8 papers
Autonomous Science Bench: Evaluating AI Agents for Autonomous Scientific Discovery
Yibo Wen, Han Liu
AI agents for autonomous scientific discovery must decide which experiments to run under a limited budget. Most benchmarks for science agents provide fixed datasets, while others t…
MolMem: Memory-Augmented Agentic Reinforcement Learning for Sample-Efficient Molecular Optimization
Ziqing Wang, Yibo Wen, Abhishek Pandy +2
In drug discovery, molecular optimization aims to iteratively refine a lead compound to improve molecular properties while preserving structural similarity to the original molecule…
Cell-JEPA: Latent Representation Learning for Single-Cell Transcriptomics
Ali ElSheikh, Rui-Xi Wang, Weimin Wu +9
Single-cell foundation models learn by reconstructing masked gene expression, implicitly treating technical noise as signal. With dropout rates exceeding 90%, reconstruction object…
POLO: Preference-Guided Multi-Turn Reinforcement Learning for Lead Optimization
Ziqing Wang, Yibo Wen, William Pattie +6
Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similar…
Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models
Weimin Wu, Xuefeng Song, Yibo Wen +5
We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify t…
A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimization
Ziqing Wang, Kexin Zhang, Zihan Zhao +4
Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic not…
Pareto-Optimal Energy Alignment for Designing Nature-Like Antibodies
Yibo Wen, Chenwei Xu, Jerry Yao-Chieh Hu +2
We present a three-stage framework for training deep learning models specializing in antibody sequence-structure co-design. We first pre-train a language model using millions of an…
Efficient Encoding of Graphics Primitives with Simplex-based Structures
Yibo Wen, Yunfan Yang
Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due t…