Publications

2026

1. LLM-to-Flow Distillation: Teaching Natural Language Goals to Scientific Generators read

   Riccardo De Santi^* , Federico Di Gennaro^* , Angelo Gnazzo^* , Sophia Tang , Pranam Chatterjee , Fanny Yang , İsmail İlkan Ceylan , Michael M. Bronstein and Andreas Krause

   arXiv preprint arXiv:2610.17246, Oct 2026

   Paper Bib Code Website

   @article{santi2026llm,
     title={LLM-to-Flow Distillation: Teaching Natural Language Goals to Scientific Generators},
     author={Riccardo De Santi and Federico Di Gennaro and Angelo Gnazzo and Sophia Tang and Pranam Chatterjee and Fanny Yang and İsmail İlkan Ceylan and Michael M. Bronstein and Andreas Krause},
     journal={arXiv preprint arXiv:2610.17246},
     year={2026},
     url={https://arxiv.org/abs/2610.17246}
   }

2. 

   Discrete Beckmann Transport Models for One-Step Language Modeling and Reasoning read

   Sophia Tang and Shiyi Wang

   arXiv preprint arXiv:2609.15903, Sep 2026

   Paper Bib Video Article Website

   @article{tang2026discrete,
     title={Discrete Beckmann Transport Models for One-Step Language Modeling and Reasoning},
     author={Sophia Tang and Shiyi Wang},
     journal={arXiv preprint arXiv:2609.15903},
     year={2026},
     url={https://arxiv.org/abs/2609.15903}
   }

3. 

   Beckmann Transport Models: From Autonomous Flows to One-Step Maps read

   Cheuk-Kit Lee , Florentin Coeurdoux , Yuyuan Chen , Sophia Tang , Peter Potaptchik , Yilun Du , Michael Samuel Albergo and Eric Vanden-Eijnden

   Advances in Neural Information Processing Systems (NeurIPS 2026), Aug 2026

   Paper Bib

   @article{lee2026beckmann,
     title={Beckmann Transport Models: From Autonomous Flows to One-Step Maps},
     author={Cheuk-Kit Lee and Florentin Coeurdoux and Yuyuan Chen and Sophia Tang and Peter Potaptchik and Yilun Du and Michael Samuel Albergo and Eric Vanden-Eijnden},
     journal={Advances in Neural Information Processing Systems (NeurIPS 2026)},
     year={2026},
     url={https://arxiv.org/abs/2608.01692}
   }

4. Expanding Flow Maps read

   Sophia Tang and Pranam Chatterjee

   Advances in Neural Information Processing Systems (NeurIPS 2026), Jul 2026

   Paper Bib Video Code Slides Website

   @article{tang2026expanding,
     title={Expanding Flow Maps},
     author={Sophia Tang and Pranam Chatterjee},
     journal={Advances in Neural Information Processing Systems (NeurIPS 2026)},
     year={2026},
     url={https://arxiv.org/abs/2607.21585}
   }

5. A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding read

   Sophia Tang , Yuchen Zhu , Molei Tao and Pranam Chatterjee

   arXiv preprint arXiv:2606.13565, Jun 2026

   Paper Bib Article Code Website

   @article{tang2026a2d2,
     title={A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding},
     author={Sophia Tang and Yuchen Zhu and Molei Tao and Pranam Chatterjee},
     journal={arXiv preprint arXiv:2606.13565},
     year={2026},
     url={https://arxiv.org/abs/2606.13565}
   }

6. 

   Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules read

   Riccardo De Santi , Bruce Lee , Cristian Perez Jensen , Kimon Protopapas , Sophia Tang , Cheng-Hao Liu , Pranam Chatterjee , Yisong Yue and Andreas Krause

   Advances in Neural Information Processing Systems (NeurIPS 2026), Jun 2026

   Paper Bib Code

   @article{desanti2026active,
     title={Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules},
     author={Riccardo De Santi and Bruce Lee and Cristian Perez Jensen and Kimon Protopapas and Sophia Tang and Cheng-Hao Liu and Pranam Chatterjee and Yisong Yue and Andreas Krause},
     journal={Advances in Neural Information Processing Systems (NeurIPS 2026)},
     year={2026},
     url={https://arxiv.org/abs/2606.08802}
   }

7. mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties read

   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 Bib Article Code Website

   @article{patel2026mrnautilus,
     title={mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties},
     author={Sawan Patel and Sophia Tang and Yesol Kim and Yinuo Zhang and Divya Srijay and Ping-Jung Lin and Shambhavi Shubham and Fengmei Pi and Cedric Wu and Sherwood Yao and Pranam Chatterjee},
     journal={arXiv preprint arXiv:2605.31296},
     year={2026},
     url={https://arxiv.org/abs/2605.31296}
   }

8. 

   TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation read

   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 Bib Code

   @article{cao2026td3b,
     title={TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation},
     author={Hanqun Cao and Aastha Pal and Sophia Tang and Yinuo Zhang and Jingjie Zhang and Pheng Ann Heng and Pranam Chatterjee},
     journal={International Conference on Machine Learning (ICML 2026) Spotlight},
     year={2026},
     url={https://arxiv.org/abs/2605.09810}
   }

9. 

   Foundations of Schrödinger Bridges for Generative Modeling read

   Sophia Tang

   arXiv, Preprint, Mar 2026

   Paper Bib Article Website

   @article{tang2026foundations,
     title={Foundations of Schrödinger Bridges for Generative Modeling},
     author={Sophia Tang},
     journal={arXiv, Preprint},
     year={2026},
     url={https://arxiv.org/abs/2603.18992}
   }

10. 

    PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction read

    Yinuo Zhang , Sophia Tang , Tong Chen , Elizabeth Mahood , Sophia Vincoff and Pranam Chatterjee

    Nature Communications, Jan 2026

    Paper Bib Code Website

    @article{zhang2026peptiverse,
      title={PeptiVerse: A Unified Platform for Therapeutic Peptide Property Prediction},
      author={Yinuo Zhang and Sophia Tang and Tong Chen and Elizabeth Mahood and Sophia Vincoff and Pranam Chatterjee},
      journal={Nature Communications},
      year={2026},
      url={https://www.nature.com/articles/s41467-026-74167-w}
    }

11. 

    High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain read

    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 Bib

    @article{han2026high,
      title={High-Throughput In Vivo Screening Identifies Structural Factors Driving mRNA Lipid Nanoparticle Delivery to the Brain},
      author={Emily L Han and Dongyoon Kim and Amanda M Murray and Kaitlin Mrksich and Alex G Hamilton and Sophia Tang and Soyeon Yoo and Audrey T Zhu and Elaine R Tong and Rohan Palanki and others},
      journal={ACS nano},
      year={2026},
      url={https://pubs.acs.org/doi/full/10.1021/acsnano.5c19138}
    }

2025

1. Entangled Schrödinger Bridge Matching read

   Sophia Tang , Yinuo Zhang and Pranam Chatterjee

   Advances in Neural Information Processing Systems (NeurIPS 2026), Nov 2025

   Paper Bib Code Poster

   @article{tang2025entangled,
     title={Entangled Schrödinger Bridge Matching},
     author={Sophia Tang and Yinuo Zhang and Pranam Chatterjee},
     journal={Advances in Neural Information Processing Systems (NeurIPS 2026)},
     year={2025},
     url={https://arxiv.org/abs/2511.07406}
   }

2. TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion read

   Sophia Tang^* , Yuchen Zhu^* , Molei Tao and Pranam Chatterjee

   arXiv, Preprint, Sep 2025

   Paper Bib Code

   @article{tang2025tr2d2,
     title={TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion},
     author={Sophia Tang and Yuchen Zhu and Molei Tao and Pranam Chatterjee},
     journal={arXiv, Preprint},
     year={2025},
     url={https://arxiv.org/abs/2509.25171}
   }

3. 

   Branched Schrödinger Bridge Matching read

   Sophia Tang , Yinuo Zhang , Alexander Tong and Pranam Chatterjee

   International Conference on Learning Representations (ICLR 2026), Jun 2025

   Paper Bib Video Code Poster Website

   @article{tang2025branched,
     title={Branched Schrödinger Bridge Matching},
     author={Sophia Tang and Yinuo Zhang and Alexander Tong and Pranam Chatterjee},
     journal={International Conference on Learning Representations (ICLR 2026)},
     year={2025},
     url={https://arxiv.org/abs/2506.09007}
   }

4. 

   Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design read

   Tong Chen , Yinuo Zhang , Sophia Tang and Pranam Chatterjee

   arXiv, Preprint, May 2025

   Paper Bib Code

   @article{chen2025multi,
     title={Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design},
     author={Tong Chen and Yinuo Zhang and Sophia Tang and Pranam Chatterjee},
     journal={arXiv, Preprint},
     year={2025},
     url={https://arxiv.org/abs/2505.07086}
   }

5. 

   Peptide-functionalized nanoparticles for brain-targeted therapeutics read

   Sophia Tang , Emily L. Han and Michael J. Mitchell

   Drug Delivery and Translational Research, Mar 2025

   Paper Bib

   @article{tang2025peptide,
     title={Peptide-functionalized nanoparticles for brain-targeted therapeutics},
     author={Sophia Tang and Emily L. Han and Michael J. Mitchell},
     journal={Drug Delivery and Translational Research},
     year={2025},
     url={http://dx.doi.org/10.1007/s13346-025-01840-w}
   }

6. 

   Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation read

   Sophia Tang , Yinuo Zhang , Alexander Tong and Pranam Chatterjee

   arXiv, Preprint, Mar 2025

   Paper Bib Poster

   @article{tang2025gumbel,
     title={Gumbel-Softmax Flow Matching with Straight-Through Guidance for Controllable Biological Sequence Generation},
     author={Sophia Tang and Yinuo Zhang and Alexander Tong and Pranam Chatterjee},
     journal={arXiv, Preprint},
     year={2025},
     url={https://arxiv.org/abs/2503.17361}
   }

2024

1. PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion read

   Sophia Tang^* , Yinuo Zhang^* and Pranam Chatterjee

   International Conference on Machine Learning (ICML 2025), Dec 2024

   Paper Bib Video Article Code Poster

   @article{tang2024peptune,
     title={PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion},
     author={Sophia Tang and Yinuo Zhang and Pranam Chatterjee},
     journal={International Conference on Machine Learning (ICML 2025)},
     year={2024},
     url={https://arxiv.org/abs/2412.17780}
   }

2. 

   Peptide-Functionalized Lipid Nanoparticles for Targeted Systemic mRNA Delivery to the Brain read

   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 Bib

   @article{han2024peptide,
     title={Peptide-Functionalized Lipid Nanoparticles for Targeted Systemic mRNA Delivery to the Brain},
     author={Emily L. Han and Sophia Tang and Dongyoon Kim and Amanda M. Murray and Kelsey L. Swingle and Alex G. Hamilton and Kaitlin Mrksich and Marshall S. Padilla and Rohan Palanki and Jacqueline J. Li and Michael J. Mitchell},
     journal={Nano Letters, American Chemical Society (ACS)},
     year={2024},
     url={http://dx.doi.org/10.1021/acs.nanolett.4c05186}
   }

3. 

   Predictive High-Throughput Platform for Dual Screening of mRNA Lipid Nanoparticle Blood–Brain Barrier Transfection and Crossing read

   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 Bib

   @article{han2024predictive,
     title={Predictive High-Throughput Platform for Dual Screening of mRNA Lipid Nanoparticle Blood–Brain Barrier Transfection and Crossing},
     author={Emily L. Han and Marshall S. Padilla and Rohan Palanki and Dongyoon Kim and Kaitlin Mrksich and Jacqueline J. Li and Sophia Tang and Il-Chul Yoon and Michael J. Mitchell},
     journal={Nano Letters, American Chemical Society (ACS)},
     year={2024},
     url={http://dx.doi.org/10.1021/acs.nanolett.3c03509}
   }

4. 

   Optimized microfluidic formulation and organic excipients for improved lipid nanoparticle mediated genome editing read

   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 Bib

   @article{palanki2024optimized,
     title={Optimized microfluidic formulation and organic excipients for improved lipid nanoparticle mediated genome editing},
     author={Rohan Palanki and Emily L. Han and Amanda M. Murray and Rohin Maganti and Sophia Tang and Kelsey L. Swingle and Dongyoon Kim and Hannah Yamagata and Hannah C. Safford and Kaitlin Mrksich and William H. Peranteau and Michael J. Mitchell},
     journal={Lab on a Chip},
     year={2024},
     url={http://dx.doi.org/10.1039/D4LC00283K}
   }