Jacky Chen

Ph.D. Student
CMU-Pitt Joint Ph.D. Program in Computational Biology

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I am a third-year Ph.D. student in the Joint Carnegie Mellon–University of Pittsburgh Ph.D. Program in Computational Biology, advised by David Koes. My research focuses on machine learning methods for molecular discovery and sampling. Prior to my Ph.D., I worked with Alan Cheng at Merck on deep learning for ADMET prediction. I received my undergraduate degree from Johns Hopkins University, where I worked with Jeffrey Gray on diffusion models for protein docking.

Selected Publications

1. WELP: Weighted Ensemble in the LooP for Committor Learning
   Jacky Chen, Rishal Aggarwal, David Ryan Koes
   NeurIPS, 2026
   BibTeX

   @inproceedings{chen2026welp,
     title={{WELP}: Weighted Ensemble in the {LooP} for Committor Learning},
     author={Chen, Jacky and Aggarwal, Rishal and Koes, David Ryan},
     booktitle={Advances in Neural Information Processing Systems},
     year={2026}
   }

2. BoltzNCE: Learning Likelihoods for Boltzmann Generation with Stochastic Interpolants and Noise Contrastive Estimation
   Rishal Aggarwal, Jacky Chen, Nicholas Boffi, David Koes
   NeurIPS, 2025
   Paper arXiv Code

   BibTeX

   @inproceedings{aggarwal2025boltznce,
     title={{BoltzNCE}: Learning Likelihoods for {Boltzmann} Generation with Stochastic Interpolants and Noise Contrastive Estimation},
     author={Aggarwal, Rishal and Chen, Jacky and Boffi, Nicholas and Koes, David},
     booktitle={Advances in Neural Information Processing Systems},
     volume={38},
     pages={167195--167227},
     year={2025},
     doi={10.52202/085713-5574}
   }

3. Data Scaling and Generalization Insights for Medicinal Chemistry Deep Learning Models
   Jacky Chen, Yunsie Chung, Jonathan Tynan, Chen Cheng, Song Yang, Alan C. Cheng
   Journal of Chemical Information and Modeling, 2025
   Paper ChemRxiv

   BibTeX

   @article{chen2025data,
     title={Data Scaling and Generalization Insights for Medicinal Chemistry Deep Learning Models},
     author={Chen, Jacky and Chung, Yunsie and Tynan, Jonathan and Cheng, Chen and Yang, Song and Cheng, Alan C.},
     journal={Journal of Chemical Information and Modeling},
     volume={65},
     number={12},
     pages={5887--5898},
     year={2025},
     publisher={American Chemical Society},
     doi={10.1021/acs.jcim.5c00538}
   }

All publications →