Removing Biases from Molecular Representations via Information Maximization. - Chenyu Wang 003; Sharut Gupta; Caroline Uhler; Tommi S. Jaakkola (ICLR, 2024)

Dirichlet Flow Matching with Applications to DNA Sequence Design. - Hannes Stärk; Bowen Jing; Chenyu Wang 003; Gabriele Corso; Bonnie Berger; Regina Barzilay; Tommi S. Jaakkola (ICML, 2024)

In-Context Symmetries: Self-Supervised Learning through Contextual World Models. - Sharut Gupta; Chenyu Wang 003; Yifei Wang 001; Tommi S. Jaakkola; Stefanie Jegelka (NeurIPS, 2024)

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding. - Xiner Li; Yulai Zhao 002; Chenyu Wang 003; Gabriele Scalia; Gökcen Eraslan; Surag Nair; Tommaso Biancalani; Aviv Regev; Sergey Levine; Masatoshi Uehara (CoRR, 2024)

Automated Generation of Challenging Multiple-Choice Questions for Vision Language Model Evaluation. - Yuhui Zhang; Yuchang Su; Yiming Liu; Xiaohan Wang; James Burgess; Elaine Sui; Chenyu Wang 003; Josiah Aklilu; Alejandro Lozano; Anjiang Wei; Ludwig Schmidt; Serena Yeung-Levy (CVPR, 2025)

An Information Criterion for Controlled Disentanglement of Multimodal Data. - Chenyu Wang 003; Sharut Gupta; Xinyi Zhang; Sana Tonekaboni; Stefanie Jegelka; Tommi S. Jaakkola; Caroline Uhler (ICLR, 2025)

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design. - Chenyu Wang 003; Masatoshi Uehara; Yichun He; Amy Wang; Avantika Lal; Tommi S. Jaakkola; Sergey Levine; Aviv Regev; Hanchen Wang 002; Tommaso Biancalani (ICLR, 2025)

Inference-Time Alignment in Diffusion Models with Reward-Guided Generation: Tutorial and Review. - Masatoshi Uehara; Yulai Zhao 002; Chenyu Wang 003; Xiner Li; Aviv Regev; Sergey Levine; Tommaso Biancalani (CoRR, 2025)

CellFlow: Simulating Cellular Morphology Changes via Flow Matching. - Yuhui Zhang; Yuchang Su; Chenyu Wang 003; Tianhong Li; Zoe Wefers; Jeffrey J. Nirschl; James Burgess; Daisy Ding; Alejandro Lozano; Emma Lundberg; Serena Yeung-Levy (CoRR, 2025)

Learning Diffusion Models with Flexible Representation Guidance. - Chenyu Wang 003; Cai Zhou; Sharut Gupta; Zongyu Lin; Stefanie Jegelka; Stephen Bates; Tommi S. Jaakkola (CoRR, 2025)