The mission of the Machine Learning Core is to support researchers in the NIMH intramural research program who want to address research problems in psychology, psychiatry, and neuroscience, using statistics and machine learning approaches. We do this by consulting with individual researchers and guiding them in the use of the appropriate tools and methods, or by taking on the analysis process ourselves, if this is more expedient. In parallel, we are a machine learning research group and, as such, develop new methods and analysis approaches, motivated by the needs of researchers or by the practical possibilities arising from advances in the field.
contact: francisco.pereira@nih.gov
Members
The Machine Learning Core supports researchers in the NIMH intramural research program who want to address research problems in clinical and cognitive neuroscience using machine learning approaches.
Team Members
Dylan Nielson
Job title
research scientist
Al Xin
Job title
postbac IRTA
Software and Resources
- VICE toolbox for creating interpretable item embeddings from odd-one-out triplet task judgments
(the developer is Lukas Muttenthaler, please see VICE paper for the method we developed jointly) - Fast Functional Mixed Models using Fast Univariate Inference
photometry_FLMM
(toolbox used in "A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments")
Preprints (under review)
- Enhancing Infant Crying Detection with Gradient Boosting for Improved Emotional and Mental Health Diagnostics
Lee K., Henry L. M., Hansen E., Tandilashvili E., Wakschlag L. S., Norton E., Pine D. S., Brotman M. A., Pereira F. - Neural and behavioral reinstatement jointly reflect retrieval of narrative events
Nau M., Greene A., Tarder-Stoll H., Lossio-Ventura J.A., Pereira F., Chen J., Baldassano C., Baker C. - More Experts Than Galaxies: Conditionally-overlapping Experts With Biologically-Inspired Fixed Routing
Shaier S., Pereira F., von der Wense K., Hunter L. E., Jones M. - In-Scanner Thoughts shape Resting-state Functional Connectivity: how participants “rest” matters
Gonzalez-Castillo J., Spurney M., Lam K. C., Gephart I. S., Pereira F., Handwerker D. A., Kam J. W. Y., Bandettini P. - Prediction of mental well-being from individual characteristics and circumstances during the COVID-19 pandemic
Harris C., Farmer C., Gibbon A., Shaw J., Thomas A., Atlas L. Y., Chung J. Y., Pereira F.
Selected publications
Methods
- A Statistical Framework for Analysis of Trial-Level Temporal Dynamics in Fiber Photometry Experiments
Loewinger G., Cui E., Lovinger D., Pereira F.
in press at eLife - Causal Inference in the Closed-Loop: Marginal Structural Models for Sequential Excursion Effects
Levis A., Loewinger G., Pereira F.
to appear in Neural Information Processing Systems, 2024 - eXponential FAmily Dynamical Systems (XFADS): Large-scale nonlinear Gaussian state-space modeling
Dowling M., Zhao Y., Park I. M.
to appear in Neural Information Processing Systems, 2024 - A Comparison of ChatGPT and Fine-Tuned Open Pre-Trained Transformers (OPT) Against Widely Used Sentiment Analysis Tools: Sentiment Analysis of COVID-19 Survey Data
Lossio-Ventura J. A., Weger R., Lee A., Guinee E., Chung J. Y., Atlas L. Y., Linos E., Pereira F.
JMIR Mental Health Vol 11, 2024 - "Improving the Interpretability of fMRI Decoding using Deep Neural Networks and Adversarial Robustness"
McClure P., Moraczewski D., Lam K. C., Thomas A., Pereira F.
Aperture Neuro, 2023 - "Manifold learning for fMRI time-varying functional connectivity"
Gonzalez-Castillo J., Fernandez I., Lam K., Handwerker D., Pereira F., Bandettini P.
Front Hum Neurosci. 2023; 17: 1134012 - "Real-time variational method for learning neural trajectory and its dynamics"
Matthew Dowling, Yuan Zhao, Il Memming Park
in International Conference on Learning Representations, 2023 - "Linear time GPs for inferring latent trajectories from neural spike trains"
Matthew Dowling, Yuan Zhao, Il Memming Park
in International Conference on Machine Learning, 2023 - "VICE: Variational Interpretable Concept Embeddings"
Muttenthaler L., Zheng C., McClure P., Vandermeulen R., Hebart M., Pereira F.
in Neural Information Processing Systems, 2022 - Semantic Projection: Recovering Human Knowledge of Multiple, Distinct, Object Features from Word Embeddings
Grand G., Blank I., Pereira F., Fedorenko E.
Nature Human Behaviour, 2022 - "Knowing What You Know in Brain Segmentation Using Bayesian Deep Neural Networks"
McClure, P., Rho, N., Lee, J., Kaczmarzyk, J., Zheng, C., Ghosh, S., Nielson, D., Thomas, A., Bandettini, P., Pereira, F.
Frontiers in Neuroinformatics, 2019 - "Revealing interpretable object representations from human behavior"
Zheng, C., Pereira, F., Baker, C., Hebart, M.
International Conference on Learning Representations, 2019 - "Validating the Representational Space of Deep Reinforcement Learning Models of Behavior with Neural Data"
Bruch S. N. , McClure P., Zhou J., Schoenbaum G., Pereira F.
bioRxiv preprint - A Deep Neural Network Tool for Automatic Segmentation of Human Body Parts in Natural Scenes
McClure P. , Reimann G., Ramot M., Pereira F.
arXiv preprint - "Deep Neural Networks in Computational Neuroscience"
Kietzmann, T., McClure, P., Kriegeskorte, N.
Oxford Research Encyclopedia of Neuroscience, 2019 - "Distributed Weight Consolidation: A Brain Segmentation Case Study"
McClure P., Zheng C., Kaczmarzyk J., Rogers-Lee J., Ghosh S., Nielson D., Bandettini P., Pereira F.
Neural Information Processing Systems, 2018 - "Extrapolating Expected Accuracies for Large Multi-Class Problems"
Zheng, C., Achanta R., Benjamini. Y.
Journal of Machine Learning Research vol. 19. 2018.
Applications
- Outcomes that matter to depressed adolescents can be identified with large language models
Xin A., Lossio-Ventura J. A., Krause, K. R., Fiorini, G., Midgley N., Pereira F., and Nielson D. M.
in press at Journal of the American Medical Informatics Association - Distinct brain-wide presynaptic networks underlie the functional identity of individual cortical neurons
Inacio A. R., Lam K. C., Zhao Y., Pereira F., Gerfen C. R., Lee S.
in press at Nature - Dynamic effects of psychiatric vulnerability, loneliness, and social distancing on distress during the first year of the COVID-19 pandemic: Insights from a large-scale longitudinal study
Atlas L. Y., Farmer C., Shaw J., Gibbon A., Guinee E.P., Lossio-Ventura J. A., Ballard E., Ernst M., Japee S., Pereira F., Chung J. Y.
in press at Nature Mental Health - Trends in Language Use During the COVID-19 Pandemic and Relationship Between Language Use and Mental Health: Text Analysis Based on Free Responses From a Longitudinal Study
Weger R., Lossio-Ventura J. A., Rose-McCandlish M., Shaw J., Sinclair S., Pereira F., Chung J., Atlas L.
JMIR Mental Health 10 (1), e40899, 2023 - "Sensory and Choice Responses in MT Distinct from Motion Encoding"
Aaron J. Levi, Yuan Zhao, Il Memming Park and Alexander C. Huk
Journal of Neuroscience 22 March 2023, 43 (12) 2090-2103 - "A Highly Replicable Decline in Mood During Rest and Simple Tasks"
Jangraw D., Keren H., Sun H., Bedder R., Rutledge R., Pereira F., Thomas A., Pine D., Zheng C., Nielson D., Stringaris A.
Nature Human Behaviour 7 (4), 596-610, 2022 - "Mood and Behaviors of Adolescents With Depression in a Longitudinal Study Before and During the COVID-19 Pandemic"
Sadeghi N., Fors P.Q., Eisner L., Taigman J., Qi K., Gorham L.S., Camp C.C., O'Callaghan G., Rodriguez D., McGuire J., Garth E.M., Engel C., Davis M., Towbin K.E., Stringaris A., Nielson D.M. - "Working memory and reward increase the accuracy of animal location encoding in the medial prefrontal cortex"
Ma X., Zheng C., Chen Y., Pereira F., Zheng L.
Cerebral Cortex, 2022, 1-15 - "Origins of Anhedonia in Childhood and Adolescence"
Prabhakar J., Nielson D.M., Stringaris A. - "The temporal representation of experience in subjective mood"
Keren H., Zheng C., Jangraw D. C., Chang K., Vitale A., Nielson D., Rutledge R. B., Pereira F., Stringaris A.
eLife 2021 - "Mental representations of objects reflect the ways in which we interact with them"
Lam K. C., Pereira F., Vaziri-Pashkam M., Woodard K., McMahon E.
Proceedings of the Cognitive Science Society Conference, 2021 [talk] - Gauging facial feature viewing preference as a stable individual trait in autism spectrum disorder.
Reimann G., Walsh C., Csumitta K., McClure P., Pereira F., Martin A., Ramot M.
Autism Research 14:1670–1683, 2021 - Cell-type-specific recruitment of GABAergic interneurons in the primary somatosensory cortex by long-range inputs
Naskar S., Qi J., Pereira F., Gerfen, C., Lee, S.
Cell Reports 34, 108774, 2021 - "Magnetoencephalographic Correlates of Mood and Reward Dynamics in Human Adolescents"
Liuzzi, L., Chang, K.K., Zheng, C., Keren, H., Saha, D., Nielson, D.M. and Stringaris, A.
Cerebral Cortex, 2021 - "Revealing the multidimensional mental representations of natural objects underlying human similarity judgments"
Hebart, M., Zheng, C., Pereira, F., Baker, C.
Nature Human Behaviour, 2020 - "Subtle predictive movements reveal actions regardless of social context"
McMahon, E.G., Zheng, C.Y., Pereira, F., Gonzalez, R., Ungerleider, L.G. and Vaziri-Pashkam, M.
Journal of vision 19 (7), 16-16, 2019 - Imaging the spontaneous flow of thought: Distinct periods of cognition contribute to dynamic functional connectivity during rest
Gonzalez-Castillo J., Caballero-Gaudes C., Topolski N., Handwerker D., Pereira F. , Bandettini P.
Neuroimage 15; 202: 116129. 2019 - Data‐driven identification of subtypes of executive function across typical development, attention deficit hyperactivity disorder, and autism spectrum disorders
Vaidya C., You X., Mostofsky S., Pereira F., Berl M., Kenworthy L.
J Child Psychol Psychiatry 61(1): 51–61. 2019 - "Toward a universal decoder of linguistic meaning from brain activation"
Pereira F., Lou B., Pritchett B., Ritter S., Gershman S., Kanwisher N., Botvinick M., Fedorenko E.
Nature Communications 9 (963), 2018
Former Team Members
Patrick McClure
Job title
Assistant Professor, Computer Science Dept., Naval Postgraduate School
Links
Yenho Chen
Job title
Machine Learning Ph.D. student
Nicole Kuznetsov
Job title
postbac IRTA / M.S. student
Carl Harris
Job title
Postbac IRTA (2021-2023)
Links
