Chenyu Wang | Massachusetts Institute of Technology

About Me

I am a third-year PhD student at MIT CSAIL, advised by Tommi Jaakkola. My research interests lie broadly in machine learning, representation learning, generative models, and AI for science. Recently my research focuses on multi-modal learning, diffusion generative models, and controlled generation.

Before my PhD, I obtained my Bachelor’s degree from Tsinghua University, working as a research assistant in Tsinghua Universal Machine Learning (THUML) Group under the supervision of Mingsheng Long. I was also fortunate to work as a research intern with Mengdi Wang at Princeton University and with Cyrus Shahabi at University of Southern California.

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Resume (Updated in Jan 2025)

Publications & Preprints

(* Equal Contribution)

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design
Chenyu Wang*, Masatoshi Uehara*, Yichun He, Amy Wang, Tommaso Biancalani, Avantika Lal, Tommi Jaakkola, Sergey Levine, Hanchen Wang, Aviv Regev
International Conference on Learning Representations. ICLR 2025.
[Paper] [Code]

An Information Criterion for Controlled Disentanglement of Multimodal Data
Chenyu Wang*, Sharut Gupta*, Xinyi Zhang, Sana Tonekaboni, Stefanie Jegelka, Tommi Jaakkola, Caroline Uhler
International Conference on Learning Representations. ICLR 2025.
Also Oral and Honorable Mention Award at NeurIPS 2024 UniReps workshop.
[Paper] [Code]

Derivative-Free Guidance in Continuous and Discrete Diffusion Models with Soft Value-Based Decoding
Xiner Li, Yulai Zhao, Chenyu Wang, Gabriele Scalia, Gokcen Eraslan, Surag Nair, Tommaso Biancalani, Aviv Regev, Sergey Levine, Masatoshi Uehara
NeurIPS 2024 Workshop on AI for New Drug Modalities.
[Paper] [Code]

In-Context Symmetries: Self-Supervised Learning through Contextual World Models
Sharut Gupta*, Chenyu Wang*, Yifei Wang*, Tommi Jaakkola, Stefanie Jegelka,
Advances in Neural Information Processing Systems. NeurIPS 2024.
Also Oral at NeurIPS 2024 SSL workshop.
[Paper] [Code]

Dirichlet Flow Matching with Applications to DNA Sequence Design
Hannes Stark*, Bowen Jing*, Chenyu Wang, Gabriele Corso, Bonnie Berger, Regina Barzilay, Tommi Jaakkola,
International Conference on Machine Learning. ICML 2024.
Also Oral at ICLR 2024 MLGenX workshop.
[Paper] [Code]

Removing Biases from Molecular Representations via Information Maximization
Chenyu Wang, Sharut Gupta, Caroline Uhler, Tommi Jaakkola
International Conference on Learning Representations. ICLR 2024.
[Paper] [Code]

Tree-Based Neural Bandits for High-Value Protein Design
Chenyu Wang*, Joseph Kim*, Le Cong, Mengdi Wang
56th Annual Conference on Information Sciences and Systems. CISS 2022.
[Paper]

HAGEN: Homophily-Aware Graph Convolutional Recurrent Network for Crime Forecasting
Chenyu Wang*, Zongyu Lin*, Xiaochen Yang, Mingxuan Yue, Jiao Sun, Cyrus Shahabi
AAAI Conference on Artificial Intelligence. AAAI 2022. (Oral Presentation)
[Paper] [Code] [Talk at TGL]

Open Domain Generalization with Domain-Augmented Meta-Learning
Yang Shu*, Zhangjie Cao*, Chenyu Wang, Jianmin Wang, Mingsheng Long
IEEE Conference on Computer Vision and Pattern Recognition. CVPR 2021.
[Paper] [Code]

Education and Research Experience

Massachusetts Institute of Technology
2022.08-Present
PhD student in Computer Science
Advisor: Tommi Jaakkola

Genentech
2024.05-2024.08
Research intern
Advisor: Aviv Regev
Mentor: Hanchen Wang, Masatoshi Uehara

Tsinghua University
2018.08-2022.06
B.S. in Economics
Minor in Data Science and Technology
Advisor: Mingsheng Long
Mentor: Yang Shu

Princeton University
2021.06-2021.12
Research intern
Advisor: Mengdi Wang, Le Cong
Mentor: Joseph Kim, Huazheng Wang

University of Southern California
2021.01-2021.06
Research intern
Advisor: Cyrus Shahabi
Mentor: Jiao Sun, Mingxuan Yue

Selected Awards

2022 MIT EECS Great Educators Fellowship
2022 Outstanding Undergraduate in Tsinghua (2% in Tsinghua)
2022 Outstanding Undergraduate in Beijing
2022 Chen Daisun Scholarship (3 in Tsinghua SEM)
2022 Undergraduate Commencement Student Speaker of Tsinghua SEM
2021 Meritorious Winner in MCM/ICM Mathematical Contest in Modelling
2020 Tang Lixin Scholarship (50 in Tsinghua)
2019 National Scholarship (0.2% in China)
2019 Athletics Excellence Scholarship of Tsinghua
2018 Gold medalist of 50th International Chemistry Olympiad (4 in China, 6th place in the world)
2016 Silver medalist of 15th China Girl’s Mathematical Olympiad (50 in China)

Internship Experience

Genentech, Research Intern at Regev Lab, May 2024 - Aug. 2024
Jane Street, Quantitative Trading Intern (return offer extended), Jun. 2021 - Sept. 2021
WizardQuant Capital Management, Quantitative Research Intern, Jun. 2020 - Aug. 2020
Techsharpe Quant Capital Management, Data Analyst Intern, Jan. 2020 - Feb. 2020

Services

Reviewer: ICLR 2025, NeurIPS 2024, PLOS Computational Biology

Miscellaneous

I enjoy (and perhaps good at) doing sports. During undergrad, I was an active member in the track team and soccer team in my school, getting 1st place in 4*400m relay, 3rd place in 1500m, women’s soccer champion etc. I’m also a fan of literature and classical music. I enjoy travelling and tasting local delicacies.