Daily Papers

With the emergence of diffusion models as the frontline of generative models, many researchers have proposed molecule generation techniques using conditional diffusion models. However, due to the fundamental nature of a molecule, which carries highly entangled correlations within a small number of atoms and bonds, it becomes difficult for a model to connect raw data with the conditions when the conditions become more complex as natural language. To address this, here we present a novel latent diffusion model dubbed LDMol, which enables a natural text-conditioned molecule generation. Specifically, LDMol is composed of three building blocks: a molecule encoder that produces a chemically informative feature space, a natural language-conditioned latent diffusion model using a Diffusion Transformer (DiT), and an autoregressive decoder for molecule re. In particular, recognizing that multiple SMILES notations can represent the same molecule, we employ a contrastive learning strategy to extract the chemical informative feature space. LDMol not only beats the existing baselines on the text-to-molecule generation benchmark but is also capable of zero-shot inference with unseen scenarios. Furthermore, we show that LDMol can be applied to downstream tasks such as molecule-to-text retrieval and text-driven molecule editing, demonstrating its versatility as a diffusion model.

While score-based generative models are the model of choice across diverse domains, there are limited tools available for controlling inference-time behavior in a principled manner, e.g. for composing multiple pretrained models. Existing classifier-free guidance methods use a simple heuristic to mix conditional and unconditional scores to approximately sample from conditional distributions. However, such methods do not approximate the intermediate distributions, necessitating additional 'corrector' steps. In this work, we provide an efficient and principled method for sampling from a sequence of annealed, geometric-averaged, or product distributions derived from pretrained score-based models. We derive a weighted simulation scheme which we call Feynman-Kac Correctors (FKCs) based on the celebrated Feynman-Kac formula by carefully accounting for terms in the appropriate partial differential equations (PDEs). To simulate these PDEs, we propose Sequential Monte Carlo (SMC) resampling algorithms that leverage inference-time scaling to improve sampling quality. We empirically demonstrate the utility of our methods by proposing amortized sampling via inference-time temperature annealing, improving multi-objective molecule generation using pretrained models, and improving classifier-free guidance for text-to-image generation. Our code is available at https://github.com/martaskrt/fkc-diffusion.

In this paper, we propose Text-based Open Molecule Generation Benchmark (TOMG-Bench), the first benchmark to evaluate the open-domain molecule generation capability of LLMs. TOMG-Bench encompasses a dataset of three major tasks: molecule editing (MolEdit), molecule optimization (MolOpt), and customized molecule generation (MolCustom). Each task further contains three subtasks, with each subtask comprising 5,000 test samples. Given the inherent complexity of open molecule generation, we have also developed an automated evaluation system that helps measure both the quality and the accuracy of the generated molecules. Our comprehensive benchmarking of 25 LLMs reveals the current limitations and potential areas for improvement in text-guided molecule discovery. Furthermore, with the assistance of OpenMolIns, a specialized instruction tuning dataset proposed for solving challenges raised by TOMG-Bench, Llama3.1-8B could outperform all the open-source general LLMs, even surpassing GPT-3.5-turbo by 46.5\% on TOMG-Bench. Our codes and datasets are available through https://github.com/phenixace/TOMG-Bench.

We present MolT5 - a self-supervised learning framework for pretraining models on a vast amount of unlabeled natural language text and molecule strings. MolT5 allows for new, useful, and challenging analogs of traditional vision-language tasks, such as molecule captioning and text-based de novo molecule generation (altogether: translation between molecules and language), which we explore for the first time. Since MolT5 pretrains models on single-modal data, it helps overcome the chemistry domain shortcoming of data scarcity. Furthermore, we consider several metrics, including a new cross-modal embedding-based metric, to evaluate the tasks of molecule captioning and text-based molecule generation. Our results show that MolT5-based models are able to generate outputs, both molecules and captions, which in many cases are high quality.

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

While various models and computational tools have been proposed for structure and property analysis of molecules, generating molecules that conform to all desired structures and properties remains a challenge. Here, we introduce a multi-constraint molecular generation large language model, TSMMG, which, akin to a student, incorporates knowledge from various small models and tools, namely, the 'teachers'. To train TSMMG, we construct a large set of text-molecule pairs by extracting molecular knowledge from these 'teachers', enabling it to generate novel molecules that conform to the descriptions through various text prompts. We experimentally show that TSMMG remarkably performs in generating molecules meeting complex, natural language-described property requirements across two-, three-, and four-constraint tasks, with an average molecular validity of over 99% and success ratio of 82.58%, 68.03%, and 67.48%, respectively. The model also exhibits adaptability through zero-shot testing, creating molecules that satisfy combinations of properties that have not been encountered. It can comprehend text inputs with various language styles, extending beyond the confines of outlined prompts, as confirmed through empirical validation. Additionally, the knowledge distillation feature of TSMMG contributes to the continuous enhancement of small models, while the innovative approach to dataset construction effectively addresses the issues of data scarcity and quality, which positions TSMMG as a promising tool in the domains of drug discovery and materials science.

Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling. Considering that text is the most important record for scientific discovery, in this paper, we propose MolXPT, a unified language model of text and molecules pre-trained on SMILES (a sequence representation of molecules) wrapped by text. Briefly, we detect the molecule names in each sequence and replace them to the corresponding SMILES. In this way, the SMILES could leverage the information from surrounding text, and vice versa. The above wrapped sequences, text sequences from PubMed and SMILES sequences from PubChem are all fed into a language model for pre-training. Experimental results demonstrate that MolXPT outperforms strong baselines of molecular property prediction on MoleculeNet, performs comparably to the best model in text-molecule translation while using less than half of its parameters, and enables zero-shot molecular generation without finetuning.

As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule. Existing template-free approaches only consider the graph structures of the target molecule, which often cannot generalize well to rare reaction types and large molecules. Here, we propose T-Rex, a text-assisted retrosynthesis prediction approach that exploits pre-trained text language models, such as ChatGPT, to assist the generation of reactants. T-Rex first exploits ChatGPT to generate a description for the target molecule and rank candidate reaction centers based both the description and the molecular graph. It then re-ranks these candidates by querying the descriptions for each reactants and examines which group of reactants can best synthesize the target molecule. We observed that T-Rex substantially outperformed graph-based state-of-the-art approaches on two datasets, indicating the effectiveness of considering text information. We further found that T-Rex outperformed the variant that only use ChatGPT-based description without the re-ranking step, demonstrate how our framework outperformed a straightforward integration of ChatGPT and graph information. Collectively, we show that text generated by pre-trained language models can substantially improve retrosynthesis prediction, opening up new avenues for exploiting ChatGPT to advance computational chemistry. And the codes can be found at https://github.com/lauyikfung/T-Rex.

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the L+M-24 dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, L+M-24 is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction.

Recent advancements in large language models have opened new possibilities for generative molecular drug design. We present Chemlactica and Chemma, two language models fine-tuned on a novel corpus of 110M molecules with computed properties, totaling 40B tokens. These models demonstrate strong performance in generating molecules with specified properties and predicting new molecular characteristics from limited samples. We introduce a novel optimization algorithm that leverages our language models to optimize molecules for arbitrary properties given limited access to a black box oracle. Our approach combines ideas from genetic algorithms, rejection sampling, and prompt optimization. It achieves state-of-the-art performance on multiple molecular optimization benchmarks, including an 8% improvement on Practical Molecular Optimization compared to previous methods. We publicly release the training corpus, the language models and the optimization algorithm.

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

Chemical language models (CLMs) are prominent for their effectiveness in exploring chemical space and enabling molecular engineering. However, while exploring chemical-linguistic space, CLMs suffer from the gap between natural language and molecular representations. This challenge is primarily due to the inherent modeling differences between molecules and texts: molecules operate unified modeling to learn chemical space, while natural language sequentially models the semantic space. Additionally, the limited availability of high-quality text-to-molecule datasets further exacerbates this challenge. To address the problem, we first verified the information bias in molecular representations from different perspectives. We then developed the Heterogeneous Molecular Encoding (HME) framework, a unified molecular encoder compressing the molecular features from fragment sequence, topology, and conformation with Q-learning. To better model chemical-linguistic space, we further constructed the MCMoD dataset, which contains over one million molecules with various conditions, including properties, fragments, and descriptions. Experimentally, HME promotes CLMs to achieve chemical-linguistic sharing space exploration: (1) chemical space exploration with linguistic guidance, where HME achieves significant improvements (+37.8\% FCD) for molecular design in multiple constraints, even in zero-shot scenarios; (2) linguistic space exploration with molecular guidance, where HME generates textual descriptions with high qualities (+11.6\% BLEU) for molecules. These results highlight the precision of HME in handling multi-objective and cross-domain tasks, as well as its remarkable generalization capability on unseen task combinations. HME offers a new perspective on navigating chemical-linguistic sharing space, advancing the potential of CLMs in both fundamental research and practical applications in chemistry.

Molecule generation with desired properties has grown immensely in popularity by disruptively changing the way scientists design molecular structures and providing support for chemical and materials design. However, despite the promising outcome, previous machine learning-based deep generative models suffer from a reliance on complex, task-specific fine-tuning, limited dimensional latent spaces, or the quality of expert rules. In this work, we propose MolGen, a pre-trained molecular language model that effectively learns and shares knowledge across multiple generation tasks and domains. Specifically, we pre-train MolGen with the chemical language SELFIES on more than 100 million unlabelled molecules. We further propose multi-task molecular prefix tuning across several molecular generation tasks and different molecular domains (synthetic & natural products) with a self-feedback mechanism. Extensive experiments show that MolGen can obtain superior performances on well-known molecular generation benchmark datasets. The further analysis illustrates that MolGen can accurately capture the distribution of molecules, implicitly learn their structural characteristics, and efficiently explore the chemical space with the guidance of multi-task molecular prefix tuning. Codes, datasets, and the pre-trained model will be available in https://github.com/zjunlp/MolGen.

Generative models have demonstrated substantial promise in Natural Language Processing (NLP) and have found application in designing molecules, as seen in General Pretrained Transformer (GPT) models. In our efforts to develop such a tool for exploring the organic chemical space in search of potentially electro-active compounds, we present "LLamol", a single novel generative transformer model based on the LLama 2 architecture, which was trained on a 13M superset of organic compounds drawn from diverse public sources. To allow for a maximum flexibility in usage and robustness in view of potentially incomplete data, we introduce "Stochastic Context Learning" as a new training procedure. We demonstrate that the resulting model adeptly handles single- and multi-conditional organic molecule generation with up to four conditions, yet more are possible. The model generates valid molecular structures in SMILES notation while flexibly incorporating three numerical and/or one token sequence into the generative process, just as requested. The generated compounds are very satisfactory in all scenarios tested. In detail, we showcase the model's capability to utilize token sequences for conditioning, either individually or in combination with numerical properties, making LLamol a potent tool for de novo molecule design, easily expandable with new properties.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

The integration of molecule and language has garnered increasing attention in molecular science. Recent advancements in Language Models (LMs) have demonstrated potential for the comprehensive modeling of molecule and language. However, existing works exhibit notable limitations. Most existing works overlook the modeling of 3D information, which is crucial for understanding molecular structures and also functions. While some attempts have been made to leverage external structure encoding modules to inject the 3D molecular information into LMs, there exist obvious difficulties that hinder the integration of molecular structure and language text, such as modality alignment and separate tuning. To bridge this gap, we propose 3D-MolT5, a unified framework designed to model both 1D molecular sequence and 3D molecular structure. The key innovation lies in our methodology for mapping fine-grained 3D substructure representations (based on 3D molecular fingerprints) to a specialized 3D token vocabulary for 3D-MolT5. This 3D structure token vocabulary enables the seamless combination of 1D sequence and 3D structure representations in a tokenized format, allowing 3D-MolT5 to encode molecular sequence (SELFIES), molecular structure, and text sequences within a unified architecture. Alongside, we further introduce 1D and 3D joint pre-training to enhance the model's comprehension of these diverse modalities in a joint representation space and better generalize to various tasks for our foundation model. Through instruction tuning on multiple downstream datasets, our proposed 3D-MolT5 shows superior performance than existing methods in molecular property prediction, molecule captioning, and text-based molecule generation tasks. Our code will be available on GitHub soon.

Molecule discovery is a pivotal research field, impacting everything from the medicines we take to the materials we use. Recently, Large Language Models (LLMs) have been widely adopted in molecule understanding and generation, yet the alignments between molecules and their corresponding captions remain a significant challenge. Previous endeavours often treat the molecule as a general SMILES string or molecular graph, neglecting the fine-grained alignments between the molecular sub-structures and the descriptive textual phrases, which are crucial for accurate and explainable predictions. In this case, we introduce MolReFlect, a novel teacher-student framework designed to contextually perform the molecule-caption alignments in a fine-grained way. Our approach initially leverages a larger teacher LLM to label the detailed alignments by directly extracting critical phrases from molecule captions or SMILES strings and implying them to corresponding sub-structures or characteristics. To refine these alignments, we propose In-Context Selective Reflection, which retrieves previous extraction results as context examples for teacher LLM to reflect and lets a smaller student LLM select from in-context reflection and previous extraction results. Finally, we enhance the learning process of the student LLM through Chain-of-Thought In-Context Molecule Tuning, integrating the fine-grained alignments and the reasoning processes within the Chain-of-Thought format. Our experimental results demonstrate that MolReFlect enables LLMs like Mistral-7B to significantly outperform the previous baselines, achieving SOTA performance on the ChEBI-20 dataset. This advancement not only enhances the generative capabilities of LLMs in the molecule-caption translation task, but also contributes to a more explainable framework.

The automatic analysis of chemical literature has immense potential to accelerate the discovery of new materials and drugs. Much of the critical information in patent documents and scientific articles is contained in figures, depicting the molecule structures. However, automatically parsing the exact chemical structure is a formidable challenge, due to the amount of detailed information, the diversity of drawing styles, and the need for training data. In this work, we introduce MolGrapher to recognize chemical structures visually. First, a deep keypoint detector detects the atoms. Second, we treat all candidate atoms and bonds as nodes and put them in a graph. This construct allows a natural graph representation of the molecule. Last, we classify atom and bond nodes in the graph with a Graph Neural Network. To address the lack of real training data, we propose a synthetic data generation pipeline producing diverse and realistic results. In addition, we introduce a large-scale benchmark of annotated real molecule images, USPTO-30K, to spur research on this critical topic. Extensive experiments on five datasets show that our approach significantly outperforms classical and learning-based methods in most settings. Code, models, and datasets are available.

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. In this paper, we present a novel generative model, BindGPT which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pretrain BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pretrained language model can serve at the same time as a 3D molecular generative model, conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such simple conceptual approach combined with pretraining and scaling can perform on par or better than the current best specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

Deep learning in computational biochemistry has traditionally focused on molecular graphs neural representations; however, recent advances in language models highlight how much scientific knowledge is encoded in text. To bridge these two modalities, we investigate how molecular property information can be transferred from natural language to graph representations. We study property prediction performance gains after using contrastive learning to align neural graph representations with representations of textual descriptions of their characteristics. We implement neural relevance scoring strategies to improve text retrieval, introduce a novel chemically-valid molecular graph augmentation strategy inspired by organic reactions, and demonstrate improved performance on downstream MoleculeNet property classification tasks. We achieve a +4.26% AUROC gain versus models pre-trained on the graph modality alone, and a +1.54% gain compared to recently proposed molecular graph/text contrastively trained MoMu model (Su et al. 2022).

Models based on machine learning can enable accurate and fast molecular property predictions, which is of interest in drug discovery and material design. Various supervised machine learning models have demonstrated promising performance, but the vast chemical space and the limited availability of property labels make supervised learning challenging. Recently, unsupervised transformer-based language models pretrained on a large unlabelled corpus have produced state-of-the-art results in many downstream natural language processing tasks. Inspired by this development, we present molecular embeddings obtained by training an efficient transformer encoder model, MoLFormer, which uses rotary positional embeddings. This model employs a linear attention mechanism, coupled with highly distributed training, on SMILES sequences of 1.1 billion unlabelled molecules from the PubChem and ZINC datasets. We show that the learned molecular representation outperforms existing baselines, including supervised and self-supervised graph neural networks and language models, on several downstream tasks from ten benchmark datasets. They perform competitively on two others. Further analyses, specifically through the lens of attention, demonstrate that MoLFormer trained on chemical SMILES indeed learns the spatial relationships between atoms within a molecule. These results provide encouraging evidence that large-scale molecular language models can capture sufficient chemical and structural information to predict various distinct molecular properties, including quantum-chemical properties.

The dominant text generation models compose the output by sequentially selecting words from a fixed vocabulary. In this paper, we formulate text generation as progressively copying text segments (e.g., words or phrases) from an existing text collection. We compute the contextualized representations of meaningful text segments and index them using efficient vector search toolkits. The task of text generation is then decomposed into a series of copy-and-paste operations: at each time step, we seek suitable text spans from the text collection rather than selecting from a standalone vocabulary. Experiments on the standard language modeling benchmark (WikiText-103) show that our approach achieves better generation quality according to both automatic and human evaluations. Besides, its inference efficiency is comparable to token-level autoregressive models thanks to the reduction of decoding steps. We also show that our approach allows for effective domain adaptation by simply switching to domain-specific text collection without extra training. Finally, we observe that our approach attains additional performance gains by simply scaling up to larger text collections, again without further training.Our source codes are publicly available at \url{https://github.com/gmftbyGMFTBY/Copyisallyouneed.}

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working on discrete data. A new accuracy schedule is proposed to improve the sampling quality by significantly reducing the reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with the state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

Large Language Models (LLMs) with strong abilities in natural language processing tasks have emerged and have been rapidly applied in various kinds of areas such as science, finance and software engineering. However, the capability of LLMs to advance the field of chemistry remains unclear. In this paper,we establish a comprehensive benchmark containing 8 practical chemistry tasks, including 1) name prediction, 2) property prediction, 3) yield prediction, 4) reaction prediction, 5) retrosynthesis (prediction of reactants from products), 6)text-based molecule design, 7) molecule captioning, and 8) reagent selection. Our analysis draws on widely recognized datasets including BBBP, Tox21, PubChem, USPTO, and ChEBI, facilitating a broad exploration of the capacities of LLMs within the context of practical chemistry. Three GPT models (GPT-4, GPT-3.5,and Davinci-003) are evaluated for each chemistry task in zero-shot and few-shot in-context learning settings with carefully selected demonstration examples and specially crafted prompts. The key results of our investigation are 1) GPT-4 outperforms the other two models among the three evaluated; 2) GPT models exhibit less competitive performance in tasks demanding precise understanding of molecular SMILES representation, such as reaction prediction and retrosynthesis;3) GPT models demonstrate strong capabilities in text-related explanation tasks such as molecule captioning; and 4) GPT models exhibit comparable or better performance to classical machine learning models when applied to chemical problems that can be transformed into classification or ranking tasks, such as property prediction, and yield prediction.

In data-to-text (D2T) generation, training on in-domain data leads to overfitting to the data representation and repeating training data noise. We examine how to avoid finetuning pretrained language models (PLMs) on D2T generation datasets while still taking advantage of surface realization capabilities of PLMs. Inspired by pipeline approaches, we propose to generate text by transforming single-item descriptions with a sequence of modules trained on general-domain text-based operations: ordering, aggregation, and paragraph compression. We train PLMs for performing these operations on a synthetic corpus WikiFluent which we build from English Wikipedia. Our experiments on two major triple-to-text datasets -- WebNLG and E2E -- show that our approach enables D2T generation from RDF triples in zero-shot settings.

Large Language Models (LLMs) have substantially driven scientific progress in various domains, and many papers have demonstrated their ability to tackle complex problems with creative solutions. Our paper introduces a new foundation model, nach0, capable of solving various chemical and biological tasks: biomedical question answering, named entity recognition, molecular generation, molecular synthesis, attributes prediction, and others. nach0 is a multi-domain and multi-task encoder-decoder LLM pre-trained on unlabeled text from scientific literature, patents, and molecule strings to incorporate a range of chemical and linguistic knowledge. We employed instruction tuning, where specific task-related instructions are utilized to fine-tune nach0 for the final set of tasks. To train nach0 effectively, we leverage the NeMo framework, enabling efficient parallel optimization of both base and large model versions. Extensive experiments demonstrate that our model outperforms state-of-the-art baselines on single-domain and cross-domain tasks. Furthermore, it can generate high-quality outputs in molecular and textual formats, showcasing its effectiveness in multi-domain setups.

We consider the task of data-to-text generation, which aims to create textual output from non-linguistic input. We focus on generating long-form text, i.e., documents with multiple paragraphs, and propose a neural model enhanced with a planning component responsible for organizing high-level information in a coherent and meaningful way. We infer latent plans sequentially with a structured variational model, while interleaving the steps of planning and generation. Text is generated by conditioning on previous variational decisions and previously generated text. Experiments on two data-to-text benchmarks (RotoWire and MLB) show that our model outperforms strong baselines and is sample efficient in the face of limited training data (e.g., a few hundred instances).

The field of bioinformatics has seen significant progress, making the cross-modal text-molecule retrieval task increasingly vital. This task focuses on accurately retrieving molecule structures based on textual descriptions, by effectively aligning textual descriptions and molecules to assist researchers in identifying suitable molecular candidates. However, many existing approaches overlook the details inherent in molecule sub-structures. In this work, we introduce the Optimal TRansport-based Multi-grained Alignments model (ORMA), a novel approach that facilitates multi-grained alignments between textual descriptions and molecules. Our model features a text encoder and a molecule encoder. The text encoder processes textual descriptions to generate both token-level and sentence-level representations, while molecules are modeled as hierarchical heterogeneous graphs, encompassing atom, motif, and molecule nodes to extract representations at these three levels. A key innovation in ORMA is the application of Optimal Transport (OT) to align tokens with motifs, creating multi-token representations that integrate multiple token alignments with their corresponding motifs. Additionally, we employ contrastive learning to refine cross-modal alignments at three distinct scales: token-atom, multitoken-motif, and sentence-molecule, ensuring that the similarities between correctly matched text-molecule pairs are maximized while those of unmatched pairs are minimized. To our knowledge, this is the first attempt to explore alignments at both the motif and multi-token levels. Experimental results on the ChEBI-20 and PCdes datasets demonstrate that ORMA significantly outperforms existing state-of-the-art (SOTA) models.

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.

Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus on 3D molecule-text interpretation, and propose 3D-MoLM: 3D-Molecular Language Modeling. Specifically, 3D-MoLM enables an LM to interpret and analyze 3D molecules by equipping the LM with a 3D molecular encoder. This integration is achieved by a 3D molecule-text projector, bridging the 3D molecular encoder's representation space and the LM's input space. Moreover, to enhance 3D-MoLM's ability of cross-modal molecular understanding and instruction following, we meticulously curated a 3D molecule-centric instruction tuning dataset -- 3D-MoIT. Through 3D molecule-text alignment and 3D molecule-centric instruction tuning, 3D-MoLM establishes an integration of 3D molecular encoder and LM. It significantly surpasses existing baselines on downstream tasks, including molecule-text retrieval, molecule captioning, and more challenging open-text molecular QA tasks, especially focusing on 3D-dependent properties.

In this work, we present the ChemNLP library that can be used for 1) curating open access datasets for materials and chemistry literature, developing and comparing traditional machine learning, transformers and graph neural network models for 2) classifying and clustering texts, 3) named entity recognition for large-scale text-mining, 4) abstractive summarization for generating titles of articles from abstracts, 5) text generation for suggesting abstracts from titles, 6) integration with density functional theory dataset for identifying potential candidate materials such as superconductors, and 7) web-interface development for text and reference query. We primarily use the publicly available arXiv and Pubchem datasets but the tools can be used for other datasets as well. Moreover, as new models are developed, they can be easily integrated in the library. ChemNLP is available at the websites: https://github.com/usnistgov/chemnlp and https://jarvis.nist.gov/jarvischemnlp.

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and significant limitations persist in their design and implementation. Notably, LLMs struggle with structured data, such as graphs, and often falter when tasked with answering domain-specific questions requiring deep expertise, such as those in biology and chemistry. In this paper, we explore a fundamental question: Can LLMs effectively handle molecule prediction tasks? Rather than pursuing top-tier performance, our goal is to assess how LLMs can contribute to diverse molecule tasks. We identify several classification and regression prediction tasks across six standard molecule datasets. Subsequently, we carefully design a set of prompts to query LLMs on these tasks and compare their performance with existing Machine Learning (ML) models, which include text-based models and those specifically designed for analysing the geometric structure of molecules. Our investigation reveals several key insights: Firstly, LLMs generally lag behind ML models in achieving competitive performance on molecule tasks, particularly when compared to models adept at capturing the geometric structure of molecules, highlighting the constrained ability of LLMs to comprehend graph data. Secondly, LLMs show promise in enhancing the performance of ML models when used collaboratively. Lastly, we engage in a discourse regarding the challenges and promising avenues to harness LLMs for molecule prediction tasks. The code and models are available at https://github.com/zhiqiangzhongddu/LLMaMol.

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language. (1) We begin by outlining the technical representations of biomolecules employed, including sequences, 2D graphs, and 3D structures. (2) We then examine in depth the rationale and key objectives underlying effective multi-modal integration of language and molecular data sources. (3) We subsequently survey the practical applications enabled to date in this developing research area. (4) We also compile and summarize the available resources and datasets to facilitate future work. (5) Looking ahead, we identify several promising research directions worthy of further exploration and investment to continue advancing the field. The related resources and contents are updating in https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling.

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at https://github.com/ChnQ/LLM4Mol.

Generative models are becoming a tool of choice for exploring the molecular space. These models learn on a large training dataset and produce novel molecular structures with similar properties. Generated structures can be utilized for virtual screening or training semi-supervised predictive models in the downstream tasks. While there are plenty of generative models, it is unclear how to compare and rank them. In this work, we introduce a benchmarking platform called Molecular Sets (MOSES) to standardize training and comparison of molecular generative models. MOSES provides a training and testing datasets, and a set of metrics to evaluate the quality and diversity of generated structures. We have implemented and compared several molecular generation models and suggest to use our results as reference points for further advancements in generative chemistry research. The platform and source code are available at https://github.com/molecularsets/moses.

Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Cross-modal Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Cross-modal Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.

In recent years, Large Language Models (LLMs) have achieved significant success in natural language processing (NLP) and various interdisciplinary areas. However, applying LLMs to chemistry is a complex task that requires specialized domain knowledge. This paper provides a thorough exploration of the nuanced methodologies employed in integrating LLMs into the field of chemistry, delving into the complexities and innovations at this interdisciplinary juncture. Specifically, our analysis begins with examining how molecular information is fed into LLMs through various representation and tokenization methods. We then categorize chemical LLMs into three distinct groups based on the domain and modality of their input data, and discuss approaches for integrating these inputs for LLMs. Furthermore, this paper delves into the pretraining objectives with adaptations to chemical LLMs. After that, we explore the diverse applications of LLMs in chemistry, including novel paradigms for their application in chemistry tasks. Finally, we identify promising research directions, including further integration with chemical knowledge, advancements in continual learning, and improvements in model interpretability, paving the way for groundbreaking developments in the field.

GNNs and chemical fingerprints are the predominant approaches to representing molecules for property prediction. However, in NLP, transformers have become the de-facto standard for representation learning thanks to their strong downstream task transfer. In parallel, the software ecosystem around transformers is maturing rapidly, with libraries like HuggingFace and BertViz enabling streamlined training and introspection. In this work, we make one of the first attempts to systematically evaluate transformers on molecular property prediction tasks via our ChemBERTa model. ChemBERTa scales well with pretraining dataset size, offering competitive downstream performance on MoleculeNet and useful attention-based visualization modalities. Our results suggest that transformers offer a promising avenue of future work for molecular representation learning and property prediction. To facilitate these efforts, we release a curated dataset of 77M SMILES from PubChem suitable for large-scale self-supervised pretraining.

One of the major challenges in training text-to-image generation models is the need of a large number of high-quality image-text pairs. While image samples are often easily accessible, the associated text descriptions typically require careful human captioning, which is particularly time- and cost-consuming. In this paper, we propose the first work to train text-to-image generation models without any text data. Our method leverages the well-aligned multi-modal semantic space of the powerful pre-trained CLIP model: the requirement of text-conditioning is seamlessly alleviated via generating text features from image features. Extensive experiments are conducted to illustrate the effectiveness of the proposed method. We obtain state-of-the-art results in the standard text-to-image generation tasks. Importantly, the proposed language-free model outperforms most existing models trained with full image-text pairs. Furthermore, our method can be applied in fine-tuning pre-trained models, which saves both training time and cost in training text-to-image generation models. Our pre-trained model obtains competitive results in zero-shot text-to-image generation on the MS-COCO dataset, yet with around only 1% of the model size and training data size relative to the recently proposed large DALL-E model.

We present a novel approach to data-to-text generation based on iterative text editing. Our approach maximizes the completeness and semantic accuracy of the output text while leveraging the abilities of recent pre-trained models for text editing (LaserTagger) and language modeling (GPT-2) to improve the text fluency. To this end, we first transform data items to text using trivial templates, and then we iteratively improve the resulting text by a neural model trained for the sentence fusion task. The output of the model is filtered by a simple heuristic and reranked with an off-the-shelf pre-trained language model. We evaluate our approach on two major data-to-text datasets (WebNLG, Cleaned E2E) and analyze its caveats and benefits. Furthermore, we show that our formulation of data-to-text generation opens up the possibility for zero-shot domain adaptation using a general-domain dataset for sentence fusion.

Molecule discovery serves as a cornerstone in numerous scientific domains, fueling the development of new materials and innovative drug designs. Recent developments of in-silico molecule discovery have highlighted the promising results of cross-modal techniques, which bridge molecular structures with their descriptive annotations. However, these cross-modal methods frequently encounter the issue of data scarcity, hampering their performance and application. In this paper, we address the low-resource challenge by utilizing artificially-real data generated by Large Language Models (LLMs). We first introduce a retrieval-based prompting strategy to construct high-quality pseudo data, then explore the optimal method to effectively leverage this pseudo data. Experiments show that using pseudo data for domain adaptation outperforms all existing methods, while also requiring a smaller model scale, reduced data size and lower training cost, highlighting its efficiency. Furthermore, our method shows a sustained improvement as the volume of pseudo data increases, revealing the great potential of pseudo data in advancing low-resource cross-modal molecule discovery.

Text generation is ubiquitous in many NLP tasks, from summarization, to dialogue and machine translation. The dominant parametric approach is based on locally normalized models which predict one word at a time. While these work remarkably well, they are plagued by exposure bias due to the greedy nature of the generation process. In this work, we investigate un-normalized energy-based models (EBMs) which operate not at the token but at the sequence level. In order to make training tractable, we first work in the residual of a pretrained locally normalized language model and second we train using noise contrastive estimation. Furthermore, since the EBM works at the sequence level, we can leverage pretrained bi-directional contextual representations, such as BERT and RoBERTa. Our experiments on two large language modeling datasets show that residual EBMs yield lower perplexity compared to locally normalized baselines. Moreover, generation via importance sampling is very efficient and of higher quality than the baseline models according to human evaluation.

The generative modeling landscape has experienced tremendous growth in recent years, particularly in generating natural images and art. Recent techniques have shown impressive potential in creating complex visual compositions while delivering impressive realism and quality. However, state-of-the-art methods have been focusing on the narrow domain of natural images, while other distributions remain unexplored. In this paper, we introduce the problem of text-to-figure generation, that is creating scientific figures of papers from text descriptions. We present FigGen, a diffusion-based approach for text-to-figure as well as the main challenges of the proposed task. Code and models are available at https://github.com/joanrod/figure-diffusion

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

In drug-discovery-related tasks such as virtual screening, machine learning is emerging as a promising way to predict molecular properties. Conventionally, molecular fingerprints (numerical representations of molecules) are calculated through rule-based algorithms that map molecules to a sparse discrete space. However, these algorithms perform poorly for shallow prediction models or small datasets. To address this issue, we present SMILES Transformer. Inspired by Transformer and pre-trained language models from natural language processing, SMILES Transformer learns molecular fingerprints through unsupervised pre-training of the sequence-to-sequence language model using a huge corpus of SMILES, a text representation system for molecules. We performed benchmarks on 10 datasets against existing fingerprints and graph-based methods and demonstrated the superiority of the proposed algorithms in small-data settings where pre-training facilitated good generalization. Moreover, we define a novel metric to concurrently measure model accuracy and data efficiency.

Large language models (LLMs) have made impressive progress in chemistry applications, including molecular property prediction, molecular generation, experimental protocol design, etc. However, the community lacks a dialogue-based model specifically designed for chemistry. The challenge arises from the fact that most chemical data and scientific knowledge are primarily stored in structured databases, and the direct use of these structured data compromises the model's ability to maintain coherent dialogue. To tackle this issue, we develop a novel template-based instruction construction method that transforms structured knowledge into plain dialogue, making it suitable for language model training. By leveraging this approach, we develop ChemLLM, the first large language model dedicated to chemistry, capable of performing various tasks across chemical disciplines with smooth dialogue interaction. ChemLLM beats GPT-3.5 on all three principal tasks in chemistry, i.e., name conversion, molecular caption, and reaction prediction, and surpasses GPT-4 on two of them. Remarkably, ChemLLM also shows exceptional adaptability to related mathematical and physical tasks despite being trained mainly on chemical-centric corpora. Furthermore, ChemLLM demonstrates proficiency in specialized NLP tasks within chemistry, such as literature translation and cheminformatic programming. ChemLLM opens up a new avenue for exploration within chemical studies, while our method of integrating structured chemical knowledge into dialogue systems sets a new frontier for developing LLMs across various scientific fields. Codes, Datasets, and Model weights are publicly accessible at hf.co/AI4Chem/ChemLLM-7B-Chat.

Recent breakthroughs in text-to-image generation has shown encouraging results via large generative models. Due to the scarcity of 3D assets, it is hardly to transfer the success of text-to-image generation to that of text-to-3D generation. Existing text-to-3D generation methods usually adopt the paradigm of DreamFusion, which conducts per-asset optimization by distilling a pretrained text-to-image diffusion model. The generation speed usually ranges from several minutes to tens of minutes per 3D asset, which degrades the user experience and also imposes a burden to the service providers due to the high computational budget. In this work, we present an efficient text-to-3D generation method, which requires only around 8 ms to generate a 3D asset given the text prompt on a consumer graphic card. The main insight is that we exploit the images generated by a large pre-trained text-to-image diffusion model, to supervise the training of a text conditioned 3D generative adversarial network. Once the network is trained, we are able to efficiently generate a 3D asset via a single forward pass. Our method requires no 3D training data and provides an alternative approach for efficient text-to-3D generation by distilling pre-trained image diffusion models.

Large language models are playing an increasingly significant role in molecular research, yet existing models often generate erroneous information, posing challenges to accurate molecular comprehension. Traditional evaluation metrics for generated content fail to assess a model's accuracy in molecular understanding. To rectify the absence of factual evaluation, we present MoleculeQA, a novel question answering (QA) dataset which possesses 62K QA pairs over 23K molecules. Each QA pair, composed of a manual question, a positive option and three negative options, has consistent semantics with a molecular description from authoritative molecular corpus. MoleculeQA is not only the first benchmark for molecular factual bias evaluation but also the largest QA dataset for molecular research. A comprehensive evaluation on MoleculeQA for existing molecular LLMs exposes their deficiencies in specific areas and pinpoints several particularly crucial factors for molecular understanding.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning.

Large-scale pre-training methodologies for chemical language models represent a breakthrough in cheminformatics. These methods excel in tasks such as property prediction and molecule generation by learning contextualized representations of input tokens through self-supervised learning on large unlabeled corpora. Typically, this involves pre-training on unlabeled data followed by fine-tuning on specific tasks, reducing dependence on annotated datasets and broadening chemical language representation understanding. This paper introduces a large encoder-decoder chemical foundation models pre-trained on a curated dataset of 91 million SMILES samples sourced from PubChem, which is equivalent to 4 billion of molecular tokens. The proposed foundation model supports different complex tasks, including quantum property prediction, and offer flexibility with two main variants (289M and 8times289M). Our experiments across multiple benchmark datasets validate the capacity of the proposed model in providing state-of-the-art results for different tasks. We also provide a preliminary assessment of the compositionality of the embedding space as a prerequisite for the reasoning tasks. We demonstrate that the produced latent space is separable compared to the state-of-the-art with few-shot learning capabilities.

Large pretrained models such as GPT-3 have had tremendous impact on modern natural language processing by leveraging self-supervised learning to learn salient representations that can be used to readily finetune on a wide variety of downstream tasks. We investigate the possibility of transferring such advances to molecular machine learning by building a chemical foundation model, ChemBERTa-2, using the language of SMILES. While labeled data for molecular prediction tasks is typically scarce, libraries of SMILES strings are readily available. In this work, we build upon ChemBERTa by optimizing the pretraining process. We compare multi-task and self-supervised pretraining by varying hyperparameters and pretraining dataset size, up to 77M compounds from PubChem. To our knowledge, the 77M set constitutes one of the largest datasets used for molecular pretraining to date. We find that with these pretraining improvements, we are competitive with existing state-of-the-art architectures on the MoleculeNet benchmark suite. We analyze the degree to which improvements in pretraining translate to improvement on downstream tasks.

We introduce SynFormer, a generative modeling framework designed to efficiently explore and navigate synthesizable chemical space. Unlike traditional molecular generation approaches, we generate synthetic pathways for molecules to ensure that designs are synthetically tractable. By incorporating a scalable transformer architecture and a diffusion module for building block selection, SynFormer surpasses existing models in synthesizable molecular design. We demonstrate SynFormer's effectiveness in two key applications: (1) local chemical space exploration, where the model generates synthesizable analogs of a reference molecule, and (2) global chemical space exploration, where the model aims to identify optimal molecules according to a black-box property prediction oracle. Additionally, we demonstrate the scalability of our approach via the improvement in performance as more computational resources become available. With our code and trained models openly available, we hope that SynFormer will find use across applications in drug discovery and materials science.

Language Models (LMs) have demonstrated impressive molecule understanding ability on various 1D text-related tasks. However, they inherently lack 2D graph perception - a critical ability of human professionals in comprehending molecules' topological structures. To bridge this gap, we propose MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter. MolCA enables an LM (e.g., Galactica) to understand both text- and graph-based molecular contents via the cross-modal projector. Specifically, the cross-modal projector is implemented as a Q-Former to connect a graph encoder's representation space and an LM's text space. Further, MolCA employs a uni-modal adapter (i.e., LoRA) for the LM's efficient adaptation to downstream tasks. Unlike previous studies that couple an LM with a graph encoder via cross-modal contrastive learning, MolCA retains the LM's ability of open-ended text generation and augments it with 2D graph information. To showcase its effectiveness, we extensively benchmark MolCA on tasks of molecule captioning, IUPAC name prediction, and molecule-text retrieval, on which MolCA significantly outperforms the baselines. Our codes and checkpoints can be found at https://github.com/acharkq/MolCA.

Over the past few years, Text-to-Image (T2I) generation approaches based on diffusion models have gained significant attention. However, vanilla diffusion models often suffer from spelling inaccuracies in the text displayed within the generated images. The capability to generate visual text is crucial, offering both academic interest and a wide range of practical applications. To produce accurate visual text images, state-of-the-art techniques adopt a glyph-controlled image generation approach, consisting of a text layout generator followed by an image generator that is conditioned on the generated text layout. Nevertheless, our study reveals that these models still face three primary challenges, prompting us to develop a testbed to facilitate future research. We introduce a benchmark, LenCom-Eval, specifically designed for testing models' capability in generating images with Lengthy and Complex visual text. Subsequently, we introduce a training-free framework to enhance the two-stage generation approaches. We examine the effectiveness of our approach on both LenCom-Eval and MARIO-Eval benchmarks and demonstrate notable improvements across a range of evaluation metrics, including CLIPScore, OCR precision, recall, F1 score, accuracy, and edit distance scores. For instance, our proposed framework improves the backbone model, TextDiffuser, by more than 23\% and 13.5\% in terms of OCR word F1 on LenCom-Eval and MARIO-Eval, respectively. Our work makes a unique contribution to the field by focusing on generating images with long and rare text sequences, a niche previously unexplored by existing literature

Recently, text-to-image generation has exhibited remarkable advancements, with the ability to produce visually impressive results. In contrast, text-to-3D generation has not yet reached a comparable level of quality. Existing methods primarily rely on text-guided score distillation sampling (SDS), and they encounter difficulties in transferring 2D attributes of the generated images to 3D content. In this work, we aim to develop an effective 3D generative model capable of synthesizing high-resolution textured meshes by leveraging both textual and image information. To this end, we introduce Guide3D, a zero-shot text-and-image-guided generative model for 3D avatar generation based on diffusion models. Our model involves (1) generating sparse-view images of a text-consistent character using diffusion models, and (2) jointly optimizing multi-resolution differentiable marching tetrahedral grids with pixel-aligned image features. We further propose a similarity-aware feature fusion strategy for efficiently integrating features from different views. Moreover, we introduce two novel training objectives as an alternative to calculating SDS, significantly enhancing the optimization process. We thoroughly evaluate the performance and components of our framework, which outperforms the current state-of-the-art in producing topologically and structurally correct geometry and high-resolution textures. Guide3D enables the direct transfer of 2D-generated images to the 3D space. Our code will be made publicly available.

Recent advances in language models have enabled framing molecule generation as sequence modeling. However, existing approaches often rely on single-objective reinforcement learning, limiting their applicability to real-world drug design, where multiple competing properties must be optimized. Traditional multi-objective reinforcement learning (MORL) methods require costly retraining for each new objective combination, making rapid exploration of trade-offs impractical. To overcome these limitations, we introduce Mol-MoE, a mixture-of-experts (MoE) architecture that enables efficient test-time steering of molecule generation without retraining. Central to our approach is a preference-based router training objective that incentivizes the router to combine experts in a way that aligns with user-specified trade-offs. This provides improved flexibility in exploring the chemical property space at test time, facilitating rapid trade-off exploration. Benchmarking against state-of-the-art methods, we show that Mol-MoE achieves superior sample quality and steerability.

Text-to-3D generation represents an exciting field that has seen rapid advancements, facilitating the transformation of textual descriptions into detailed 3D models. However, current progress often neglects the intricate high-order correlation of geometry and texture within 3D objects, leading to challenges such as over-smoothness, over-saturation and the Janus problem. In this work, we propose a method named ``3D Gaussian Generation via Hypergraph (Hyper-3DG)'', designed to capture the sophisticated high-order correlations present within 3D objects. Our framework is anchored by a well-established mainflow and an essential module, named ``Geometry and Texture Hypergraph Refiner (HGRefiner)''. This module not only refines the representation of 3D Gaussians but also accelerates the update process of these 3D Gaussians by conducting the Patch-3DGS Hypergraph Learning on both explicit attributes and latent visual features. Our framework allows for the production of finely generated 3D objects within a cohesive optimization, effectively circumventing degradation. Extensive experimentation has shown that our proposed method significantly enhances the quality of 3D generation while incurring no additional computational overhead for the underlying framework. (Project code: https://github.com/yjhboy/Hyper3DG)

Table-to-text generation refers to generating a descriptive text from a key-value table. Traditional autoregressive methods, though can generate text with high fluency, suffer from low coverage and poor faithfulness problems. To mitigate these problems, we propose a novel Skeleton-based two-stage method that combines both Autoregressive and Non-Autoregressive generations (SANA). Our approach includes: (1) skeleton generation with an autoregressive pointer network to select key tokens from the source table; (2) edit-based non-autoregressive generation model to produce texts via iterative insertion and deletion operations. By integrating hard constraints from the skeleton, the non-autoregressive model improves the generation's coverage over the source table and thus enhances its faithfulness. We conduct automatic and human evaluations on both WikiPerson and WikiBio datasets. Experimental results demonstrate that our method outperforms the previous state-of-the-art methods in both automatic and human evaluation, especially on coverage and faithfulness. In particular, we achieve PARENT-T recall of 99.47 in WikiPerson, improving over the existing best results by more than 10 points.

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

Current AI-assisted protein design mainly utilizes protein sequential and structural information. Meanwhile, there exists tremendous knowledge curated by humans in the text format describing proteins' high-level properties. Yet, whether the incorporation of such text data can help protein design tasks has not been explored. To bridge this gap, we propose ProteinDT, a multi-modal framework that leverages textual descriptions for protein design. ProteinDT consists of three subsequent steps: ProteinCLAP that aligns the representation of two modalities, a facilitator that generates the protein representation from the text modality, and a decoder that generates the protein sequences from the representation. To train ProteinDT, we construct a large dataset, SwissProtCLAP, with 441K text and protein pairs. We empirically verify the effectiveness of ProteinDT from three aspects: (1) consistently superior performance on four out of six protein property prediction benchmarks; (2) over 90% accuracy for text-guided protein generation; and (3) promising results for zero-shot text-guided protein editing.

Text-to-image synthesis refers to computational methods which translate human written textual descriptions, in the form of keywords or sentences, into images with similar semantic meaning to the text. In earlier research, image synthesis relied mainly on word to image correlation analysis combined with supervised methods to find best alignment of the visual content matching to the text. Recent progress in deep learning (DL) has brought a new set of unsupervised deep learning methods, particularly deep generative models which are able to generate realistic visual images using suitably trained neural network models. In this paper, we review the most recent development in the text-to-image synthesis research domain. Our survey first introduces image synthesis and its challenges, and then reviews key concepts such as generative adversarial networks (GANs) and deep convolutional encoder-decoder neural networks (DCNN). After that, we propose a taxonomy to summarize GAN based text-to-image synthesis into four major categories: Semantic Enhancement GANs, Resolution Enhancement GANs, Diversity Enhancement GANS, and Motion Enhancement GANs. We elaborate the main objective of each group, and further review typical GAN architectures in each group. The taxonomy and the review outline the techniques and the evolution of different approaches, and eventually provide a clear roadmap to summarize the list of contemporaneous solutions that utilize GANs and DCNNs to generate enthralling results in categories such as human faces, birds, flowers, room interiors, object reconstruction from edge maps (games) etc. The survey will conclude with a comparison of the proposed solutions, challenges that remain unresolved, and future developments in the text-to-image synthesis domain.

Recent advances in large-scale pre-training such as GPT-3 allow seemingly high quality text to be generated from a given prompt. However, such generation systems often suffer from problems of hallucinated facts, and are not inherently designed to incorporate useful external information. Grounded generation models appear to offer remedies, but their training typically relies on rarely-available parallel data where information-relevant documents are provided for context. We propose a framework that alleviates this data constraint by jointly training a grounded generator and document retriever on the language model signal. The model learns to reward retrieval of the documents with the highest utility in generation, and attentively combines them using a Mixture-of-Experts (MoE) ensemble to generate follow-on text. We demonstrate that both generator and retriever can take advantage of this joint training and work synergistically to produce more informative and relevant text in both prose and dialogue generation.

Most text-to-3D generators build upon off-the-shelf text-to-image models trained on billions of images. They use variants of Score Distillation Sampling (SDS), which is slow, somewhat unstable, and prone to artifacts. A mitigation is to fine-tune the 2D generator to be multi-view aware, which can help distillation or can be combined with reconstruction networks to output 3D objects directly. In this paper, we further explore the design space of text-to-3D models. We significantly improve multi-view generation by considering video instead of image generators. Combined with a 3D reconstruction algorithm which, by using Gaussian splatting, can optimize a robust image-based loss, we directly produce high-quality 3D outputs from the generated views. Our new method, IM-3D, reduces the number of evaluations of the 2D generator network 10-100x, resulting in a much more efficient pipeline, better quality, fewer geometric inconsistencies, and higher yield of usable 3D assets.

Understanding molecules is key to understanding organisms and driving advances in drug discovery, requiring interdisciplinary knowledge across chemistry and biology. Although large molecular language models have achieved notable success in interpreting molecular structures, their instruction datasets are limited to the specific knowledge from task-oriented datasets and do not fully cover the fundamental characteristics of molecules, hindering their abilities as general-purpose molecular assistants. To address this issue, we propose Mol-LLaMA, a large molecular language model that grasps the general knowledge centered on molecules via multi-modal instruction tuning. To this end, we design key data types that encompass the fundamental features of molecules, incorporating essential knowledge from molecular structures. In addition, to improve understanding of molecular features, we introduce a module that integrates complementary information from different molecular encoders, leveraging the distinct advantages of different molecular representations. Our experimental results demonstrate that Mol-LLaMA is capable of comprehending the general features of molecules and generating relevant responses to users' queries with detailed explanations, implying its potential as a general-purpose assistant for molecular analysis.

Text-to-video is a rapidly growing research area that aims to generate a semantic, identical, and temporal coherence sequence of frames that accurately align with the input text prompt. This study focuses on zero-shot text-to-video generation considering the data- and cost-efficient. To generate a semantic-coherent video, exhibiting a rich portrayal of temporal semantics such as the whole process of flower blooming rather than a set of "moving images", we propose a novel Free-Bloom pipeline that harnesses large language models (LLMs) as the director to generate a semantic-coherence prompt sequence, while pre-trained latent diffusion models (LDMs) as the animator to generate the high fidelity frames. Furthermore, to ensure temporal and identical coherence while maintaining semantic coherence, we propose a series of annotative modifications to adapting LDMs in the reverse process, including joint noise sampling, step-aware attention shift, and dual-path interpolation. Without any video data and training requirements, Free-Bloom generates vivid and high-quality videos, awe-inspiring in generating complex scenes with semantic meaningful frame sequences. In addition, Free-Bloom is naturally compatible with LDMs-based extensions.

The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to optimize laboratory operations and fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose a multi-domain, multi-task language model to solve a wide range of tasks in both the chemical and natural language domains. By leveraging multi-task learning, our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements and bonds respectively. Although existing deep learning models perform remarkably well at predicting physicochemical properties and binding affinities, the generation of new molecules with optimized properties remains challenging. Inherently, most GNNs perform poorly in whole-graph representation due to the limitations of the message-passing paradigm. Furthermore, step-by-step graph generation frameworks that use reinforcement learning or other sequential processing can be slow and result in a high proportion of invalid molecules with substantial post-processing needed in order to satisfy the principles of stoichiometry. To address these issues, we propose a representation-first approach to molecular graph generation. We guide the latent representation of an autoencoder by capturing graph structure information with the geometric scattering transform and apply penalties that structure the representation also by molecular properties. We show that this highly structured latent space can be directly used for molecular graph generation by the use of a GAN. We demonstrate that our architecture learns meaningful representations of drug datasets and provides a platform for goal-directed drug synthesis.

We propose fine-tuning large language models for generation of stable materials. While unorthodox, fine-tuning large language models on text-encoded atomistic data is simple to implement yet reliable, with around 90% of sampled structures obeying physical constraints on atom positions and charges. Using energy above hull calculations from both learned ML potentials and gold-standard DFT calculations, we show that our strongest model (fine-tuned LLaMA-2 70B) can generate materials predicted to be metastable at about twice the rate (49% vs 28%) of CDVAE, a competing diffusion model. Because of text prompting's inherent flexibility, our models can simultaneously be used for unconditional generation of stable material, infilling of partial structures and text-conditional generation. Finally, we show that language models' ability to capture key symmetries of crystal structures improves with model scale, suggesting that the biases of pretrained LLMs are surprisingly well-suited for atomistic data.

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

One critical prerequisite for faithful text-to-image generation is the accurate understanding of text inputs. Existing methods leverage the text encoder of the CLIP model to represent input prompts. However, the pre-trained CLIP model can merely encode English with a maximum token length of 77. Moreover, the model capacity of the text encoder from CLIP is relatively limited compared to Large Language Models (LLMs), which offer multilingual input, accommodate longer context, and achieve superior text representation. In this paper, we investigate LLMs as the text encoder to improve the language understanding in text-to-image generation. Unfortunately, training text-to-image generative model with LLMs from scratch demands significant computational resources and data. To this end, we introduce a three-stage training pipeline that effectively and efficiently integrates the existing text-to-image model with LLMs. Specifically, we propose a lightweight adapter that enables fast training of the text-to-image model using the textual representations from LLMs. Extensive experiments demonstrate that our model supports not only multilingual but also longer input context with superior image generation quality.

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language Models (LVLMs). However, the competency of the LLMs and instruction tuning have been less explored in the molecular domain. Thus, we propose LLaMo: Large Language Model-based Molecular graph assistant, which is an end-to-end trained large molecular graph-language model. To bridge the discrepancy between the language and graph modalities, we present the multi-level graph projector that transforms graph representations into graph tokens by abstracting the output representations of each GNN layer and motif representations with the cross-attention mechanism. We also introduce machine-generated molecular graph instruction data to instruction-tune the large molecular graph-language model for general-purpose molecule and language understanding. Our extensive experiments demonstrate that LLaMo shows the best performance on diverse tasks, such as molecular description generation, property prediction, and IUPAC name prediction. The code of LLaMo is available at https://github.com/mlvlab/LLaMo.

Molecular structure recognition is the task of translating a molecular image into its graph structure. Significant variation in drawing styles and conventions exhibited in chemical literature poses a significant challenge for automating this task. In this paper, we propose MolScribe, a novel image-to-graph generation model that explicitly predicts atoms and bonds, along with their geometric layouts, to construct the molecular structure. Our model flexibly incorporates symbolic chemistry constraints to recognize chirality and expand abbreviated structures. We further develop data augmentation strategies to enhance the model robustness against domain shifts. In experiments on both synthetic and realistic molecular images, MolScribe significantly outperforms previous models, achieving 76-93% accuracy on public benchmarks. Chemists can also easily verify MolScribe's prediction, informed by its confidence estimation and atom-level alignment with the input image. MolScribe is publicly available through Python and web interfaces: https://github.com/thomas0809/MolScribe.

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction.

Automated computational analysis of the vast chemical space is critical for numerous fields of research such as drug discovery and material science. Representation learning techniques have recently been employed with the primary objective of generating compact and informative numerical expressions of complex data. One approach to efficiently learn molecular representations is processing string-based notations of chemicals via natural language processing (NLP) algorithms. Majority of the methods proposed so far utilize SMILES notations for this purpose; however, SMILES is associated with numerous problems related to validity and robustness, which may prevent the model from effectively uncovering the knowledge hidden in the data. In this study, we propose SELFormer, a transformer architecture-based chemical language model that utilizes a 100% valid, compact and expressive notation, SELFIES, as input, in order to learn flexible and high-quality molecular representations. SELFormer is pre-trained on two million drug-like compounds and fine-tuned for diverse molecular property prediction tasks. Our performance evaluation has revealed that, SELFormer outperforms all competing methods, including graph learning-based approaches and SMILES-based chemical language models, on predicting aqueous solubility of molecules and adverse drug reactions. We also visualized molecular representations learned by SELFormer via dimensionality reduction, which indicated that even the pre-trained model can discriminate molecules with differing structural properties. We shared SELFormer as a programmatic tool, together with its datasets and pre-trained models. Overall, our research demonstrates the benefit of using the SELFIES notations in the context of chemical language modeling and opens up new possibilities for the design and discovery of novel drug candidates with desired features.

The goal of text generation is to make machines express in human language. It is one of the most important yet challenging tasks in natural language processing (NLP). Since 2014, various neural encoder-decoder models pioneered by Seq2Seq have been proposed to achieve the goal by learning to map input text to output text. However, the input text alone often provides limited knowledge to generate the desired output, so the performance of text generation is still far from satisfaction in many real-world scenarios. To address this issue, researchers have considered incorporating various forms of knowledge beyond the input text into the generation models. This research direction is known as knowledge-enhanced text generation. In this survey, we present a comprehensive review of the research on knowledge enhanced text generation over the past five years. The main content includes two parts: (i) general methods and architectures for integrating knowledge into text generation; (ii) specific techniques and applications according to different forms of knowledge data. This survey can have broad audiences, researchers and practitioners, in academia and industry.

Recent text-to-image generative models have enabled us to transform our words into vibrant, captivating imagery. The surge of personalization techniques that has followed has also allowed us to imagine unique concepts in new scenes. However, an intriguing question remains: How can we generate a new, imaginary concept that has never been seen before? In this paper, we present the task of creative text-to-image generation, where we seek to generate new members of a broad category (e.g., generating a pet that differs from all existing pets). We leverage the under-studied Diffusion Prior models and show that the creative generation problem can be formulated as an optimization process over the output space of the diffusion prior, resulting in a set of "prior constraints". To keep our generated concept from converging into existing members, we incorporate a question-answering model that adaptively adds new constraints to the optimization problem, encouraging the model to discover increasingly more unique creations. Finally, we show that our prior constraints can also serve as a strong mixing mechanism allowing us to create hybrids between generated concepts, introducing even more flexibility into the creative process.

Current vision-language generative models rely on expansive corpora of paired image-text data to attain optimal performance and generalization capabilities. However, automatically collecting such data (e.g. via large-scale web scraping) leads to low quality and poor image-text correlation, while human annotation is more accurate but requires significant manual effort and expense. We introduce ITIT (InTegrating Image Text): an innovative training paradigm grounded in the concept of cycle consistency which allows vision-language training on unpaired image and text data. ITIT is comprised of a joint image-text encoder with disjoint image and text decoders that enable bidirectional image-to-text and text-to-image generation in a single framework. During training, ITIT leverages a small set of paired image-text data to ensure its output matches the input reasonably well in both directions. Simultaneously, the model is also trained on much larger datasets containing only images or texts. This is achieved by enforcing cycle consistency between the original unpaired samples and the cycle-generated counterparts. For instance, it generates a caption for a given input image and then uses the caption to create an output image, and enforces similarity between the input and output images. Our experiments show that ITIT with unpaired datasets exhibits similar scaling behavior as using high-quality paired data. We demonstrate image generation and captioning performance on par with state-of-the-art text-to-image and image-to-text models with orders of magnitude fewer (only 3M) paired image-text data.

Recently, with the rapid advancements of generative models, the field of visual text generation has witnessed significant progress. However, it is still challenging to render high-quality text images in real-world scenarios, as three critical criteria should be satisfied: (1) Fidelity: the generated text images should be photo-realistic and the contents are expected to be the same as specified in the given conditions; (2) Reasonability: the regions and contents of the generated text should cohere with the scene; (3) Utility: the generated text images can facilitate related tasks (e.g., text detection and recognition). Upon investigation, we find that existing methods, either rendering-based or diffusion-based, can hardly meet all these aspects simultaneously, limiting their application range. Therefore, we propose in this paper a visual text generator (termed SceneVTG), which can produce high-quality text images in the wild. Following a two-stage paradigm, SceneVTG leverages a Multimodal Large Language Model to recommend reasonable text regions and contents across multiple scales and levels, which are used by a conditional diffusion model as conditions to generate text images. Extensive experiments demonstrate that the proposed SceneVTG significantly outperforms traditional rendering-based methods and recent diffusion-based methods in terms of fidelity and reasonability. Besides, the generated images provide superior utility for tasks involving text detection and text recognition. Code and datasets are available at AdvancedLiterateMachinery.

Traditionally, most data-to-text applications have been designed using a modular pipeline architecture, in which non-linguistic input data is converted into natural language through several intermediate transformations. In contrast, recent neural models for data-to-text generation have been proposed as end-to-end approaches, where the non-linguistic input is rendered in natural language with much less explicit intermediate representations in-between. This study introduces a systematic comparison between neural pipeline and end-to-end data-to-text approaches for the generation of text from RDF triples. Both architectures were implemented making use of state-of-the art deep learning methods as the encoder-decoder Gated-Recurrent Units (GRU) and Transformer. Automatic and human evaluations together with a qualitative analysis suggest that having explicit intermediate steps in the generation process results in better texts than the ones generated by end-to-end approaches. Moreover, the pipeline models generalize better to unseen inputs. Data and code are publicly available.

Recent text-to-image generation methods provide a simple yet exciting conversion capability between text and image domains. While these methods have incrementally improved the generated image fidelity and text relevancy, several pivotal gaps remain unanswered, limiting applicability and quality. We propose a novel text-to-image method that addresses these gaps by (i) enabling a simple control mechanism complementary to text in the form of a scene, (ii) introducing elements that substantially improve the tokenization process by employing domain-specific knowledge over key image regions (faces and salient objects), and (iii) adapting classifier-free guidance for the transformer use case. Our model achieves state-of-the-art FID and human evaluation results, unlocking the ability to generate high fidelity images in a resolution of 512x512 pixels, significantly improving visual quality. Through scene controllability, we introduce several new capabilities: (i) Scene editing, (ii) text editing with anchor scenes, (iii) overcoming out-of-distribution text prompts, and (iv) story illustration generation, as demonstrated in the story we wrote.

Large language models (LLMs) have shown remarkable ability on controllable text generation. However, the potential of LLMs in generating text from structured tables remains largely under-explored. In this paper, we study the capabilities of LLMs for table-to-text generation tasks, particularly aiming to investigate their performance in generating natural language statements that can be logically entailed by a provided table. First, we investigate how LLMs compare to state-of-the-art table-to-text fine-tuned models, and demonstrate that LLMs can generate statements with higher faithfulness compared with previous state-of-the-art fine-tuned models. Given this finding, we next explore whether LLMs can serve as faithfulness-level automated evaluation metrics. Through human evaluation, we show that evaluation metrics adopted from LLMs correlates better with human judgments compared with existing faithfulness-level metrics. Finally, we demonstrate that LLMs using chain-of-thought prompting can generate high-fidelity natural language feedback for other table-to-text models' generations, provide insights for future work regarding the distillation of text generation capabilities from LLMs to smaller models.

Existing text-to-image generation approaches have set high standards for photorealism and text-image correspondence, largely benefiting from web-scale text-image datasets, which can include up to 5~billion pairs. However, text-to-image generation models trained on domain-specific datasets, such as urban scenes, medical images, and faces, still suffer from low text-image correspondence due to the lack of text-image pairs. Additionally, collecting billions of text-image pairs for a specific domain can be time-consuming and costly. Thus, ensuring high text-image correspondence without relying on web-scale text-image datasets remains a challenging task. In this paper, we present a novel approach for enhancing text-image correspondence by leveraging available semantic layouts. Specifically, we propose a Gaussian-categorical diffusion process that simultaneously generates both images and corresponding layout pairs. Our experiments reveal that we can guide text-to-image generation models to be aware of the semantics of different image regions, by training the model to generate semantic labels for each pixel. We demonstrate that our approach achieves higher text-image correspondence compared to existing text-to-image generation approaches in the Multi-Modal CelebA-HQ and the Cityscapes dataset, where text-image pairs are scarce. Codes are available in this https://pmh9960.github.io/research/GCDP

Large-scale diffusion-based generative models have led to breakthroughs in text-conditioned high-resolution image synthesis. Starting from random noise, such text-to-image diffusion models gradually synthesize images in an iterative fashion while conditioning on text prompts. We find that their synthesis behavior qualitatively changes throughout this process: Early in sampling, generation strongly relies on the text prompt to generate text-aligned content, while later, the text conditioning is almost entirely ignored. This suggests that sharing model parameters throughout the entire generation process may not be ideal. Therefore, in contrast to existing works, we propose to train an ensemble of text-to-image diffusion models specialized for different synthesis stages. To maintain training efficiency, we initially train a single model, which is then split into specialized models that are trained for the specific stages of the iterative generation process. Our ensemble of diffusion models, called eDiff-I, results in improved text alignment while maintaining the same inference computation cost and preserving high visual quality, outperforming previous large-scale text-to-image diffusion models on the standard benchmark. In addition, we train our model to exploit a variety of embeddings for conditioning, including the T5 text, CLIP text, and CLIP image embeddings. We show that these different embeddings lead to different behaviors. Notably, the CLIP image embedding allows an intuitive way of transferring the style of a reference image to the target text-to-image output. Lastly, we show a technique that enables eDiff-I's "paint-with-words" capability. A user can select the word in the input text and paint it in a canvas to control the output, which is very handy for crafting the desired image in mind. The project page is available at https://deepimagination.cc/eDiff-I/

Language models (LMs) have revolutionized the way we interact with information, but they often generate nonfactual text, raising concerns about their reliability. Previous methods use external knowledge as references for text generation to enhance factuality but often struggle with the knowledge mix-up(e.g., entity mismatch) of irrelevant references. Besides,as the length of the output text grows, the randomness of sampling can escalate, detrimentally impacting the factual accuracy of the generated text. In this paper, we present DKGen, which divide the text generation process into an iterative process. In each iteration, DKGen takes the input query, the previously generated text and a subset of the reference passages as input to generate short text. During the process, the subset is dynamically selected from the full passage set based on their relevance to the previously generated text and the query, largely eliminating the irrelevant references from input. To further enhance DKGen's ability to correctly use these external knowledge, DKGen distills the relevance order of reference passages to the cross-attention distribution of decoder. We train and evaluate DKGen on a large-scale benchmark dataset. Experiment results show that DKGen outperforms all baseline models.

Self-supervised neural language models have recently achieved unprecedented success, from natural language processing to learning the languages of biological sequences and organic molecules. These models have demonstrated superior performance in the generation, structure classification, and functional predictions for proteins and molecules with learned representations. However, most of the masking-based pre-trained language models are not designed for generative design, and their black-box nature makes it difficult to interpret their design logic. Here we propose BLMM Crystal Transformer, a neural network based probabilistic generative model for generative and tinkering design of inorganic materials. Our model is built on the blank filling language model for text generation and has demonstrated unique advantages in learning the "materials grammars" together with high-quality generation, interpretability, and data efficiency. It can generate chemically valid materials compositions with as high as 89.7\% charge neutrality and 84.8\% balanced electronegativity, which are more than 4 and 8 times higher compared to a pseudo random sampling baseline. The probabilistic generation process of BLMM allows it to recommend tinkering operations based on learned materials chemistry and makes it useful for materials doping. Combined with the TCSP crysal structure prediction algorithm, We have applied our model to discover a set of new materials as validated using DFT calculations. Our work thus brings the unsupervised transformer language models based generative artificial intelligence to inorganic materials. A user-friendly web app has been developed for computational materials doping and can be accessed freely at www.materialsatlas.org/blmtinker.

We propose a method to fuse frozen text-only large language models (LLMs) with pre-trained image encoder and decoder models, by mapping between their embedding spaces. Our model demonstrates a wide suite of multimodal capabilities: image retrieval, novel image generation, and multimodal dialogue. Ours is the first approach capable of conditioning on arbitrarily interleaved image and text inputs to generate coherent image (and text) outputs. To achieve strong performance on image generation, we propose an efficient mapping network to ground the LLM to an off-the-shelf text-to-image generation model. This mapping network translates hidden representations of text into the embedding space of the visual models, enabling us to leverage the strong text representations of the LLM for visual outputs. Our approach outperforms baseline generation models on tasks with longer and more complex language. In addition to novel image generation, our model is also capable of image retrieval from a prespecified dataset, and decides whether to retrieve or generate at inference time. This is done with a learnt decision module which conditions on the hidden representations of the LLM. Our model exhibits a wider range of capabilities compared to prior multimodal language models. It can process image-and-text inputs, and produce retrieved images, generated images, and generated text -- outperforming non-LLM based generation models across several text-to-image tasks that measure context dependence.

Recent text-to-image models have achieved impressive results. However, since they require large-scale datasets of text-image pairs, it is impractical to train them on new domains where data is scarce or not labeled. In this work, we propose using large-scale retrieval methods, in particular, efficient k-Nearest-Neighbors (kNN), which offers novel capabilities: (1) training a substantially small and efficient text-to-image diffusion model without any text, (2) generating out-of-distribution images by simply swapping the retrieval database at inference time, and (3) performing text-driven local semantic manipulations while preserving object identity. To demonstrate the robustness of our method, we apply our kNN approach on two state-of-the-art diffusion backbones, and show results on several different datasets. As evaluated by human studies and automatic metrics, our method achieves state-of-the-art results compared to existing approaches that train text-to-image generation models using images only (without paired text data)

Large language models (LLMs) such as generative pretrained transformers (GPTs) have shown potential for various commercial applications, but their applicability for materials design remains underexplored. In this article, we introduce AtomGPT, a model specifically developed for materials design based on transformer architectures, to demonstrate the capability for both atomistic property prediction and structure generation. We show that a combination of chemical and structural text descriptions can efficiently predict material properties with accuracy comparable to graph neural network models, including formation energies, electronic bandgaps from two different methods and superconducting transition temperatures. Furthermore, we demonstrate that AtomGPT can generate atomic structures for tasks such as designing new superconductors, with the predictions validated through density functional theory calculations. This work paves the way for leveraging LLMs in forward and inverse materials design, offering an efficient approach to the discovery and optimization of materials.

Text-to-Image (T2I) generation methods based on diffusion model have garnered significant attention in the last few years. Although these image synthesis methods produce visually appealing results, they frequently exhibit spelling errors when rendering text within the generated images. Such errors manifest as missing, incorrect or extraneous characters, thereby severely constraining the performance of text image generation based on diffusion models. To address the aforementioned issue, this paper proposes a novel approach for text image generation, utilizing a pre-trained diffusion model (i.e., Stable Diffusion [27]). Our approach involves the design and training of a light-weight character-level text encoder, which replaces the original CLIP encoder and provides more robust text embeddings as conditional guidance. Then, we fine-tune the diffusion model using a large-scale dataset, incorporating local attention control under the supervision of character-level segmentation maps. Finally, by employing an inference stage refinement process, we achieve a notably high sequence accuracy when synthesizing text in arbitrarily given images. Both qualitative and quantitative results demonstrate the superiority of our method to the state of the art. Furthermore, we showcase several potential applications of the proposed UDiffText, including text-centric image synthesis, scene text editing, etc. Code and model will be available at https://github.com/ZYM-PKU/UDiffText .

Retrosynthesis planning poses a formidable challenge in the organic chemical industry, particularly in pharmaceuticals. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, Our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

This paper introduces M^{3}-20M, a large-scale Multi-Modal Molecular dataset that contains over 20 million molecules. Designed to support AI-driven drug design and discovery, M^{3}-20M is 71 times more in the number of molecules than the largest existing dataset, providing an unprecedented scale that can highly benefit training or fine-tuning large (language) models with superior performance for drug design and discovery. This dataset integrates one-dimensional SMILES, two-dimensional molecular graphs, three-dimensional molecular structures, physicochemical properties, and textual descriptions collected through web crawling and generated by using GPT-3.5, offering a comprehensive view of each molecule. To demonstrate the power of M^{3}-20M in drug design and discovery, we conduct extensive experiments on two key tasks: molecule generation and molecular property prediction, using large language models including GLM4, GPT-3.5, and GPT-4. Our experimental results show that M^{3}-20M can significantly boost model performance in both tasks. Specifically, it enables the models to generate more diverse and valid molecular structures and achieve higher property prediction accuracy than the existing single-modal datasets, which validates the value and potential of M^{3}-20M in supporting AI-driven drug design and discovery. The dataset is available at https://github.com/bz99bz/M-3.

Developing therapeutics is a lengthy and expensive process that requires the satisfaction of many different criteria, and AI models capable of expediting the process would be invaluable. However, the majority of current AI approaches address only a narrowly defined set of tasks, often circumscribed within a particular domain. To bridge this gap, we introduce Tx-LLM, a generalist large language model (LLM) fine-tuned from PaLM-2 which encodes knowledge about diverse therapeutic modalities. Tx-LLM is trained using a collection of 709 datasets that target 66 tasks spanning various stages of the drug discovery pipeline. Using a single set of weights, Tx-LLM simultaneously processes a wide variety of chemical or biological entities(small molecules, proteins, nucleic acids, cell lines, diseases) interleaved with free-text, allowing it to predict a broad range of associated properties, achieving competitive with state-of-the-art (SOTA) performance on 43 out of 66 tasks and exceeding SOTA on 22. Among these, Tx-LLM is particularly powerful and exceeds best-in-class performance on average for tasks combining molecular SMILES representations with text such as cell line names or disease names, likely due to context learned during pretraining. We observe evidence of positive transfer between tasks with diverse drug types (e.g.,tasks involving small molecules and tasks involving proteins), and we study the impact of model size, domain finetuning, and prompting strategies on performance. We believe Tx-LLM represents an important step towards LLMs encoding biochemical knowledge and could have a future role as an end-to-end tool across the drug discovery development pipeline.

In recent decades, chemistry publications and patents have increased rapidly. A significant portion of key information is embedded in molecular structure figures, complicating large-scale literature searches and limiting the application of large language models in fields such as biology, chemistry, and pharmaceuticals. The automatic extraction of precise chemical structures is of critical importance. However, the presence of numerous Markush structures in real-world documents, along with variations in molecular image quality, drawing styles, and noise, significantly limits the performance of existing optical chemical structure recognition (OCSR) methods. We present MolParser, a novel end-to-end OCSR method that efficiently and accurately recognizes chemical structures from real-world documents, including difficult Markush structure. We use a extended SMILES encoding rule to annotate our training dataset. Under this rule, we build MolParser-7M, the largest annotated molecular image dataset to our knowledge. While utilizing a large amount of synthetic data, we employed active learning methods to incorporate substantial in-the-wild data, specifically samples cropped from real patents and scientific literature, into the training process. We trained an end-to-end molecular image captioning model, MolParser, using a curriculum learning approach. MolParser significantly outperforms classical and learning-based methods across most scenarios, with potential for broader downstream applications. The dataset is publicly available.

Text generation is of great importance to many natural language processing applications. However, maximization-based decoding methods (e.g. beam search) of neural language models often lead to degenerate solutions -- the generated text is unnatural and contains undesirable repetitions. Existing approaches introduce stochasticity via sampling or modify training objectives to decrease probabilities of certain tokens (e.g., unlikelihood training). However, they often lead to solutions that lack coherence. In this work, we show that an underlying reason for model degeneration is the anisotropic distribution of token representations. We present a contrastive solution: (i) SimCTG, a contrastive training objective to calibrate the model's representation space, and (ii) a decoding method -- contrastive search -- to encourage diversity while maintaining coherence in the generated text. Extensive experiments and analyses on three benchmarks from two languages demonstrate that our proposed approach significantly outperforms current state-of-the-art text generation methods as evaluated by both human and automatic metrics.

Text-to-image diffusion models have demonstrated an impressive ability to produce high-quality outputs. However, they often struggle to accurately follow fine-grained spatial information in an input text. To this end, we propose a compositional approach for text-to-image generation based on two stages. In the first stage, we design a diffusion-based generative model to produce one or more aligned intermediate representations (such as depth or segmentation maps) conditioned on text. In the second stage, we map these representations, together with the text, to the final output image using a separate diffusion-based generative model. Our findings indicate that such compositional approach can improve image generation, resulting in a notable improvement in FID score and a comparable CLIP score, when compared to the standard non-compositional baseline.

In this technical report, we propose ChemVLM, the first open-source multimodal large language model dedicated to the fields of chemistry, designed to address the incompatibility between chemical image understanding and text analysis. Built upon the VIT-MLP-LLM architecture, we leverage ChemLLM-20B as the foundational large model, endowing our model with robust capabilities in understanding and utilizing chemical text knowledge. Additionally, we employ InternVIT-6B as a powerful image encoder. We have curated high-quality data from the chemical domain, including molecules, reaction formulas, and chemistry examination data, and compiled these into a bilingual multimodal question-answering dataset. We test the performance of our model on multiple open-source benchmarks and three custom evaluation sets. Experimental results demonstrate that our model achieves excellent performance, securing state-of-the-art results in five out of six involved tasks. Our model can be found at https://huggingface.co/AI4Chem/ChemVLM-26B.

Large diffusion-based Text-to-Image (T2I) models have shown impressive generative powers for text-to-image generation as well as spatially conditioned image generation. For most applications, we can train the model end-toend with paired data to obtain photorealistic generation quality. However, to add an additional task, one often needs to retrain the model from scratch using paired data across all modalities to retain good generation performance. In this paper, we tackle this issue and propose a novel strategy to scale a generative model across new tasks with minimal compute. During our experiments, we discovered that the variance maps of intermediate feature maps of diffusion models capture the intensity of conditioning. Utilizing this prior information, we propose MaxFusion, an efficient strategy to scale up text-to-image generation models to accommodate new modality conditions. Specifically, we combine aligned features of multiple models, hence bringing a compositional effect. Our fusion strategy can be integrated into off-the-shelf models to enhance their generative prowess.

Groundbreaking advancements in text-to-image generation have recently been achieved with the emergence of diffusion models. These models exhibit a remarkable ability to generate highly artistic and intricately detailed images based on textual prompts. However, obtaining desired generation outcomes often necessitates repetitive trials of manipulating text prompts just like casting spells on a magic mirror, and the reason behind that is the limited capability of semantic understanding inherent in current image generation models. Specifically, existing diffusion models encode the text prompt input with a pre-trained encoder structure, which is usually trained on a limited number of image-caption pairs. The state-of-the-art large language models (LLMs) based on the decoder-only structure have shown a powerful semantic understanding capability as their architectures are more suitable for training on very large-scale unlabeled data. In this work, we propose to enhance text-to-image diffusion models by borrowing the strength of semantic understanding from large language models, and devise a simple yet effective adapter to allow the diffusion models to be compatible with the decoder-only structure. Meanwhile, we also provide a supporting theoretical analysis with various architectures (e.g., encoder-only, encoder-decoder, and decoder-only), and conduct extensive empirical evaluations to verify its effectiveness. The experimental results show that the enhanced models with our adapter module are superior to the stat-of-the-art models in terms of text-to-image generation quality and reliability.

Chemical similarity searches are widely used in-silico methods for identifying new drug-like molecules. These methods have historically relied on structure-based comparisons to compute molecular similarity. Here, we use a chemical language model to create a vector-based chemical search. We extend implementations by creating a prompt engineering strategy that utilizes two different chemical string representation algorithms: one for the query and the other for the database. We explore this method by reviewing the search results from five drug-like query molecules (penicillin G, nirmatrelvir, zidovudine, lysergic acid diethylamide, and fentanyl) and three dye-like query molecules (acid blue 25, avobenzone, and 2-diphenylaminocarbazole). We find that this novel method identifies molecules that are functionally similar to the query, indicated by the associated patent literature, and that many of these molecules are structurally distinct from the query, making them unlikely to be found with traditional chemical similarity search methods. This method may aid in the discovery of novel structural classes of molecules that achieve target functionality.

Leveraging new data sources is a key step in accelerating the pace of materials design and discovery. To complement the strides in synthesis planning driven by historical, experimental, and computed data, we present an automated method for connecting scientific literature to synthesis insights. Starting from natural language text, we apply word embeddings from language models, which are fed into a named entity recognition model, upon which a conditional variational autoencoder is trained to generate syntheses for arbitrary materials. We show the potential of this technique by predicting precursors for two perovskite materials, using only training data published over a decade prior to their first reported syntheses. We demonstrate that the model learns representations of materials corresponding to synthesis-related properties, and that the model's behavior complements existing thermodynamic knowledge. Finally, we apply the model to perform synthesizability screening for proposed novel perovskite compounds.

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

It has always been an important yet challenging problem to control language models to avoid generating texts with undesirable attributes, such as toxic language and unnatural repetition. We introduce Click for controllable text generation, which needs no modification to the model architecture and facilitates out-of-the-box use of trained models. It employs a contrastive loss on sequence likelihood, which fundamentally decreases the generation probability of negative samples (i.e., generations with undesirable attributes). It also adopts a novel likelihood ranking-based strategy to construct contrastive samples from model generations. On the tasks of language detoxification, sentiment steering, and repetition reduction, we show that Click outperforms strong baselines of controllable text generation and demonstrate the superiority of Click's sample construction strategy.

We observe that the mapping between an image's representation in one model to its representation in another can be learned surprisingly well with just a linear layer, even across diverse models. Building on this observation, we propose text-to-concept, where features from a fixed pretrained model are aligned linearly to the CLIP space, so that text embeddings from CLIP's text encoder become directly comparable to the aligned features. With text-to-concept, we convert fixed off-the-shelf vision encoders to surprisingly strong zero-shot classifiers for free, with accuracy at times even surpassing that of CLIP, despite being much smaller models and trained on a small fraction of the data compared to CLIP. We show other immediate use-cases of text-to-concept, like building concept bottleneck models with no concept supervision, diagnosing distribution shifts in terms of human concepts, and retrieving images satisfying a set of text-based constraints. Lastly, we demonstrate the feasibility of concept-to-text, where vectors in a model's feature space are decoded by first aligning to the CLIP before being fed to a GPT-based generative model. Our work suggests existing deep models, with presumably diverse architectures and training, represent input samples relatively similarly, and a two-way communication across model representation spaces and to humans (through language) is viable.

Diffusion-based generative models have significantly advanced text-to-image generation but encounter challenges when processing lengthy and intricate text prompts describing complex scenes with multiple objects. While excelling in generating images from short, single-object descriptions, these models often struggle to faithfully capture all the nuanced details within longer and more elaborate textual inputs. In response, we present a novel approach leveraging Large Language Models (LLMs) to extract critical components from text prompts, including bounding box coordinates for foreground objects, detailed textual descriptions for individual objects, and a succinct background context. These components form the foundation of our layout-to-image generation model, which operates in two phases. The initial Global Scene Generation utilizes object layouts and background context to create an initial scene but often falls short in faithfully representing object characteristics as specified in the prompts. To address this limitation, we introduce an Iterative Refinement Scheme that iteratively evaluates and refines box-level content to align them with their textual descriptions, recomposing objects as needed to ensure consistency. Our evaluation on complex prompts featuring multiple objects demonstrates a substantial improvement in recall compared to baseline diffusion models. This is further validated by a user study, underscoring the efficacy of our approach in generating coherent and detailed scenes from intricate textual inputs.

Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

This work delved into the realm of automatic text generation, exploring a variety of techniques ranging from traditional deterministic approaches to more modern stochastic methods. Through analysis of greedy search, beam search, top-k sampling, top-p sampling, contrastive searching, and locally typical searching, this work has provided valuable insights into the strengths, weaknesses, and potential applications of each method. Each text-generating method is evaluated using several standard metrics and a comparative study has been made on the performance of the approaches. Finally, some future directions of research in the field of automatic text generation are also identified.

Text-to-image synthesis has made encouraging progress and attracted lots of public attention recently. However, popular evaluation metrics in this area, like the Inception Score and Fr'echet Inception Distance, incur several issues. First of all, they cannot explicitly assess the perceptual quality of generated images and poorly reflect the semantic alignment of each text-image pair. Also, they are inefficient and need to sample thousands of images to stabilise their evaluation results. In this paper, we propose to evaluate text-to-image generation performance by directly estimating the likelihood of the generated images using a pre-trained likelihood-based text-to-image generative model, i.e., a higher likelihood indicates better perceptual quality and better text-image alignment. To prevent the likelihood of being dominated by the non-crucial part of the generated image, we propose several new designs to develop a credit assignment strategy based on the semantic and perceptual significance of the image patches. In the experiments, we evaluate the proposed metric on multiple popular text-to-image generation models and datasets in accessing both the perceptual quality and the text-image alignment. Moreover, it can successfully assess the generation ability of these models with as few as a hundred samples, making it very efficient in practice.

Methods for designing organic materials with desired properties have high potential impact across fields such as medicine, renewable energy, petrochemical engineering, and agriculture. However, using generative modeling to design substances with desired properties is difficult because candidate compounds must satisfy multiple constraints, including synthetic accessibility and other metrics that are intuitive to domain experts but challenging to quantify. We propose C5T5, a novel self-supervised pretraining method that enables transformers to make zero-shot select-and-replace edits, altering organic substances towards desired property values. C5T5 operates on IUPAC names -- a standardized molecular representation that intuitively encodes rich structural information for organic chemists but that has been largely ignored by the ML community. Our technique requires no edited molecule pairs to train and only a rough estimate of molecular properties, and it has the potential to model long-range dependencies and symmetric molecular structures more easily than graph-based methods. C5T5 also provides a powerful interface to domain experts: it grants users fine-grained control over the generative process by selecting and replacing IUPAC name fragments, which enables experts to leverage their intuitions about structure-activity relationships. We demonstrate C5T5's effectiveness on four physical properties relevant for drug discovery, showing that it learns successful and chemically intuitive strategies for altering molecules towards desired property values.

Conditional neural text generation models generate high-quality outputs, but often concentrate around a mode when what we really want is a diverse set of options. We present a search algorithm to construct lattices encoding a massive number of generation options. First, we restructure decoding as a best-first search, which explores the space differently than beam search and improves efficiency by avoiding pruning paths. Second, we revisit the idea of hypothesis recombination: we can identify pairs of similar generation candidates during search and merge them as an approximation. On both summarization and machine translation, we show that our algorithm encodes thousands of diverse options that remain grammatical and high-quality into one lattice. This algorithm provides a foundation for building downstream generation applications on top of massive-scale diverse outputs.

This paper introduces a neural model for concept-to-text generation that scales to large, rich domains. We experiment with a new dataset of biographies from Wikipedia that is an order of magnitude larger than existing resources with over 700k samples. The dataset is also vastly more diverse with a 400k vocabulary, compared to a few hundred words for Weathergov or Robocup. Our model builds upon recent work on conditional neural language model for text generation. To deal with the large vocabulary, we extend these models to mix a fixed vocabulary with copy actions that transfer sample-specific words from the input database to the generated output sentence. Our neural model significantly out-performs a classical Kneser-Ney language model adapted to this task by nearly 15 BLEU.

Text-to-3D generation is to craft a 3D object according to a natural language description. This can significantly reduce the workload for manually designing 3D models and provide a more natural way of interaction for users. However, this problem remains challenging in recovering the fine-grained details effectively and optimizing a large-size 3D output efficiently. Inspired by the success of progressive learning, we propose a Multi-Scale Triplane Network (MTN) and a new progressive learning strategy. As the name implies, the Multi-Scale Triplane Network consists of four triplanes transitioning from low to high resolution. The low-resolution triplane could serve as an initial shape for the high-resolution ones, easing the optimization difficulty. To further enable the fine-grained details, we also introduce the progressive learning strategy, which explicitly demands the network to shift its focus of attention from simple coarse-grained patterns to difficult fine-grained patterns. Our experiment verifies that the proposed method performs favorably against existing methods. For even the most challenging descriptions, where most existing methods struggle to produce a viable shape, our proposed method consistently delivers. We aspire for our work to pave the way for automatic 3D prototyping via natural language descriptions.

Standard language models generate text by selecting tokens from a fixed, finite, and standalone vocabulary. We introduce a novel method that selects context-aware phrases from a collection of supporting documents. One of the most significant challenges for this paradigm shift is determining the training oracles, because a string of text can be segmented in various ways and each segment can be retrieved from numerous possible documents. To address this, we propose to initialize the training oracles using linguistic heuristics and, more importantly, bootstrap the oracles through iterative self-reinforcement. Extensive experiments show that our model not only outperforms standard language models on a variety of knowledge-intensive tasks but also demonstrates improved generation quality in open-ended text generation. For instance, compared to the standard language model counterpart, our model raises the accuracy from 23.47% to 36.27% on OpenbookQA, and improves the MAUVE score from 42.61% to 81.58% in open-ended text generation. Remarkably, our model also achieves the best performance and the lowest latency among several retrieval-augmented baselines. In conclusion, we assert that retrieval is more accurate generation and hope that our work will encourage further research on this new paradigm shift.

A wide variety of NLP applications, such as machine translation, summarization, and dialog, involve text generation. One major challenge for these applications is how to evaluate whether such generated texts are actually fluent, accurate, or effective. In this work, we conceptualize the evaluation of generated text as a text generation problem, modeled using pre-trained sequence-to-sequence models. The general idea is that models trained to convert the generated text to/from a reference output or the source text will achieve higher scores when the generated text is better. We operationalize this idea using BART, an encoder-decoder based pre-trained model, and propose a metric BARTScore with a number of variants that can be flexibly applied in an unsupervised fashion to evaluation of text from different perspectives (e.g. informativeness, fluency, or factuality). BARTScore is conceptually simple and empirically effective. It can outperform existing top-scoring metrics in 16 of 22 test settings, covering evaluation of 16 datasets (e.g., machine translation, text summarization) and 7 different perspectives (e.g., informativeness, factuality). Code to calculate BARTScore is available at https://github.com/neulab/BARTScore, and we have released an interactive leaderboard for meta-evaluation at http://explainaboard.nlpedia.ai/leaderboard/task-meval/ on the ExplainaBoard platform, which allows us to interactively understand the strengths, weaknesses, and complementarity of each metric.

Literature research, vital for scientific work, faces the challenge of the surging torrent of information in the vast ocean of literature exceeding researchers' processing capabilities. To address this issue, we present an automated review generation method based on Large Language Models (LLMs), aimed at overcoming efficiency bottlenecks in literature processing and reducing cognitive load. Our statistically validated evaluation framework demonstrates that the generated reviews match or exceed manual quality, offering broad applicability across research fields due to minimal domain knowledge requirements. In a case study on propane dehydrogenation (PDH) catalysts, our method swiftly analyzed 343 articles, averaging seconds per article per LLM account, producing comprehensive reviews spanning 35 topics. Extended analysis of 1041 articles provided deep insights into catalysts' composition, structure, and performance. Recognizing LLMs' hallucinations, we implemented a multi-layered quality control strategy, effectively mitigating risks and ensuring reliability, as quantitatively demonstrated through manual verification. Expert verification confirms the accuracy and citation integrity of generated reviews, demonstrating LLM hallucination risks reduced to below 0.5\% with over 95\% confidence. Released Windows application enables one-click review generation, aiding researchers in tracking advancements and recommending literature. This approach showcases LLMs' role in enhancing scientific research productivity and sets the stage for further exploration.

The task of condensing large chunks of textual information into concise and structured tables has gained attention recently due to the emergence of Large Language Models (LLMs) and their potential benefit for downstream tasks, such as text summarization and text mining. Previous approaches often generate tables that directly replicate information from the text, limiting their applicability in broader contexts, as text-to-table generation in real-life scenarios necessitates information extraction, reasoning, and integration. However, there is a lack of both datasets and methodologies towards this task. In this paper, we introduce LiveSum, a new benchmark dataset created for generating summary tables of competitions based on real-time commentary texts. We evaluate the performances of state-of-the-art LLMs on this task in both fine-tuning and zero-shot settings, and additionally propose a novel pipeline called T^3(Text-Tuple-Table) to improve their performances. Extensive experimental results demonstrate that LLMs still struggle with this task even after fine-tuning, while our approach can offer substantial performance gains without explicit training. Further analyses demonstrate that our method exhibits strong generalization abilities, surpassing previous approaches on several other text-to-table datasets. Our code and data can be found at https://github.com/HKUST-KnowComp/LiveSum-TTT.

With increasing usage of generative models for text generation and widespread use of machine generated texts in various domains, being able to distinguish between human written and machine generated texts is a significant challenge. While existing models and proprietary systems focus on identifying whether given text is entirely human written or entirely machine generated, only a few systems provide insights at sentence or paragraph level at likelihood of being machine generated at a non reliable accuracy level, working well only for a set of domains and generators. This paper introduces few reliable approaches for the novel task of identifying which part of a given text is machine generated at a word level while comparing results from different approaches and methods. We present a comparison with proprietary systems , performance of our model on unseen domains' and generators' texts. The findings reveal significant improvements in detection accuracy along with comparison on other aspects of detection capabilities. Finally we discuss potential avenues for improvement and implications of our work. The proposed model is also well suited for detecting which parts of a text are machine generated in outputs of Instruct variants of many LLMs.

We introduce Meta 3D Gen (3DGen), a new state-of-the-art, fast pipeline for text-to-3D asset generation. 3DGen offers 3D asset creation with high prompt fidelity and high-quality 3D shapes and textures in under a minute. It supports physically-based rendering (PBR), necessary for 3D asset relighting in real-world applications. Additionally, 3DGen supports generative retexturing of previously generated (or artist-created) 3D shapes using additional textual inputs provided by the user. 3DGen integrates key technical components, Meta 3D AssetGen and Meta 3D TextureGen, that we developed for text-to-3D and text-to-texture generation, respectively. By combining their strengths, 3DGen represents 3D objects simultaneously in three ways: in view space, in volumetric space, and in UV (or texture) space. The integration of these two techniques achieves a win rate of 68% with respect to the single-stage model. We compare 3DGen to numerous industry baselines, and show that it outperforms them in terms of prompt fidelity and visual quality for complex textual prompts, while being significantly faster.

Large language models (LLMs) have established great success in the general domain of natural language processing. Their emerging task generalization and free-form dialogue capabilities can greatly help to design Chemical General Intelligence (CGI) to assist real-world research in chemistry. However, the existence of specialized language and knowledge in the field of chemistry, such as the highly informative SMILES notation, hinders the performance of general-domain LLMs in chemistry. To this end, we develop ChemDFM, the first LLM towards CGI. ChemDFM-13B is trained on 34B tokens from chemical literature, textbooks, and instructions as well as various data from the general domain. Therefore, it can store, understand, and reason over chemical knowledge and languages while still possessing advanced free-form language comprehension capabilities. Extensive quantitative evaluation shows that ChemDFM can significantly outperform the representative open-sourced LLMs. Moreover, ChemDFM can also surpass GPT-4 on a great portion of chemical tasks, despite the significant size difference. Further qualitative evaluations demonstrate the efficiency and effectiveness of ChemDFM in real-world research scenarios. We will open-source the ChemDFM model soon.

Despite rapid advancement in the field of Constrained Natural Language Generation, little time has been spent on exploring the potential of language models which have had their vocabularies lexically, semantically, and/or phonetically constrained. We find that most language models generate compelling text even under significant constraints. We present a simple and universally applicable technique for modifying the output of a language model by compositionally applying filter functions to the language models vocabulary before a unit of text is generated. This approach is plug-and-play and requires no modification to the model. To showcase the value of this technique, we present an easy to use AI writing assistant called Constrained Text Generation Studio (CTGS). CTGS allows users to generate or choose from text with any combination of a wide variety of constraints, such as banning a particular letter, forcing the generated words to have a certain number of syllables, and/or forcing the words to be partial anagrams of another word. We introduce a novel dataset of prose that omits the letter e. We show that our method results in strictly superior performance compared to fine-tuning alone on this dataset. We also present a Huggingface space web-app presenting this technique called Gadsby. The code is available to the public here: https://github.com/Hellisotherpeople/Constrained-Text-Generation-Studio

Traditional molecular string representations, such as SMILES, often pose challenges for AI-driven molecular design due to their non-sequential depiction of molecular substructures. To address this issue, we introduce Sequential Attachment-based Fragment Embedding (SAFE), a novel line notation for chemical structures. SAFE reimagines SMILES strings as an unordered sequence of interconnected fragment blocks while maintaining full compatibility with existing SMILES parsers. It streamlines complex generative tasks, including scaffold decoration, fragment linking, polymer generation, and scaffold hopping, while facilitating autoregressive generation for fragment-constrained design, thereby eliminating the need for intricate decoding or graph-based models. We demonstrate the effectiveness of SAFE by training an 87-million-parameter GPT2-like model on a dataset containing 1.1 billion SAFE representations. Through extensive experimentation, we show that our SAFE-GPT model exhibits versatile and robust optimization performance. SAFE opens up new avenues for the rapid exploration of chemical space under various constraints, promising breakthroughs in AI-driven molecular design.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

This project aims to investigate a novel sequence generation method inspired by the AlphaGo paradigm, adapting it for use with large language models (LLMs). The proposed approach involves creating search trees of different possible completions and evaluating these completions based on model confidence. By considering various paths in the search tree and scoring them according to the model's confidence in each completion, we can generate diverse and high-quality sequences. This research explores the implementation of this paradigm by using confidence as a proxy for response quality akin to beam search vijayakumar2016diverse. The primary goal of this paper is to outline the paradigm and demonstrate its potential, rather than focusing on achieving perfect results. The paper will outline the reasons why we believe this paradigm has the potential to improve LLMs in the following manners: 1) increase output quality, 2) decrease errors, 3) eliminate or reduce the compound error problems, 4) generate diverse and creative completions, 5) allow for iterative problem-solving, and 6) self-training. We expect this approach to yield a set of diverse and coherent sequences, offering insights into balancing exploration and exploitation in sequence generation. Potential applications include creative text generation tasks, such as storytelling and content creation, as well as other natural language processing domains, like machine translation and automated summarization. The goal is that the model will be far more effective as it will be able to consider many possible variations allowing it to find the ideal completion. This research aims to contribute to the understanding of effective search strategies in sequence generation and their impact on generating high-quality, varied textual outputs.

Despite recent progress of pre-trained language models on generating fluent text, existing methods still suffer from incoherence problems in long-form text generation tasks that require proper content control and planning to form a coherent high-level logical flow. In this work, we propose PLANET, a novel generation framework leveraging autoregressive self-attention mechanism to conduct content planning and surface realization dynamically. To guide the generation of output sentences, our framework enriches the Transformer decoder with latent representations to maintain sentence-level semantic plans grounded by bag-of-words. Moreover, we introduce a new coherence-based contrastive learning objective to further improve the coherence of output. Extensive experiments are conducted on two challenging long-form text generation tasks including counterargument generation and opinion article generation. Both automatic and human evaluations show that our method significantly outperforms strong baselines and generates more coherent texts with richer contents.

The recent availability and adaptability of text-to-image models has sparked a new era in many related domains that benefit from the learned text priors as well as high-quality and fast generation capabilities, one of which is texture generation for 3D objects. Although recent texture generation methods achieve impressive results by using text-to-image networks, the combination of global consistency, quality, and speed, which is crucial for advancing texture generation to real-world applications, remains elusive. To that end, we introduce Meta 3D TextureGen: a new feedforward method comprised of two sequential networks aimed at generating high-quality and globally consistent textures for arbitrary geometries of any complexity degree in less than 20 seconds. Our method achieves state-of-the-art results in quality and speed by conditioning a text-to-image model on 3D semantics in 2D space and fusing them into a complete and high-resolution UV texture map, as demonstrated by extensive qualitative and quantitative evaluations. In addition, we introduce a texture enhancement network that is capable of up-scaling any texture by an arbitrary ratio, producing 4k pixel resolution textures.

Recent strides in Text-to-3D techniques have been propelled by distilling knowledge from powerful large text-to-image diffusion models (LDMs). Nonetheless, existing Text-to-3D approaches often grapple with challenges such as over-saturation, inadequate detailing, and unrealistic outputs. This study presents a novel strategy that leverages explicitly synthesized multi-view images to address these issues. Our approach involves the utilization of image-to-image pipelines, empowered by LDMs, to generate posed high-quality images based on the renderings of coarse 3D models. Although the generated images mostly alleviate the aforementioned issues, challenges such as view inconsistency and significant content variance persist due to the inherent generative nature of large diffusion models, posing extensive difficulties in leveraging these images effectively. To overcome this hurdle, we advocate integrating a discriminator alongside a novel Diffusion-GAN dual training strategy to guide the training of 3D models. For the incorporated discriminator, the synthesized multi-view images are considered real data, while the renderings of the optimized 3D models function as fake data. We conduct a comprehensive set of experiments that demonstrate the effectiveness of our method over baseline approaches.

Natural Language Generation (NLG) accepts input data in the form of images, videos, or text and generates corresponding natural language text as output. Existing NLG methods mainly adopt a supervised approach and rely heavily on coupled data-to-text pairs. However, for many targeted scenarios and for non-English languages, sufficient quantities of labeled data are often not available. To relax the dependency on labeled data of downstream tasks, we propose an intuitive and effective zero-shot learning framework, ZeroNLG, which can deal with multiple NLG tasks, including image-to-text (image captioning), video-to-text (video captioning), and text-to-text (neural machine translation), across English, Chinese, German, and French within a unified framework. ZeroNLG does not require any labeled downstream pairs for training. During training, ZeroNLG (i) projects different domains (across modalities and languages) to corresponding coordinates in a shared common latent space; (ii) bridges different domains by aligning their corresponding coordinates in this space; and (iii) builds an unsupervised multilingual auto-encoder to learn to generate text by reconstructing the input text given its coordinate in shared latent space. Consequently, during inference, based on the data-to-text pipeline, ZeroNLG can generate target sentences across different languages given the coordinate of input data in the common space. Within this unified framework, given visual (imaging or video) data as input, ZeroNLG can perform zero-shot visual captioning; given textual sentences as input, ZeroNLG can perform zero-shot machine translation. We present the results of extensive experiments on twelve NLG tasks, showing that, without using any labeled downstream pairs for training, ZeroNLG generates high-quality and believable outputs and significantly outperforms existing zero-shot methods.

Despite recent advancements, most computational methods for molecule optimization are constrained to single- or double-property optimization tasks and suffer from poor scalability and generalizability to novel optimization tasks. Meanwhile, Large Language Models (LLMs) demonstrate remarkable out-of-domain generalizability to novel tasks. To demonstrate LLMs' potential for molecule optimization, we introduce MoMUInstruct, the first high-quality instruction-tuning dataset specifically focused on complex multi-property molecule optimization tasks. Leveraging MoMUInstruct, we develop GeLLM^3Os, a series of instruction-tuned LLMs for molecule optimization. Extensive evaluations across 5 in-domain and 5 out-of-domain tasks demonstrate that GeLLM^3Os consistently outperform state-of-the-art baselines. GeLLM^3Os also exhibit outstanding zero-shot generalization to unseen tasks, significantly outperforming powerful closed-source LLMs. Such strong generalizability demonstrates the tremendous potential of GeLLM^3Os as foundational models for molecule optimization, thereby tackling novel optimization tasks without resource-intensive retraining. MoMUInstruct, models, and code are accessible through https://github.com/ninglab/GeLLMO.

We study the text generation task under the approach of pre-trained language models (PLMs). Typically, an auto-regressive (AR) method is adopted for generating texts in a token-by-token manner. Despite many advantages of AR generation, it usually suffers from inefficient inference. Therefore, non-autoregressive (NAR) models are proposed to generate all target tokens simultaneously. However, NAR models usually generate texts of lower quality due to the absence of token dependency in the output text. In this paper, we propose ELMER: an efficient and effective PLM for NAR text generation to explicitly model the token dependency during NAR generation. By leveraging the early exit technique, ELMER enables the token generations at different layers, according to their prediction confidence (a more confident token will exit at a lower layer). Besides, we propose a novel pre-training objective, Layer Permutation Language Modeling, to pre-train ELMER by permuting the exit layer for each token in sequences. Experiments on three text generation tasks show that ELMER significantly outperforms NAR models and further narrows the performance gap with AR PLMs (\eg ELMER (29.92) vs BART (30.61) ROUGE-L in XSUM) while achieving over 10 times inference speedup.

Machine learning, notably deep learning, has significantly propelled molecular investigations within the biochemical sphere. Traditionally, modeling for such research has centered around a handful of paradigms. For instance, the prediction paradigm is frequently deployed for tasks such as molecular property prediction. To enhance the generation and decipherability of purely data-driven models, scholars have integrated biochemical domain knowledge into these molecular study models. This integration has sparked a surge in paradigm transfer, which is solving one molecular learning task by reformulating it as another one. With the emergence of Large Language Models, these paradigms have demonstrated an escalating trend towards harmonized unification. In this work, we delineate a literature survey focused on knowledge-informed molecular learning from the perspective of paradigm transfer. We classify the paradigms, scrutinize their methodologies, and dissect the contribution of domain knowledge. Moreover, we encapsulate prevailing trends and identify intriguing avenues for future exploration in molecular learning.

Large-scale text-to-image generative models have been a revolutionary breakthrough in the evolution of generative AI, allowing us to synthesize diverse images that convey highly complex visual concepts. However, a pivotal challenge in leveraging such models for real-world content creation tasks is providing users with control over the generated content. In this paper, we present a new framework that takes text-to-image synthesis to the realm of image-to-image translation -- given a guidance image and a target text prompt, our method harnesses the power of a pre-trained text-to-image diffusion model to generate a new image that complies with the target text, while preserving the semantic layout of the source image. Specifically, we observe and empirically demonstrate that fine-grained control over the generated structure can be achieved by manipulating spatial features and their self-attention inside the model. This results in a simple and effective approach, where features extracted from the guidance image are directly injected into the generation process of the target image, requiring no training or fine-tuning and applicable for both real or generated guidance images. We demonstrate high-quality results on versatile text-guided image translation tasks, including translating sketches, rough drawings and animations into realistic images, changing of the class and appearance of objects in a given image, and modifications of global qualities such as lighting and color.

We present ToTTo, an open-domain English table-to-text dataset with over 120,000 training examples that proposes a controlled generation task: given a Wikipedia table and a set of highlighted table cells, produce a one-sentence description. To obtain generated targets that are natural but also faithful to the source table, we introduce a dataset construction process where annotators directly revise existing candidate sentences from Wikipedia. We present systematic analyses of our dataset and annotation process as well as results achieved by several state-of-the-art baselines. While usually fluent, existing methods often hallucinate phrases that are not supported by the table, suggesting that this dataset can serve as a useful research benchmark for high-precision conditional text generation.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

Text-to-image generation models have grown in popularity due to their ability to produce high-quality images from a text prompt. One use for this technology is to enable the creation of more accessible art creation software. In this paper, we document the development of an alternative user interface that reduces the typing effort needed to enter image prompts by providing suggestions from a large language model, developed through iterative design and testing within the project team. The results of this testing demonstrate how generative text models can support the accessibility of text-to-image models, enabling users with a range of abilities to create visual art.

We consider the task of text generation in language models with constraints specified in natural language. To this end, we first create a challenging benchmark Cognac that provides as input to the model a topic with example text, along with a constraint on text to be avoided. Unlike prior work, our benchmark contains knowledge-intensive constraints sourced from databases like Wordnet and Wikidata, which allows for straightforward evaluation while striking a balance between broad attribute-level and narrow lexical-level controls. We find that even state-of-the-art language models like GPT-3 fail often on this task, and propose a solution to leverage a language model's own internal knowledge to guide generation. Our method, called CognacGen, first queries the language model to generate guidance terms for a specified topic or constraint, and uses the guidance to modify the model's token generation probabilities. We propose three forms of guidance (binary verifier, top-k tokens, textual example), and employ prefix-tuning approaches to distill the guidance to tackle diverse natural language constraints. Through extensive empirical evaluations, we demonstrate that CognacGen can successfully generalize to unseen instructions and outperform competitive baselines in generating constraint conforming text.

Text-to-motion generation is a crucial task in computer vision, which generates the target 3D motion by the given text. The existing annotated datasets are limited in scale, resulting in most existing methods overfitting to the small datasets and unable to generalize to the motions of the open domain. Some methods attempt to solve the open-vocabulary motion generation problem by aligning to the CLIP space or using the Pretrain-then-Finetuning paradigm. However, the current annotated dataset's limited scale only allows them to achieve mapping from sub-text-space to sub-motion-space, instead of mapping between full-text-space and full-motion-space (full mapping), which is the key to attaining open-vocabulary motion generation. To this end, this paper proposes to leverage the atomic motion (simple body part motions over a short time period) as an intermediate representation, and leverage two orderly coupled steps, i.e., Textual Decomposition and Sub-motion-space Scattering, to address the full mapping problem. For Textual Decomposition, we design a fine-grained description conversion algorithm, and combine it with the generalization ability of a large language model to convert any given motion text into atomic texts. Sub-motion-space Scattering learns the compositional process from atomic motions to the target motions, to make the learned sub-motion-space scattered to form the full-motion-space. For a given motion of the open domain, it transforms the extrapolation into interpolation and thereby significantly improves generalization. Our network, DSO-Net, combines textual decomposition and sub-motion-space scattering to solve the open-vocabulary motion generation. Extensive experiments demonstrate that our DSO-Net achieves significant improvements over the state-of-the-art methods on open-vocabulary motion generation. Code is available at https://vankouf.github.io/DSONet/.

Personalized text generation is an emerging research area that has attracted much attention in recent years. Most studies in this direction focus on a particular domain by designing bespoke features or models. In this work, we propose a general approach for personalized text generation using large language models (LLMs). Inspired by the practice of writing education, we develop a multistage and multitask framework to teach LLMs for personalized generation. In writing instruction, the task of writing from sources is often decomposed into multiple steps that involve finding, evaluating, summarizing, synthesizing, and integrating information. Analogously, our approach to personalized text generation consists of multiple stages: retrieval, ranking, summarization, synthesis, and generation. In addition, we introduce a multitask setting that helps the model improve its generation ability further, which is inspired by the observation in education that a student's reading proficiency and writing ability are often correlated. We evaluate our approach on three public datasets, each of which covers a different and representative domain. Our results show significant improvements over a variety of baselines.

Text-to-image generation has traditionally focused on finding better modeling assumptions for training on a fixed dataset. These assumptions might involve complex architectures, auxiliary losses, or side information such as object part labels or segmentation masks supplied during training. We describe a simple approach for this task based on a transformer that autoregressively models the text and image tokens as a single stream of data. With sufficient data and scale, our approach is competitive with previous domain-specific models when evaluated in a zero-shot fashion.

Generative models trained at scale can now produce text, video, and more recently, scientific data such as crystal structures. In applications of generative approaches to materials science, and in particular to crystal structures, the guidance from the domain expert in the form of high-level instructions can be essential for an automated system to output candidate crystals that are viable for downstream research. In this work, we formulate end-to-end language-to-structure generation as a multi-objective optimization problem, and propose Generative Hierarchical Materials Search (GenMS) for controllable generation of crystal structures. GenMS consists of (1) a language model that takes high-level natural language as input and generates intermediate textual information about a crystal (e.g., chemical formulae), and (2) a diffusion model that takes intermediate information as input and generates low-level continuous value crystal structures. GenMS additionally uses a graph neural network to predict properties (e.g., formation energy) from the generated crystal structures. During inference, GenMS leverages all three components to conduct a forward tree search over the space of possible structures. Experiments show that GenMS outperforms other alternatives of directly using language models to generate structures both in satisfying user request and in generating low-energy structures. We confirm that GenMS is able to generate common crystal structures such as double perovskites, or spinels, solely from natural language input, and hence can form the foundation for more complex structure generation in near future.

Recent breakthroughs in the field of language-guided image generation have yielded impressive achievements, enabling the creation of high-quality and diverse images based on user instructions.Although the synthesis performance is fascinating, one significant limitation of current image generation models is their insufficient ability to generate text coherently within images, particularly for complex glyph structures like Chinese characters. To address this problem, we introduce GlyphDraw, a general learning framework aiming to endow image generation models with the capacity to generate images coherently embedded with text for any specific language.We first sophisticatedly design the image-text dataset's construction strategy, then build our model specifically on a diffusion-based image generator and carefully modify the network structure to allow the model to learn drawing language characters with the help of glyph and position information.Furthermore, we maintain the model's open-domain image synthesis capability by preventing catastrophic forgetting by using parameter-efficient fine-tuning techniques.Extensive qualitative and quantitative experiments demonstrate that our method not only produces accurate language characters as in prompts, but also seamlessly blends the generated text into the background.Please refer to our https://1073521013.github.io/glyph-draw.github.io/{project page}. abstract

Data-to-text (D2T) generation is a crucial task in many natural language understanding (NLU) applications and forms the foundation of task-oriented dialog systems. In the context of conversational AI solutions that can work directly with local data on the user's device, architectures utilizing large pre-trained language models (PLMs) are impractical for on-device deployment due to a high memory footprint. To this end, we propose TrICy, a novel lightweight framework for an enhanced D2T task that generates text sequences based on the intent in context and may further be guided by user-provided triggers. We leverage an attention-copy mechanism to predict out-of-vocabulary (OOV) words accurately. Performance analyses on E2E NLG dataset (BLEU: 66.43%, ROUGE-L: 70.14%), WebNLG dataset (BLEU: Seen 64.08%, Unseen 52.35%), and our Custom dataset related to text messaging applications, showcase our architecture's effectiveness. Moreover, we show that by leveraging an optional trigger input, data-to-text generation quality increases significantly and achieves the new SOTA score of 69.29% BLEU for E2E NLG. Furthermore, our analyses show that TrICy achieves at least 24% and 3% improvement in BLEU and METEOR respectively over LLMs like GPT-3, ChatGPT, and Llama 2. We also demonstrate that in some scenarios, performance improvement due to triggers is observed even when they are absent in training.

Despite the crucial importance of accelerating text generation in large language models (LLMs) for efficiently producing content, the sequential nature of this process often leads to high inference latency, posing challenges for real-time applications. Various techniques have been proposed and developed to address these challenges and improve efficiency. This paper presents a comprehensive survey of accelerated generation techniques in autoregressive language models, aiming to understand the state-of-the-art methods and their applications. We categorize these techniques into several key areas: speculative decoding, early exiting mechanisms, and non-autoregressive methods. We discuss each category's underlying principles, advantages, limitations, and recent advancements. Through this survey, we aim to offer insights into the current landscape of techniques in LLMs and provide guidance for future research directions in this critical area of natural language processing.

Text generation has become more accessible than ever, and the increasing interest in these systems, especially those using large language models, has spurred an increasing number of related publications. We provide a systematic literature review comprising 244 selected papers between 2017 and 2024. This review categorizes works in text generation into five main tasks: open-ended text generation, summarization, translation, paraphrasing, and question answering. For each task, we review their relevant characteristics, sub-tasks, and specific challenges (e.g., missing datasets for multi-document summarization, coherence in story generation, and complex reasoning for question answering). Additionally, we assess current approaches for evaluating text generation systems and ascertain problems with current metrics. Our investigation shows nine prominent challenges common to all tasks and sub-tasks in recent text generation publications: bias, reasoning, hallucinations, misuse, privacy, interpretability, transparency, datasets, and computing. We provide a detailed analysis of these challenges, their potential solutions, and which gaps still require further engagement from the community. This systematic literature review targets two main audiences: early career researchers in natural language processing looking for an overview of the field and promising research directions, as well as experienced researchers seeking a detailed view of tasks, evaluation methodologies, open challenges, and recent mitigation strategies.

Existing large language models have to run K times to generate a sequence of K tokens. In this paper, we present RecycleGPT, a generative language model with fast decoding speed by recycling pre-generated model states without running the whole model in multiple steps. Our approach relies on the observation that adjacent tokens in a sequence usually have strong correlations and the next token in a sequence can be reasonably guessed or inferred based on the preceding ones. Through theoretical evaluations and practical tests on downstream text generation tasks, we demonstrate the effectiveness of our approach in lowering inference latency, achieving up to 1.4x speedup while preserving high performance.

Natural Language Generation (NLG) has improved exponentially in recent years thanks to the development of sequence-to-sequence deep learning technologies such as Transformer-based language models. This advancement has led to more fluent and coherent NLG, leading to improved development in downstream tasks such as abstractive summarization, dialogue generation and data-to-text generation. However, it is also apparent that deep learning based generation is prone to hallucinate unintended text, which degrades the system performance and fails to meet user expectations in many real-world scenarios. To address this issue, many studies have been presented in measuring and mitigating hallucinated texts, but these have never been reviewed in a comprehensive manner before. In this survey, we thus provide a broad overview of the research progress and challenges in the hallucination problem in NLG. The survey is organized into two parts: (1) a general overview of metrics, mitigation methods, and future directions; and (2) an overview of task-specific research progress on hallucinations in the following downstream tasks, namely abstractive summarization, dialogue generation, generative question answering, data-to-text generation, machine translation, and visual-language generation. This survey serves to facilitate collaborative efforts among researchers in tackling the challenge of hallucinated texts in NLG.

Text-to-3D generation has achieved remarkable progress in recent years, yet evaluating these methods remains challenging for two reasons: i) Existing benchmarks lack fine-grained evaluation on different prompt categories and evaluation dimensions. ii) Previous evaluation metrics only focus on a single aspect (e.g., text-3D alignment) and fail to perform multi-dimensional quality assessment. To address these problems, we first propose a comprehensive benchmark named MATE-3D. The benchmark contains eight well-designed prompt categories that cover single and multiple object generation, resulting in 1,280 generated textured meshes. We have conducted a large-scale subjective experiment from four different evaluation dimensions and collected 107,520 annotations, followed by detailed analyses of the results. Based on MATE-3D, we propose a novel quality evaluator named HyperScore. Utilizing hypernetwork to generate specified mapping functions for each evaluation dimension, our metric can effectively perform multi-dimensional quality assessment. HyperScore presents superior performance over existing metrics on MATE-3D, making it a promising metric for assessing and improving text-to-3D generation. The project is available at https://mate-3d.github.io/.

Recent text-to-image generative models can generate high-fidelity images from text prompts. However, these models struggle to consistently generate the same objects in different contexts with the same appearance. Consistent object generation is important to many downstream tasks like generating comic book illustrations with consistent characters and setting. Numerous approaches attempt to solve this problem by extending the vocabulary of diffusion models through fine-tuning. However, even lightweight fine-tuning approaches can be prohibitively expensive to run at scale and in real-time. We introduce a method called ObjectComposer for generating compositions of multiple objects that resemble user-specified images. Our approach is training-free, leveraging the abilities of preexisting models. We build upon the recent BLIP-Diffusion model, which can generate images of single objects specified by reference images. ObjectComposer enables the consistent generation of compositions containing multiple specific objects simultaneously, all without modifying the weights of the underlying models.

Keyphrase generation is the task consisting in generating a set of words or phrases that highlight the main topics of a document. There are few datasets for keyphrase generation in the biomedical domain and they do not meet the expectations in terms of size for training generative models. In this paper, we introduce kp-biomed, the first large-scale biomedical keyphrase generation dataset with more than 5M documents collected from PubMed abstracts. We train and release several generative models and conduct a series of experiments showing that using large scale datasets improves significantly the performances for present and absent keyphrase generation. The dataset is available under CC-BY-NC v4.0 license at https://huggingface.co/ datasets/taln-ls2n/kpbiomed.

Diffusion models have become a new generative paradigm for text generation. Considering the discrete categorical nature of text, in this paper, we propose GlyphDiffusion, a novel diffusion approach for text generation via text-guided image generation. Our key idea is to render the target text as a glyph image containing visual language content. In this way, conditional text generation can be cast as a glyph image generation task, and it is then natural to apply continuous diffusion models to discrete texts. Specially, we utilize a cascaded architecture (ie a base and a super-resolution diffusion model) to generate high-fidelity glyph images, conditioned on the input text. Furthermore, we design a text grounding module to transform and refine the visual language content from generated glyph images into the final texts. In experiments over four conditional text generation tasks and two classes of metrics (ie quality and diversity), GlyphDiffusion can achieve comparable or even better results than several baselines, including pretrained language models. Our model also makes significant improvements compared to the recent diffusion model.

The text-to-image synthesis by diffusion models has recently shown remarkable performance in generating high-quality images. Although performs well for simple texts, the models may get confused when faced with complex texts that contain multiple objects or spatial relationships. To get the desired images, a feasible way is to manually adjust the textual descriptions, i.e., narrating the texts or adding some words, which is labor-consuming. In this paper, we propose a framework to learn the proper textual descriptions for diffusion models through prompt learning. By utilizing the quality guidance and the semantic guidance derived from the pre-trained diffusion model, our method can effectively learn the prompts to improve the matches between the input text and the generated images. Extensive experiments and analyses have validated the effectiveness of the proposed method.

People primarily consult tables to conduct data analysis or answer specific questions. Text generation systems that can provide accurate table summaries tailored to users' information needs can facilitate more efficient access to relevant data insights. However, existing table-to-text generation studies primarily focus on converting tabular data into coherent statements, rather than addressing information-seeking purposes. In this paper, we define a new query-focused table summarization task, where text generation models have to perform human-like reasoning and analysis over the given table to generate a tailored summary, and we introduce a new benchmark named QTSumm for this task. QTSumm consists of 5,625 human-annotated query-summary pairs over 2,437 tables on diverse topics. Moreover, we investigate state-of-the-art models (i.e., text generation, table-to-text generation, and large language models) on the QTSumm dataset. Experimental results and manual analysis reveal that our benchmark presents significant challenges in table-to-text generation for future research.

Transformer-based deep neural networks have revolutionized the field of molecular-related prediction tasks by treating molecules as symbolic sequences. These models have been successfully applied in various organic chemical applications by pretraining them with extensive compound libraries and subsequently fine-tuning them with smaller in-house datasets for specific tasks. However, many conventional methods primarily focus on single molecules, with limited exploration of pretraining for reactions involving multiple molecules. In this paper, we propose ReactionT5, a novel model that leverages pretraining on the Open Reaction Database (ORD), a publicly available large-scale resource. We further fine-tune this model for yield prediction and product prediction tasks, demonstrating its impressive performance even with limited fine-tuning data compared to traditional models. The pre-trained ReactionT5 model is publicly accessible on the Hugging Face platform.

Large language models (LLMs) have emerged as pivotal contributors in contemporary natural language processing and are increasingly being applied across a diverse range of industries. However, these large-scale probabilistic statistical models cannot currently ensure the requisite quality in professional content generation. These models often produce hallucinated text, compromising their practical utility in professional contexts. To assess the authentic reliability of LLMs in text generation, numerous initiatives have developed benchmark evaluations for hallucination phenomena. Nevertheless, these benchmarks frequently utilize constrained generation techniques due to cost and temporal constraints. These techniques encompass the use of directed hallucination induction and strategies that deliberately alter authentic text to produce hallucinations. These approaches are not congruent with the unrestricted text generation demanded by real-world applications. Furthermore, a well-established Chinese-language dataset dedicated to the evaluation of hallucinations in text generation is presently lacking. Consequently, we have developed an Unconstrained Hallucination Generation Evaluation (UHGEval) benchmark, designed to compile outputs produced with minimal restrictions by LLMs. Concurrently, we have established a comprehensive benchmark evaluation framework to aid subsequent researchers in undertaking scalable and reproducible experiments. We have also executed extensive experiments, evaluating prominent Chinese language models and the GPT series models to derive professional performance insights regarding hallucination challenges.

Recent advancements in specialized large-scale architectures for training image and language have profoundly impacted the field of computer vision and natural language processing (NLP). Language models, such as the recent ChatGPT and GPT4 have demonstrated exceptional capabilities in processing, translating, and generating human languages. These breakthroughs have also been reflected in protein research, leading to the rapid development of numerous new methods in a short time, with unprecedented performance. Language models, in particular, have seen widespread use in protein research, as they have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we provide an overview of the use of protein generative models, reviewing 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches.

Diffusion-based text-to-image models have demonstrated impressive achievements in diversity and aesthetics but struggle to generate images with legible visual texts. Existing backbone models have limitations such as misspelling, failing to generate texts, and lack of support for Chinese text, but their development shows promising potential. In this paper, we propose a series of methods, aiming to empower backbone models to generate visual texts in English and Chinese. We first conduct a preliminary study revealing that Byte Pair Encoding (BPE) tokenization and the insufficient learning of cross-attention modules restrict the performance of the backbone models. Based on these observations, we make the following improvements: (1) We design a mixed granularity input strategy to provide more suitable text representations; (2) We propose to augment the conventional training objective with three glyph-aware training losses, which enhance the learning of cross-attention modules and encourage the model to focus on visual texts. Through experiments, we demonstrate that our methods can effectively empower backbone models to generate semantic relevant, aesthetically appealing, and accurate visual text images, while maintaining their fundamental image generation quality.

Existing approaches to multilingual text detoxification are hampered by the scarcity of parallel multilingual datasets. In this work, we introduce a pipeline for the generation of multilingual parallel detoxification data. We also introduce SynthDetoxM, a manually collected and synthetically generated multilingual parallel text detoxification dataset comprising 16,000 high-quality detoxification sentence pairs across German, French, Spanish and Russian. The data was sourced from different toxicity evaluation datasets and then rewritten with nine modern open-source LLMs in few-shot setting. Our experiments demonstrate that models trained on the produced synthetic datasets have superior performance to those trained on the human-annotated MultiParaDetox dataset even in data limited setting. Models trained on SynthDetoxM outperform all evaluated LLMs in few-shot setting. We release our dataset and code to help further research in multilingual text detoxification.

In open-ended natural-language generation, existing text decoding methods typically struggle to produce text which is both diverse and high-quality. Greedy and beam search are known to suffer from text degeneration and linguistic diversity issues, while temperature, top-k, and nucleus sampling often yield diverse but low-quality outputs. In this work, we present crowd sampling, a family of decoding methods based on Bayesian risk minimization, to address this diversity-quality trade-off. Inspired by the principle of "the wisdom of the crowd," crowd sampling seeks to select a candidate from a pool of candidates that has the least expected risk (i.e., highest expected reward) under a generative model according to a given utility function. Crowd sampling can be seen as a generalization of numerous existing methods, including majority voting, and in practice, it can be used as a drop-in replacement for existing sampling methods. Extensive experiments show that crowd sampling delivers improvements of 3-7 ROUGE and BLEU points across a wide range of tasks, including summarization, data-to-text, translation, and textual style transfer, while achieving new state-of-the-art results on WebNLG and WMT'16.

Generative Artificial Intelligence (AI) has enabled the development of sophisticated models that are capable of producing high-caliber text, images, and other outputs through the utilization of large pre-trained models. Nevertheless, assessing the quality of the generation is an even more arduous task than the generation itself, and this issue has not been given adequate consideration recently. This paper proposes a novel evaluation framework, GPTScore, which utilizes the emergent abilities (e.g., zero-shot instruction) of generative pre-trained models to score generated texts. There are 19 pre-trained models explored in this paper, ranging in size from 80M (e.g., FLAN-T5-small) to 175B (e.g., GPT3). Experimental results on four text generation tasks, 22 evaluation aspects, and corresponding 37 datasets demonstrate that this approach can effectively allow us to achieve what one desires to evaluate for texts simply by natural language instructions. This nature helps us overcome several long-standing challenges in text evaluation--how to achieve customized, multi-faceted evaluation without the need for annotated samples. We make our code publicly available at https://github.com/jinlanfu/GPTScore.

In this paper, we present VideoGen, a text-to-video generation approach, which can generate a high-definition video with high frame fidelity and strong temporal consistency using reference-guided latent diffusion. We leverage an off-the-shelf text-to-image generation model, e.g., Stable Diffusion, to generate an image with high content quality from the text prompt, as a reference image to guide video generation. Then, we introduce an efficient cascaded latent diffusion module conditioned on both the reference image and the text prompt, for generating latent video representations, followed by a flow-based temporal upsampling step to improve the temporal resolution. Finally, we map latent video representations into a high-definition video through an enhanced video decoder. During training, we use the first frame of a ground-truth video as the reference image for training the cascaded latent diffusion module. The main characterises of our approach include: the reference image generated by the text-to-image model improves the visual fidelity; using it as the condition makes the diffusion model focus more on learning the video dynamics; and the video decoder is trained over unlabeled video data, thus benefiting from high-quality easily-available videos. VideoGen sets a new state-of-the-art in text-to-video generation in terms of both qualitative and quantitative evaluation.

Text-to-image generation has made significant advancements with the introduction of text-to-image diffusion models. These models typically consist of a language model that interprets user prompts and a vision model that generates corresponding images. As language and vision models continue to progress in their respective domains, there is a great potential in exploring the replacement of components in text-to-image diffusion models with more advanced counterparts. A broader research objective would therefore be to investigate the integration of any two unrelated language and generative vision models for text-to-image generation. In this paper, we explore this objective and propose LaVi-Bridge, a pipeline that enables the integration of diverse pre-trained language models and generative vision models for text-to-image generation. By leveraging LoRA and adapters, LaVi-Bridge offers a flexible and plug-and-play approach without requiring modifications to the original weights of the language and vision models. Our pipeline is compatible with various language models and generative vision models, accommodating different structures. Within this framework, we demonstrate that incorporating superior modules, such as more advanced language models or generative vision models, results in notable improvements in capabilities like text alignment or image quality. Extensive evaluations have been conducted to verify the effectiveness of LaVi-Bridge. Code is available at https://github.com/ShihaoZhaoZSH/LaVi-Bridge.

Diffusion-based text-to-video generation has witnessed impressive progress in the past year yet still falls behind text-to-image generation. One of the key reasons is the limited scale of publicly available data (e.g., 10M video-text pairs in WebVid10M vs. 5B image-text pairs in LAION), considering the high cost of video captioning. Instead, it could be far easier to collect unlabeled clips from video platforms like YouTube. Motivated by this, we come up with a novel text-to-video generation framework, termed TF-T2V, which can directly learn with text-free videos. The rationale behind is to separate the process of text decoding from that of temporal modeling. To this end, we employ a content branch and a motion branch, which are jointly optimized with weights shared. Following such a pipeline, we study the effect of doubling the scale of training set (i.e., video-only WebVid10M) with some randomly collected text-free videos and are encouraged to observe the performance improvement (FID from 9.67 to 8.19 and FVD from 484 to 441), demonstrating the scalability of our approach. We also find that our model could enjoy sustainable performance gain (FID from 8.19 to 7.64 and FVD from 441 to 366) after reintroducing some text labels for training. Finally, we validate the effectiveness and generalizability of our ideology on both native text-to-video generation and compositional video synthesis paradigms. Code and models will be publicly available at https://tf-t2v.github.io/.

In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about synthetic procedures. By taking advantage of recent advances in natural language processing for procedural texts, SynKB supports more flexible queries about reaction conditions, and thus has the potential to help chemists search the literature for conditions used in relevant reactions as they design new synthetic routes. Using customized Transformer models to automatically extract information from 6 million synthesis procedures described in U.S. and EU patents, we show that for many queries, SynKB has higher recall than Reaxsys, while maintaining high precision. We plan to make SynKB available as an open-source tool; in contrast, proprietary chemistry databases require costly subscriptions.

Existing visual parsers for molecule diagrams translate pixel-based raster images such as PNGs to chemical structure representations (e.g., SMILES). However, PDFs created by word processors including LaTeX and Word provide explicit locations and shapes for characters, lines, and polygons. We extract symbols from born-digital PDF molecule images and then apply simple graph transformations to capture both visual and chemical structure in editable ChemDraw files (CDXML). Our fast ( PDF rightarrow visual graph rightarrow chemical graph ) pipeline does not require GPUs, Optical Character Recognition (OCR) or vectorization. We evaluate on standard benchmarks using SMILES strings, along with a novel evaluation that provides graph-based metrics and error compilation using LgEval. The geometric information in born-digital PDFs produces a highly accurate parser, motivating generating training data for visual parsers that recognize from raster images, with extracted graphics, visual structure, and chemical structure as annotations. To do this we render SMILES strings in Indigo, parse molecule structure, and then validate recognized structure to select correct files.

Large pre-trained language models are capable of generating realistic text. However, controlling these models so that the generated text satisfies lexical constraints, i.e., contains specific words, is a challenging problem. Given that state-of-the-art language models are too large to be trained from scratch in a manageable time, it is desirable to control these models without re-training them. Methods capable of doing this are called plug-and-play. Recent plug-and-play methods have been successful in constraining small bidirectional language models as well as forward models in tasks with a restricted search space, e.g., machine translation. However, controlling large transformer-based models to meet lexical constraints without re-training them remains a challenge. In this work, we propose Directed Beam Search (DBS), a plug-and-play method for lexically constrained language generation. Our method can be applied to any language model, is easy to implement and can be used for general language generation. In our experiments we use DBS to control GPT-2. We demonstrate its performance on keyword-to-phrase generation and we obtain comparable results as a state-of-the-art non-plug-and-play model for lexically constrained story generation.

Diffusion Models have exhibited substantial success in text-to-image generation. However, they often encounter challenges when dealing with complex and dense prompts that involve multiple objects, attribute binding, and long descriptions. This paper proposes a framework called LLM4GEN, which enhances the semantic understanding ability of text-to-image diffusion models by leveraging the semantic representation of Large Language Models (LLMs). Through a specially designed Cross-Adapter Module (CAM) that combines the original text features of text-to-image models with LLM features, LLM4GEN can be easily incorporated into various diffusion models as a plug-and-play component and enhances text-to-image generation. Additionally, to facilitate the complex and dense prompts semantic understanding, we develop a LAION-refined dataset, consisting of 1 million (M) text-image pairs with improved image descriptions. We also introduce DensePrompts which contains 7,000 dense prompts to provide a comprehensive evaluation for the text-to-image generation task. With just 10\% of the training data required by recent ELLA, LLM4GEN significantly improves the semantic alignment of SD1.5 and SDXL, demonstrating increases of 7.69\% and 9.60\% in color on T2I-CompBench, respectively. The extensive experiments on DensePrompts also demonstrate that LLM4GEN surpasses existing state-of-the-art models in terms of sample quality, image-text alignment, and human evaluation. The project website is at: magenta{https://xiaobul.github.io/LLM4GEN/}

Large Language Models (LLMs) have garnered significant attention for their advancements in natural language processing, demonstrating unparalleled prowess in text comprehension and generation. Yet, the simultaneous generation of images with coherent textual narratives remains an evolving frontier. In response, we introduce an innovative interleaved vision-and-language generation technique anchored by the concept of "generative vokens," acting as the bridge for harmonized image-text outputs. Our approach is characterized by a distinctive two-staged training strategy focusing on description-free multimodal generation, where the training requires no comprehensive descriptions of images. To bolster model integrity, classifier-free guidance is incorporated, enhancing the effectiveness of vokens on image generation. Our model, MiniGPT-5, exhibits substantial improvement over the baseline Divter model on the MMDialog dataset and consistently delivers superior or comparable multimodal outputs in human evaluations on the VIST dataset, highlighting its efficacy across diverse benchmarks.

Probabilistic text generators have been used to produce fake scientific papers for more than a decade. Such nonsensical papers are easily detected by both human and machine. Now more complex AI-powered generation techniques produce texts indistinguishable from that of humans and the generation of scientific texts from a few keywords has been documented. Our study introduces the concept of tortured phrases: unexpected weird phrases in lieu of established ones, such as 'counterfeit consciousness' instead of 'artificial intelligence.' We combed the literature for tortured phrases and study one reputable journal where these concentrated en masse. Hypothesising the use of advanced language models we ran a detector on the abstracts of recent articles of this journal and on several control sets. The pairwise comparisons reveal a concentration of abstracts flagged as 'synthetic' in the journal. We also highlight irregularities in its operation, such as abrupt changes in editorial timelines. We substantiate our call for investigation by analysing several individual dubious articles, stressing questionable features: tortured writing style, citation of non-existent literature, and unacknowledged image reuse. Surprisingly, some websites offer to rewrite texts for free, generating gobbledegook full of tortured phrases. We believe some authors used rewritten texts to pad their manuscripts. We wish to raise the awareness on publications containing such questionable AI-generated or rewritten texts that passed (poor) peer review. Deception with synthetic texts threatens the integrity of the scientific literature.

Recently, retrieval-augmented text generation attracted increasing attention of the computational linguistics community. Compared with conventional generation models, retrieval-augmented text generation has remarkable advantages and particularly has achieved state-of-the-art performance in many NLP tasks. This paper aims to conduct a survey about retrieval-augmented text generation. It firstly highlights the generic paradigm of retrieval-augmented generation, and then it reviews notable approaches according to different tasks including dialogue response generation, machine translation, and other generation tasks. Finally, it points out some important directions on top of recent methods to facilitate future research.

Multiple business scenarios require an automated generation of descriptive human-readable text from structured input data. Hence, fact-to-text generation systems have been developed for various downstream tasks like generating soccer reports, weather and financial reports, medical reports, person biographies, etc. Unfortunately, previous work on fact-to-text (F2T) generation has focused primarily on English mainly due to the high availability of relevant datasets. Only recently, the problem of cross-lingual fact-to-text (XF2T) was proposed for generation across multiple languages alongwith a dataset, XALIGN for eight languages. However, there has been no rigorous work on the actual XF2T generation problem. We extend XALIGN dataset with annotated data for four more languages: Punjabi, Malayalam, Assamese and Oriya. We conduct an extensive study using popular Transformer-based text generation models on our extended multi-lingual dataset, which we call XALIGNV2. Further, we investigate the performance of different text generation strategies: multiple variations of pretraining, fact-aware embeddings and structure-aware input encoding. Our extensive experiments show that a multi-lingual mT5 model which uses fact-aware embeddings with structure-aware input encoding leads to best results on average across the twelve languages. We make our code, dataset and model publicly available, and hope that this will help advance further research in this critical area.

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset.

Recent improvements in KG-to-text generation are due to additional auxiliary pre-training tasks designed to give the fine-tune task a boost in performance. These tasks require extensive computational resources while only suggesting marginal improvements. Here, we demonstrate that by fusing graph-aware elements into existing pre-trained language models, we are able to outperform state-of-the-art models and close the gap imposed by additional pre-training tasks. We do so by proposing a mask structure to capture neighborhood information and a novel type encoder that adds a bias to the graph-attention weights depending on the connection type. Experiments on two KG-to-text benchmark datasets show our models are competitive while involving fewer parameters and no additional pre-training tasks. By formulating the problem as a framework, we can interchange the various proposed components and begin interpreting KG-to-text generative models based on the topological and type information found in a graph.