Smita Krishnaswamy, PhD
Research & Publications
Biography
News
Research Summary
Smita Krishnaswamy is an Assistant Professor in the department of Genetics at the Yale School of Medicine and Department of Computer Science in the Yale School of Applied Science and engineering. Smita’s research is at the intersection of applied math, machine learning and computational biology. She focuses on developing deep representation learning methods for unsupervised data exploration. Some of the key projects developed in her Lab include MAGIC (a tool for imputation and denoising of data), PHATE (a powerful new visualization method for high dimensional data that can unveil progression and cluster structures, and SAUCIE (an autoencoder-based deep learning approach for automatically batch correcting, visualizing, denoising and clustering data). These methods have been applied to a variety of biological applications in neuroscience, immunology, cancer biology, and clinical outcomes.
At Yale, Smita teaches two machine learning courses: Unsupervised Learning for Big Data and Deep learning theory and applications. She completed her postdoctoral training at Columbia University in the systems biology department where she focused on learning computational models of cellular signaling from single-cell mass cytometry data. She was trained as a computer scientist with a Ph.D. from the University of Michigan’s EECS department where her research focused on algorithms for automated synthesis and verification of nanoscale logic circuits that exhibit probabilistic effects.
Coauthors
Research Interests
Allergy and Immunology; Neurosciences; Computational Biology; Machine Learning; Deep Learning
Selected Publications
- StrokeClassifier: ischemic stroke etiology classification by ensemble consensus modeling using electronic health recordsLee H, Schwamm L, Sansing L, Kamel H, de Havenon A, Turner A, Sheth K, Krishnaswamy S, Brandt C, Zhao H, Krumholz H, Sharma R. StrokeClassifier: ischemic stroke etiology classification by ensemble consensus modeling using electronic health records. Npj Digital Medicine 2024, 7: 130. PMID: 38760474, PMCID: PMC11101464, DOI: 10.1038/s41746-024-01120-w.
- Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep LearningSteach H, Viswanath S, He Y, Zhang X, Ivanova N, Hirn M, Perlmutter M, Krishnaswamy S. Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning. 2024, 14758: 235-252. DOI: 10.1007/978-1-0716-3989-4_15.
- Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer’s disease progressionHodgson L, Li Y, Iturria-Medina Y, Stratton J, Wolf G, Krishnaswamy S, Bennett D, Bzdok D. Supervised latent factor modeling isolates cell-type-specific transcriptomic modules that underlie Alzheimer’s disease progression. Communications Biology 2024, 7: 591. PMID: 38760483, PMCID: PMC11101463, DOI: 10.1038/s42003-024-06273-8.
- Geometric scattering on measure spacesChew J, Hirn M, Krishnaswamy S, Needell D, Perlmutter M, Steach H, Viswanath S, Wu H. Geometric scattering on measure spaces. Applied And Computational Harmonic Analysis 2024, 70: 101635. DOI: 10.1016/j.acha.2024.101635.
- Directed Scattering for Knowledge Graph-Based Cellular Signaling AnalysisVenkat A, Chew J, Rodriguez F, Tape C, Perlmutter M, Krishnaswamy S. Directed Scattering for Knowledge Graph-Based Cellular Signaling Analysis. 2024, 9761-9765. DOI: 10.1109/icassp48485.2024.10446530.
- Parasympathetic neurons derived from human pluripotent stem cells model human diseases and developmentWu H, Saito-Diaz K, Huang C, McAlpine J, Seo D, Magruder D, Ishan M, Bergeron H, Delaney W, Santori F, Krishnaswamy S, Hart G, Chen Y, Hogan R, Liu H, Ivanova N, Zeltner N. Parasympathetic neurons derived from human pluripotent stem cells model human diseases and development. Cell Stem Cell 2024, 31: 734-753.e8. PMID: 38608707, PMCID: PMC11069445, DOI: 10.1016/j.stem.2024.03.011.
- Learnable Filters for Geometric Scattering ModulesTong A, Wenkel F, Bhaskar D, Macdonald K, Grady J, Perlmutter M, Krishnaswamy S, Wolf G. Learnable Filters for Geometric Scattering Modules. IEEE Transactions On Signal Processing 2024, 72: 2939-2952. DOI: 10.1109/tsp.2024.3378001.
- Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral EntropyLiao D, Liu C, Christensen B, Tong A, Huguet G, Wolf G, Nickel M, Adelstein I, Krishnaswamy S. Assessing Neural Network Representations During Training Using Noise-Resilient Diffusion Spectral Entropy. 2024, 00: 1-6. DOI: 10.1109/ciss59072.2024.10480166.
- Bayesian Spectral Graph Denoising with Smoothness PriorLeone S, Sun X, Perlmutter M, Krishnaswamy S. Bayesian Spectral Graph Denoising with Smoothness Prior. 2024, 00: 1-6. DOI: 10.1109/ciss59072.2024.10480177.
- Correction: Cell cycle controls long-range calcium signaling in the regenerating epidermisMoore J, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V. Correction: Cell cycle controls long-range calcium signaling in the regenerating epidermis. Journal Of Cell Biology 2024, 223: e20230209503052024c. PMID: 38477880, PMCID: PMC10938063, DOI: 10.1083/jcb.20230209503052024c.
- Stem cell migration drives lung repair in living miceChioccioli M, Liu S, Magruder S, Tata A, Borriello L, McDonough J, Konkimalla A, Kim S, Nouws J, Gonzalez D, Traub B, Ye X, Yang T, Entenberg D, Krishnaswamy S, Hendry C, Kaminski N, Tata P, Sauler M. Stem cell migration drives lung repair in living mice. Developmental Cell 2024, 59: 830-840.e4. PMID: 38377991, PMCID: PMC11003834, DOI: 10.1016/j.devcel.2024.02.003.
- Abstract B049: Pancreatic beta cell stress pathways drive pancreatic ductal adenocarcinoma development in obesityGarcia C, Venkat A, Tong A, Agabiti S, Lawres L, Cardone R, Kibbey R, Krishnaswamy S, Muzumdar M. Abstract B049: Pancreatic beta cell stress pathways drive pancreatic ductal adenocarcinoma development in obesity. Cancer Research 2024, 84: b049-b049. DOI: 10.1158/1538-7445.panca2023-b049.
- Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responsesRamos Zapatero M, Tong A, Opzoomer J, O'Sullivan R, Cardoso Rodriguez F, Sufi J, Vlckova P, Nattress C, Qin X, Claus J, Hochhauser D, Krishnaswamy S, Tape C. Trellis tree-based analysis reveals stromal regulation of patient-derived organoid drug responses. Cell 2023, 186: 5606-5619.e24. PMID: 38065081, DOI: 10.1016/j.cell.2023.11.005.
- Wire Before You WalkAsmara T, Bhaskar D, Adelstein I, Krishnaswamy S, Perlmutter M. Wire Before You Walk. 2023, 00: 714-716. DOI: 10.1109/ieeeconf59524.2023.10477089.
- Graph Fourier MMD for Signals on GraphsLeone S, Venkat A, Huguet G, Tong A, Wolf G, Krishnaswamy S. Graph Fourier MMD for Signals on Graphs. 2023, 00: 1-6. DOI: 10.1109/sampta59647.2023.10301384.
- Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithmZunder ER, Finck R, Behbehani GK, Amir el-AD, Krishnaswamy S, Gonzalez VD, Lorang CG, Bjornson Z, Spitzer MH, Bodenmiller B, Fantl WJ, Pe'er D, Nolan GP. Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm. Nature Protocols 2015, 10: 316-333. PMID: 25612231, PMCID: PMC4347881, DOI: 10.1038/nprot.2015.020.
- Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD miceMingueneau M, Krishnaswamy S, Spitzer MH, Bendall SC, Stone EL, Hedrick SM, Pe'er D, Mathis D, Nolan GP, Benoist C. Single-cell mass cytometry of TCR signaling: Amplification of small initial differences results in low ERK activation in NOD mice. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 16466-16471. PMID: 25362052, PMCID: PMC4246343, DOI: 10.1073/pnas.1419337111.
- Conditional density-based analysis of T cell signaling in single-cell dataKrishnaswamy S, Spitzer MH, Mingueneau M, Bendall SC, Litvin O, Stone E, Pe'er D, Nolan GP. Conditional density-based analysis of T cell signaling in single-cell data. Science 2014, 346: 1250689. PMID: 25342659, PMCID: PMC4334155, DOI: 10.1126/science.1250689.
- viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemiaAmir el-AD, Davis KL, Tadmor MD, Simonds EF, Levine JH, Bendall SC, Shenfeld DK, Krishnaswamy S, Nolan GP, Pe'er D. viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia. Nature Biotechnology 2013, 31: 545-552. PMID: 23685480, PMCID: PMC4076922, DOI: 10.1038/nbt.2594.
- Design, Analysis and Test of Logic Circuits under UncertaintySmita Krishnaswamy, Igor L. Markov, John P. Hayes Lecture Notes in Electrical Engineering, Springer DOI:10.1007/978-90-481-9644-9