This wiki supports the activities of the NIH BRAIN Theories, Models and Methods grantees.

TMM FOA requirements

Working Group Lead

Bill Lytton, Fidel Santamaria

This Working Group supports the activities of the awardees in the NIH BRAIN Initiative developing new theories, models and methods to understand complex brain circuits.

Slack: https://braincircuits.slack.com/

Activities

1. DATA Scholar Project

Expanding Theories of Brain Circuits Using Knowledge Integration: Solving knowledge integration challenges and develop the BRAIN initiative Workspace to ORganize the Knowledge Space (BRAINWORKS) platform

All TMM Projects are encouraged to utilize the NIH BRAINWORKS platform (that organizes, integrates, and represents nuanced knowledge contained within the growing body of the scientific literature) to assist in the development of Theories, Models and Methods for understanding brain circuits from the cellular and subsecond resolution to behavior.

2. BRAIN Awardee Welcome Meeting/Intro to DATA Scholar

3. 2021 BRAIN BOOTH

4. U19/TMM Data & Model Match for Reuse

Deadline to upload abstracts was September 25th, 2020.

5. RFAs and other calls

BRAIN Initiative: Theories Models and Methods RFA
Current FOA: https://grants.nih.gov/grants/guide/rfa-files/RFA-EB-20-002.html {Released June 29, 2020}

Letter of Intent Due Date(s) August 14, 2020

Application Due Date(s) September 14, 2020, All applications are due by 5:00 PM local time of applicant organization.

Past FOAs:

https://grants.nih.gov/grants/guide/rfa-files/rfa-eb-17-005.html

https://grants.nih.gov/grants/guide/rfa-files/rfa-eb-15-006.html

1-Slide Template: to explain the math inside the tools being developed NIBIB Math Project Template_final.pptx {use this to post in your project pages!}

6. Activity Log

6.1 Discussion on roadblocks to theoretical neuroscience from 2020 BRAIN PI meeting

THEORIES Discussion {Please post your thoughts!}

6.2 Meeting notes

July 27, 2020 Call

notes from July 27, 2020 TMM grantee meeting219.42 KB

2020 BRAIN PI Meeting - TMM vitual booth materials

February 14, 2020 Call

2019 BRAIN PI Meeting Materials

2019 TMM group shot

Additional Information

TMM Projects

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1-slide template for TMM Projects953.5 KB
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All BRAIN Theories, Models and Methods Awardees

*Participating in Data Reuse Effort and Abstract is Linked

PI Name(s) All	Title	Grant #
BROWN, EMERY N	Filtered Point Process Inference Framework for Modeling Neural Data	EB022726
*CARLSON, DAVID E	Uncovering Population-Level Cellular Relationships to Behavior via Mesoscale Networks	EB026937
CHEN, ZHE SAGE (contact); BUZSAKI, GYORGY	Dissection of spatiotemporal activity from large-scale, mutli-modal, multi-resolution hippocampal-neocortical recordings	DA056394
*CHING, SHINUNG (contact); SNYDER, LAWRENCE H	Efficient resource allocation and information retention in working memory circuits	EB028154
CHUNG, MOO K	BRAIN Initiative: Theories, Models and Methods for Analysis of Complex Data from the Brain	EB022856
COEN-CAGLI, RUBEN	Computational Tools for assessing mechanisms and functional relevance of divisive normalization	DA056400
CURTO, CARINA	Emergent dynamics from network connectivity: a minimal model	EB022862

*DAVID, STEPHEN V (contact); MESGARANI, NIMA	Tools for modeling state-dependent sensory encoding by neural populations across spatial and temporal scales	EB028155
*DOIRON, BRENT D (contact); SMITH, MATTHEW A; YU, BYRON M	Neuronal population dynamics within and across cortical areas	EB026953
*DRUCKMANN, SHAUL	Dissecting distributed representations by advanced population activity analysis methods and modeling	EB028171
DYER, EVA	A comparative framework for modeling the low-dimensional geometry of neural population states	EB029852
*ENGEL, TATIANA	Discovering dynamic computations from large-scale neural activity recordings	EB026949
ENGEL, TATIANA	Multiscale computational frameworks for integrating large-scale cortical dynamics, connectivity, and behavior	DA055666
FLETCHER, PRESTON THOMAS	Beyond Diagnostic Classification of Autism: Neuroanatomical, Functional, and Behavioral Phenotypes	EB022876
GATES, KATHLEEN	Network Connectivity Modeling of Heterogeneous Brain Data to Examine Ensembles of Activity Across Two Levels of Dimensionality	EB022904
GOLD, JOSHUA I (contact); BALASUBRAMANIAN, VIJAY	Mental, measurement, and model complexity in neuroscience	EB026945
HANSON, STEPHEN JOSE	EFFECTIVE CONNECTIVITY IN BRAIN NETWORKS: Discovering Latent Structure, Network Complexity and Recurrence	EB022858
*HOWARD, MARC W	Toward a Theory for Macroscopic Neural Computation Based on Laplace Transform	EB022864
JONES, STEPHANIE RUGGIANO (contact); HAMALAINEN, MATTI ; HINES, MICHAEL L	Human Neocortical Neurosolver	EB022889
KEILHOLZ, SHELLA D	Crossing space and time: uncovering the nonlinear dynamics of multimodal and multiscale brain activity	EB029857
*KILPATRICK, ZACHARY PETER	Connecting neural circuit architecture and experience-driven probabilistic computations	EB029847
KORDING, KONRAD P	Quantifying causality for neuroscience	EB028162
*KRAMER, MARK ALAN (contact); EDEN, URI TZVI	Measuring, Modeling, and Modulating Cross-Frequency Coupling	EB026938
LITWIN-KUMAR, ASHOK	Relating structure and function in synapse-level wiring diagrams	EB029858
LUO, XI	Large-scale Network Modeling for Brain Dynamics: Statistical Learning and Optimization	EB022911
*LYTTON, WILLIAM W (contact); ANTIC, SRDJAN D	Embedded Ensemble Encoding	EB022903
*MAKSE, HERNAN	Application of the principle of symmetry to neural circuitry: from building blocks to neural synchronization in the connectome	EB028157
MAKSE, HERNAN (contact); HOLODNY, ANDREI I	Graph theoretical analysis of the effect of brain tumors on functional MRI networks	EB022720
MENON, VINOD	Novel Bayesian linear dynamical systems-based methods for discovering human brain circuit dynamics in health and disease	EB022907
MIHALAS, STEFAN (contact);SHEA-BROWN, ERIC TODD	From diverse dynamics to diverse computation via neural cell types	DA055669
MIHALAS, STEFAN (contact); ARKHIPOV, ANTON	Modeling the structure-function relation in a reconstructed cortical tissue	EB029813
MILLER, KENNETH D.	Modeling the development of orientation selectivity, maps, and the associated recurrent circuit	DA056397
*MISHNE, GAL	Data-driven analysis for neuronal dynamic modeling	EB026936
MITRA, PARTHA PRATIM (contact); WANG, YUSU	Methods from Computational Topology and Geometry for Analysing Neuronal Tree and Graph Data	EB022899
MJOLSNESS, ErRIC	Multiscale theory of synapse function with model reduction by machine learning	DA055668
NEMENMAN, ILYA M (contact); SOBER, SAMUEL	Neural mechanisms and behavioral consequences of non-Gaussian likelihoods in sensorimotor learning	EB022872
PALMER, STEPHANIE E (contact); BIALEK, WILLIAM ; SCHWAB, DAVID JASON	Coarse-graining approaches to networks, learning, and behavior	EB026943
PANDARINATH, CHETHAN (contact); MILLER, LEE E	Robust modeling of within-and across-area population dynamics using recurrent neural networks	DA055667
PANINSKI, LIAM M	Next-Generation Calcium Imaging Analysis Methods	EB022913
*PARK, IL MEMMING (contact); PILLOW, JONATHAN WILLIAM	Real-time statistical algorithms for controlling neural dynamics and behavior	EB026946
PEARSON, JOHN	Real-time mapping and adaptive testing for neural population hypotheses	DA056376
PILLOW, JONATHAN WILLIAM (contact); PARK, IL MEMMING	Adaptive statistical algorithms for learning and control of neural dynamics	DA065404
RAJ, ASHISH (contact); NAGARAJAN, SRIKANTAN S	Multimodal modeling framework for fusing structural and functional connectome data	EB022717

*RAJAN, KANAKA	Multi-region Network of Networks Recurrent Neural Network Models of Adaptive and Maladaptive Learning	EB028166
RAJAN, KANAKA	Neural Network Models Constrained by Multiscale Data to Infer Minimal Functional Motifs in the Brain	DA056403
RINGACH, DARIO L	Bayesian estimation of network connectivity and motifs	EB022915
*SANTAMARIA, FIDEL	A unified framework to study history dependence in the nervous system	EB026939
SAXENA, SHREYA	Elucidating Principles of Sensorimotor Control using Deep Learning	DA056377
SEJNOWSKI, TERRENCE J	Nonlinear Causal Analysis of Neural Signals	EB026899
SHADMEHR, RAZA	A new theory of population coding in the cerebellum	EB028156
SHEN, DINGGANG (contact); YAP, PEW-THIAN	Diagnosis of Alzheimers Disease Using Dynamic High-Order Brain Networks	EB022880
*SHOUVAL, HAREL ZEEV (contact); BRUNEL, NICOLAS	Learning spatio-temporal statistics from the environment in recurrent networks	EB022891
SINGH, VIKAS (contact); JOHNSON, STERLING C	Manifold-valued statistical models for longitudinal morphometic analysis in preclinical Alzheimers disease (AD)	EB022883
*SOMMER, FRIEDRICH T	Building analysis tools and a theory framework for inferring principles of neural computation from multi-scale organization in brain recordings	EB026955
SONG, DONG	Combined Mechanistic and Input-Output Modeling of the Hippocampus During Spatial Navigation	DA055665
*WITTEN, DANIELA (contact); BUICE, MICHAEL	Models and Methods for Calcium Imaging Data with Application to the Allen Brain Observatory	EB026908
WOMELSDORF, THILO	Mechanisms of Information Routing in Primate Fronto-striatal Circuits	EB028161
*YE, BING (contact); DIERSSEN, MARA	New methods and theories to interrogate organizational principles from single cell to neuronal networks	EB028159

Interagency Modeling and Analysis Group

BRAIN Initiative - Theories, Models and Methods