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Çatal Y, Keskin K, Wolman A, Klar P, Smith D, Northoff G. Flexibility of intrinsic neural timescales during distinct behavioral states. Commun Biol 2024; 7:1667. [PMID: 39702547 DOI: 10.1038/s42003-024-07349-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 12/02/2024] [Indexed: 12/21/2024] Open
Abstract
Recent neuroimaging studies demonstrate a heterogeneity of timescales prevalent in the brain's ongoing spontaneous activity, labeled intrinsic neural timescales (INT). At the same time, neural timescales also reflect stimulus- or task-related activity. The relationship of the INT during the brain's spontaneous activity with their involvement in task states including behavior remains unclear. To address this question, we combined calcium imaging data of spontaneously behaving mice and human electroencephalography (EEG) during rest and task states with computational modeling. We obtained four primary findings: (i) the distinct behavioral states can be accurately predicted from INT, (ii) INT become longer during behavioral states compared to rest, (iii) INT change from rest to task is correlated negatively with the variability of INT during rest, (iv) neural mass modeling shows a key role of recurrent connections in mediating the rest-task change of INT. Extending current findings, our results show the dynamic nature of the brain's INT in reflecting continuous behavior through their flexible rest-task modulation possibly mediated by recurrent connections.
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Affiliation(s)
- Yasir Çatal
- Mind, Brain Imaging and Neuroethics Research Unit, University of Ottawa, Ontario, ON, Canada.
- University of Ottawa Institute of Mental Health Research, Ottawa, ON, Canada.
| | - Kaan Keskin
- University of Ottawa Institute of Mental Health Research, Ottawa, ON, Canada
- Department of Psychiatry, Ege University, Izmir, Turkey
- SoCAT Lab, Ege University, Izmir, Turkey
| | - Angelika Wolman
- Mind, Brain Imaging and Neuroethics Research Unit, University of Ottawa, Ontario, ON, Canada
- University of Ottawa Institute of Mental Health Research, Ottawa, ON, Canada
| | - Philipp Klar
- Faculty of Mathematics and Natural Sciences, Institute of Experimental Psychology, Heinrich Heine University of Düsseldorf, Düsseldorf, Germany
- Institute of Neuroscience and Medicine, Brain & Behaviour (INM-7), Research Centre Jülich, Jülich, Germany
| | - David Smith
- University of Ottawa Institute of Mental Health Research, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Georg Northoff
- Mind, Brain Imaging and Neuroethics Research Unit, University of Ottawa, Ontario, ON, Canada
- University of Ottawa Institute of Mental Health Research, Ottawa, ON, Canada
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2
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Pavuluri A, Kohn A. The representational geometry for naturalistic textures in macaque V1 and V2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.18.619102. [PMID: 39484570 PMCID: PMC11526966 DOI: 10.1101/2024.10.18.619102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Our understanding of visual cortical processing has relied primarily on studying the selectivity of individual neurons in different areas. A complementary approach is to study how the representational geometry of neuronal populations differs across areas. Though the geometry is derived from individual neuronal selectivity, it can reveal encoding strategies difficult to infer from single neuron responses. In addition, recent theoretical work has begun to relate distinct functional objectives to different representational geometries. To understand how the representational geometry changes across stages of processing, we measured neuronal population responses in primary visual cortex (V1) and area V2 of macaque monkeys to an ensemble of synthetic, naturalistic textures. Responses were lower dimensional in V2 than V1, and there was a better alignment of V2 population responses to different textures. The representational geometry in V2 afforded better discriminability between out-of-sample textures. We performed complementary analyses of standard convolutional network models, which did not replicate the representational geometry of cortex. We conclude that there is a shift in the representational geometry between V1 and V2, with the V2 representation exhibiting features of a low-dimensional, systematic encoding of different textures and of different instantiations of each texture. Our results suggest that comparisons of representational geometry can reveal important transformations that occur across successive stages of visual processing.
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3
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Srinath R, Ni AM, Marucci C, Cohen MR, Brainard DH. Orthogonal neural representations support perceptual judgements of natural stimuli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580134. [PMID: 38464018 PMCID: PMC10925131 DOI: 10.1101/2024.02.14.580134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
In natural behavior, observers must separate relevant information from a barrage of irrelevant information. Many studies have investigated the neural underpinnings of this ability using artificial stimuli presented on simple backgrounds. Natural viewing, however, carries a set of challenges that are inaccessible using artificial stimuli, including neural responses to background objects that are task-irrelevant. An emerging body of evidence suggests that the visual abilities of humans and animals can be modeled through the linear decoding of task-relevant information from visual cortex. This idea suggests the hypothesis that irrelevant features of a natural scene should impair performance on a visual task only if their neural representations intrude on the linear readout of the task relevant feature, as would occur if the representations of task-relevant and irrelevant features are not orthogonal in the underlying neural population. We tested this hypothesis using human psychophysics and monkey neurophysiology, in response to parametrically variable naturalistic stimuli. We demonstrate that 1) the neural representation of one feature (the position of a central object) in visual area V4 is orthogonal to those of several background features, 2) the ability of human observers to precisely judge object position was largely unaffected by task-irrelevant variation in those background features, and 3) many features of the object and the background are orthogonally represented by V4 neural responses. Our observations are consistent with the hypothesis that orthogonal neural representations can support stable perception of objects and features despite the tremendous richness of natural visual scenes.
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Affiliation(s)
- Ramanujan Srinath
- equal contribution
- Department of Neurobiology and Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Amy M. Ni
- equal contribution
- Department of Neurobiology and Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Claire Marucci
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marlene R. Cohen
- Department of Neurobiology and Neuroscience Institute, The University of Chicago, Chicago, IL 60637, USA
- equal contribution
| | - David H. Brainard
- Department of Psychology, University of Pennsylvania, Philadelphia, PA 19104, USA
- equal contribution
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4
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Heusser MR, Jagadisan UK, Gandhi NJ. Drifting population dynamics with transient resets characterize sensorimotor transformation in the monkey superior colliculus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.03.522634. [PMID: 36711849 PMCID: PMC9881850 DOI: 10.1101/2023.01.03.522634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
To produce goal-directed eye movements known as saccades, we must channel sensory input from our environment through a process known as sensorimotor transformation. The behavioral output of this phenomenon (an accurate eye movement) is straightforward, but the coordinated activity of neurons underlying its dynamics is not well understood. We searched for a neural correlate of sensorimotor transformation in the activity patterns of simultaneously recorded neurons in the superior colliculus (SC) of three male rhesus monkeys performing a visually guided, delayed saccade task. Neurons in the intermediate layers produce a burst of spikes both following the appearance of a visual (sensory) stimulus and preceding an eye movement command, but many also exhibit a sustained activity level during the intervening time ("delay period"). This sustained activity could be representative of visual processing or motor preparation, along with countless cognitive processes. Using a novel measure we call the Visuomotor Proximity Index (VMPI), we pitted visual and motor signals against each other by measuring the degree to which each session's population activity (as summarized in a low-dimensional framework) could be considered more visual-like or more motor-like. The analysis highlighted two salient features of sensorimotor transformation. One, population activity on average drifted systematically toward a motor-like representation and intermittently reverted to a visual-like representation following a microsaccade. Two, activity patterns that drift to a stronger motor-like representation by the end of the delay period may enable a more rapid initiation of a saccade, substantiating the idea that this movement initiation mechanism is conserved across motor systems.
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Affiliation(s)
- Michelle R Heusser
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Uday K Jagadisan
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Neeraj J Gandhi
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
- Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
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5
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Affiliation(s)
- Max Dabagia
- School of Computer Science, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konrad P Kording
- Department of Biomedical Engineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Eva L Dyer
- Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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6
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Salners T, Avila KE, Nicholson B, Myers CR, Beggs J, Dahmen KA. Recurrent activity in neuronal avalanches. Sci Rep 2023; 13:4871. [PMID: 36964158 PMCID: PMC10039060 DOI: 10.1038/s41598-023-31851-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/17/2023] [Indexed: 03/26/2023] Open
Abstract
A new statistical analysis of large neuronal avalanches observed in mouse and rat brain tissues reveals a substantial degree of recurrent activity and cyclic patterns of activation not seen in smaller avalanches. To explain these observations, we adapted a model of structural weakening in materials. In this model, dynamical weakening of neuron firing thresholds closely replicates experimental avalanche size distributions, firing number distributions, and patterns of cyclic activity. This agreement between model and data suggests that a mechanism like dynamical weakening plays a key role in recurrent activity found in large neuronal avalanches. We expect these results to illuminate the causes and dynamics of large avalanches, like those seen in seizures.
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Affiliation(s)
- Tyler Salners
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA.
| | - Karina E Avila
- Physics Department, University Kaiserslautern, Erwin-Schrödinger-Straße, 67663, Kaiserslautern, Germany
| | - Benjamin Nicholson
- Laboratory of Atomic and Solid State Physics, Clark Hall, Cornell University, Ithaca, NY, 14853-2501, USA
| | - Christopher R Myers
- Laboratory of Atomic and Solid State Physics, Clark Hall, Cornell University, Ithaca, NY, 14853-2501, USA
- Center for Advanced Computing, Cornell University, Ithaca, NY, 14853, USA
| | - John Beggs
- Department of Physics, Indiana University, Bloomington, IN, 47405, USA
| | - Karin A Dahmen
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, USA
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7
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Avitan L, Stringer C. Not so spontaneous: Multi-dimensional representations of behaviors and context in sensory areas. Neuron 2022; 110:3064-3075. [PMID: 35863344 DOI: 10.1016/j.neuron.2022.06.019] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Sensory areas are spontaneously active in the absence of sensory stimuli. This spontaneous activity has long been studied; however, its functional role remains largely unknown. Recent advances in technology, allowing large-scale neural recordings in the awake and behaving animal, have transformed our understanding of spontaneous activity. Studies using these recordings have discovered high-dimensional spontaneous activity patterns, correlation between spontaneous activity and behavior, and dissimilarity between spontaneous and sensory-driven activity patterns. These findings are supported by evidence from developing animals, where a transition toward these characteristics is observed as the circuit matures, as well as by evidence from mature animals across species. These newly revealed characteristics call for the formulation of a new role for spontaneous activity in neural sensory computation.
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Affiliation(s)
- Lilach Avitan
- Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel.
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8
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Dimensionality of the intermediate-level representation of shape and texture in monkey V4. Neural Netw 2022; 153:444-449. [DOI: 10.1016/j.neunet.2022.06.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 04/26/2022] [Accepted: 06/22/2022] [Indexed: 11/19/2022]
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9
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Yu Y, Stirman JN, Dorsett CR, Smith SL. Selective representations of texture and motion in mouse higher visual areas. Curr Biol 2022; 32:2810-2820.e5. [PMID: 35609609 DOI: 10.1016/j.cub.2022.04.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/22/2022] [Accepted: 04/28/2022] [Indexed: 10/18/2022]
Abstract
The mouse visual cortex contains interconnected higher visual areas, but their functional specializations are unclear. Here, we used a data-driven approach to examine the representations of complex visual stimuli by L2/3 neurons across mouse higher visual areas, measured using large-field-of-view two-photon calcium imaging. Using specialized stimuli, we found higher fidelity representations of texture in area LM, compared to area AL. Complementarily, we found higher fidelity representations of motion in area AL, compared to area LM. We also observed this segregation of information in response to naturalistic videos. Finally, we explored how receptive field models of visual cortical neurons could produce the segregated representations of texture and motion we observed. These selective representations could aid in behaviors such as visually guided navigation.
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Affiliation(s)
- Yiyi Yu
- Department of Electrical & Computer Engineering, Center for BioEngineering, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Jeffrey N Stirman
- Neuroscience Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christopher R Dorsett
- Neuroscience Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Spencer L Smith
- Department of Electrical & Computer Engineering, Center for BioEngineering, Neuroscience Research Institute, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
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11
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Srinath R, Ruff DA, Cohen MR. Attention improves information flow between neuronal populations without changing the communication subspace. Curr Biol 2021; 31:5299-5313.e4. [PMID: 34699782 PMCID: PMC8665027 DOI: 10.1016/j.cub.2021.09.076] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/22/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
Visual attention allows observers to change the influence of different parts of a visual scene on their behavior, suggesting that information can be flexibly shared between visual cortex and neurons involved in decision making. We investigated the neural substrate of flexible information routing by analyzing the activity of populations of visual neurons in the medial temporal area (MT) and oculo-motor neurons in the superior colliculus (SC) while rhesus monkeys switched spatial attention. We demonstrated that attention increases the efficacy of visuomotor communication: trial-to-trial variability in SC population activity could be better predicted by the activity of the MT population (and vice versa) when attention was directed toward their joint receptive fields. Surprisingly, this improvement in prediction was not explained by changes in the dimensionality of the shared subspace or in the magnitude of local or shared pairwise noise correlations. These results lay a foundation for future theoretical and experimental studies into how visual attention can flexibly change information flow between sensory and decision neurons.
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Affiliation(s)
- Ramanujan Srinath
- Department of Neuroscience and Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Douglas A Ruff
- Department of Neuroscience and Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marlene R Cohen
- Department of Neuroscience and Center for the Neural Basis of Cognition, University of Pittsburgh, Pittsburgh, PA, USA
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12
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Sokoloski S, Aschner A, Coen-Cagli R. Modelling the neural code in large populations of correlated neurons. eLife 2021; 10:64615. [PMID: 34608865 PMCID: PMC8577837 DOI: 10.7554/elife.64615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 10/01/2021] [Indexed: 01/02/2023] Open
Abstract
Neurons respond selectively to stimuli, and thereby define a code that associates stimuli with population response patterns. Certain correlations within population responses (noise correlations) significantly impact the information content of the code, especially in large populations. Understanding the neural code thus necessitates response models that quantify the coding properties of modelled populations, while fitting large-scale neural recordings and capturing noise correlations. In this paper, we propose a class of response model based on mixture models and exponential families. We show how to fit our models with expectation-maximization, and that they capture diverse variability and covariability in recordings of macaque primary visual cortex. We also show how they facilitate accurate Bayesian decoding, provide a closed-form expression for the Fisher information, and are compatible with theories of probabilistic population coding. Our framework could allow researchers to quantitatively validate the predictions of neural coding theories against both large-scale neural recordings and cognitive performance.
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Affiliation(s)
- Sacha Sokoloski
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, United States.,Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Amir Aschner
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States
| | - Ruben Coen-Cagli
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, United States.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, United States
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13
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Umakantha A, Morina R, Cowley BR, Snyder AC, Smith MA, Yu BM. Bridging neuronal correlations and dimensionality reduction. Neuron 2021; 109:2740-2754.e12. [PMID: 34293295 PMCID: PMC8505167 DOI: 10.1016/j.neuron.2021.06.028] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 05/05/2021] [Accepted: 06/25/2021] [Indexed: 01/01/2023]
Abstract
Two commonly used approaches to study interactions among neurons are spike count correlation, which describes pairs of neurons, and dimensionality reduction, applied to a population of neurons. Although both approaches have been used to study trial-to-trial neuronal variability correlated among neurons, they are often used in isolation and have not been directly related. We first established concrete mathematical and empirical relationships between pairwise correlation and metrics of population-wide covariability based on dimensionality reduction. Applying these insights to macaque V4 population recordings, we found that the previously reported decrease in mean pairwise correlation associated with attention stemmed from three distinct changes in population-wide covariability. Overall, our work builds the intuition and formalism to bridge between pairwise correlation and population-wide covariability and presents a cautionary tale about the inferences one can make about population activity by using a single statistic, whether it be mean pairwise correlation or dimensionality.
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Affiliation(s)
- Akash Umakantha
- Carnegie Mellon Neuroscience Institute, Pittsburgh, PA 15213, USA; Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Rudina Morina
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Benjamin R Cowley
- Machine Learning Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA
| | - Adam C Snyder
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Brain and Cognitive Sciences, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, University of Rochester, Rochester, NY 14642, USA; Center for Visual Science, University of Rochester, Rochester, NY 14642, USA
| | - Matthew A Smith
- Carnegie Mellon Neuroscience Institute, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
| | - Byron M Yu
- Carnegie Mellon Neuroscience Institute, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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14
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Ruff DA, Xue C, Kramer LE, Baqai F, Cohen MR. Low rank mechanisms underlying flexible visual representations. Proc Natl Acad Sci U S A 2020; 117:29321-29329. [PMID: 33229536 PMCID: PMC7703603 DOI: 10.1073/pnas.2005797117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuronal population responses to sensory stimuli are remarkably flexible. The responses of neurons in visual cortex have heterogeneous dependence on stimulus properties (e.g., contrast), processes that affect all stages of visual processing (e.g., adaptation), and cognitive processes (e.g., attention or task switching). Understanding whether these processes affect similar neuronal populations and whether they have similar effects on entire populations can provide insight into whether they utilize analogous mechanisms. In particular, it has recently been demonstrated that attention has low rank effects on the covariability of populations of visual neurons, which impacts perception and strongly constrains mechanistic models. We hypothesized that measuring changes in population covariability associated with other sensory and cognitive processes could clarify whether they utilize similar mechanisms or computations. Our experimental design included measurements in multiple visual areas using four distinct sensory and cognitive processes. We found that contrast, adaptation, attention, and task switching affect the variability of responses of populations of neurons in primate visual cortex in a similarly low rank way. These results suggest that a given circuit may use similar mechanisms to perform many forms of modulation and likely reflects a general principle that applies to a wide range of brain areas and sensory, cognitive, and motor processes.
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Affiliation(s)
- Douglas A Ruff
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260
| | - Cheng Xue
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260
| | - Lily E Kramer
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260
| | - Faisal Baqai
- Program in Neural Computation, Carnegie Mellon University, Pittsburgh, PA 15260
| | - Marlene R Cohen
- Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA 15260;
- Program in Neural Computation, Carnegie Mellon University, Pittsburgh, PA 15260
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Cowley BR, Snyder AC, Acar K, Williamson RC, Yu BM, Smith MA. Slow Drift of Neural Activity as a Signature of Impulsivity in Macaque Visual and Prefrontal Cortex. Neuron 2020; 108:551-567.e8. [PMID: 32810433 PMCID: PMC7822647 DOI: 10.1016/j.neuron.2020.07.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/15/2020] [Accepted: 07/17/2020] [Indexed: 12/22/2022]
Abstract
An animal's decision depends not only on incoming sensory evidence but also on its fluctuating internal state. This state embodies multiple cognitive factors, such as arousal and fatigue, but it is unclear how these factors influence the neural processes that encode sensory stimuli and form a decision. We discovered that, unprompted by task conditions, animals slowly shifted their likelihood of detecting stimulus changes over the timescale of tens of minutes. Neural population activity from visual area V4, as well as from prefrontal cortex, slowly drifted together with these behavioral fluctuations. We found that this slow drift, rather than altering the encoding of the sensory stimulus, acted as an impulsivity signal, overriding sensory evidence to dictate the final decision. Overall, this work uncovers an internal state embedded in population activity across multiple brain areas and sheds further light on how internal states contribute to the decision-making process.
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Affiliation(s)
- Benjamin R Cowley
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA; Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Adam C Snyder
- Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Brain and Cognitive Sciences, University of Rochester, Rochester, NY 14642, USA; Department of Neuroscience, University of Rochester, Rochester, NY 14642, USA; Center for Visual Science, University of Rochester, Rochester, NY 14642, USA
| | - Katerina Acar
- Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Center for Neuroscience, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ryan C Williamson
- Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA 15213, USA; University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Byron M Yu
- Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Matthew A Smith
- Center for the Neural Basis of Cognition, Pittsburgh, PA 15213, USA; Neuroscience Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA; Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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16
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Jin C, Chen W, Cao Y, Xu Z, Tan Z, Zhang X, Deng L, Zheng C, Zhou J, Shi H, Feng J. Development and evaluation of an artificial intelligence system for COVID-19 diagnosis. Nat Commun 2020; 11:5088. [PMID: 33037212 DOI: 10.1101/823377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 05/22/2023] Open
Abstract
Early detection of COVID-19 based on chest CT enables timely treatment of patients and helps control the spread of the disease. We proposed an artificial intelligence (AI) system for rapid COVID-19 detection and performed extensive statistical analysis of CTs of COVID-19 based on the AI system. We developed and evaluated our system on a large dataset with more than 10 thousand CT volumes from COVID-19, influenza-A/B, non-viral community acquired pneumonia (CAP) and non-pneumonia subjects. In such a difficult multi-class diagnosis task, our deep convolutional neural network-based system is able to achieve an area under the receiver operating characteristic curve (AUC) of 97.81% for multi-way classification on test cohort of 3,199 scans, AUC of 92.99% and 93.25% on two publicly available datasets, CC-CCII and MosMedData respectively. In a reader study involving five radiologists, the AI system outperforms all of radiologists in more challenging tasks at a speed of two orders of magnitude above them. Diagnosis performance of chest x-ray (CXR) is compared to that of CT. Detailed interpretation of deep network is also performed to relate system outputs with CT presentations. The code is available at https://github.com/ChenWWWeixiang/diagnosis_covid19 .
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Affiliation(s)
- Cheng Jin
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Weixiang Chen
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Yukun Cao
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Zhanwei Xu
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Zimeng Tan
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Xin Zhang
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Lei Deng
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Chuansheng Zheng
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China
| | - Jie Zhou
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China
| | - Heshui Shi
- Department of Radiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Hubei Province Key Laboratory of Molecular Imaging, Wuhan, China.
| | - Jianjiang Feng
- Department of Automation, Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
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17
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Kohn A, Jasper AI, Semedo JD, Gokcen E, Machens CK, Yu BM. Principles of Corticocortical Communication: Proposed Schemes and Design Considerations. Trends Neurosci 2020; 43:725-737. [PMID: 32771224 PMCID: PMC7484382 DOI: 10.1016/j.tins.2020.07.001] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 07/01/2020] [Accepted: 07/05/2020] [Indexed: 12/22/2022]
Abstract
Nearly all brain functions involve routing neural activity among a distributed network of areas. Understanding this routing requires more than a description of interareal anatomical connectivity: it requires understanding what controls the flow of signals through interareal circuitry and how this communication might be modulated to allow flexible behavior. Here we review proposals of how communication, particularly between visual cortical areas, is instantiated and modulated, highlighting recent work that offers new perspectives. We suggest transitioning from a focus on assessing changes in the strength of interareal interactions, as often seen in studies of interareal communication, to a broader consideration of how different signaling schemes might contribute to computation. To this end, we discuss a set of features that might be desirable for a communication scheme.
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Affiliation(s)
- Adam Kohn
- Dominik Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, NY, USA; Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, NY, USA.
| | - Anna I Jasper
- Dominik Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, NY, USA
| | - João D Semedo
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Evren Gokcen
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Christian K Machens
- Champalimaud Research, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Byron M Yu
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA
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18
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Bartolo R, Saunders RC, Mitz AR, Averbeck BB. Dimensionality, information and learning in prefrontal cortex. PLoS Comput Biol 2020; 16:e1007514. [PMID: 32330126 PMCID: PMC7202668 DOI: 10.1371/journal.pcbi.1007514] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 05/06/2020] [Accepted: 03/11/2020] [Indexed: 01/12/2023] Open
Abstract
Learning leads to changes in population patterns of neural activity. In this study we wanted to examine how these changes in patterns of activity affect the dimensionality of neural responses and information about choices. We addressed these questions by carrying out high channel count recordings in dorsal-lateral prefrontal cortex (dlPFC; 768 electrodes) while monkeys performed a two-armed bandit reinforcement learning task. The high channel count recordings allowed us to study population coding while monkeys learned choices between actions or objects. We found that the dimensionality of neural population activity was higher across blocks in which animals learned the values of novel pairs of objects, than across blocks in which they learned the values of actions. The increase in dimensionality with learning in object blocks was related to less shared information across blocks, and therefore patterns of neural activity that were less similar, when compared to learning in action blocks. Furthermore, these differences emerged with learning, and were not a simple function of the choice of a visual image or action. Therefore, learning the values of novel objects increases the dimensionality of neural representations in dlPFC. In this study we found that learning to choose rewarding objects increased the diversity of patterns of activity, measured as the dimensionality of the response, observed in dorsal-lateral prefrontal cortex. The dimensionality increase for learning to choose rewarding objects was larger than the dimensionality increase for learning to choose rewarding actions. The dimensionality increase was not a simple function of the diverse set of images used, as the patterns of activity only appeared after learning.
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Affiliation(s)
- Ramon Bartolo
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Richard C. Saunders
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew R. Mitz
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Bruno B. Averbeck
- Laboratory of Neuropsychology, National Institute of Mental Health, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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19
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Stabilization of a brain-computer interface via the alignment of low-dimensional spaces of neural activity. Nat Biomed Eng 2020; 4:672-685. [PMID: 32313100 DOI: 10.1038/s41551-020-0542-9] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 02/21/2020] [Indexed: 12/31/2022]
Abstract
The instability of neural recordings can render clinical brain-computer interfaces (BCIs) uncontrollable. Here, we show that the alignment of low-dimensional neural manifolds (low-dimensional spaces that describe specific correlation patterns between neurons) can be used to stabilize neural activity, thereby maintaining BCI performance in the presence of recording instabilities. We evaluated the stabilizer with non-human primates during online cursor control via intracortical BCIs in the presence of severe and abrupt recording instabilities. The stabilized BCIs recovered proficient control under different instability conditions and across multiple days. The stabilizer does not require knowledge of user intent and can outperform supervised recalibration. It stabilized BCIs even when neural activity contained little information about the direction of cursor movement. The stabilizer may be applicable to other neural interfaces and may improve the clinical viability of BCIs.
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20
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Whiteway MR, Butts DA. The quest for interpretable models of neural population activity. Curr Opin Neurobiol 2019; 58:86-93. [PMID: 31426024 DOI: 10.1016/j.conb.2019.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 07/14/2019] [Indexed: 11/24/2022]
Abstract
Many aspects of brain function arise from the coordinated activity of large populations of neurons. Recent developments in neural recording technologies are providing unprecedented access to the activity of such populations during increasingly complex experimental contexts; however, extracting scientific insights from such recordings requires the concurrent development of analytical tools that relate this population activity to system-level function. This is a primary motivation for latent variable models, which seek to provide a low-dimensional description of population activity that can be related to experimentally controlled variables, as well as uncontrolled variables such as internal states (e.g. attention and arousal) and elements of behavior. While deriving an understanding of function from traditional latent variable methods relies on low-dimensional visualizations, new approaches are targeting more interpretable descriptions of the components underlying system-level function.
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Affiliation(s)
- Matthew R Whiteway
- Zuckerman Mind Brain Behavior Institute, Jerome L Greene Science Center, Columbia University, 3227 Broadway, 5th Floor, Quad D, New York, NY 10027, USA
| | - Daniel A Butts
- Department of Biology and Program in Neuroscience and Cognitive Science, University of Maryland, 1210 Biology-Psychology Bldg. #144, College Park, MD 20742, USA.
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21
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Stringer C, Pachitariu M, Steinmetz N, Carandini M, Harris KD. High-dimensional geometry of population responses in visual cortex. Nature 2019; 571:361-365. [PMID: 31243367 PMCID: PMC6642054 DOI: 10.1038/s41586-019-1346-5] [Citation(s) in RCA: 279] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 05/29/2019] [Indexed: 01/13/2023]
Abstract
A neuronal population encodes information most efficiently when its stimulus responses are high-dimensional and uncorrelated, and most robustly when they are lower-dimensional and correlated. Here we analysed the dimensionality of the encoding of natural images by large populations of neurons in the visual cortex of awake mice. The evoked population activity was high-dimensional, and correlations obeyed an unexpected power law: the nth principal component variance scaled as 1/n. This scaling was not inherited from the power law spectrum of natural images, because it persisted after stimulus whitening. We proved mathematically that if the variance spectrum was to decay more slowly then the population code could not be smooth, allowing small changes in input to dominate population activity. The theory also predicts larger power-law exponents for lower-dimensional stimulus ensembles, which we validated experimentally. These results suggest that coding smoothness may represent a fundamental constraint that determines correlations in neural population codes.
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Affiliation(s)
- Carsen Stringer
- HHMI Janelia Research Campus, Ashburn, VA, USA.
- UCL Gatsby Computational Neuroscience Unit, University College London, London, UK.
| | - Marius Pachitariu
- HHMI Janelia Research Campus, Ashburn, VA, USA.
- UCL Institute of Neurology, University College London, London, UK.
| | - Nicholas Steinmetz
- UCL Institute of Neurology, University College London, London, UK
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Kenneth D Harris
- UCL Institute of Neurology, University College London, London, UK.
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22
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Tripp B. Approximating the Architecture of Visual Cortex in a Convolutional Network. Neural Comput 2019; 31:1551-1591. [PMID: 31260392 DOI: 10.1162/neco_a_01211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Deep convolutional neural networks (CNNs) have certain structural, mechanistic, representational, and functional parallels with primate visual cortex and also many differences. However, perhaps some of the differences can be reconciled. This study develops a cortex-like CNN architecture, via (1) a loss function that quantifies the consistency of a CNN architecture with neural data from tract tracing, cell reconstruction, and electrophysiology studies; (2) a hyperparameter-optimization approach for reducing this loss, and (3) heuristics for organizing units into convolutional-layer grids. The optimized hyperparameters are consistent with neural data. The cortex-like architecture differs from typical CNN architectures. In particular, it has longer skip connections, larger kernels and strides, and qualitatively different connection sparsity. Importantly, layers of the cortex-like network have one-to-one correspondences with cortical neuron populations. This should allow unambiguous comparison of model and brain representations in the future and, consequently, more precise measurement of progress toward more biologically realistic deep networks.
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Affiliation(s)
- Bryan Tripp
- Department of Systems Design Engineering and Centre for Theoretical Neuroscience, University of Waterloo, Waterloo, ON N2L 3G1
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23
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Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O'Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV. Accurate Estimation of Neural Population Dynamics without Spike Sorting. Neuron 2019; 103:292-308.e4. [PMID: 31171448 DOI: 10.1016/j.neuron.2019.05.003] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 02/06/2019] [Accepted: 04/30/2019] [Indexed: 11/25/2022]
Abstract
A central goal of systems neuroscience is to relate an organism's neural activity to behavior. Neural population analyses often reduce the data dimensionality to focus on relevant activity patterns. A major hurdle to data analysis is spike sorting, and this problem is growing as the number of recorded neurons increases. Here, we investigate whether spike sorting is necessary to estimate neural population dynamics. The theory of random projections suggests that we can accurately estimate the geometry of low-dimensional manifolds from a small number of linear projections of the data. We recorded data using Neuropixels probes in motor cortex of nonhuman primates and reanalyzed data from three previous studies and found that neural dynamics and scientific conclusions are quite similar using multiunit threshold crossings rather than sorted neurons. This finding unlocks existing data for new analyses and informs the design and use of new electrode arrays for laboratory and clinical use.
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Affiliation(s)
- Eric M Trautmann
- Neurosciences Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Sergey D Stavisky
- Neurosciences Program, Stanford University, Stanford, CA, USA; Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Subhaneil Lahiri
- Department of Applied Physics, Stanford University, Stanford, CA, USA
| | - Katherine C Ames
- Neurosciences Program, Stanford University, Stanford, CA, USA; Department of Neuroscience, Columbia University, New York, NY, USA
| | - Matthew T Kaufman
- Neurosciences Program, Stanford University, Stanford, CA, USA; Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Daniel J O'Shea
- Neurosciences Program, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Saurabh Vyas
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Xulu Sun
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Stephen I Ryu
- Palo Alto Medical Foundation, Palo Alto, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Surya Ganguli
- Department of Applied Physics, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Department of Neurobiology, Stanford University, Stanford, CA, USA; Stanford Neurosciences Institute, Stanford, CA, USA; Bio-X Program, Stanford University, Stanford, CA, USA
| | - Krishna V Shenoy
- Neurosciences Program, Stanford University, Stanford, CA, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Department of Neurobiology, Stanford University, Stanford, CA, USA; Stanford Neurosciences Institute, Stanford, CA, USA; Bio-X Program, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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24
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Beyeler M, Rounds EL, Carlson KD, Dutt N, Krichmar JL. Neural correlates of sparse coding and dimensionality reduction. PLoS Comput Biol 2019; 15:e1006908. [PMID: 31246948 PMCID: PMC6597036 DOI: 10.1371/journal.pcbi.1006908] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Supported by recent computational studies, there is increasing evidence that a wide range of neuronal responses can be understood as an emergent property of nonnegative sparse coding (NSC), an efficient population coding scheme based on dimensionality reduction and sparsity constraints. We review evidence that NSC might be employed by sensory areas to efficiently encode external stimulus spaces, by some associative areas to conjunctively represent multiple behaviorally relevant variables, and possibly by the basal ganglia to coordinate movement. In addition, NSC might provide a useful theoretical framework under which to understand the often complex and nonintuitive response properties of neurons in other brain areas. Although NSC might not apply to all brain areas (for example, motor or executive function areas) the success of NSC-based models, especially in sensory areas, warrants further investigation for neural correlates in other regions.
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Affiliation(s)
- Michael Beyeler
- Department of Psychology, University of Washington, Seattle, Washington, United States of America
- Institute for Neuroengineering, University of Washington, Seattle, Washington, United States of America
- eScience Institute, University of Washington, Seattle, Washington, United States of America
- Department of Computer Science, University of California, Irvine, California, United States of America
| | - Emily L. Rounds
- Department of Cognitive Sciences, University of California, Irvine, California, United States of America
| | - Kristofor D. Carlson
- Department of Cognitive Sciences, University of California, Irvine, California, United States of America
- Sandia National Laboratories, Albuquerque, New Mexico, United States of America
| | - Nikil Dutt
- Department of Computer Science, University of California, Irvine, California, United States of America
- Department of Cognitive Sciences, University of California, Irvine, California, United States of America
| | - Jeffrey L. Krichmar
- Department of Computer Science, University of California, Irvine, California, United States of America
- Department of Cognitive Sciences, University of California, Irvine, California, United States of America
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25
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Abstract
The sense of touch affords a remarkable sensitivity to the microstructure of surfaces, affording us the ability to sense elements ranging in size from tens of nanometers to tens of millimeters. The hand sends signals about texture to the brain using three classes of nerve fibers through two neural codes: coarse features in spatial patterns of activation and fine features in precise temporal spiking patterns. In this study, we show that these nerve signals culminate in a complex, high-dimensional representation of texture in somatosensory cortex, whose structure can account for the structure of texture perception. This complexity arises from the neurons that act as idiosyncratic detectors of spatial and/or temporal motifs in the afferent input. In the somatosensory nerves, the tactile perception of texture is driven by spatial and temporal patterns of activation distributed across three populations of afferents. These disparate streams of information must then be integrated centrally to achieve a unified percept of texture. To investigate the representation of texture in somatosensory cortex, we scanned a wide range of natural textures across the fingertips of rhesus macaques and recorded the responses evoked in Brodmann’s areas 3b, 1, and 2. We found that texture identity is reliably encoded in the idiosyncratic responses of populations of cortical neurons, giving rise to a high-dimensional representation of texture. Cortical neurons fall along a continuum in their sensitivity to fine vs. coarse texture, and neurons at the extrema of this continuum seem to receive their major input from different afferent populations. Finally, we show that cortical responses can account for several aspects of texture perception in humans.
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26
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Williamson RC, Doiron B, Smith MA, Yu BM. Bridging large-scale neuronal recordings and large-scale network models using dimensionality reduction. Curr Opin Neurobiol 2019; 55:40-47. [PMID: 30677702 DOI: 10.1016/j.conb.2018.12.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 12/21/2022]
Abstract
A long-standing goal in neuroscience has been to bring together neuronal recordings and neural network modeling to understand brain function. Neuronal recordings can inform the development of network models, and network models can in turn provide predictions for subsequent experiments. Traditionally, neuronal recordings and network models have been related using single-neuron and pairwise spike train statistics. We review here recent studies that have begun to relate neuronal recordings and network models based on the multi-dimensional structure of neuronal population activity, as identified using dimensionality reduction. This approach has been used to study working memory, decision making, motor control, and more. Dimensionality reduction has provided common ground for incisive comparisons and tight interplay between neuronal recordings and network models.
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Affiliation(s)
- Ryan C Williamson
- Center for the Neural Basis of Cognition, Pittsburgh, PA, USA; Department of Machine Learning, Carnegie Mellon University, Pittsburgh, PA, USA; School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brent Doiron
- Center for the Neural Basis of Cognition, Pittsburgh, PA, USA; Department of Mathematics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew A Smith
- Center for the Neural Basis of Cognition, Pittsburgh, PA, USA; Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Byron M Yu
- Center for the Neural Basis of Cognition, Pittsburgh, PA, USA; Department of Electrical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Biomedical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA.
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27
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Kaplan HS, Nichols ALA, Zimmer M. Sensorimotor integration in Caenorhabditis elegans: a reappraisal towards dynamic and distributed computations. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170371. [PMID: 30201836 PMCID: PMC6158224 DOI: 10.1098/rstb.2017.0371] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/03/2022] Open
Abstract
The nematode Caenorhabditis elegans is a tractable model system to study locomotion, sensory navigation and decision-making. In its natural habitat, it is thought to navigate complex multisensory environments in order to find food and mating partners, while avoiding threats like predators or toxic environments. While research in past decades has shed much light on the functions and mechanisms of selected sensory neurons, we are just at the brink of understanding how sensory information is integrated by interneuron circuits for action selection in the worm. Recent technological advances have enabled whole-brain Ca2+ imaging and Ca2+ imaging of neuronal activity in freely moving worms. A common principle emerging across multiple studies is that most interneuron activities are tightly coupled to the worm's instantaneous behaviour; notably, these observations encompass neurons receiving direct sensory neuron inputs. The new findings suggest that in the C. elegans brain, sensory and motor representations are integrated already at the uppermost sensory processing layers. Moreover, these results challenge a perhaps more intuitive view of sequential feed-forward sensory pathways that converge onto premotor interneurons and motor neurons. We propose that sensorimotor integration occurs rather in a distributed dynamical fashion. In this perspective article, we will explore this view, discuss the challenges and implications of these discoveries on the interpretation and design of neural activity experiments, and discuss possible functions. Furthermore, we will discuss the broader context of similar findings in fruit flies and rodents, which suggest generalizable principles that can be learnt from this amenable nematode model organism.This article is part of a discussion meeting issue 'Connectome to behaviour: modelling C. elegans at cellular resolution'.
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Affiliation(s)
- Harris S Kaplan
- Research Institute of Molecular Pathology, Vienna Biocenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Annika L A Nichols
- Research Institute of Molecular Pathology, Vienna Biocenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Manuel Zimmer
- Research Institute of Molecular Pathology, Vienna Biocenter, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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28
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Adjusted regularization of cortical covariance. J Comput Neurosci 2018; 45:83-101. [PMID: 30191352 DOI: 10.1007/s10827-018-0692-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 07/13/2018] [Accepted: 07/30/2018] [Indexed: 12/31/2022]
Abstract
It is now common to record dozens to hundreds or more neurons simultaneously, and to ask how the network activity changes across experimental conditions. A natural framework for addressing questions of functional connectivity is to apply Gaussian graphical modeling to neural data, where each edge in the graph corresponds to a non-zero partial correlation between neurons. Because the number of possible edges is large, one strategy for estimating the graph has been to apply methods that aim to identify large sparse effects using an [Formula: see text] penalty. However, the partial correlations found in neural spike count data are neither large nor sparse, so techniques that perform well in sparse settings will typically perform poorly in the context of neural spike count data. Fortunately, the correlated firing for any pair of cortical neurons depends strongly on both their distance apart and the features for which they are tuned. We introduce a method that takes advantage of these known, strong effects by allowing the penalty to depend on them: thus, for example, the connection between pairs of neurons that are close together will be penalized less than pairs that are far apart. We show through simulations that this physiologically-motivated procedure performs substantially better than off-the-shelf generic tools, and we illustrate by applying the methodology to populations of neurons recorded with multielectrode arrays implanted in macaque visual cortex areas V1 and V4.
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29
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Frégnac Y. Big data and the industrialization of neuroscience: A safe roadmap for understanding the brain? Science 2018; 358:470-477. [PMID: 29074766 DOI: 10.1126/science.aan8866] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
New technologies in neuroscience generate reams of data at an exponentially increasing rate, spurring the design of very-large-scale data-mining initiatives. Several supranational ventures are contemplating the possibility of achieving, within the next decade(s), full simulation of the human brain.
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Affiliation(s)
- Yves Frégnac
- Unité de Neuroscience, Information et Complexité (UNIC-CNRS), Gif-sur-Yvette, France.
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30
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Gallego JA, Perich MG, Miller LE, Solla SA. Neural Manifolds for the Control of Movement. Neuron 2017; 94:978-984. [PMID: 28595054 DOI: 10.1016/j.neuron.2017.05.025] [Citation(s) in RCA: 327] [Impact Index Per Article: 40.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 05/11/2017] [Accepted: 05/18/2017] [Indexed: 10/19/2022]
Abstract
The analysis of neural dynamics in several brain cortices has consistently uncovered low-dimensional manifolds that capture a significant fraction of neural variability. These neural manifolds are spanned by specific patterns of correlated neural activity, the "neural modes." We discuss a model for neural control of movement in which the time-dependent activation of these neural modes is the generator of motor behavior. This manifold-based view of motor cortex may lead to a better understanding of how the brain controls movement.
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Affiliation(s)
- Juan A Gallego
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA; Neural and Cognitive Engineering Group, Centre for Robotics and Automation CSIC-UPM, Arganda del Rey 28500, Spain
| | - Matthew G Perich
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Lee E Miller
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA; Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA; Department of Physical Medicine and Rehabilitation, Northwestern University, Chicago, IL 60611, USA
| | - Sara A Solla
- Department of Physiology, Northwestern University, Chicago, IL 60611, USA; Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.
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31
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Jancke D. Catching the voltage gradient-asymmetric boost of cortical spread generates motion signals across visual cortex: a brief review with special thanks to Amiram Grinvald. NEUROPHOTONICS 2017; 4:031206. [PMID: 28217713 PMCID: PMC5301132 DOI: 10.1117/1.nph.4.3.031206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 01/12/2017] [Indexed: 06/06/2023]
Abstract
Wide-field voltage imaging is unique in its capability to capture snapshots of activity-across the full gradient of average changes in membrane potentials from subthreshold to suprathreshold levels-of hundreds of thousands of superficial cortical neurons that are simultaneously active. Here, I highlight two examples where voltage-sensitive dye imaging (VSDI) was exploited to track gradual space-time changes of activity within milliseconds across several millimeters of cortex at submillimeter resolution: the line-motion condition, measured in Amiram Grinvald's Laboratory more than 10 years ago and-coming full circle running VSDI in my laboratory-another motion-inducing condition, in which two neighboring stimuli counterchange luminance simultaneously. In both examples, cortical spread is asymmetrically boosted, creating suprathreshold activity drawn out over primary visual cortex. These rapidly propagating waves may integrate brain signals that encode motion independent of direction-selective circuits.
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Affiliation(s)
- Dirk Jancke
- Ruhr University Bochum, Optical Imaging Group, Institut für Neuroinformatik, Bochum, Germany
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