publications

2026

1. Preprint

   MIOFlow 2.0: A Unified Framework for Inferring Cellular Stochastic Dynamics from Single Cell and Spatial Transcriptomics Data

   Xinran Sun, João Felipe Rocha, Brian Phelan, and 6 more authors

   arXiv preprint arXiv:2603.22564, 2026

   arXiv Bib

   @article{sun2026mioflow2,
     title = {MIOFlow 2.0: A Unified Framework for Inferring Cellular Stochastic Dynamics from Single Cell and Spatial Transcriptomics Data},
     author = {Sun, Xinran and Rocha, Jo{\~a}o Felipe and Phelan, Brian and Bhaskar, Dhananjay and Huguet, Guillaume and Zhang, Yanlei and Magruder, Daniel S. and Xu, Ke and others},
     journal = {arXiv preprint arXiv:2603.22564},
     year = {2026},
   }

2. Preprint

   Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models

   Corey Liu, Xinran Sun, Xia Xiao, and 8 more authors

   arXiv preprint arXiv:2602.00217, 2026

   arXiv Bib

   @article{liu2026dispersion,
     title = {Dispersion Loss Counteracts Embedding Condensation and Improves Generalization in Small Language Models},
     author = {Liu, Corey and Sun, Xinran and Xiao, Xia and Van Tassel, Adam and Xu, Ke and Reimann, Kilian and Liao, Dan and Gerstein, Mark and Wang, Tao and Wang, Xiao and Krishnaswamy, Smita},
     journal = {arXiv preprint arXiv:2602.00217},
     year = {2026},
   }

2025

1. MLCB

   STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics

   João Felipe Rocha^*, Ke Xu^*, Xinran Sun^*, and 6 more authors

   In Machine Learning in Computational Biology (MLCB), 2025

   arXiv Bib

   @inproceedings{rocha2025staged,
     title = {STAGED: A Multi-Agent Neural Network for Learning Cellular Interaction Dynamics},
     author = {Rocha, Jo{\~a}o Felipe and Xu, Ke and Sun, Xinran and Krishna, Adi and Bhaskar, Dhananjay and Mongeon, Beatrice and Craig, Michael and Gerstein, Mark and Krishnaswamy, Smita},
     booktitle = {Machine Learning in Computational Biology (MLCB)},
     year = {2025},
     publisher = {PMLR},
   }

2. ICASSP

   ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression

   Corey Liu^*, Ke Xu^*, Luca Liebeskind Shen^†, and 8 more authors

   In IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP), 2025

   arXiv Bib

   @inproceedings{liu2025imageflownet,
     title = {ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression},
     author = {Liu, Corey and Xu, Ke and Shendagger;, Luca Liebeskind and Huguetdagger;, Guillaume and Wang, Ziyang and Tong, Alexander and Bzdok, Danilo and Stewart, Jay and Wang, Jia Cheng and Del Priore, Lucian V. and Krishnaswamy, Smita},
     booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)},
     year = {2025},
   }

3. Nat Commun

   The chronODE Framework for Modelling Multi-Omic Time Series with Ordinary Differential Equations and Machine Learning

   Beatrice Borsari^*, Matthew Frank^*, Eric S. Wattenberg^†, and 4 more authors

   Nature Communications, 2025

   Bib HTML

   @article{borsari2025chronode,
     title = {The chronODE Framework for Modelling Multi-Omic Time Series with Ordinary Differential Equations and Machine Learning},
     author = {Borsari, Beatrice and Frank, Matthew and Wattenbergdagger;, Eric S. and Xudagger;, Ke and Liudagger;, Sherry X. and Yu, Xinchen and Gerstein, Mark},
     journal = {Nature Communications},
     volume = {16},
     pages = {7021},
     year = {2025},
   }