publications

2025

1. arXiv

   Graph Contrastive Learning versus Untrained Baselines: The Role of Dataset Size

   Smayan Khanna, Doruk Efe Gökmen, Risi Kondor, and 1 more author

   Sep 2025

   HTML
2. JCIM

   FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping

   Mike Jones, Smayan Khanna, and Andrew Ferguson

   Journal of Chemical Information and Modeling, American Chemical Society (ACS), Jan 2025

   DOI Bib HTML

   @article{JCIM,
     title = {FlowBack: A Generalized Flow-Matching Approach for Biomolecular Backmapping},
     author = {Jones, Mike and Khanna, Smayan and Ferguson, Andrew},
     journal = {Journal of Chemical Information and Modeling, American Chemical Society (ACS)},
     year = {2025},
     month = jan,
     pages = {672-692},
     doi = {10.1021/acs.jcim.4c02046},
   }

2024

1. ICML

   FlowBack: A Flow-matching Approach for Generative Backmapping of Macromolecules

   Mike Jones, Smayan Khanna, and Andrew Ferguson

   ICML’24 Workshop - ML4LMS, Jul 2024

   HTML

2023

1. Biophys. J.

   Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs

   Brennan Ashwood, Michael S. Jones, Aleksandar Radakovic, and 6 more authors

   Biophysical Journal, Chicago, Jul 2023

   DOI Bib HTML

   @article{BPJ,
     title = {Thermodynamics and kinetics of DNA and RNA dinucleotide hybridization to gaps and overhangs},
     author = {Ashwood, Brennan and Jones, Michael S. and Radakovic, Aleksandar and Khanna, Smayan and Lee, Yumin and Sachleben, Joseph R. and Szostak, Jack W. and Ferguson, Andrew L. and Tokmakoff, Andrei},
     journal = {Biophysical Journal},
     location = {Chicago},
     volume = {122},
     issue = {16},
     pages = {3323-3329},
     year = {2023},
     month = jul,
     publisher = {Cell Press},
     doi = {10.1016/j.bpj.2023.07.009},
     url = {https://www.sciencedirect.com/science/article/abs/pii/S0006349523004605?via%3Dihub},
     dimensions = {true},
   }