Shreya Saxena


Saxena Lab
Assistant Professor of Biomedical Engineering
Office Address:
55 Prospect Street
New Haven, CT 06511
Mailing Address:
P.O. Box 208260
New Haven, CT 06520
  • Ph.D., Massachusetts Institute of Technology
  • M.S., Johns Hopkins University
  • B.S., Ecole Polytechnique Federale de Lausanne (EPFL), Switzerland


Our ability to record large-scale neural and behavioral data has substantially improved in the last decade. However, the inference of quantitative dynamical models for cognition and motor control remains challenging due to their unconstrained nature. In the Saxena Lab, we incorporate constraints from anatomy and physiology to tame machine learning models of neural activity and behavior. We are interested in a constraints-based modeling approach that allows us to predictively understand the relationship between neural activity and behavior.

Selected Awards & Honors:

  • Rising Stars in Electrical Engineering, UIUC (2019)
  • Rising Stars in Biomedical Engineering, Johns Hopkins University (2018)
  • Honoree of the Graduate Women of Excellence Award, MIT (2017)

Selected Publications:

  • Yi, D., Musall, S., Churchland, A. , Padilla-Coreano, N., Saxena, S.*, "Disentangled multi- subject and social behavioral representations through a constrained subspace variational autoencoder (CS-VAE)" eLife (To Appear), 2023.
  • Mitelut, C., Zhang, Y.G, Sekino, Y., Boyd, J., Bolanos, F., Swindale, N. V., Silasi, G., Saxena, S.*, Murphy, T. H.* "Mesoscale cortex-wide neural dynamics predict self-initiated actions in mice several seconds prior to movement." eLife, 2022.
  • Koch, C., Svoboda, K., Bernard, A., Basso, M. A., Churchland, A. K., Fairhall, A. L., Groblewski, P. A., Lecoq, J. A., Mainen, Z. F., Mathis, M. W., Olsen, S.R., Pouget, A., Saxena, S. , Siegle, J. H. , Zador, A. M. (2022). "Next-generation brain observatories". Neuron, 2022.
  • Saxena S.*, Russo A.*, Cunningham J., Churchland M. "The hypothesis of low trajectory tangling predicts motor cortex population activity across movement speeds" eLife, 2022.
  • Warriner, C. L., Fageiry, S., Saxena, S. , Costa, R. M., Miri, A. "Motor cortical influence relies on task-specific activity covariation". Cell Reports, 2022.
  • Abe T., Kinsella I., Saxena S., Paninski L., Cunningham J. "Neuroscience Cloud Analysis As a Service" Neuron, 2022.
  • Couto J., Musall S., Sun X., Khanal A., Gluf S., Saxena S., Kinsella I., Abe T., Cunningham J., Paninski L., Churchland A. "Chronic, cortex-wide imaging of specific cell populations during behavior " Nature Protocols, 2021.
  • Saxena S., Kinsella I., Musall S., Kim S., Meszaros J., Thibodeaux D., Kim C., Cunningham J., Hillman E., Churchland A., Paninski L. "Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data" PLOS Computational Biology, 2020.
  • Saxena S., Sarma S.V., Dahleh M. "Performance Limitations in Sensorimotor Control: Tradeoffs between Neural Computing and Accuracy in Fast Tracking." Neural Computation, 2020.
  • Hernandez D., Moretti A., Saxena S., Wei Z., Cunningham J., Paninski L. "Nonlinear Evolution via Spatially-Dependent Linear Dynamics for Electrophysiology and Calcium Data" Neurons, Behavior, Data analysis, and Theory (NBDT), 2020.
  • Saxena S., Cunningham J.P. "Towards the Neural Population Doctrine" Current Opinion in Neurobiology, 2019.
  • Saxena S., Sarma S.V., Patel S.R., Santaniello S., Eskandar, E., Gale, J.T."Modulations in Oscillatory Activity of Globus Pallidus internus Neurons During a Directed Hand Movement Task - A Primary Mechanism for Motor Planning." Frontiers in Systems Neuroscience, 2019.
  • Kahn K., Saxena S., Eskandar E.N., Thakor N., Schieber M., Gale J.T., Averbeck B., Eden U. and Sarma S.V. "A Systematic Approach to Selecting Task Relevant Neurons." Journal of Neuroscience Methods, 2015.
  • Saxena S., Santaniello S., Gale J.T., Montgomery E. and Sarma S.V. "Aggregate Input-Output Models of Neuronal Populations." IEEE Transactions on Biomedical Engineering, 2012.


Shreya Saxena is broadly interested in the neural control of complex, coordinated behavior. She is an Assistant Professor in the Biomedical Engineering Department and a core member of the Center for Neurocomputation and Machine Intelligence at the Wu Tsai Institute at Yale. From 2020 to 2023, she was an Assistant Professor at the University of Florida's Department of Electrical and Computer Engineering. Before this, Shreya was a Swiss National Science Foundation Postdoctoral Fellow at Columbia University's Zuckerman Mind Brain Behavior Institute in the Center for Theoretical Neuroscience. She did her PhD in the Department of Electrical Engineering and Computer Science at the Massachusetts Institute of Technology studying the closed-loop control of fast movements from a control theory perspective. Shreya received a B.S. in Mechanical Engineering from the Swiss Federal Institute of Technology (EPFL), and an M.S. in Biomedical Engineering from Johns Hopkins University. She is honored to have been selected as a Rising Star in both Electrical Engineering (2019) and Biomedical Engineering (2018).