1
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Chen Y, Chien J, Dai B, Lin D, Chen ZS. Identifying behavioral links to neural dynamics of multifiber photometry recordings in a mouse social behavior network. J Neural Eng 2024; 21:036051. [PMID: 38861996 DOI: 10.1088/1741-2552/ad5702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/11/2024] [Indexed: 06/13/2024]
Abstract
Objective.Distributed hypothalamic-midbrain neural circuits help orchestrate complex behavioral responses during social interactions. Given rapid advances in optical imaging, it is a fundamental question how population-averaged neural activity measured by multi-fiber photometry (MFP) for calcium fluorescence signals correlates with social behaviors is a fundamental question. This paper aims to investigate the correspondence between MFP data and social behaviors.Approach:We propose a state-space analysis framework to characterize mouse MFP data based on dynamic latent variable models, which include a continuous-state linear dynamical system and a discrete-state hidden semi-Markov model. We validate these models on extensive MFP recordings during aggressive and mating behaviors in male-male and male-female interactions, respectively.Main results:Our results show that these models are capable of capturing both temporal behavioral structure and associated neural states, and produce interpretable latent states. Our approach is also validated in computer simulations in the presence of known ground truth.Significance:Overall, these analysis approaches provide a state-space framework to examine neural dynamics underlying social behaviors and reveals mechanistic insights into the relevant networks.
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Affiliation(s)
- Yibo Chen
- Department of Psychiatry, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, United States of America
- Program in Artificial Intelligence, University of Science and Technology of China, Hefei, Anhui, People's Republic of China
| | - Jonathan Chien
- Department of Psychiatry, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, United States of America
| | - Bing Dai
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States of America
| | - Dayu Lin
- Department of Psychiatry, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, United States of America
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States of America
- Center for Neural Science, New York University, New York, NY, United States of America
| | - Zhe Sage Chen
- Department of Psychiatry, Department of Neuroscience and Physiology, New York University School of Medicine, New York, NY, United States of America
- Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, United States of America
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, United States of America
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2
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Camaglia F, Nemenman I, Mora T, Walczak AM. Bayesian estimation of the Kullback-Leibler divergence for categorical systems using mixtures of Dirichlet priors. Phys Rev E 2024; 109:024305. [PMID: 38491647 DOI: 10.1103/physreve.109.024305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/18/2024] [Indexed: 03/18/2024]
Abstract
In many applications in biology, engineering, and economics, identifying similarities and differences between distributions of data from complex processes requires comparing finite categorical samples of discrete counts. Statistical divergences quantify the difference between two distributions. However, their estimation is very difficult and empirical methods often fail, especially when the samples are small. We develop a Bayesian estimator of the Kullback-Leibler divergence between two probability distributions that makes use of a mixture of Dirichlet priors on the distributions being compared. We study the properties of the estimator on two examples: probabilities drawn from Dirichlet distributions and random strings of letters drawn from Markov chains. We extend the approach to the squared Hellinger divergence. Both estimators outperform other estimation techniques, with better results for data with a large number of categories and for higher values of divergences.
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Affiliation(s)
- Francesco Camaglia
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université and Université de Paris, 75005 Paris, France
| | - Ilya Nemenman
- Department of Physics, Department of Biology, and Initiative for Theory and Modeling of Living Systems, Emory University, Atlanta, Georgia 30322, USA
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université and Université de Paris, 75005 Paris, France
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL University, Sorbonne Université and Université de Paris, 75005 Paris, France
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3
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Chung B, Zia M, Thomas KA, Michaels JA, Jacob A, Pack A, Williams MJ, Nagapudi K, Teng LH, Arrambide E, Ouellette L, Oey N, Gibbs R, Anschutz P, Lu J, Wu Y, Kashefi M, Oya T, Kersten R, Mosberger AC, O'Connell S, Wang R, Marques H, Mendes AR, Lenschow C, Kondakath G, Kim JJ, Olson W, Quinn KN, Perkins P, Gatto G, Thanawalla A, Coltman S, Kim T, Smith T, Binder-Markey B, Zaback M, Thompson CK, Giszter S, Person A, Goulding M, Azim E, Thakor N, O'Connor D, Trimmer B, Lima SQ, Carey MR, Pandarinath C, Costa RM, Pruszynski JA, Bakir M, Sober SJ. Myomatrix arrays for high-definition muscle recording. eLife 2023; 12:RP88551. [PMID: 38113081 PMCID: PMC10730117 DOI: 10.7554/elife.88551] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023] Open
Abstract
Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous system's actual motor output - the activation of muscle fibers by motor neurons - typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices ('Myomatrix arrays') that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a 'motor unit,' during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous system's motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and identifying pathologies of the motor system.
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Affiliation(s)
- Bryce Chung
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Muneeb Zia
- School of Electrical and Computer Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Kyle A Thomas
- Graduate Program in Biomedical Engineering at Emory University and Georgia TechAtlantaUnited States
| | | | - Amanda Jacob
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Andrea Pack
- Neuroscience Graduate Program, Emory UniversityAtlantaUnited States
| | - Matthew J Williams
- Graduate Program in Biomedical Engineering at Emory University and Georgia TechAtlantaUnited States
| | | | - Lay Heng Teng
- Department of Biology, Emory UniversityAtlantaUnited States
| | | | | | - Nicole Oey
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Rhuna Gibbs
- Department of Biology, Emory UniversityAtlantaUnited States
| | - Philip Anschutz
- Graduate Program in BioEngineering, Georgia TechAtlantaUnited States
| | - Jiaao Lu
- Graduate Program in Electrical and Computer Engineering, Georgia TechAtlantaUnited States
| | - Yu Wu
- School of Electrical and Computer Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Mehrdad Kashefi
- Department of Physiology and Pharmacology, Western UniversityLondonCanada
| | - Tomomichi Oya
- Department of Physiology and Pharmacology, Western UniversityLondonCanada
| | - Rhonda Kersten
- Department of Physiology and Pharmacology, Western UniversityLondonCanada
| | - Alice C Mosberger
- Zuckerman Mind Brain Behavior Institute at Columbia UniversityNew YorkUnited States
| | - Sean O'Connell
- Graduate Program in Biomedical Engineering at Emory University and Georgia TechAtlantaUnited States
| | - Runming Wang
- Department of Biomedical Engineering at Emory University and Georgia TechAtlantaUnited States
| | - Hugo Marques
- Champalimaud Neuroscience Programme, Champalimaud FoundationLisbonPortugal
| | - Ana Rita Mendes
- Champalimaud Neuroscience Programme, Champalimaud FoundationLisbonPortugal
| | - Constanze Lenschow
- Champalimaud Neuroscience Programme, Champalimaud FoundationLisbonPortugal
| | | | - Jeong Jun Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
| | - William Olson
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Kiara N Quinn
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Pierce Perkins
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Graziana Gatto
- Salk Institute for Biological StudiesLa JollaUnited States
| | | | - Susan Coltman
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
| | - Taegyo Kim
- Department of Neurobiology & Anatomy, Drexel University, College of MedicinePhiladelphiaUnited States
| | - Trevor Smith
- Department of Neurobiology & Anatomy, Drexel University, College of MedicinePhiladelphiaUnited States
| | - Ben Binder-Markey
- Department of Physical Therapy and Rehabilitation Sciences, Drexel University College of Nursing and Health ProfessionsPhiladelphiaUnited States
| | - Martin Zaback
- Department of Health and Rehabilitation Sciences, Temple UniversityPhiladelphiaUnited States
| | - Christopher K Thompson
- Department of Health and Rehabilitation Sciences, Temple UniversityPhiladelphiaUnited States
| | - Simon Giszter
- Department of Neurobiology & Anatomy, Drexel University, College of MedicinePhiladelphiaUnited States
| | - Abigail Person
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical CampusAuroraUnited States
- Allen InstituteSeattleUnited States
| | | | - Eiman Azim
- Salk Institute for Biological StudiesLa JollaUnited States
| | - Nitish Thakor
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Daniel O'Connor
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of MedicineBaltimoreUnited States
| | - Barry Trimmer
- Department of Biology, Tufts UniversityMedfordUnited States
| | - Susana Q Lima
- Champalimaud Neuroscience Programme, Champalimaud FoundationLisbonPortugal
| | - Megan R Carey
- Champalimaud Neuroscience Programme, Champalimaud FoundationLisbonPortugal
| | - Chethan Pandarinath
- Department of Biomedical Engineering at Emory University and Georgia TechAtlantaUnited States
| | - Rui M Costa
- Zuckerman Mind Brain Behavior Institute at Columbia UniversityNew YorkUnited States
| | | | - Muhannad Bakir
- School of Electrical and Computer Engineering, Georgia Institute of TechnologyAtlantaUnited States
| | - Samuel J Sober
- Department of Biology, Emory UniversityAtlantaUnited States
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Chung B, Zia M, Thomas KA, Michaels JA, Jacob A, Pack A, Williams MJ, Nagapudi K, Teng LH, Arrambide E, Ouellette L, Oey N, Gibbs R, Anschutz P, Lu J, Wu Y, Kashefi M, Oya T, Kersten R, Mosberger AC, O'Connell S, Wang R, Marques H, Mendes AR, Lenschow C, Kondakath G, Kim JJ, Olson W, Quinn KN, Perkins P, Gatto G, Thanawalla A, Coltman S, Kim T, Smith T, Binder-Markey B, Zaback M, Thompson CK, Giszter S, Person A, Goulding M, Azim E, Thakor N, O'Connor D, Trimmer B, Lima SQ, Carey MR, Pandarinath C, Costa RM, Pruszynski JA, Bakir M, Sober SJ. Myomatrix arrays for high-definition muscle recording. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529200. [PMID: 36865176 PMCID: PMC9980060 DOI: 10.1101/2023.02.21.529200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Neurons coordinate their activity to produce an astonishing variety of motor behaviors. Our present understanding of motor control has grown rapidly thanks to new methods for recording and analyzing populations of many individual neurons over time. In contrast, current methods for recording the nervous system's actual motor output - the activation of muscle fibers by motor neurons - typically cannot detect the individual electrical events produced by muscle fibers during natural behaviors and scale poorly across species and muscle groups. Here we present a novel class of electrode devices ("Myomatrix arrays") that record muscle activity at unprecedented resolution across muscles and behaviors. High-density, flexible electrode arrays allow for stable recordings from the muscle fibers activated by a single motor neuron, called a "motor unit", during natural behaviors in many species, including mice, rats, primates, songbirds, frogs, and insects. This technology therefore allows the nervous system's motor output to be monitored in unprecedented detail during complex behaviors across species and muscle morphologies. We anticipate that this technology will allow rapid advances in understanding the neural control of behavior and in identifying pathologies of the motor system.
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Affiliation(s)
- Bryce Chung
- Department of Biology, Emory University (Atlanta, GA, USA)
| | - Muneeb Zia
- School of Electrical and Computer Engineering, Georgia Institute of Technology (Atlanta, GA, USA)
| | - Kyle A Thomas
- Graduate Program in Biomedical Engineering at Emory University and Georgia Tech (Atlanta, GA, USA)
| | - Jonathan A Michaels
- Department of Physiology and Pharmacology, Western University (London, ON, Canada)
| | - Amanda Jacob
- Department of Biology, Emory University (Atlanta, GA, USA)
| | - Andrea Pack
- Neuroscience Graduate Program, Emory University (Atlanta, GA, USA)
| | - Matthew J Williams
- Graduate Program in Biomedical Engineering at Emory University and Georgia Tech (Atlanta, GA, USA)
| | | | - Lay Heng Teng
- Department of Biology, Emory University (Atlanta, GA, USA)
| | | | | | - Nicole Oey
- Department of Biology, Emory University (Atlanta, GA, USA)
| | - Rhuna Gibbs
- Department of Biology, Emory University (Atlanta, GA, USA)
| | - Philip Anschutz
- Graduate Program in BioEngineering, Georgia Tech (Atlanta, GA, USA)
| | - Jiaao Lu
- Graduate Program in Electrical and Computer Engineering, Georgia Tech (Atlanta, GA, USA)
| | - Yu Wu
- School of Electrical and Computer Engineering, Georgia Institute of Technology (Atlanta, GA, USA)
| | - Mehrdad Kashefi
- Department of Physiology and Pharmacology, Western University (London, ON, Canada)
| | - Tomomichi Oya
- Department of Physiology and Pharmacology, Western University (London, ON, Canada)
| | - Rhonda Kersten
- Department of Physiology and Pharmacology, Western University (London, ON, Canada)
| | - Alice C Mosberger
- Zuckerman Mind Brain Behavior Institute at Columbia University (New York, NY, USA)
| | - Sean O'Connell
- Graduate Program in Biomedical Engineering at Emory University and Georgia Tech (Atlanta, GA, USA)
| | - Runming Wang
- Department of Biomedical Engineering at Emory University and Georgia Tech (Atlanta, GA, USA)
| | - Hugo Marques
- Champalimaud Neuroscience Programme, Champalimaud Foundation (Lisbon, Portugal)
| | - Ana Rita Mendes
- Champalimaud Neuroscience Programme, Champalimaud Foundation (Lisbon, Portugal)
| | - Constanze Lenschow
- Champalimaud Neuroscience Programme, Champalimaud Foundation (Lisbon, Portugal)
- current address: Institute of Biology, Otto-von-Guericke University, (Magdeburg, Germany)
| | | | - Jeong Jun Kim
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - William Olson
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - Kiara N Quinn
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - Pierce Perkins
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - Graziana Gatto
- Salk Institute for Biological Studies (La Jolla, CA, USA)
- current address: Department of Neurology, University Hospital of Cologne (Cologne, Germany)
| | | | - Susan Coltman
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus (Aurora, CO, USA)
| | - Taegyo Kim
- Department of Neurobiology & Anatomy, Drexel University, College of Medicine (Philadelphia, PA, USA)
| | - Trevor Smith
- Department of Neurobiology & Anatomy, Drexel University, College of Medicine (Philadelphia, PA, USA)
| | - Ben Binder-Markey
- Department of Physical Therapy and Rehabilitation Sciences, Drexel University College of Nursing and Health Professions (Philadelphia, PA)
| | - Martin Zaback
- Department of Health and Rehabilitation Sciences, Temple University (Philadelphia, PA, USA)
| | - Christopher K Thompson
- Department of Health and Rehabilitation Sciences, Temple University (Philadelphia, PA, USA)
| | - Simon Giszter
- Department of Neurobiology & Anatomy, Drexel University, College of Medicine (Philadelphia, PA, USA)
| | - Abigail Person
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus (Aurora, CO, USA)
| | | | - Eiman Azim
- Salk Institute for Biological Studies (La Jolla, CA, USA)
| | - Nitish Thakor
- Departments of Biomedical Engineering and Neurology, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - Daniel O'Connor
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins School of Medicine (Baltimore, MD, USA)
| | - Barry Trimmer
- Department of Biology, Tufts University (Medford, MA, USA)
| | - Susana Q Lima
- Champalimaud Neuroscience Programme, Champalimaud Foundation (Lisbon, Portugal)
| | - Megan R Carey
- Champalimaud Neuroscience Programme, Champalimaud Foundation (Lisbon, Portugal)
| | - Chethan Pandarinath
- Department of Biomedical Engineering at Emory University and Georgia Tech (Atlanta, GA, USA)
| | - Rui M Costa
- Zuckerman Mind Brain Behavior Institute at Columbia University (New York, NY, USA)
- Allen Institute (Seattle, WA, USA)
| | - J Andrew Pruszynski
- Department of Physiology and Pharmacology, Western University (London, ON, Canada)
| | - Muhannad Bakir
- School of Electrical and Computer Engineering, Georgia Institute of Technology (Atlanta, GA, USA)
| | - Samuel J Sober
- Department of Biology, Emory University (Atlanta, GA, USA)
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Ning Y, Wan G, Liu T, Zhang S. Volitional Generation of Reproducible, Efficient Temporal Patterns. Brain Sci 2022; 12:1269. [PMID: 36291203 PMCID: PMC9599309 DOI: 10.3390/brainsci12101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/26/2023] Open
Abstract
One of the extraordinary characteristics of the biological brain is the low energy expense it requires to implement a variety of biological functions and intelligence as compared to the modern artificial intelligence (AI). Spike-based energy-efficient temporal codes have long been suggested as a contributor for the brain to run on low energy expense. Despite this code having been largely reported in the sensory cortex, whether this code can be implemented in other brain areas to serve broader functions and how it evolves throughout learning have remained unaddressed. In this study, we designed a novel brain-machine interface (BMI) paradigm. Two macaques could volitionally generate reproducible energy-efficient temporal patterns in the primary motor cortex (M1) by learning the BMI paradigm. Moreover, most neurons that were not directly assigned to control the BMI did not boost their excitability, and they demonstrated an overall energy-efficient manner in performing the task. Over the course of learning, we found that the firing rates and temporal precision of selected neurons co-evolved to generate the energy-efficient temporal patterns, suggesting that a cohesive rather than dissociable processing underlies the refinement of energy-efficient temporal patterns.
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Affiliation(s)
- Yuxiao Ning
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou 310027, China
- Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Guihua Wan
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou 310027, China
| | - Tengjun Liu
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou 310027, China
- Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
| | - Shaomin Zhang
- Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou 310027, China
- Department of Biomedical Engineering, Zhejiang University, Hangzhou 310027, China
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang University, Hangzhou 310027, China
- Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou 310027, China
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