Lu Zhu

Yunhui Jang, Lu Zhu, Jake Fawkes et al.

Large language models (LLMs) have recently gained significant attention as a promising approach to accelerate scientific discovery. However, their application in open-ended scientific domains such as biology remains limited, primarily due to the lack of factually grounded and actionable explanations. To address this, we introduce a structured explanation formalism for virtual cells that represents biological reasoning as mechanistic action graphs, enabling systematic verification and falsification. Building upon this, we propose VCR-Agent, a multi-agent framework that integrates biologically grounded knowledge retrieval with a verifier-based filtering approach to generate and validate mechanistic reasoning autonomously. Using this framework, we release VC-TRACES dataset, which consists of verified mechanistic explanations derived from the Tahoe-100M atlas. Empirically, we demonstrate that training with these explanations improves factual precision and provides a more effective supervision signal for downstream gene expression prediction. These results underscore the importance of reliable mechanistic reasoning for virtual cells, achieved through the synergy of multi-agent and rigorous verification.

Lu Zhu, Tiantian Geng, Yangye Chen et al.

Recently, rapid advancements have been made in multimodal large language models (MLLMs), especially in video understanding tasks. However, current research focuses on simple video scenarios, failing to reflect the complex and diverse nature of real-world audio-visual events in videos. To bridge this gap, we firstly introduce R-AVST, a dataset for audio-visual reasoning featuring fine-grained spatio-temporal annotations. In constructing this, we design a pipeline consisting of LLM-based key object extraction, automatic spatial annotation and manual quality inspection, resulting in over 5K untrimmed videos with 27K objects across 100 types of audio-visual events. Building on this dataset, we define three core tasks for spatio-temporal reasoning in audio-visual scenes and generate more than 8K high-quality, evenly distributed question-answer pairs to effectively benchmark model performance. To further enhance reasoning, we propose AVST-Zero, a reinforcement learning-based model that avoids intermediate supervision, directly optimizing behavior via carefully designed multi-dimensional rewards. Extensive experiments validate the effectiveness of our R-AVST in advancing audio-visual spatio-temporal reasoning, upon which AVST-Zero demonstrates competitive performance compared to existing models. To the best of our knowledge, R-AVST is the first dataset designed for real-world audio-visual spatio-temporal reasoning, and AVST-Zero offers a novel perspective for tackling future challenges in this domain.

Lu Zhu, Emmanuel Noutahi

Generative chemical language models (CLMs) have demonstrated strong capabilities in molecular design, yet their impact in drug discovery remains limited by the absence of reliable reward signals and the lack of interpretability in their outputs. We present SAFE-T, a generalist chemical modeling framework that conditions on biological context -- such as protein targets or mechanisms of action -- to prioritize and design molecules without relying on structural information or engineered scoring functions. SAFE-T models the conditional likelihood of fragment-based molecular sequences given a biological prompt, enabling principled scoring of molecules across tasks such as virtual screening, drug-target interaction prediction, and activity cliff detection. Moreover, it supports goal-directed generation by sampling from this learned distribution, aligning molecular design with biological objectives. In comprehensive zero-shot evaluations across predictive (LIT-PCBA, DAVIS, KIBA, ACNet) and generative (DRUG, PMO) benchmarks, SAFE-T consistently achieves performance comparable to or better than existing approaches while being significantly faster. Fragment-level attribution further reveals that SAFE-T captures known structure-activity relationships, supporting interpretable and biologically grounded design. Together with its computational efficiency, these results demonstrate that conditional generative CLMs can unify scoring and generation to accelerate early-stage drug discovery.