Publications

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* Indicates equal contribution

2026

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    Beckmann Transport Models: From Autonomous Flows to One-Step Maps
    Lee Cheuk-Kit , Florentin Coeurdoux , Yuyuan Chen , Sophia Tang , Peter Potaptchik , Yilun Du , Michael Samuel Albergo and Eric Vanden-Eijnden
    arXiv preprint arXiv:2608.01692, Aug 2026
    Paper
  2. Expanding Flow Maps
    Sophia Tang and Pranam Chatterjee
    arXiv preprint arXiv:2607.21585, Jul 2026
    Paper Video Code Slides Website
  3. 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
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    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 Code
  5. 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
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    PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction
    Yinuo Zhang , Sophia Tang , Tong Chen , Elizabeth Mahood , Sophia Vincoff and Pranam Chatterjee
    Nature Communications, Jan 2026
    Paper Code Website
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    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
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    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
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    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
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    Peptide-functionalized nanoparticles for brain-targeted therapeutics
    Sophia Tang , Emily L. Han and Michael J. Mitchell
    Drug Delivery and Translational Research, Mar 2025
    Paper
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    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
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    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
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    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
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    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