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Mar 14

Exploiting Pretrained Biochemical Language Models for Targeted Drug Design

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

Two-in-One Depth: Bridging the Gap Between Monocular and Binocular Self-supervised Depth Estimation

Monocular and binocular self-supervised depth estimations are two important and related tasks in computer vision, which aim to predict scene depths from single images and stereo image pairs respectively. In literature, the two tasks are usually tackled separately by two different kinds of models, and binocular models generally fail to predict depth from single images, while the prediction accuracy of monocular models is generally inferior to binocular models. In this paper, we propose a Two-in-One self-supervised depth estimation network, called TiO-Depth, which could not only compatibly handle the two tasks, but also improve the prediction accuracy. TiO-Depth employs a Siamese architecture and each sub-network of it could be used as a monocular depth estimation model. For binocular depth estimation, a Monocular Feature Matching module is proposed for incorporating the stereo knowledge between the two images, and the full TiO-Depth is used to predict depths. We also design a multi-stage joint-training strategy for improving the performances of TiO-Depth in both two tasks by combining the relative advantages of them. Experimental results on the KITTI, Cityscapes, and DDAD datasets demonstrate that TiO-Depth outperforms both the monocular and binocular state-of-the-art methods in most cases, and further verify the feasibility of a two-in-one network for monocular and binocular depth estimation. The code is available at https://github.com/ZM-Zhou/TiO-Depth_pytorch.

Once for Both: Single Stage of Importance and Sparsity Search for Vision Transformer Compression

Recent Vision Transformer Compression (VTC) works mainly follow a two-stage scheme, where the importance score of each model unit is first evaluated or preset in each submodule, followed by the sparsity score evaluation according to the target sparsity constraint. Such a separate evaluation process induces the gap between importance and sparsity score distributions, thus causing high search costs for VTC. In this work, for the first time, we investigate how to integrate the evaluations of importance and sparsity scores into a single stage, searching the optimal subnets in an efficient manner. Specifically, we present OFB, a cost-efficient approach that simultaneously evaluates both importance and sparsity scores, termed Once for Both (OFB), for VTC. First, a bi-mask scheme is developed by entangling the importance score and the differentiable sparsity score to jointly determine the pruning potential (prunability) of each unit. Such a bi-mask search strategy is further used together with a proposed adaptive one-hot loss to realize the progressive-and-efficient search for the most important subnet. Finally, Progressive Masked Image Modeling (PMIM) is proposed to regularize the feature space to be more representative during the search process, which may be degraded by the dimension reduction. Extensive experiments demonstrate that OFB can achieve superior compression performance over state-of-the-art searching-based and pruning-based methods under various Vision Transformer architectures, meanwhile promoting search efficiency significantly, e.g., costing one GPU search day for the compression of DeiT-S on ImageNet-1K.

BigNAS: Scaling Up Neural Architecture Search with Big Single-Stage Models

Neural architecture search (NAS) has shown promising results discovering models that are both accurate and fast. For NAS, training a one-shot model has become a popular strategy to rank the relative quality of different architectures (child models) using a single set of shared weights. However, while one-shot model weights can effectively rank different network architectures, the absolute accuracies from these shared weights are typically far below those obtained from stand-alone training. To compensate, existing methods assume that the weights must be retrained, finetuned, or otherwise post-processed after the search is completed. These steps significantly increase the compute requirements and complexity of the architecture search and model deployment. In this work, we propose BigNAS, an approach that challenges the conventional wisdom that post-processing of the weights is necessary to get good prediction accuracies. Without extra retraining or post-processing steps, we are able to train a single set of shared weights on ImageNet and use these weights to obtain child models whose sizes range from 200 to 1000 MFLOPs. Our discovered model family, BigNASModels, achieve top-1 accuracies ranging from 76.5% to 80.9%, surpassing state-of-the-art models in this range including EfficientNets and Once-for-All networks without extra retraining or post-processing. We present ablative study and analysis to further understand the proposed BigNASModels.

EAGAN: Efficient Two-stage Evolutionary Architecture Search for GANs

Generative adversarial networks (GANs) have proven successful in image generation tasks. However, GAN training is inherently unstable. Although many works try to stabilize it by manually modifying GAN architecture, it requires much expertise. Neural architecture search (NAS) has become an attractive solution to search GANs automatically. The early NAS-GANs search only generators to reduce search complexity but lead to a sub-optimal GAN. Some recent works try to search both generator (G) and discriminator (D), but they suffer from the instability of GAN training. To alleviate the instability, we propose an efficient two-stage evolutionary algorithm-based NAS framework to search GANs, namely EAGAN. We decouple the search of G and D into two stages, where stage-1 searches G with a fixed D and adopts the many-to-one training strategy, and stage-2 searches D with the optimal G found in stage-1 and adopts the one-to-one training and weight-resetting strategies to enhance the stability of GAN training. Both stages use the non-dominated sorting method to produce Pareto-front architectures under multiple objectives (e.g., model size, Inception Score (IS), and Fr\'echet Inception Distance (FID)). EAGAN is applied to the unconditional image generation task and can efficiently finish the search on the CIFAR-10 dataset in 1.2 GPU days. Our searched GANs achieve competitive results (IS=8.81pm0.10, FID=9.91) on the CIFAR-10 dataset and surpass prior NAS-GANs on the STL-10 dataset (IS=10.44pm0.087, FID=22.18). Source code: https://github.com/marsggbo/EAGAN.

StageInteractor: Query-based Object Detector with Cross-stage Interaction

Previous object detectors make predictions based on dense grid points or numerous preset anchors. Most of these detectors are trained with one-to-many label assignment strategies. On the contrary, recent query-based object detectors depend on a sparse set of learnable queries and a series of decoder layers. The one-to-one label assignment is independently applied on each layer for the deep supervision during training. Despite the great success of query-based object detection, however, this one-to-one label assignment strategy demands the detectors to have strong fine-grained discrimination and modeling capacity. To solve the above problems, in this paper, we propose a new query-based object detector with cross-stage interaction, coined as StageInteractor. During the forward propagation, we come up with an efficient way to improve this modeling ability by reusing dynamic operators with lightweight adapters. As for the label assignment, a cross-stage label assigner is applied subsequent to the one-to-one label assignment. With this assigner, the training target class labels are gathered across stages and then reallocated to proper predictions at each decoder layer. On MS COCO benchmark, our model improves the baseline by 2.2 AP, and achieves 44.8 AP with ResNet-50 as backbone, 100 queries and 12 training epochs. With longer training time and 300 queries, StageInteractor achieves 51.1 AP and 52.2 AP with ResNeXt-101-DCN and Swin-S, respectively.

Towards All-in-one Pre-training via Maximizing Multi-modal Mutual Information

To effectively exploit the potential of large-scale models, various pre-training strategies supported by massive data from different sources are proposed, including supervised pre-training, weakly-supervised pre-training, and self-supervised pre-training. It has been proved that combining multiple pre-training strategies and data from various modalities/sources can greatly boost the training of large-scale models. However, current works adopt a multi-stage pre-training system, where the complex pipeline may increase the uncertainty and instability of the pre-training. It is thus desirable that these strategies can be integrated in a single-stage manner. In this paper, we first propose a general multi-modal mutual information formula as a unified optimization target and demonstrate that all existing approaches are special cases of our framework. Under this unified perspective, we propose an all-in-one single-stage pre-training approach, named Maximizing Multi-modal Mutual Information Pre-training (M3I Pre-training). Our approach achieves better performance than previous pre-training methods on various vision benchmarks, including ImageNet classification, COCO object detection, LVIS long-tailed object detection, and ADE20k semantic segmentation. Notably, we successfully pre-train a billion-level parameter image backbone and achieve state-of-the-art performance on various benchmarks. Code shall be released at https://github.com/OpenGVLab/M3I-Pretraining.

PoseTalk: Text-and-Audio-based Pose Control and Motion Refinement for One-Shot Talking Head Generation

While previous audio-driven talking head generation (THG) methods generate head poses from driving audio, the generated poses or lips cannot match the audio well or are not editable. In this study, we propose PoseTalk, a THG system that can freely generate lip-synchronized talking head videos with free head poses conditioned on text prompts and audio. The core insight of our method is using head pose to connect visual, linguistic, and audio signals. First, we propose to generate poses from both audio and text prompts, where the audio offers short-term variations and rhythm correspondence of the head movements and the text prompts describe the long-term semantics of head motions. To achieve this goal, we devise a Pose Latent Diffusion (PLD) model to generate motion latent from text prompts and audio cues in a pose latent space. Second, we observe a loss-imbalance problem: the loss for the lip region contributes less than 4\% of the total reconstruction loss caused by both pose and lip, making optimization lean towards head movements rather than lip shapes. To address this issue, we propose a refinement-based learning strategy to synthesize natural talking videos using two cascaded networks, i.e., CoarseNet, and RefineNet. The CoarseNet estimates coarse motions to produce animated images in novel poses and the RefineNet focuses on learning finer lip motions by progressively estimating lip motions from low-to-high resolutions, yielding improved lip-synchronization performance. Experiments demonstrate our pose prediction strategy achieves better pose diversity and realness compared to text-only or audio-only, and our video generator model outperforms state-of-the-art methods in synthesizing talking videos with natural head motions. Project: https://junleen.github.io/projects/posetalk.

Scaling of Search and Learning: A Roadmap to Reproduce o1 from Reinforcement Learning Perspective

OpenAI o1 represents a significant milestone in Artificial Inteiligence, which achieves expert-level performances on many challanging tasks that require strong reasoning ability.OpenAI has claimed that the main techinique behinds o1 is the reinforcement learining. Recent works use alternative approaches like knowledge distillation to imitate o1's reasoning style, but their effectiveness is limited by the capability ceiling of the teacher model. Therefore, this paper analyzes the roadmap to achieving o1 from the perspective of reinforcement learning, focusing on four key components: policy initialization, reward design, search, and learning. Policy initialization enables models to develop human-like reasoning behaviors, equipping them with the ability to effectively explore solution spaces for complex problems. Reward design provides dense and effective signals via reward shaping or reward modeling, which is the guidance for both search and learning. Search plays a crucial role in generating high-quality solutions during both training and testing phases, which can produce better solutions with more computation. Learning utilizes the data generated by search for improving policy, which can achieve the better performance with more parameters and more searched data. Existing open-source projects that attempt to reproduce o1 can be seem as a part or a variant of our roadmap. Collectively, these components underscore how learning and search drive o1's advancement, making meaningful contributions to the development of LLM.