arXiv:2602.18476v1 Announce Type: cross Abstract: Protein-ligand scoring is a central component of structure-based drug design, underpinning molecular docking, virtual screening, and pose optimization. Conventional physics-based energy functions are often computationally expensive, limiting their utility in large-scale screening. In contrast, deep learning-based scoring models offer improved computational efficiency but frequently suffer from limited cross-target generalization and poor interpretability, which restrict their practical applicability. Here we present BioLM-Score, a simple yet generalizable protein-ligand scoring model that couples geometric modeling with representation learning. Specifically, it employs modality-specific and structure-aware encoders for proteins and ligands, each augmented with biomolecular language models to enrich structural and chemical representations. Subsequently, these representations are integrated through a mixture density network to predict multimodal interatomic distance distributions, from which statistically grounded likelihood-based scores are derived. Evaluations on the CASF-2016 benchmark demonstrate that BioLM-Score achieves significant improvements across docking, scoring, ranking, and screening tasks. Moreover, the proposed scoring function serves as an effective optimization objective for guiding docking protocols and conformational search. In summary, BioLM-Score provides a principled and practical alternative to existing scoring functions, combining efficiency, generalization, and interpretability for structure-based drug discovery.

arXiv:2602.14879v1 Announce Type: cross Abstract: Artificial intelligence (AI) can automatically delineate lesions on computed tomography (CT) and generate radiology report content, yet progress is limited by the scarcity of publicly available CT datasets with lesion-level annotations. To bridge this gap, we introduce CT-Bench, a first-of-its-kind benchmark dataset comprising two components: a Lesion Image and Metadata Set containing 20,335 lesions from 7,795 CT studies with bounding boxes, descriptions, and size information, and a multitask visual question answering benchmark with 2,850 QA pairs covering lesion localization, description, size estimation, and attribute categorization. Hard negative examples are included to reflect real-world diagnostic challenges. We evaluate multiple state-of-the-art multimodal models, including vision-language and medical CLIP variants, by comparing their performance to radiologist assessments, demonstrating the value of CT-Bench as a comprehensive benchmark for lesion analysis. Moreover, fine-tuning models on the Lesion Image and Metadata Set yields significant performance gains across both components, underscoring the clinical utility of CT-Bench.

arXiv:2410.15756v3 Announce Type: replace-cross Abstract: Ensuring correctness is crucial for code generation. Formal verification offers a definitive assurance of correctness, but demands substantial human effort in proof construction and hence raises a pressing need for automation. The primary obstacle lies in the severe lack of data-there is much fewer proofs than code snippets for Large Language Models (LLMs) to train upon. In this paper, we introduce SAFE, a framework that overcomes the lack of human-written proofs to enable automated proof generation of Rust code. SAFE establishes a self-evolving cycle where data synthesis and fine-tuning collaborate to enhance the model capability, leveraging the definitive power of a symbolic verifier in telling correct proofs from incorrect ones. SAFE also re-purposes the large number of synthesized incorrect proofs to train the self-debugging capability of the fine-tuned models, empowering them to fix incorrect proofs based on the verifier's feedback. SAFE demonstrates superior efficiency and precision compared to GPT-4o. Through tens of thousands of synthesized proofs and the self-debugging mechanism, we improve the capability of open-source models, initially unacquainted with formal verification, to automatically write proofs for Rust code. This advancement leads to a significant improvement in performance, achieving a 52.52% accuracy rate in a benchmark crafted by human experts, a significant leap over GPT-4o's performance of 14.39%.