Daily Papers

Recently, Large language models (LLMs) have revolutionized Natural Language Processing (NLP). Pretrained LLMs, due to limited training context size, struggle with handling long token sequences, limiting their performance on various downstream tasks. Current solutions toward long context modeling often employ multi-stage continual pertaining, which progressively increases the effective context length through several continual pretraining stages. However, those approaches require extensive manual tuning and human expertise. In this paper, we introduce a novel single-stage continual pretraining method, Head-Adaptive Rotary Position Encoding (HARPE), to equip LLMs with long context modeling capabilities while simplifying the training process. Our HARPE leverages different Rotary Position Encoding (RoPE) base frequency values across different attention heads and directly trains LLMs on the target context length. Extensive experiments on 4 language modeling benchmarks, including the latest RULER benchmark, demonstrate that HARPE excels in understanding and integrating long-context tasks with single-stage training, matching and even outperforming existing multi-stage methods. Our results highlight that HARPE successfully breaks the stage barrier for training LLMs with long context modeling capabilities.

Accurate prediction of Drug-Target Affinity (DTA) is of vital importance in early-stage drug discovery, facilitating the identification of drugs that can effectively interact with specific targets and regulate their activities. While wet experiments remain the most reliable method, they are time-consuming and resource-intensive, resulting in limited data availability that poses challenges for deep learning approaches. Existing methods have primarily focused on developing techniques based on the available DTA data, without adequately addressing the data scarcity issue. To overcome this challenge, we present the SSM-DTA framework, which incorporates three simple yet highly effective strategies: (1) A multi-task training approach that combines DTA prediction with masked language modeling (MLM) using paired drug-target data. (2) A semi-supervised training method that leverages large-scale unpaired molecules and proteins to enhance drug and target representations. This approach differs from previous methods that only employed molecules or proteins in pre-training. (3) The integration of a lightweight cross-attention module to improve the interaction between drugs and targets, further enhancing prediction accuracy. Through extensive experiments on benchmark datasets such as BindingDB, DAVIS, and KIBA, we demonstrate the superior performance of our framework. Additionally, we conduct case studies on specific drug-target binding activities, virtual screening experiments, drug feature visualizations, and real-world applications, all of which showcase the significant potential of our work. In conclusion, our proposed SSM-DTA framework addresses the data limitation challenge in DTA prediction and yields promising results, paving the way for more efficient and accurate drug discovery processes. Our code is available at https://github.com/QizhiPei/SSM-DTA{Github}.

Enhancing reasoning in Large Multimodal Models (LMMs) faces unique challenges from the complex interplay between visual perception and logical reasoning, particularly in compact 3B-parameter architectures where architectural constraints limit reasoning capacity and modality alignment. While rule-based reinforcement learning (RL) excels in text-only domains, its multimodal extension confronts two critical barriers: (1) data limitations due to ambiguous answers and scarce complex reasoning examples, and (2) degraded foundational reasoning induced by multimodal pretraining. To address these challenges, we propose \method, a two-stage framework adapting rule-based RL for multimodal reasoning through Foundational Reasoning Enhancement (FRE) followed by Multimodal Generalization Training (MGT). The FRE stage first strengthens reasoning abilities using text-only data with rule-based RL, then the MGT stage generalizes these reasoning capabilities to multimodal domains. Experiments on Qwen2.5-VL-Instruct-3B demonstrate that \method achieves 4.83\% and 4.5\% average improvements over baselines in multimodal and text-only benchmarks, respectively, with a 3.63\% gain in complex Football Game tasks. These results validate that text-based reasoning enhancement enables effective multimodal generalization, offering a data-efficient paradigm that bypasses costly high-quality multimodal training data.