Daily Papers

Pretrained transformer-encoder models like DeBERTaV3 and ModernBERT introduce architectural advancements aimed at improving efficiency and performance. Although the authors of ModernBERT report improved performance over DeBERTaV3 on several benchmarks, the lack of disclosed training data and the absence of comparisons using a shared dataset make it difficult to determine whether these gains are due to architectural improvements or differences in training data. In this work, we conduct a controlled study by pretraining ModernBERT on the same dataset as CamemBERTaV2, a DeBERTaV3 French model, isolating the effect of model design. Our results show that the previous model generation remains superior in sample efficiency and overall benchmark performance, with ModernBERT's primary advantage being faster training and inference speed. However, the new proposed model still provides meaningful architectural improvements compared to earlier models such as BERT and RoBERTa. Additionally, we observe that high-quality pre-training data accelerates convergence but does not significantly improve final performance, suggesting potential benchmark saturation. These findings show the importance of disentangling pretraining data from architectural innovations when evaluating transformer models.

Objective: This study aims to evaluate and compare the performance of two Japanese language models-conventional Bidirectional Encoder Representations from Transformers (BERT) and the newer ModernBERT-in classifying findings from chest CT reports, with a focus on tokenization efficiency, processing time, and classification performance. Methods: We conducted a retrospective study using the CT-RATE-JPN dataset containing 22,778 training reports and 150 test reports. Both models were fine-tuned for multi-label classification of 18 common chest CT conditions. The training data was split in 18,222:4,556 for training and validation. Performance was evaluated using F1 scores for each condition and exact match accuracy across all 18 labels. Results: ModernBERT demonstrated superior tokenization efficiency, requiring 24.0% fewer tokens per document (258.1 vs. 339.6) compared to BERT Base. This translated to significant performance improvements, with ModernBERT completing training in 1877.67 seconds versus BERT's 3090.54 seconds (39% reduction). ModernBERT processed 38.82 samples per second during training (1.65x faster) and 139.90 samples per second during inference (1.66x faster). Despite these efficiency gains, classification performance remained comparable, with ModernBERT achieving superior F1 scores in 8 conditions, while BERT performed better in 4 conditions. Overall exact match accuracy was slightly higher for ModernBERT (74.67% vs. 72.67%), though this difference was not statistically significant (p=0.6291). Conclusion: ModernBERT offers substantial improvements in tokenization efficiency and training speed without sacrificing classification performance. These results suggest that ModernBERT is a promising candidate for clinical applications in Japanese radiology reports analysis.

We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.

Extracting tables and key-value pairs from financial documents is essential for business workflows such as auditing, data analytics, and automated invoice processing. In this work, we introduce Spatial ModernBERT-a transformer-based model augmented with spatial embeddings-to accurately detect and extract tabular data and key-value fields from complex financial documents. We cast the extraction task as token classification across three heads: (1) Label Head, classifying each token as a label (e.g., PO Number, PO Date, Item Description, Quantity, Base Cost, MRP, etc.); (2) Column Head, predicting column indices; (3) Row Head, distinguishing the start of item rows and header rows. The model is pretrained on the PubTables-1M dataset, then fine-tuned on a financial document dataset, achieving robust performance through cross-entropy loss on each classification head. We propose a post-processing method to merge tokens using B-I-IB tagging, reconstruct the tabular layout, and extract key-value pairs. Empirical evaluation shows that Spatial ModernBERT effectively leverages both textual and spatial cues, facilitating highly accurate table and key-value extraction in real-world financial documents.

Encoder-based transformer models are central to biomedical and clinical Natural Language Processing (NLP), as their bidirectional self-attention makes them well-suited for efficiently extracting structured information from unstructured text through discriminative tasks. However, encoders have seen slower development compared to decoder models, leading to limited domain adaptation in biomedical and clinical settings. We introduce BioClinical ModernBERT, a domain-adapted encoder that builds on the recent ModernBERT release, incorporating long-context processing and substantial improvements in speed and performance for biomedical and clinical NLP. BioClinical ModernBERT is developed through continued pretraining on the largest biomedical and clinical corpus to date, with over 53.5 billion tokens, and addresses a key limitation of prior clinical encoders by leveraging 20 datasets from diverse institutions, domains, and geographic regions, rather than relying on data from a single source. It outperforms existing biomedical and clinical encoders on four downstream tasks spanning a broad range of use cases. We release both base (150M parameters) and large (396M parameters) versions of BioClinical ModernBERT, along with training checkpoints to support further research.

Encoder-only transformer models like BERT are widely adopted as a pre-trained backbone for tasks like sentence classification and retrieval. However, pretraining of encoder models with large-scale corpora and long contexts has been relatively underexplored compared to decoder-only transformers. In this work, we present llm-jp-modernbert, a ModernBERT model trained on a publicly available, massive Japanese corpus with a context length of 8192 tokens. While our model does not surpass existing baselines on downstream tasks, it achieves good results on fill-mask test evaluations. We also analyze the effect of context length expansion through pseudo-perplexity experiments. Furthermore, we investigate sentence embeddings in detail, analyzing their transitions during training and comparing them with those from other existing models, confirming similar trends with models sharing the same architecture. To support reproducibility and foster the development of long-context BERT, we release our model, along with the training and evaluation code.

Modern information retrieval systems often employ a two-stage pipeline: an efficient initial retrieval stage followed by a computationally intensive reranking stage. Cross-encoders have shown strong effectiveness for reranking due to their deep analysis of query-document pairs. This paper studies the impact of the Lion optimizer, a recent alternative to AdamW, during fine-tuning of cross-encoder rerankers. We fine-tune three transformer models-MiniLM, GTE, and ModernBERT-on the MS MARCO passage ranking dataset using both optimizers. GTE and ModernBERT support extended context lengths (up to 8192 tokens). We evaluate effectiveness using TREC 2019 Deep Learning Track and MS MARCO dev set (MRR@10). Experiments, run on the Modal cloud platform, reveal that ModernBERT with Lion achieves the best NDCG@10 (0.7225) and MAP (0.5121) on TREC DL 2019, while MiniLM with Lion ties ModernBERT for MRR@10 (0.5988) on MS MARCO dev. Lion also provides superior GPU efficiency, improving utilization by 2.67% to 10.33% across models. We analyze performance trends using standard IR metrics and discuss the optimizer's impact on training dynamics across architectures.

Encoder-only transformer models such as BERT offer a great performance-size tradeoff for retrieval and classification tasks with respect to larger decoder-only models. Despite being the workhorse of numerous production pipelines, there have been limited Pareto improvements to BERT since its release. In this paper, we introduce ModernBERT, bringing modern model optimizations to encoder-only models and representing a major Pareto improvement over older encoders. Trained on 2 trillion tokens with a native 8192 sequence length, ModernBERT models exhibit state-of-the-art results on a large pool of evaluations encompassing diverse classification tasks and both single and multi-vector retrieval on different domains (including code). In addition to strong downstream performance, ModernBERT is also the most speed and memory efficient encoder and is designed for inference on common GPUs.

While encoder-only models such as BERT and ModernBERT are ubiquitous in real-world NLP applications, their conventional reliance on task-specific classification heads can limit their applicability compared to decoder-based large language models (LLMs). In this work, we introduce ModernBERT-Large-Instruct, a 0.4B-parameter encoder model that leverages its masked language modelling (MLM) head for generative classification. Our approach employs an intentionally simple training loop and inference mechanism that requires no heavy pre-processing, heavily engineered prompting, or architectural modifications. ModernBERT-Large-Instruct exhibits strong zero-shot performance on both classification and knowledge-based tasks, outperforming similarly sized LLMs on MMLU and achieving 93% of Llama3-1B's MMLU performance with 60% less parameters. We also demonstrate that, when fine-tuned, the generative approach using the MLM head matches or even surpasses traditional classification-head methods across diverse NLU tasks.This capability emerges specifically in models trained on contemporary, diverse data mixes, with models trained on lower volume, less-diverse data yielding considerably weaker performance. Although preliminary, these results demonstrate the potential of using the original generative masked language modelling head over traditional task-specific heads for downstream tasks. Our work suggests that further exploration into this area is warranted, highlighting many avenues for future improvements.

Large Language Models (LLMs) are increasingly powerful but remain vulnerable to prompt injection attacks, where malicious inputs cause the model to deviate from its intended instructions. This paper introduces Sentinel, a novel detection model, qualifire/prompt-injection-sentinel, based on the \answerdotai/ModernBERT-large architecture. By leveraging ModernBERT's advanced features and fine-tuning on an extensive and diverse dataset comprising a few open-source and private collections, Sentinel achieves state-of-the-art performance. This dataset amalgamates varied attack types, from role-playing and instruction hijacking to attempts to generate biased content, alongside a broad spectrum of benign instructions, with private datasets specifically targeting nuanced error correction and real-world misclassifications. On a comprehensive, unseen internal test set, Sentinel demonstrates an average accuracy of 0.987 and an F1-score of 0.980. Furthermore, when evaluated on public benchmarks, it consistently outperforms strong baselines like protectai/deberta-v3-base-prompt-injection-v2. This work details Sentinel's architecture, its meticulous dataset curation, its training methodology, and a thorough evaluation, highlighting its superior detection capabilities.

Retrieval Augmented Generation (RAG) systems remain vulnerable to hallucinated answers despite incorporating external knowledge sources. We present LettuceDetect a framework that addresses two critical limitations in existing hallucination detection methods: (1) the context window constraints of traditional encoder-based methods, and (2) the computational inefficiency of LLM based approaches. Building on ModernBERT's extended context capabilities (up to 8k tokens) and trained on the RAGTruth benchmark dataset, our approach outperforms all previous encoder-based models and most prompt-based models, while being approximately 30 times smaller than the best models. LettuceDetect is a token-classification model that processes context-question-answer triples, allowing for the identification of unsupported claims at the token level. Evaluations on the RAGTruth corpus demonstrate an F1 score of 79.22% for example-level detection, which is a 14.8% improvement over Luna, the previous state-of-the-art encoder-based architecture. Additionally, the system can process 30 to 60 examples per second on a single GPU, making it more practical for real-world RAG applications.

The computational cost of softmax-based attention in transformers limits their applicability to long-context tasks. Adaptive sparsity, of which alpha-entmax attention is an example, offers a flexible data-dependent alternative, but existing implementations are inefficient and do not leverage the sparsity to obtain runtime and memory gains. In this work, we propose AdaSplash, which combines the efficiency of GPU-optimized algorithms with the sparsity benefits of alpha-entmax. We first introduce a hybrid Halley-bisection algorithm, resulting in a 7-fold reduction in the number of iterations needed to compute the alpha-entmax transformation. Then, we implement custom Triton kernels to efficiently handle adaptive sparsity. Experiments with RoBERTa and ModernBERT for text classification and single-vector retrieval, along with GPT-2 for language modeling, show that our method achieves substantial improvements in runtime and memory efficiency compared to existing alpha-entmax implementations. It approaches -- and in some cases surpasses -- the efficiency of highly optimized softmax implementations like FlashAttention-2, enabling long-context training while maintaining strong task performance.

Small molecules are essential to drug discovery, and graph-language models hold promise for learning molecular properties and functions from text. However, existing molecule-text datasets are limited in scale and informativeness, restricting the training of generalizable multimodal models. We present MolTextNet, a dataset of 2.5 million high-quality molecule-text pairs designed to overcome these limitations. To construct it, we propose a synthetic text generation pipeline that integrates structural features, computed properties, bioactivity data, and synthetic complexity. Using GPT-4o-mini, we create structured descriptions for 2.5 million molecules from ChEMBL35, with text over 10 times longer than prior datasets. MolTextNet supports diverse downstream tasks, including property prediction and structure retrieval. Pretraining CLIP-style models with Graph Neural Networks and ModernBERT on MolTextNet yields improved performance, highlighting its potential for advancing foundational multimodal modeling in molecular science. Our dataset is available at https://huggingface.co/datasets/liuganghuggingface/moltextnet.

Tracking how data is mentioned and used in research papers provides critical insights for improving data discoverability, quality, and production. However, manually identifying and classifying dataset mentions across vast academic literature is resource-intensive and not scalable. This paper presents a machine learning framework that automates dataset mention detection across research domains by leveraging large language models (LLMs), synthetic data, and a two-stage fine-tuning process. We employ zero-shot extraction from research papers, an LLM-as-a-Judge for quality assessment, and a reasoning agent for refinement to generate a weakly supervised synthetic dataset. The Phi-3.5-mini instruct model is pre-fine-tuned on this dataset, followed by fine-tuning on a manually annotated subset. At inference, a ModernBERT-based classifier efficiently filters dataset mentions, reducing computational overhead while maintaining high recall. Evaluated on a held-out manually annotated sample, our fine-tuned model outperforms NuExtract-v1.5 and GLiNER-large-v2.1 in dataset extraction accuracy. Our results highlight how LLM-generated synthetic data can effectively address training data scarcity, improving generalization in low-resource settings. This framework offers a pathway toward scalable monitoring of dataset usage, enhancing transparency, and supporting researchers, funders, and policymakers in identifying data gaps and strengthening data accessibility for informed decision-making.

This paper presents AI Wizards' participation in the CLEF 2025 CheckThat! Lab Task 1: Subjectivity Detection in News Articles, classifying sentences as subjective/objective in monolingual, multilingual, and zero-shot settings. Training/development datasets were provided for Arabic, German, English, Italian, and Bulgarian; final evaluation included additional unseen languages (e.g., Greek, Romanian, Polish, Ukrainian) to assess generalization. Our primary strategy enhanced transformer-based classifiers by integrating sentiment scores, derived from an auxiliary model, with sentence representations, aiming to improve upon standard fine-tuning. We explored this sentiment-augmented architecture with mDeBERTaV3-base, ModernBERT-base (English), and Llama3.2-1B. To address class imbalance, prevalent across languages, we employed decision threshold calibration optimized on the development set. Our experiments show sentiment feature integration significantly boosts performance, especially subjective F1 score. This framework led to high rankings, notably 1st for Greek (Macro F1 = 0.51).

Recent innovations in architecture, pre-training, and fine-tuning have led to the remarkable in-context learning and reasoning abilities of large auto-regressive language models such as LLaMA and DeepSeek. In contrast, encoders like BERT and RoBERTa have not seen the same level of progress despite being foundational for many downstream NLP applications. To bridge this gap, we introduce NeoBERT, a next-generation encoder that redefines the capabilities of bidirectional models by integrating state-of-the-art advancements in architecture, modern data, and optimized pre-training methodologies. NeoBERT is designed for seamless adoption: it serves as a plug-and-play replacement for existing base models, relies on an optimal depth-to-width ratio, and leverages an extended context length of 4,096 tokens. Despite its compact 250M parameter footprint, it achieves state-of-the-art results on the massive MTEB benchmark, outperforming BERT large, RoBERTa large, NomicBERT, and ModernBERT under identical fine-tuning conditions. In addition, we rigorously evaluate the impact of each modification on GLUE and design a uniform fine-tuning and evaluation framework for MTEB. We release all code, data, checkpoints, and training scripts to accelerate research and real-world adoption.

The large language model (LLM) community focuses almost exclusively on decoder-only language models, since they are easier to use for text generation. However, a large subset of the community still uses encoder-only models for tasks such as classification or retrieval. Previous work has attempted to compare these architectures, but is forced to make comparisons with models that have different numbers of parameters, training techniques, and datasets. We introduce the SOTA open-data Ettin suite of models: paired encoder-only and decoder-only models ranging from 17 million parameters to 1 billion, trained on up to 2 trillion tokens. Using the same recipe for both encoder-only and decoder-only models produces SOTA recipes in both categories for their respective sizes, beating ModernBERT as an encoder and Llama 3.2 and SmolLM2 as decoders. Like previous work, we find that encoder-only models excel at classification and retrieval tasks while decoders excel at generative tasks. However, we show that adapting a decoder model to encoder tasks (and vice versa) through continued training is subpar compared to using only the reverse objective (i.e. a 400M encoder outperforms a 1B decoder on MNLI, and vice versa for generative tasks). We open-source all artifacts of this study including training data, training order segmented by checkpoint, and 200+ checkpoints to allow future work to analyze or extend all aspects of training.

Detecting AI-generated code, deepfakes, and other synthetic content is an emerging research challenge. As code generated by Large Language Models (LLMs) becomes more common, identifying the specific model behind each sample is increasingly important. This paper presents the first systematic study of LLM authorship attribution for C programs. We released CodeT5-Authorship, a novel model that uses only the encoder layers from the original CodeT5 encoder-decoder architecture, discarding the decoder to focus on classification. Our model's encoder output (first token) is passed through a two-layer classification head with GELU activation and dropout, producing a probability distribution over possible authors. To evaluate our approach, we introduce LLM-AuthorBench, a benchmark of 32,000 compilable C programs generated by eight state-of-the-art LLMs across diverse tasks. We compare our model to seven traditional ML classifiers and eight fine-tuned transformer models, including BERT, RoBERTa, CodeBERT, ModernBERT, DistilBERT, DeBERTa-V3, Longformer, and LoRA-fine-tuned Qwen2-1.5B. In binary classification, our model achieves 97.56% accuracy in distinguishing C programs generated by closely related models such as GPT-4.1 and GPT-4o, and 95.40% accuracy for multi-class attribution among five leading LLMs (Gemini 2.5 Flash, Claude 3.5 Haiku, GPT-4.1, Llama 3.3, and DeepSeek-V3). To support open science, we release the CodeT5-Authorship architecture, the LLM-AuthorBench benchmark, and all relevant Google Colab scripts on GitHub: https://github.com/LLMauthorbench/.

Despite the prominence of decoder-only language models, encoders remain crucial for resource-constrained applications. We introduce ModernGBERT (134M, 1B), a fully transparent family of German encoder models trained from scratch, incorporating architectural innovations from ModernBERT. To evaluate the practical trade-offs of training encoders from scratch, we also present LL\"aMmlein2Vec (120M, 1B, 7B), a family of encoders derived from German decoder-only models via LLM2Vec. We benchmark all models on natural language understanding, text embedding, and long-context reasoning tasks, enabling a controlled comparison between dedicated encoders and converted decoders. Our results show that ModernGBERT 1B outperforms prior state-of-the-art German encoders as well as encoders adapted via LLM2Vec, with regard to performance and parameter-efficiency. All models, training data, checkpoints and code are publicly available, advancing the German NLP ecosystem with transparent, high-performance encoder models.

This study explores strategies for efficiently classifying scientific full texts using both small, BERT-based models and local large language models like Llama-3.1 8B. We focus on developing methods for selecting subsets of input sentences to reduce input size while simultaneously enhancing classification performance. To this end, we compile a novel dataset consisting of full-text scientific papers from the field of invasion biology, specifically addressing the impacts of invasive species. These papers are aligned with publicly available impact assessments created by researchers for the International Union for Conservation of Nature (IUCN). Through extensive experimentation, we demonstrate that various sources like human evidence annotations, LLM-generated annotations or explainability scores can be used to train sentence selection models that improve the performance of both encoder- and decoder-based language models while optimizing efficiency through the reduction in input length, leading to improved results even if compared to models like ModernBERT that are able to handle the complete text as input. Additionally, we find that repeated sampling of shorter inputs proves to be a very effective strategy that, at a slightly increased cost, can further improve classification performance.