Smita Krishnaswamy, Ph.D., University of Michigan; M.S., University of Michigan; B.A., Kalamazoo College, B.S., University of Michigan. Joined Yale Faculty in 2015

Smita Krishnaswamy's picture
Associate Professor of Computer Science and Genetics
Dunham Lab 227
+1 (734) 678-7428
Research Areas: 

Machine Learning, Deep Learning, Computational Biology

Representative Publications: 
  • M. Kuchroo, J. Huang, P. Wong, J.C. Grenier, D. Shung, A. Tong,  C. Lucas., J. Klein, Gamache I., Poujol R., Burkhardt D.B., Gigante S., Godavarthi A., Rieck B., Israelow B., Simonov M., Mao T., Eun Oh J., Silva J., Pesaranghader A., Takahashi T. Odio C.D., Casanovas-Massana A., Fournier J., Yale IMPACT Team, Farhadian S., Dela Cruz C.S., Ko A.I., Wilson F.P., Hussin J., Wolf G., A.S. Iwasaki*., S. Krishnaswamy*. “Multiscale PHATE Exploration of SARS-CoV-2 Data Reveals Multimodal Signatures of Disease.’ Nature Biotechnology. March 2022,
  • A. Tong, G. Huguet, A. Natik, K. MacDonald, M. Kuchroo, R. R. Coifman, G. Wolf, S. Krishnaswamy*, Diffusion Earth Mover’s Distance and Distribution Embeddings,”  ICML 2021.
  • A. Tong,G.  Wolf, & S. Krishnaswamy, Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators. Journal of Signal Processing Systems (2021). doi:10.1007/s11265-021-01715-6
  • D.B. Burkhardt, J.S. Stanley, A. L. Perdigoto, S. A., Gigante, K.C. Herold, G. Wolf, A.J. Giraldez, D. van Dijk*, and S. Krishnaswamy*,  2019. Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing. Nature biotechnology, 37(12), 1482-1492 (2021).
  • A. Tong, J. Huang, G. Wolf, D. van Dijk, S. Krishnaswamy*, “TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics,” in Proceedings of the 37th International Conference on Machine Learning (ICML) 2020.
  • B. Rieck, T. Yates, C. Bock, K. Borgwardt, G. Wolf, N. Turk-Browne, S. Krishnaswamy*. Uncovering the Topology of Time-Varying fMRI Data using Cubical Persistence. Advances in Neural Information Processing Systems. 2020;33.
  • M. Amodio, D. van Dijk, K. Srinivasan, W. S. Chen, K. R. Moon, A. Campbell, Y. Zhao, X. Wang, M. Venkataswamy, A. Desai, V. Ravi, P. Kumar, R. Montgomery, G. Wolf, and S. Krishnaswamy,* “Exploring single-cell data with multitasking deep neural networks,” Nature Methods 2019, vol. 16, pp. 1139–1145, doi:10.1038/s41592-019-0576-7.
  • J.S. Stanley III, S. Gigante, G. Wolf, and S. Krishnaswamy*. “Harmonic Alignment.” In Proceedings of the 2020 SIAM International Conference on Data Mining, pp. 316-324. Society for Industrial and Applied Mathematics (SIAM), 2020.
  • K.R. Moon, D. van Dijk, Z. Wang, W. Chen, M.J. Hirn, R. R. Coifman, N.B. Ivanova, G. Wolf, and S. Krishnaswamy,* “Visualizing structure and transitions in high-dimensional biological data,” Nature Biotechnology 2019, vol. 37, n. 12, pp. 1482-1492, doi: 10.1038/s41587-019-0395-5.
  • van Dijk, D,. Sharma, R. Nainys, J., Yim, K., Kathail, P., Carr, A., Burdziak, C., Moon, K. R., Chaffer, C. L., Pattabiraman, D., Bierie, B., Mazutis, L. and Wolf, Guy, S. Krishnaswamy*, D. Pe’er*, “Recovering Gene Interactions from Single-Cell Data Using Data Diffusion,” Cell 2018, no. 174(3), pp. 716 – 729

NSF CAREER Award, Sloan Faculty Fellowship, FASEB Excellence in Science Award