Publications

@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}
}

@article{sarma2026extract,
  title={Can We Extract Physics-like Energies from Generative Protein Diffusion Models?},
  author={Sarma, Sudeep and Truscott, Harrison and Xu, Da and Reid, Kendall and Chu, Lee-Shin and Chen, Jacky and Gray, Jeffrey J.},
  journal={PRX Life},
  year={2026},
  doi={10.1103/m7qr-gnjc}
}

@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}
}

@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}
}

@article{chen2023unsupervised,
  title={Unsupervised Machine Learning Unveil Easily Identifiable Subphenotypes of {COVID-19} With Differing Disease Trajectories},
  author={Chen, Jacky and Hsu, Jocelyn and Szewc, Alexandra and Balucini, Clotilde and Azad, Tej D. and Gong, Kirby and Kim, Han and Stevens, Robert D.},
  journal={medRxiv},
  year={2023},
  doi={10.1101/2023.04.07.23288152}
}