11 citations · 28 across the 16 of their papers we have counts for
6 papers · 1 filter
Contextualizing Biological Language Models across Modalities via Logit-Space Contrastive Alignment
Yanjun Shao, Yundi Chen, Yashvi Patel +2
Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, var…
FORGE: Fragment-Oriented Ranking and Generation for Context-Aware Molecular Optimization
Qingchuan Zhang, He Cao, Hao Li +6
Molecular optimization seeks to improve a molecule through small structural edits while preserving similarity to the starting compound. Recent language-model approaches typically t…
AI Scientists for Building Virtual-Cell Models
Xiangru Tang, Zhuoyun Yu, Jiapeng Chen +12
Autonomous agents, from virtual laboratories to biological data-analysis agents and co-scientists, have begun to turn scientific goals into hypotheses. Whether they can go further…
Revisiting Convolution Architecture in the Realm of DNA Foundation Models
Yu Bo, Weian Mao, Yanjun Shao +6
In recent years, a variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there…
PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes
He Cao, Yanjun Shao, Zhiyuan Liu +4
Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling…
Colossal-Auto: Unified Automation of Parallelization and Activation Checkpoint for Large-scale Models
Yuliang Liu, Shenggui Li, Jiarui Fang +3
In recent years, large-scale models have demonstrated state-of-the-art performance across various domains. However, training such models requires various techniques to address the…