I am a student of chemistry and computer science. I am a postdoctoral fellow at Caltech supervised by Prof. Frances Arnold (2025-present). I completed by my Ph.D. at McGill University (2019-2024) supervised by Prof. Dmytro (Dima) Perepichka, and I concurrently studied at Mila with Prof. Yoshua Bengio. I was a co-founder of the protein design startup Dreamfold (2021-2025). I was a Vanier scholar (2021-2024). I obtained my BSc (Hons) from McGill University (2016-2019) working with Prof. Perepichka, and earlier with Prof. Reinhard Hesse in geology. I have also been supervised by Dr. Jean-Michel Sellier at Mila. Before undergraduate studies, I spent my younger years in Germany, the Netherlands, and China.

My research is focused on understanding how uncharted physical properties emerge from molecular and supramolecular structures, and their design from the infinite chemical space. Feel free to reach out to me at chl@caltech.edu. My Google Scholar is here.

I am an organizer of the workshop series of integrating Generative and Experimental platforms for bioMolecular design (GEM) at ICLR. GEM at ICLR’25 was held in Singapore, and GEM at ICLR’24 was held in Vienna. Stay tuned for our next workshop.

Publications

2025

• SynCoGen: Synthesizable 3D Molecule Generation via Joint Reaction and Coordinate Modeling
  Andrei Rekesh, Miruna Cretu, Dmytro Shevchuk, Vignesh Ram Somnath, Pietro Lio, Robert A. Batey, Mike Tyers, Michał Koziarski, Cheng-Hao Liu, under review. 2025. DOI: 10.48550/arXiv.2507.11818

• Structural Control of Band Gap and Polaron Delocalization in 2D Azatriangulene Covalent Organic Frameworks
  Chang Wan Kang, Ehsan Hamzehpoor, Pegah Ghamari, Yuze Tao, Mohammad Hossein Gohari, Cheng-Hao Liu, Zhenzhe Zhang, Rustam Z. Khaliullin, Dmytro F. Perepichka, under review. 2025. DOI: 10.26434/chemrxiv-2025-mr7kv

• Generating π-Functional Molecules Using STGG+ with Active Learning
  Alexia Jolicoeur-Martineau, Yan Zhang, Boris Knyazev, Artisde Baratin, Cheng-Hao Liu, under review. 2025. DOI: 10.48550/arXiv.250214842. Also Spotlight at ICLR Machine Learning Multiscale Processes Workshop, 2025.

• Substrate-aware Zero-Shot Predictors for Non-Native Enzyme Activities
  Francesca-Zhoufan Li, Lukas Alexander Radtke, Kadina E Johnston, Cheng-Hao Liu, Yisong Yue, Frances H. Arnold, under review. 2025. Also at ICLR GEM Workshop, 2025.

• [Invited News and Views] Bilayer Covalent Organic Frameworks Take a Twist
  Cheng-Hao Liu, Dmytro F. Perepichka, Nat. Chem., 2025. Not peer-reviewed. DOI: 10.1038/s41557-025-01782-3

2024

• Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction
  Jarrid Rector-Brooks, Mohsin Hasan, Zhangzhi Peng, Zachary Quinn, Cheng-Hao Liu, Sarthak Mittal, Nouha Dziri, Michael Bronstein, Yoshua Bengio, Pranam Chatterjee, Alexander Tong, Avishek Joey Bose, ICLR, 2025.

• Flow Factorization for Efficient Generative Flow Networks
  Jiashun Liu, Chunhui Li, Cheng-Hao Liu, Dianbo Liu, Qingpeng Cai, Ling Pan, AAAI, 2024. Oral presentation.

• RGFN: Synthesizable Molecular Generation Using GFlowNets
  Michał Koziarski, Andrei Rekesh, Dmytro Shevchuk, Almer van der Sloot, Piotr Gaiński, Yoshua Bengio, Cheng-Hao Liu, Mike Tyers, Robert A. Batey, NeurIPS, 2024.

• Sequence-Augmented SE(3)-Flow Matching For Conditional Protein Backbone Generation
  Guillaume Huguet, James Vuckovic, Kilian Fatras, Eric Thibodeau-Laufer, Pablo Lemos, Riashat Islam, Cheng-Hao Liu, Jarrid Rector-Brooks, Tara Akhound-Sadegh, Michael Bronstein, Alexander Tong, Avishek Joey Bose, NeurIPS, 2024.

• Generative Active Learning for the Search of Small-molecule Protein Binders
  Maksym Korablyov†, Cheng-Hao Liu†, Moksh Jain†, Almer M. van der Sloot†, Eric Jolicoeur†, Edward Ruediger†, Andrei Cristian Nica†, Emmanuel Bengio, Kostiantyn Lapchevskyi, Daniel St-Cyr, Doris Alexandra Schuetz, Victor Ion Butoi, Jarrid Rector-Brooks, Simon Blackburn, Leo Feng, Hadi Nekoei, SaiKrishna Gottipati, Priyesh Vijayan, Prateek Gupta, Ladislav Rampášek, Sasikanth Avancha, Pierre-Luc Bacon, William L. Hamilton, Brooks Paige, Sanchit Misra, Stanislaw Kamil Jastrzebski, Bharat Kaul, Doina Precup, José Miguel Hernández-Lobato, Marwin Segler, Michael M. Bronstein, Anne Marinier, Mike Tyers, Yoshua Bengio, under review. Also at ICLR GEM Workshop, 2024. DOI: 10.48550/arXiv.2405.01616 †: equal contribution

• Stabilization of Na-ion Cathode Surfaces: Combinatorial Experiments with Insights from Machine Learning Models
  Shipeng Jia, Marzieh Abdolhosseini , Cheng-Hao Liu, Antranik Jonderian, Yixuan Li, Hunbo Kwak, Shinichi Kumakura, Maddison Eisnor, Michael Sieffert, Eric McCalla, Adv. Energy Sustainability Res., 2024. DOI: 10.1002/aesr.202400051

• Iterated Denoising Energy Matching for Sampling from Boltzmann Densities
  Tara Akhound-Sadegh, Jarrid Rector-Brooks, Avishek Joey Bose, Sarath Mittal, Pablo Lemos, Cheng-Hao Liu, Marcin Sendera, Siamak Ravanbakhsh, Gauthier Gidel, Yoshua Bengio, Nikolay Malkin, Alexander Tong, ICML, 2024. DOI: 10.48550/arXiv.2402.06121

2023

• SE(3)-Stochastic Flow Matching for Protein Backbone Generation
  Avishek Joey Bose, Tara Akhound-Sadegh, Kilian Fatras, Guillaume Huguet, Jarrid Rector-Brooks, Cheng-Hao Liu, Andrei Cristian Nica, Maksym Korablyov, Michael Bronstein, Alexander Tong, ICLR, 2024. DOI: 10.48550/arXiv.2310.02391

• Diffusion Generative Flow Samplers: Improving Learning Signals through Partial Trajectory Optimization
  Dinghuai Zhang, Ricky Tian Qi Chen, Cheng-Hao Liu, Aaron Courville, Yoshua Bengio, ICLR, 2024. DOI: 10.48550/arXiv.2310.02679.

• Towards Equilibrium Molecular Conformation Generation with GFlowNets
  Alexandra Volokhova, Michał Koziarski, Alex Hernández-García, Cheng-Hao Liu, Santiago Miret, Pablo Lemos, Luca Thiede, Zichao Yan, Alan Aspuru-Guzik, Yoshua Bengio, Digital Discovery, 2024, 3, 1038-1047. Also at NeurIPS AI4Mat Workshop, 2023. DOI: 10.1039/D4DD00023D.

• Thompson Sampling for Improved Exploration in GFlowNets
  Jarrid Rector-Brooks, Kanika Madan, Moksh Jain, Maksym Korablyov, Cheng-Hao Liu, Sarath Chandar, Nikolay Malkin, Yoshua Bengio, ICML SPIGM Workshop, 2023.

• Multi-Fidelity Active Learning with GFlowNets
  Alex Hernández-García, Nikita Saxena, Moksh Jain, Cheng-Hao Liu, Yoshua Bengio, TMLR, 2024. Also at NeurIPS RealML Workshop, 2023.

• Thiele’s Fluorocarbons: Stable Diradicaloids with Efficient Vis-NIR Fluorescence from a Zwitterionic Excited State
  Cheng-Hao Liu†, Zhechang He†, Cory Ruchlin†, Yuxuan Che, Kyle Somers, Dmytro F. Perepichka, J. Am. Chem. Soc, 2023, 145, 15702. †: equal contribution

• A community effort to discover small molecule SARS-CoV-2 inhibitors
  Johannes Schimunek et al., Mol. Inform., 2024, 43, e202300262.

• GFlowNets for AI-Driven Scientific Discovery
  Moksh Jain, Tristan Deleu, Jason Hartford, Cheng-Hao Liu, Alex Hernandez-Garcia, Yoshua Bengio, Digital Discovery, 2023, 2, 557.

• Nitrofluorene-Based A–D–A Electron Acceptors for Organic Photovoltaics
  Yuxuan Che, Muhammad Rizwan Niazi, Ting Yu, Thierry Maris, Cheng-Hao Liu, Dongling Ma, Ricardo Izquierdo, Igor F. Perepichka, Dmytro F. Perepichka, J. Mater. Chem. C., 2023, 11, 8186.

• Silver Nanoparticle Enhanced Metal-organic Matrix with Interface-engineering for Efficient Photocatalytic Hydrogen Evolution
  Yannan Liu†, Cheng-Hao Liu†, Tushar Debnath, Yong Wang, Darius Pohl, Lucas V. Besteiro, Déboa Meira, Shengyun Huang, Fan Yang, Bernd Rellinghaus, Mohamed Chaker, Dmytro F. Perepichka, Dongling Ma, Nat. Commun., 2023, 14, 541. †: equal contribution

2022

• Efficient Room-Temperature Phosphorescence of Covalent Organic Frameworks through Covalent Halogen Doping
  Ehsan Hamzehpoor, Cory Ruchlin, Yuze Tao, Cheng-Hao Liu, Hatem M. Titi, Dmytro F. Perepichka, Nat. Chem., 2023, 15, 83.

• Vanishing Electronic Band-gap in Two-dimensional Hydrogen-Bonded Organic Frameworks
  Cheng-Hao Liu, Allan Wei, Maïline Fok Cheung, Dmytro F. Perepichka, Chem. Mater., 2022, 34, 3461-3467. Supplemental Cover. Selected in the Virtual Issue π-Conjugated Materials: Here, There, and Everywhere.

• A 2D Perchlorinated sp²-Carbon Framework
  Cheng-Hao Liu, Yoko Sakai-Otsuka, Paul Richardson, Muhammad Rizwan Niazi, Ehsan Hamzehpoor, Thaksen Jadhav, Akaela Michels-Gualteri, Yuan Fang, Muralee Murugesu, Dmytro F. Perepichka, Cell Rep. Phys. Sci., 2022, 3, 100858.

• RetroGNN: Fast Estimation of Synthesizability for Virtual Screening and De Novo Design by Learning From Slow Retrosynthesis Software
  Cheng-Hao Liu, Maksym Korablyov, Stanisław Jastrzębski, Paweł Włodarczyk-Pruszyński, Yoshua Bengio, and Marwin Segler. J. Chem. Inf. Model., 2022, 62, 2293–2300. See 2020 NeurIPS workshop paper for the first version.

• Evaluating Generalization in GFlowNets for Molecule Design
  Andrei Cristian Nica, Moksh Jain, Emmanuel Bengio, Cheng-Hao Liu, Maksym Korablyov, Michael M. Bronstein, Yoshua Bengio, ICLR MLDD Workshop, 2022.

• Bidirectional Phase Transformation of Supramolecular Networks Using Two Molecular Signals
  Daling Cui, Cheng-Hao Liu, Federico Rosei, and Dmitrii F. Perepichka, ACS Nano, 2022, 16, 1560-1566.

2021

• Glaser Coupling of Substituted Anthracene Diynes on a Non-metallic Surface at the Vapor-Solid Interface
  Yuan Fang, Zahra Heydari, Cheng-Hao Liu, Nianyue Zhang, Louis A. Cuccia, Oleksandr Ivasenko, and Dmitrii F. Perepichka, Chem. Res. Chin. Univ., 2021, 37, 1143. Invited contribution for special issue ‘Women in Chemistry’

• Phase-enabled metal-organic framework homojunction for highly selective CO₂ photoreduction
  Yannan Liu, Chuanshuang Chen, Jesus Valdez, Debora Motta Meira, Wanting He, Yong Wang, Catalin Harnagea, Qiongqiong Lu, Tugrul Guner, Hao Wang, Cheng-Hao Liu, Qingzhe Zhang, Shengyun Huang, Aycan Yurtsever, Mohamed Chaker, and Dongling Ma, Nat. Commun., 2021, 12, 1231.

2020

• RetroGNN: Approximating Retrosynthesis by Graph Neural Networks for De Novo Drug Design
  Cheng-Hao Liu, Maksym Korablyov, Stanisław Jastrzębski, Paweł Włodarczyk-Pruszyński, Yoshua Bengio, and Marwin Segler. NeurIPS Machine Learning for Molecules Workshop, 2020. See 2022 JCIM paper for the latest version.

• A Pure Red Doublet Emission with 90% Quantum Yield: Stable, Colorless, Iodinated Triphenylmethane Solid
  Cheng-Hao Liu, Ehsan Hamzehpoor, Yoko Otsuka-Sakai, Thaksen Jadhav, and Dmitrii F. Perepichka. Angew. Chem. Int. Ed., 2020, 59, 23030.

• Transformation Between 2D and 3D Covalent Organic Frameworks via Reversible [2+2] Cycloaddition
  Thaksen Jadhav†, Yuan Fang†, Cheng-Hao Liu†, Afshin Dadvand, Ehsan Hamzehpoor, William Patterson, Antranik Jonderian, Robin Stein, and Dmitrii F. Perepichka. J. Am. Chem. Soc., 2020, 142, 8862. †: equal contribution

• A Two-dimensional Poly(azatriangulene) Covalent Organic Framework with Semiconducting and Paramagnetic State
  Lakshmi Vellanki, Cheng-Hao Liu, Malakalapalli Rajeswara Rao, Yulan Chen, Yuan Fang, Afshin Dadvand, Ehsan Hamzehpoor, Yoko Sakai-Otsuka, Robin S. Stein, and Dmitrii F. Perepichka. J. Am. Chem. Soc., 2020, 142, 2155.

• Understanding the Photovoltaic Behavior of A–D–A Molecular Semiconductors through a Permutation of End Groups
  Yuxuan Che, Yuliang Zhang, Yali Yang, Cheng-Hao Liu, Ricardo Izquierdo, Steven Shuyong Xiao, and Dmitrii F. Perepichka. J. Org. Chem., 2020, 85, 52.

2019

• Strong Enhancement of Electron Donor/Acceptor Ability by DD/AA Complementary Hydrogen Bonding
  Cheng-Hao Liu, Muhammad R. Niazi, Dmitrii F. Perepichka. Angew. Chem. Int. Ed., 2019, 58, 17312. Frontispiece.

• 2D Poly(arylene vinylene) Covalent Organic Frameworks via Aldol Condensation of Trimethyltriazine
  Thaksen Jadhav, Yuan Fang, William Patterson, Cheng-Hao Liu, Ehsan Hamzehpoor, and Dmitrii F. Perepichka. Angew. Chem. Int. Ed., 2019, 58, 13753.