Publications

* Indicates equal contribution

2026

  1. A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding
    Sophia Tang , Yuchen Zhu , Molei Tao and Pranam Chatterjee
    arXiv preprint arXiv:2606.13565, Jun 2026
    Paper Article Code Website
  2. actflow.png
    Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules
    Riccardo De Santi , Bruce Lee , Cristian Perez Jensen , Kimon Protopapas , Sophia Tang , Cheng-Hao Liu , Pranam Chatterjee , Yisong Yue and Andreas Krause
    arXiv preprint arXiv:2606.08802, Jun 2026
    Paper
  3. mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties
    Sawan Patel* , Sophia Tang* , Yesol Kim* , Yinuo Zhang , Divya Srijay , Ping-Jung Lin , Shambhavi Shubham , Fengmei Pi , Cedric Wu , Sherwood Yao and Pranam Chatterjee
    arXiv preprint arXiv:2605.31296, Jun 2026
    Paper Article Code Website
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    TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
    Hanqun Cao* , Aastha Pal* , Sophia Tang , Yinuo Zhang , Jingjie Zhang , Pheng Ann Heng and Pranam Chatterjee
    International Conference on Machine Learning (ICML 2026) Spotlight, May 2026
    Paper Code
  5. foundations-sbm.png
    Foundations of Schrödinger Bridges for Generative Modeling
    Sophia Tang
    arXiv, Preprint, Mar 2026
    Paper Article Website
  6. peptiverse-cover.png
    PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction
    Yinuo Zhang , Sophia Tang , Tong Chen , Elizabeth Mahood , Sophia Vincoff and Pranam Chatterjee
    bioRxiv, Preprint, Jan 2026
    Paper Code Website
  7. hts-brain.jpeg
    High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain
    Emily L Han , Dongyoon Kim , Amanda M Murray , Kaitlin Mrksich , Alex G Hamilton , Sophia Tang , Soyeon Yoo , Audrey T Zhu , Elaine R Tong , Rohan Palanki and others
    ACS nano, Jan 2026
    Paper

2025

  1. Entangled Schrödinger Bridge Matching
    Sophia Tang , Yinuo Zhang and Pranam Chatterjee
    arXiv, Preprint, Nov 2025
    Paper Code Poster
  2. TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion
    Sophia Tang* , Yuchen Zhu* , Molei Tao and Pranam Chatterjee
    arXiv, Preprint, Sep 2025
    Paper Code
  3. branchsbm.png
    Branched Schrödinger Bridge Matching
    Sophia Tang , Yinuo Zhang , Alexander Tong and Pranam Chatterjee
    International Conference on Learning Representations (ICLR 2026), Jun 2025
    Paper Video Code Poster Website
  4. mog-dfm.png
    Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
    Tong Chen , Yinuo Zhang , Sophia Tang and Pranam Chatterjee
    arXiv, Preprint, May 2025
    Paper Code
  5. ddtr.jpg
    Peptide-functionalized nanoparticles for brain-targeted therapeutics
    Sophia Tang , Emily L. Han and Michael J. Mitchell
    Drug Delivery and Translational Research, Mar 2025
    Paper
  6. guidance.png
    Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation
    Sophia Tang , Yinuo Zhang , Alexander Tong and Pranam Chatterjee
    arXiv, Preprint, Mar 2025
    Paper Poster

2024

  1. PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion
    Sophia Tang* , Yinuo Zhang* and Pranam Chatterjee
    International Conference on Machine Learning (ICML 2025), Dec 2024
    Paper Video Article Code Poster
  2. nanoletters.jpeg
    Peptide-Functionalized Lipid Nanoparticles for Targeted Systemic mRNA Delivery to the Brain
    Emily L. Han , Sophia Tang , Dongyoon Kim , Amanda M. Murray , Kelsey L. Swingle , Alex G. Hamilton , Kaitlin Mrksich , Marshall S. Padilla , Rohan Palanki , Jacqueline J. Li and Michael J. Mitchell
    Nano Letters, American Chemical Society (ACS), Dec 2024
    Paper
  3. predictive.jpeg
    Predictive High-Throughput Platform for Dual Screening of mRNA Lipid Nanoparticle Blood–Brain Barrier Transfection and Crossing
    Emily L. Han , Marshall S. Padilla , Rohan Palanki , Dongyoon Kim , Kaitlin Mrksich , Jacqueline J. Li , Sophia Tang , Il-Chul Yoon and Michael J. Mitchell
    Nano Letters, American Chemical Society (ACS), Jan 2024
    Paper
  4. optimized.jpeg
    Optimized microfluidic formulation and organic excipients for improved lipid nanoparticle mediated genome editing
    Rohan Palanki , Emily L. Han , Amanda M. Murray , Rohin Maganti , Sophia Tang , Kelsey L. Swingle , Dongyoon Kim , Hannah Yamagata , Hannah C. Safford , Kaitlin Mrksich , William H. Peranteau and Michael J. Mitchell
    Lab on a Chip, Jan 2024
    Paper