Ryan Raut | Allen Institute

About

Hello! I am currently a Shanahan Foundation Fellow at the Allen Institute and the University of Washington, Seattle – where I split my time between the AI Institute in Dynamic Systems and the UW Computational Neuroscience Center. Prior to Seattle I completed my PhD in neuroscience with Marcus Raichle at Washington University in St. Louis.

Research interests

In a nutshell, I am interested in understanding general principles of how brains work – uncovering the rules and regularities of how brain dynamics unfold across spatiotemporal scales and species. I’m especially focused on discovering and integrating this knowledge into holistic accounts of what brains do: specifically, mathematical, physiological, and behavioral descriptions considered in a context that spans the whole brain, organism, and its environmental interactions. This perspective motivates a data-centric dynamical modeling approach to the study of brain function, placing my research agenda at the intersection of neuroscience, dynamical systems theory, and scientific machine learning.

I’m fortunate to be in a unique position that enables the interdisciplinary training and collaboration this agenda requires. At UW, I primarily work with Professors Nathan Kutz, Bing Brunton, and Steve Brunton, where I seek to combine machine learning and dynamical systems theory to improve our ability to draw inferences about brains and other complex systems from the incomplete, noisy measurements that we typically access. At the Allen Institute I primarily work with Anton Arkhipov, where I seek to bring insights derived from these data-driven methods to biologically detailed datasets and models. The goal is to synthesize wide-ranging empirical observations within mathematical frameworks, clarifying specific biological hypotheses that can be tested through close collaboration with experimentalists.

Papers

For the most up-to-date listing, please visit my Google Scholar page.

Preprints

Raut, R.V., Rosenthal, Z.P., Wang, X., Miao, H., Zhang, Z., Lee, J.M., Raichle, M.E., Bauer, A.Q., Brunton, B.W., Brunton, S.L., Kutz, J.N. (2023). Arousal as a universal embedding for spatiotemporal brain dynamics. bioRxiv. [paper]
Jacobs, M., Brunton, B.W., Brunton, S.L., Kutz, J.N., Raut, R.V. (2023). HyperSINDy: deep generative modeling of nonlinear stochastic governing equations. arXiv preprint arXiv:2310.04832. [paper]
*Carroll, C.M., *Stanley, M., Raut, R.V., Constantino, N.J., Irmen, R.E., Mitra, A., Snipes, J.A., Raichle, M.E., Holtzman, D.M., Gould, R.W., Kishida, K.T., Macauley, S.L. (2022). Acute hyper-and hypoglycemia uncouples the metabolic cooperation between glucose and lactate to disrupt sleep. bioRxiv, pp.2022-09. [paper]

Peer-reviewed

Colbrook, M.J., Li, Q., Raut, R.V., Townsend, A. (2023). Beyond expectations: residual dynamic mode decomposition and variance for stochastic dynamical systems. Nonlinear Dynamics, 1-25. [paper]
Luckett, P.H., Lee, J.J., Park, K.Y., Raut, R.V., Meeker, K.L., Gordon, E.M., Snyder, A.Z., Ances, B.M., Leuthardt, E.C., Shimony, J.S. (2023). Resting state network mapping in individuals using deep learning. Frontiers in Neurology, 13, p.1055437. [paper]
Raut, R.V., Snyder, A.Z., Mitra, A., Yellin, D.M., Fujii, N., Malach, R., Raichle, M.E. (2021). Global waves synchronize the brain’s functional systems with fluctuating arousal. Science Advances, 7 (30), eabf2709. [paper][code]
Rosenthal, Z.P., Raut, R.V., Snyder, A.Z., Culver, J.P., Raichle, M.E., Lee, J. (2021). Peripheral sensory stimulation elicits global slow waves by recruiting somatosensory cortex bilaterally. Proceedings of the National Academy of Sciences, 118 (8), e2021252118. [paper]
Raut, R.V., Snyder, A.Z., Raichle, M.E. (2020). Hierarchical dynamics as a macroscopic organizing principle of the human brain. Proceedings of the National Academy of Sciences, 117 (34), 20890-20897. [paper][code]
Gordon, E.M., Laumann, T.O., Marek, S., Raut, R.V., Gratton, C., Gilmore, A.W., Newbold, D.J., Greene, D.J., Coalson, R.S., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E., Dosenbach, N.U.F., Nelson, S.M. (2020). Default mode network streams for coupling to language and control systems. Proceedings of the National Academy of Sciences, 117 (29), 17308-17319. [paper]
Newbold, D.J., Laumann, T.O., Hoyt, C.R., Hampton, J.M., Montez, D.F., Raut, R.V., Ortega, M., Mitra, A., Nielsen, A.N., Miller, D.B., Adeyemo, B., Nguyen, A.L., Scheidter, K.M., Tanenbaum, A.B., Van, A.N., Marek, S., Schlaggar, B.L., Carter, A.R., Greene, D.J., Gordon, E.M., Raichle, M.E., Petersen, S.E., Snyder, A.Z., Dosenbach, N.U.F. (2020). Plasticity and spontaneous activity pulses in disused human brain circuits. Neuron, 107, 580-589. [paper]
Sylvester, C.M., Yu, Q., Srivastava, A.B., Marek, S., Zheng, A., Alexopoulos, D., Smyser, C.D., Shimony, J.S., Ortega, M., Dierker, D.L., Patel, G.H., Nelson, S.M., Gilmore, A.W., McDermott, K.B., Berg, J.J., Drysdale, A.T., Perino, M., Snyder, A.Z., Raut, R.V., Laumann, T.O., Gordon, E., Barch, D.M., Rogers, C.E., Greene, D.J., Raichle, M.E., Dosenbach, N.U.F. (2020). Individual-specific functional connectivity of the amygdala: A substrate for precision psychiatry. Proceedings of the National Academy of Sciences, 177 (7), 3808-3818. [paper]
Rosenthal, Z.P., Raut, R.V., Yan, P., Koko, D., Kraft, A.W., Czerniewski, L., Acland, B., Mitra, A., Snyder, L.H., Bauer, A.Q., Snyder, A.Z., Culver, J.P., Raichle, M.E., Lee, J. (2020). Local perturbations of cortical excitability propagate differentially through large-scale functional networks. Cerebral Cortex, 30 (5), 3352-3369. [paper]
Seitzman, B.A., Gratton, C., Marek, S., Raut, R.V., Dosenbach, N.U.F., Schlaggar, B.L., Petersen, S.E., Greene, D.J. (2020). A set of functionally-defined brain regions with improved representation of the subcortex and cerebellum. NeuroImage, 206, 116-290. [paper]
Raut, R.V., Mitra, A., Marek, S., Ortega, M., Snyder, A.Z., Tanenbaum, A., Laumann, T.O., Dosenbach, N.U.F., Raichle, M.E. (2020). Organization of propagated intrinsic brain activity in individual humans. Cerebral Cortex, 30 (3), 1716-1734. [paper][code]
Raut, R.V., Mitra, A., Snyder, A.Z., Raichle, M.E. (2019). On time delay estimation and sampling error in resting-state fMRI. NeuroImage, 194, 211-227. [paper][code]
Raichle, M.E., Raut, R.V., Mitra, A. (2019). Brain networks: How many types are there?, in The Neocortex. Singer, W., Sejnowski, T., Rakic, P. eds. Strüngmann Forum Reports (27), Lupp, J.R. series ed. MIT Press, MA, 97-108. [paper]
Marek, S., Siegel, J.S., Gordon, E.M., Raut, R.V., Gratton, C., Newbold, D.J., Ortega, M., Laumann, T.O., Miller, D.B., Zheng, A., Lopez, K.C., Berg., J.J., Coalson, R.S., Nguyen, A.L., Dierker, D., Van., A.N., Hoyt, C.R., McDermott, K.B., Norris, S.A., Shimony, J.S., Snyder, A.Z., Nelson, S.M., Barch, D.M., Schlaggar, B.L., Raichle, M.E., Petersen, S.E., Greene, D.J., Dosenbach, N.U.F. (2018) Spatial and temporal organization of the individual human cerebellum. Neuron, 100 (4), 977-993. [paper]
Nair, V.A., Raut, R.V., Prabhakaran, V. (2017). Investigating the BOLD fMRI response to a verbal fluency task in early stroke before and after hemodynamic scaling. Frontiers in Neurology, 8-23. [paper]
Raut, R.V., Nair, V.A., Sattin, J.A., Prabhakaran, V. (2016). Hypercapnic evaluation of vascular reactivity in healthy aging and acute stroke via functional MRI. NeuroImage: Clinical, 12, 173-179. [paper]
DeYoe, E.A. & Raut, R.V. (2014). Visual mapping using blood oxygen level dependent functional magnetic resonance imaging. Neuroimag Clin N Am, 24, 573-584. [paper]