Chao Shen

Jike Wang, Rui Qin, Mingyang Wang et al.

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D) structures, thereby limiting their effectiveness in tasks that explicitly involve molecular conformations. In this study, we introduced Token-Mol, a token-only 3D drug design model. This model encodes all molecular information, including 2D and 3D structures, as well as molecular property data, into tokens, which transforms classification and regression tasks in drug discovery into probabilistic prediction problems, thereby enabling learning through a unified paradigm. Token-Mol is built on the transformer decoder architecture and trained using random causal masking techniques. Additionally, we proposed the Gaussian cross-entropy (GCE) loss function to overcome the challenges in regression tasks, significantly enhancing the capacity of LLMs to learn continuous numerical values. Through a combination of fine-tuning and reinforcement learning (RL), Token-Mol achieves performance comparable to or surpassing existing task-specific methods across various downstream tasks, including pocket-based molecular generation, conformation generation, and molecular property prediction. Compared to existing molecular pre-trained models, Token-Mol exhibits superior proficiency in handling a wider range of downstream tasks essential for drug design. Notably, our approach improves regression task accuracy by approximately 30% compared to similar token-only methods. Token-Mol overcomes the precision limitations of token-only models and has the potential to integrate seamlessly with general models such as ChatGPT, paving the way for the development of a universal artificial intelligence drug design model that facilitates rapid and high-quality drug design by experts.

Yingmao Miao, Zhanpeng Huang, Rui Han et al.

While virtual try-on for clothes and shoes with diffusion models has gained attraction, virtual try-on for ornaments, such as bracelets, rings, earrings, and necklaces, remains largely unexplored. Due to the intricate tiny patterns and repeated geometric sub-structures in most ornaments, it is much more difficult to guarantee identity and appearance consistency under large pose and scale variances between ornaments and models. This paper proposes the task of virtual try-on for ornaments and presents a method to improve the geometric and appearance preservation of ornament virtual try-ons. Specifically, we estimate an accurate wearing mask to improve the alignments between ornaments and models in an iterative scheme alongside the denoising process. To preserve structure details, we further regularize attention layers to map the reference ornament mask to the wearing mask in an implicit way. Experimental results demonstrate that our method successfully wears ornaments from reference images onto target models, handling substantial differences in scale and pose while preserving identity and achieving realistic visual effects.

Junjie Chu, Mingjie Li, Ziqing Yang et al.

Accurately determining whether a jailbreak attempt has succeeded is a fundamental yet unresolved challenge. Existing evaluation methods rely on misaligned proxy indicators or naive holistic judgments. They frequently misinterpret model responses, leading to inconsistent and subjective assessments that misalign with human perception. To address this gap, we introduce JADES (Jailbreak Assessment via Decompositional Scoring), a universal jailbreak evaluation framework. Its key mechanism is to automatically decompose an input harmful question into a set of weighted sub-questions, score each sub-answer, and weight-aggregate the sub-scores into a final decision. JADES also incorporates an optional fact-checking module to strengthen the detection of hallucinations in jailbreak responses. We validate JADES on JailbreakQR, a newly introduced benchmark proposed in this work, consisting of 400 pairs of jailbreak prompts and responses, each meticulously annotated by humans. In a binary setting (success/failure), JADES achieves 98.5% agreement with human evaluators, outperforming strong baselines by over 9%. Re-evaluating five popular attacks on four LLMs reveals substantial overestimation (e.g., LAA's attack success rate on GPT-3.5-Turbo drops from 93% to 69%). Our results show that JADES could deliver accurate, consistent, and interpretable evaluations, providing a reliable basis for measuring future jailbreak attacks.

Yuchen Zhu, Jihong Chen, Yitong Li et al.

Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often lack generalizability across diverse biomolecular systems. We present BioScore, a foundational scoring function that addresses key challenges -- data sparsity, cross-system representation, and task compatibility -- through a dual-scale geometric graph learning framework with tailored modules for structure assessment and affinity prediction. BioScore supports a wide range of tasks, including affinity prediction, conformation ranking, and structure-based virtual screening. Evaluated on 16 benchmarks spanning proteins, nucleic acids, small molecules, and carbohydrates, BioScore consistently outperforms or matches 70 traditional and deep learning methods. Our newly proposed PPI Benchmark further enables comprehensive evaluation of protein-protein complex scoring. BioScore demonstrates broad applicability: (1) pretraining on mixed-structure data boosts protein-protein affinity prediction by up to 40% and antigen-antibody binding correlation by over 90%; (2) cross-system generalizability enables zero- and few-shot prediction with up to 71% correlation gain; and (3) its unified representation captures chemically challenging systems such as cyclic peptides, improving affinity prediction by over 60%. BioScore establishes a robust and generalizable framework for structural assessment across complex biomolecular landscapes.