publications

2026

1. Preprint

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

   Xingzhi Sun, João Felipe Rocha, Brett Phelan, and 12 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, Xingzhi and Rocha, Jo{\~a}o Felipe and Phelan, Brett and Bhaskar, Dhananjay and Huguet, Guillaume and Zhang, Yanlei and Magruder, Daniel S. and Tong, Alexander and Xu, Ke and Fasina, Oluwadamilola and Gerstein, Mark and Wolf, Guy and Ivanova, Natalia and Chaffer, Christine L. and Krishnaswamy, Smita},
     journal = {arXiv preprint arXiv:2603.22564},
     year = {2026},
   }

2. Preprint

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

   Chen Liu, Xingzhi Sun, Xi 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, Chen and Sun, Xingzhi and Xiao, Xi and Van Tassel, Alexandre and Xu, Ke and Reimann, Kristof and Liao, Danqi and Gerstein, Mark and Wang, Tianyang 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^*, Xingzhi 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, Xingzhi and Krishna, Ananya and Bhaskar, Dhananjay and Mongeon, Blanche and Craig, Morgan 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

   Chen Liu^*, Ke Xu^*, Liangbo L. 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, Chen and Xu, Ke and Shen, Liangbo L. and Huguet, Guillaume and Wang, Zilong and Tong, Alexander and Bzdok, Danilo and Stewart, Jay and Wang, Jay C. 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^*, Mor Frank^*, Eve 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, Mor and Wattenberg, Eve S. and Xu, Ke and Liu, Susanna X. and Yu, Xuezhu and Gerstein, Mark},
     journal = {Nature Communications},
     volume = {16},
     pages = {7021},
     year = {2025},
   }