
Stefan Mihalas, Ph.D.
Bio:
Stefan Mihalas joined the Allen Institute in 2011 from Johns Hopkins University, where he was a postdoctoral fellow in neuroscience and subsequently an associate research scientist. As a computational neuroscientist, Mihalas has worked on models of both molecular and systems neuroscience including nervous system development, synaptic plasticity, minimalistic spiking neuron models, self-organized criticality, visual attention and figure ground segregation. His current research interests are aimed at building models to elucidate how large networks of interacting neurons produce cognitive behaviors. At the Allen Institute, Mihalas integrates anatomical and physiological connectivity data to generate models of visual perception in the mouse. To this end, he works to build a series of models of increasing complexity for both individual components, i.e., neurons, synapses, and microcircuits, as well as for large portions of the entire system. This series of models will be compared to the simplified theoretical predictions from statistical physics, information theory and computer vision. Mihalas received his Diploma in physics and M.S. in mathematics from West University of Timisoara in Romania. He received his Ph.D. in physics from the California Institute of Technology.
Publications
Cell Reports
Simple synaptic modulations implement diverse novelty computations
May 28, 2024
Kyle Aitken, Luke Campagnola, Marina E. Garrett, Shawn R. Olsen, Stefan Mihalas
Read MoreNature Neuroscience
Backward masking in mice requires visual cortex
Jan 01, 2024
Samuel D. Gale, Chelsea Strawder, Corbett Bennett, Stefan Mihalas, Christof Koch, Shawn R. Olsen
Read MoreNeural Networks: The Official Journal of the International Neural Network Society
A biologically inspired architecture with switching units can learn to generalize across backgrounds
Sep 17, 2023
Doris Voina, Eric Shea-Brown, Stefan Mihalas
Read MoreeLife
Neural population dynamics of computing with synaptic modulations
Feb 23, 2023
Kyle Aitken, Stefan Mihalas
Read MoreNeural Computation
Heterogeneity in Neuronal Dynamics Is Learned by Gradient Descent for Temporal Processing Tasks
Feb 13, 2023
Chloe N. Winston, Dana Mastrovito, Eric Shea-Brown, Stefan Mihalas
Read MoreNature Neuroscience
A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex
Feb 01, 2023
Shenqin Yao, Quanxin Wang, Karla E. Hirokawa, Benjamin Ouellette, Ruweida Ahmed, Jasmin Bomben, Krissy Brouner, Linzy Casal, Shiella Caldejon, Andy Cho, Nadezhda I. Dotson, Tanya L. Daigle, Tom Egdorf, Rachel Enstrom, Amanda Gary, Emily Gelfand, Melissa Gorham, Fiona Griffin, Hong Gu, Nicole Hancock, Robert Howard, Leonard Kuan, Sophie Lambert, Eric Kenji Lee, Jennifer Luviano, Kyla Mace, Michelle Maxwell, Marty T. Mortrud, Maitham Naeemi, Chelsea Nayan, Nhan-Kiet Ngo, Thuyanh Nguyen, Kat North, Shea Ransford, Augustin Ruiz, Sam Seid, Jackie Swapp, Michael J. Taormina, Wayne Wakeman, Thomas Zhou, Philip R. Nicovich, Ali Williford, Lydia Potekhina, Medea McGraw, Lydia Ng, Peter A. Groblewski, Bosiljka Tasic, Stefan Mihalas, Julie A. Harris, Ali Cetin, Hongkui Zeng
Read MoreNetwork Neuroscience (Cambridge, Mass.)
Modeling the cell-type-specific mesoscale murine connectome with anterograde tracing experiments
Jan 01, 2023
Samson Koelle, Dana Mastrovito, Jennifer D. Whitesell, Karla E. Hirokawa, Hongkui Zeng, Marina Meila, Julie A. Harris, Stefan Mihalas
Read MoreScience (New York, N.Y.)
Mesolimbic dopamine release conveys causal associations
Dec 23, 2022
Huijeong Jeong, Annie Taylor, Joseph R. Floeder, Martin Lohmann, Stefan Mihalas, Brenda Wu, Mingkang Zhou, Dennis A. Burke, Vijay Mohan K. Namboodiri
Read MorePLoS computational biology
The geometry of representational drift in natural and artificial neural networks
Nov 01, 2022
Kyle Aitken, Marina Garrett, Shawn Olsen, Stefan Mihalas
Read MorePLoS computational biology
MouseNet: A biologically constrained convolutional neural network model for the mouse visual cortex
Sep 01, 2022
Jianghong Shi, Bryan Tripp, Eric Shea-Brown, Stefan Mihalas, Michael A Buice
Read MoreNeural Computation
Single Circuit in V1 Capable of Switching Contexts During Movement Using an Inhibitory Population as a Switch
Feb 17, 2022
Doris Voina, Stefano Recanatesi, Brian Hu, Eric Shea-Brown, Stefan Mihalas
Read MoreProceedings of the National Academy of Sciences of the United States of America
Cell-type-specific neuromodulation guides synaptic credit assignment in a spiking neural network
Dec 21, 2021
Yuhan Helena Liu, Stephen Smith, Stefan Mihalas, Eric Shea-Brown, Uygar Sümbül
Read MorePLoS computational biology
Adaptation supports short-term memory in a visual change detection task
Sep 01, 2021
Brian Hu, Marina E. Garrett, Peter A. Groblewski, Douglas R. Ollerenshaw, Jiaqi Shang, Kate Roll, Sahar Manavi, Christof Koch, Shawn R. Olsen, Stefan Mihalas
Read MoreNeural Networks: The Official Journal of the International Neural Network Society
Autoencoder networks extract latent variables and encode these variables in their connectomes
Sep 01, 2021
Matthew Farrell, Stefano Recanatesi, R. Clay Reid, Stefan Mihalas, Eric Shea-Brown
Read MoreNature
Survey of spiking in the mouse visual system reveals functional hierarchy
Apr 01, 2021
Joshua H. Siegle, Xiaoxuan Jia, Séverine Durand, Sam Gale, Corbett Bennett, Nile Graddis, Greggory Heller, Tamina K. Ramirez, Hannah Choi, Jennifer A. Luviano, Peter A. Groblewski, Ruweida Ahmed, Anton Arkhipov, Amy Bernard, Yazan N. Billeh, Dillan Brown, Michael A. Buice, Nicolas Cain, Shiella Caldejon, Linzy Casal, Andrew Cho, Maggie Chvilicek, Timothy C. Cox, Kael Dai, Daniel J. Denman, Saskia E. J. de Vries, Roald Dietzman, Luke Esposito, Colin Farrell, David Feng, John Galbraith, Marina Garrett, Emily C. Gelfand, Nicole Hancock, Julie A. Harris, Robert Howard, Brian Hu, Ross Hytnen, Ramakrishnan Iyer, Erika Jessett, Katelyn Johnson, India Kato, Justin Kiggins, Sophie Lambert, Jerome Lecoq, Peter Ledochowitsch, Jung Hoon Lee, Arielle Leon, Yang Li, Elizabeth Liang, Fuhui Long, Kyla Mace, Jose Melchior, Daniel Millman, Tyler Mollenkopf, Chelsea Nayan, Lydia Ng, Kiet Ngo, Thuyahn Nguyen, Philip R. Nicovich, Kat North, Gabriel Koch Ocker, Doug Ollerenshaw, Michael Oliver, Marius Pachitariu, Jed Perkins, Melissa Reding, David Reid, Miranda Robertson, Kara Ronellenfitch, Sam Seid, Cliff Slaughterbeck, Michelle Stoecklin, David Sullivan, Ben Sutton, Jackie Swapp, Carol Thompson, Kristen Turner, Wayne Wakeman, Jennifer D. Whitesell, Derric Williams, Ali Williford, Rob Young, Hongkui Zeng, Sarah Naylor, John W. Phillips, R. Clay Reid, Stefan Mihalas, Shawn R. Olsen, Christof Koch
Read MoreNeuron
Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network
Feb 03, 2021
Jennifer D. Whitesell, Adam Liska, Ludovico Coletta, Karla E. Hirokawa, Phillip Bohn, Ali Williford, Peter A. Groblewski, Nile Graddis, Leonard Kuan, Joseph E. Knox, Anh Ho, Wayne Wakeman, Philip R. Nicovich, Thuc Nghi Nguyen, Cindy T. J. van Velthoven, Emma Garren, Olivia Fong, Maitham Naeemi, Alex M. Henry, Nick Dee, Kimberly A. Smith, Boaz Levi, David Feng, Lydia Ng, Bosiljka Tasic, Hongkui Zeng, Stefan Mihalas, Alessandro Gozzi, Julie A. Harris
Read MoreFrontiers in Synaptic Neuroscience
A Multisubcellular Compartment Model of AMPA Receptor Trafficking for Neuromodulation of Hebbian Synaptic Plasticity
Jan 01, 2021
Stefan Mihalas, Alvaro Ardiles, Kaiwen He, Adrian Palacios, Alfredo Kirkwood
Read MorePLoS computational biology
Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits
Nov 01, 2020
Kael Dai, Sergey L. Gratiy, Yazan N. Billeh, Richard Xu, Binghuang Cai, Nicholas Cain, Atle E. Rimehaug, Alexander J. Stasik, Gaute T. Einevoll, Stefan Mihalas, Christof Koch, Anton Arkhipov
Read MoreNeuron
Systematic Integration of Structural and Functional Data into Multi-scale Models of Mouse Primary Visual Cortex
May 06, 2020
Yazan N. Billeh, Binghuang Cai, Sergey L. Gratiy, Kael Dai, Ramakrishnan Iyer, Nathan W. Gouwens, Reza Abbasi-Asl, Xiaoxuan Jia, Joshua H. Siegle, Shawn R. Olsen, Christof Koch, Stefan Mihalas, Anton Arkhipov
Read MoreeLife
Experience shapes activity dynamics and stimulus coding of VIP inhibitory cells
Feb 26, 2020
Marina Garrett, Sahar Manavi, Kate Roll, Douglas R. Ollerenshaw, Peter A. Groblewski, Nicholas D. Ponvert, Justin T. Kiggins, Linzy Casal, Kyla Mace, Ali Williford, Arielle Leon, Xiaoxuan Jia, Peter Ledochowitsch, Michael A. Buice, Wayne Wakeman, Stefan Mihalas, Shawn R. Olsen
Read MoreNature Neuroscience
A large-scale standardized physiological survey reveals functional organization of the mouse visual cortex
Jan 01, 2020
Saskia E. J. de Vries, Jerome A. Lecoq, Michael A. Buice, Peter A. Groblewski, Gabriel K. Ocker, Michael Oliver, David Feng, Nicholas Cain, Peter Ledochowitsch, Daniel Millman, Kate Roll, Marina Garrett, Tom Keenan, Leonard Kuan, Stefan Mihalas, Shawn Olsen, Carol Thompson, Wayne Wakeman, Jack Waters, Derric Williams, Chris Barber, Nathan Berbesque, Brandon Blanchard, Nicholas Bowles, Shiella D. Caldejon, Linzy Casal, Andrew Cho, Sissy Cross, Chinh Dang, Tim Dolbeare, Melise Edwards, John Galbraith, Nathalie Gaudreault, Terri L. Gilbert, Fiona Griffin, Perry Hargrave, Robert Howard, Lawrence Huang, Sean Jewell, Nika Keller, Ulf Knoblich, Josh D. Larkin, Rachael Larsen, Chris Lau, Eric Lee, Felix Lee, Arielle Leon, Lu Li, Fuhui Long, Jennifer Luviano, Kyla Mace, Thuyanh Nguyen, Jed Perkins, Miranda Robertson, Sam Seid, Eric Shea-Brown, Jianghong Shi, Nathan Sjoquist, Cliff Slaughterbeck, David Sullivan, Ryan Valenza, Casey White, Ali Williford, Daniela M. Witten, Jun Zhuang, Hongkui Zeng, Colin Farrell, Lydia Ng, Amy Bernard, John W. Phillips, R. Clay Reid, Christof Koch
Read MoreFrontiers in Behavioral Neuroscience
Characterization of Learning, Motivation, and Visual Perception in Five Transgenic Mouse Lines Expressing GCaMP in Distinct Cell Populations
Jan 01, 2020
Peter A. Groblewski, Douglas R. Ollerenshaw, Justin T. Kiggins, Marina E. Garrett, Chris Mochizuki, Linzy Casal, Sissy Cross, Kyla Mace, Jackie Swapp, Sahar Manavi, Derric Williams, Stefan Mihalas, Shawn R. Olsen
Read MoreFrontiers in Computational Neuroscience
Contextual Integration in Cortical and Convolutional Neural Networks
Jan 01, 2020
Ramakrishnan Iyer, Brian Hu, Stefan Mihalas
Read MoreNature
Hierarchical organization of cortical and thalamic connectivity
Nov 01, 2019
Julie A. Harris, Stefan Mihalas, Karla E. Hirokawa, Jennifer D. Whitesell, Hannah Choi, Amy Bernard, Phillip Bohn, Shiella Caldejon, Linzy Casal, Andrew Cho, Aaron Feiner, David Feng, Nathalie Gaudreault, Charles R. Gerfen, Nile Graddis, Peter A. Groblewski, Alex M. Henry, Anh Ho, Robert Howard, Joseph E. Knox, Leonard Kuan, Xiuli Kuang, Jerome Lecoq, Phil Lesnar, Yaoyao Li, Jennifer Luviano, Stephen McConoughey, Marty T. Mortrud, Maitham Naeemi, Lydia Ng, Seung Wook Oh, Benjamin Ouellette, Elise Shen, Staci A. Sorensen, Wayne Wakeman, Quanxin Wang, Yun Wang, Ali Williford, John W. Phillips, Allan R. Jones, Christof Koch, Hongkui Zeng
Read MoreNature Neuroscience
Single-cell activity tracking reveals that orbitofrontal neurons acquire and maintain a long-term memory to guide behavioral adaptation
Jul 01, 2019
Vijay Mohan K. Namboodiri, James M. Otis, Kay van Heeswijk, Elisa S. Voets, Rizk A. Alghorazi, Jose Rodriguez-Romaguera, Stefan Mihalas, Garret D. Stuber
Read MoreNature Neuroscience
Classification of electrophysiological and morphological neuron types in the mouse visual cortex
Jul 01, 2019
Nathan W. Gouwens, Staci A. Sorensen, Jim Berg, Changkyu Lee, Tim Jarsky, Jonathan Ting, Susan M. Sunkin, David Feng, Costas A. Anastassiou, Eliza Barkan, Kris Bickley, Nicole Blesie, Thomas Braun, Krissy Brouner, Agata Budzillo, Shiella Caldejon, Tamara Casper, Dan Castelli, Peter Chong, Kirsten Crichton, Christine Cuhaciyan, Tanya L. Daigle, Rachel Dalley, Nick Dee, Tsega Desta, Song-Lin Ding, Samuel Dingman, Alyse Doperalski, Nadezhda Dotson, Tom Egdorf, Michael Fisher, Rebecca A. de Frates, Emma Garren, Marissa Garwood, Amanda Gary, Nathalie Gaudreault, Keith Godfrey, Melissa Gorham, Hong Gu, Caroline Habel, Kristen Hadley, James Harrington, Julie A. Harris, Alex Henry, DiJon Hill, Sam Josephsen, Sara Kebede, Lisa Kim, Matthew Kroll, Brian Lee, Tracy Lemon, Katherine E. Link, Xiaoxiao Liu, Brian Long, Rusty Mann, Medea McGraw, Stefan Mihalas, Alice Mukora, Gabe J. Murphy, Lindsay Ng, Kiet Ngo, Thuc Nghi Nguyen, Philip R. Nicovich, Aaron Oldre, Daniel Park, Sheana Parry, Jed Perkins, Lydia Potekhina, David Reid, Miranda Robertson, David Sandman, Martin Schroedter, Cliff Slaughterbeck, Gilberto Soler-Llavina, Josef Sulc, Aaron Szafer, Bosiljka Tasic, Naz Taskin, Corinne Teeter, Nivretta Thatra, Herman Tung, Wayne Wakeman, Grace Williams, Rob Young, Zhi Zhou, Colin Farrell, Hanchuan Peng, Michael J. Hawrylycz, Ed Lein, Lydia Ng, Anton Arkhipov, Amy Bernard, John W. Phillips, Hongkui Zeng, Christof Koch
Read MorePLoS computational biology
Synchronization dependent on spatial structures of a mesoscopic whole-brain network
Apr 01, 2019
Hannah Choi, Stefan Mihalas
Read MoreNetwork Neuroscience (Cambridge, Mass.)
High-resolution data-driven model of the mouse connectome
Jan 01, 2019
Joseph E. Knox, Kameron Decker Harris, Nile Graddis, Jennifer D. Whitesell, Hongkui Zeng, Julie A. Harris, Eric Shea-Brown, Stefan Mihalas
Read MorePLoS computational biology
Visual physiology of the layer 4 cortical circuit in silico
Nov 01, 2018
Anton Arkhipov, Nathan W. Gouwens, Yazan N. Billeh, Sergey Gratiy, Ramakrishnan Iyer, Ziqiang Wei, Zihao Xu, Reza Abbasi-Asl, Jim Berg, Michael Buice, Nicholas Cain, Nuno da Costa, Saskia de Vries, Daniel Denman, Severine Durand, David Feng, Tim Jarsky, Jérôme Lecoq, Brian Lee, Lu Li, Stefan Mihalas, Gabriel K. Ocker, Shawn R. Olsen, R. Clay Reid, Gilberto Soler-Llavina, Staci A. Sorensen, Quanxin Wang, Jack Waters, Massimo Scanziani, Christof Koch
Read MoreeLife
Sparse recurrent excitatory connectivity in the microcircuit of the adult mouse and human cortex
Sep 26, 2018
Stephanie C. Seeman, Luke Campagnola, Pasha A. Davoudian, Alex Hoggarth, Travis A. Hage, Alice Bosma-Moody, Christopher A. Baker, Jung Hoon Lee, Stefan Mihalas, Corinne Teeter, Andrew L. Ko, Jeffrey G. Ojemann, Ryder P. Gwinn, Daniel L. Silbergeld, Charles Cobbs, John Phillips, Ed Lein, Gabe Murphy, Christof Koch, Hongkui Zeng, Tim Jarsky
Read MoreNature Communications
Generalized leaky integrate-and-fire models classify multiple neuron types
Feb 19, 2018
Corinne Teeter, Ramakrishnan Iyer, Vilas Menon, Nathan Gouwens, David Feng, Jim Berg, Aaron Szafer, Nicholas Cain, Hongkui Zeng, Michael Hawrylycz, Christof Koch, Stefan Mihalas
Read MoreScientific Reports
Visual processing mode switching regulated by VIP cells
May 12, 2017
Jung Hoon Lee, Stefan Mihalas
Read MorePhilosophical Transactions of the Royal Society of London. Series B, Biological Sciences
Experience-dependent homeostasis of 'noise' at inhibitory synapses preserves information coding in adult visual cortex
Mar 05, 2017
Ming Gao, Jessica L. Whitt, Shiyong Huang, Angela Lee, Stefan Mihalas, Alfredo Kirkwood, Hey-Kyoung Lee
Read MoreFrontiers in Computational Neuroscience
A Computational Analysis of the Function of Three Inhibitory Cell Types in Contextual Visual Processing
Jan 01, 2017
Jung H. Lee, Christof Koch, Stefan Mihalas
Read MoreThe Journal of Neuroscience: The Official Journal of the Society for Neuroscience
A Comparison of Visual Response Properties in the Lateral Geniculate Nucleus and Primary Visual Cortex of Awake and Anesthetized Mice
Nov 30, 2016
Séverine Durand, Ramakrishnan Iyer, Kenji Mizuseki, Saskia de Vries, Stefan Mihalas, R. Clay Reid
Read MorePLoS computational biology
The Computational Properties of a Simplified Cortical Column Model
Sep 01, 2016
Nicholas Cain, Ramakrishnan Iyer, Christof Koch, Stefan Mihalas
Read MoreProceedings of the National Academy of Sciences of the United States of America
Inferring cortical function in the mouse visual system through large-scale systems neuroscience
Jul 05, 2016
Michael Hawrylycz, Costas Anastassiou, Anton Arkhipov, Jim Berg, Michael Buice, Nicholas Cain, Nathan W. Gouwens, Sergey Gratiy, Ramakrishnan Iyer, Jung Hoon Lee, Stefan Mihalas, Catalin Mitelut, Shawn Olsen, R. Clay Reid, Corinne Teeter, Saskia de Vries, Jack Waters, Hongkui Zeng, Christof Koch, MindScope
Read MoreeNeuro
Effects of Chronic Sleep Restriction during Early Adolescence on the Adult Pattern of Connectivity of Mouse Secondary Motor Cortex
Apr 01, 2016
Yazan N. Billeh, Alexander V. Rodriguez, Michele Bellesi, Amy Bernard, Luisa de Vivo, Chadd M. Funk, Julie Harris, Sakiko Honjoh, Stefan Mihalas, Lydia Ng, Christof Koch, Chiara Cirelli, Giulio Tononi
Read MoreNeural Computation
Analytical Calculation of Errors in Time and Value Perception Due to a Subjective Time Accumulator: A Mechanistic Model and the Generation of Weber's Law
Jan 01, 2016
Vijay Mohan K. Namboodiri, Stefan Mihalas, Marshall G. Hussain Shuler
Read MoreNature Neuroscience
Canonical genetic signatures of the adult human brain
Dec 01, 2015
Michael Hawrylycz, Jeremy A. Miller, Vilas Menon, David Feng, Tim Dolbeare, Angela L. Guillozet-Bongaarts, Anil G. Jegga, Bruce J. Aronow, Chang-Kyu Lee, Amy Bernard, Matthew F. Glasser, Donna L. Dierker, Jörg Menche, Aaron Szafer, Forrest Collman, Pascal Grange, Kenneth A. Berman, Stefan Mihalas, Zizhen Yao, Lance Stewart, Albert-László Barabási, Jay Schulkin, John Phillips, Lydia Ng, Chinh Dang, David R. Haynor, Allan Jones, David C. Van Essen, Christof Koch, Ed Lein
Read MoreProceedings of the National Academy of Sciences of the United States of America
Large-scale topology and the default mode network in the mouse connectome
Dec 30, 2014
James M. Stafford, Benjamin R. Jarrett, Oscar Miranda-Dominguez, Brian D. Mills, Nicholas Cain, Stefan Mihalas, Garet P. Lahvis, K. Matthew Lattal, Suzanne H. Mitchell, Stephen V. David, John D. Fryer, Joel T. Nigg, Damien A. Fair
Read MoreVision Research
Local spectral anisotropy is a valid cue for figure-ground organization in natural scenes
Oct 01, 2014
Sudarshan Ramenahalli, Stefan Mihalas, Ernst Niebur
Read MoreNature
A mesoscale connectome of the mouse brain
Apr 10, 2014
Seung Wook Oh, Julie A. Harris, Lydia Ng, Brent Winslow, Nicholas Cain, Stefan Mihalas, Quanxin Wang, Chris Lau, Leonard Kuan, Alex M. Henry, Marty T. Mortrud, Benjamin Ouellette, Thuc Nghi Nguyen, Staci A. Sorensen, Clifford R. Slaughterbeck, Wayne Wakeman, Yang Li, David Feng, Anh Ho, Eric Nicholas, Karla E. Hirokawa, Phillip Bohn, Kevin M. Joines, Hanchuan Peng, Michael J. Hawrylycz, John W. Phillips, John G. Hohmann, Paul Wohnoutka, Charles R. Gerfen, Christof Koch, Amy Bernard, Chinh Dang, Allan R. Jones, Hongkui Zeng
Read MoreFrontiers in Integrative Neuroscience
A temporal basis for Weber's law in value perception
Jan 01, 2014
Vijay Mohan K. Namboodiri, Stefan Mihalas, Marshall G. Hussain Shuler
Read MoreFrontiers in Behavioral Neuroscience
A general theory of intertemporal decision-making and the perception of time
Jan 01, 2014
Vijay M. K. Namboodiri, Stefan Mihalas, Tanya M. Marton, Marshall G. Hussain Shuler
Read MorePLoS computational biology
The influence of synaptic weight distribution on neuronal population dynamics
Oct 01, 2013
Ramakrishnan Iyer, Vilas Menon, Michael Buice, Christof Koch, Stefan Mihalas
Read MoreSIAM journal on applied dynamical systems
Locally Contractive Dynamics in Generalized Integrate-and-Fire Neurons
Sep 10, 2013
Nicolas D. Jimenez, Stefan Mihalas, Richard Brown, Ernst Niebur, Jonathan Rubin
Read More