Dimensionality reduction for large-scale neural recordings

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Objective and efficient inference for couplings in neuronal network*

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A Simple Self-Decoding Model for Neural Coding

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Automated customization of large-scale spiking network models to neuronal population activity

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Reconstruction of in-vivo subthreshold activity of single neurons from large-scale spiking recordingsPreprint

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Conditional Finite Mixtures of Poisson Distributions for Context-Dependent Neural CorrelationsPreprint

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Demixed shared component analysis of neural population data from multiple brain areasPreprint

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Signatures of processing complexity during global cognitive states in ventromedial prefrontal cortexPreprint

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Neuronal Learning Analysis using Cycle-Consistent Adversarial NetworksPreprint

Li, B. M., Amvrosiadis, T., Rochefort, N. L., & Onken, A. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2111.13073 · Cited by 1

A graph-based approach to identify motor neuron synergiesPreprint

Avrillon, S., Hug, F., & Farina, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.07.527433

Neuroelectrophysiology-Compatible Electrolytic LesioningPreprint

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Somatic Calcium Signals from Layer II/III Motor Cortex for Continuous Neural DecodingPreprint

Wang, R., Han, J., Hu, X., You, H., & Zhang, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.04.11.536319 · Cited by 1

Directed networks and resting-state effective brain connectivity with state-space reconstruction using reservoir computing causalityPreprint

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Music's manifold emotions for mental well-being: a topological approachPreprint

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Insights in neuronal tuning: Navigating the statistical challenges of autocorrelation and missing variablesPreprint

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Reconfigurations of cortical manifold structure during reward-based motor learningPreprint

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Neuroelectrophysiology-Compatible Electrolytic LesioningPreprint

Bray, I. E., Clarke, S. E., Casey, K. M., & Nuyujukian, P. (2024) · eLife · doi:10.7554/elife.84385.2 · Cited by 1

Revealing unexpected complex encoding but simple decoding mechanisms in motor cortex via separating behaviorally relevant neural signalsPreprint

Li, Y., Zhu, X., Qi, Y., & Wang, Y. (2024) · eLife · doi:10.7554/elife.87881.3 · Cited by 1

Electrical diversity of neurons in sensory corticesPreprint

Calcini, N., Zeldenrust, F., & Celikel, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.07.617007 · Cited by 1

From spiking neuronal networks to interpretable dynamics: a diffusion-approximation frameworkPreprint

Mohammadi, N., Truccolo, W., Cash, S. S., Giraud, A., & Proix, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.12.17.628339 · Cited by 1

The Geometry and Dimensionality of Brain-wide ActivityPreprint

Wang, Z., Mai, W., Chai, Y., Qi, K., Ren, H., Shen, C., Zhang, S., Tan, G., Hu, Y., & Wen, Q. (2025) · eLife · doi:10.7554/elife.100666.1 · Cited by 1

The Geometry and Dimensionality of Brain-wide ActivityPreprint

Wang, Z., Mai, W., Chai, Y., Qi, K., Ren, H., Shen, C., Zhang, S., Tan, G., Hu, Y., & Wen, Q. (2025) · eLife · doi:10.7554/elife.100666.2 · Cited by 3

Human brain network control of creativityPreprint

Rabinovich, R. J., Cowan, R. L., Libowitz, M. R., Davis, T. S., Rahimpour, S., Beaty, R. E., Bartoli, E., Sheth, S. A., Smith, E. H., & Shofty, B. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.06.03.657648 · Cited by 1

Predictive variational autoencoder for learning robust representations of time-series dataPreprint

Wang, J. H., Tsin, D., & Engel, T. A. (2023) · PubMed · doi:10.48550/arxiv.2312.06932 · Cited by 1

Context-dependent low-dimensional neural dynamics unfold in distinct subspaces, dimensionality, and dynamical strength for natural walking and reachingPreprint

Ling, A. S., Silvernagel, M. P., Clarke, S. E., Jun, E. J., Abdulla, M. U., & Nuyujukian, P. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.19.695640 · Cited by 1

Anterior inferotemporal cortex represents decision formation and termination without rampsPreprint

Okazawa, G., & Kiani, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.24.696440 · Cited by 1

Neural Latching Switch Circuits for implementing Finite-State AutomataPreprint

Dubreuil, A. M., Leblois, A., & Monasson, R. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.27.696649 · Cited by 1

Non-saturating dimensionality, contextual dependence, and the limits of unsupervised decoding in motor cortexPreprint

Silvernagel, M. P., Tor, A., Jun, E. J., Clarke, S. E., Sutherland, R., Marshall, K., Wu, Y., Abdulla, M. U., Even-Chen, N., & Nuyujukian, P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.26.701668 · Cited by 1

SIMPL: Scalable and hassle-free optimisation of neural representations from behaviourPreprint

George, T. M., Glaser, P., Stachenfeld, K., Barry, C., & Clopath, C. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.11.11.623030 · Cited by 1

The hippocampus as a small-world cognitive mapPreprint

Kim, J. Z., Sethna, J. P., Cohen, I., & Sun, W. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.07.704615 · Cited by 1

Learning sculpts orthogonal task manifolds for continual skill learning in recurrent networksPreprint

Liu, Z., Kurth, A. C., Osako, Y., & Asabuki, T. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.02.15.705283 · Cited by 1

Neural signatures of impaired semantic contextualization in Autism Spectrum DisorderPreprint

Franch, M. C., Katlowitz, K. A., Mickiewicz, E. A., Belanger, J. L., Mathura, R. K., Zhu, H., Yan, X., Ismail, T., Chavez, A. G., Chericoni, A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.16.712048 · Cited by 1

Probabilistic Co-Control in Brain-Computer Interfaces: Uncertainty as a Control Signal in Brain-to-Text DecodingPreprint

Huang, J., Narasimha, S. M., Patel, A. N., Sristi, R. D., Mishne, G., & Gilja, V. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.02.715749 · Cited by 1

Distinct tasks engage a shared neural subspace in human hippocampus and anterior cingulate cortexPreprint

Lu, H., Chericoni, A., Franch, M. C., Katlowitz, K. A., Mickiewicz, E. A., Paulo, D. L., Watrous, A. J., Bartoli, E., Provenza, N. R., Sheth, S. A., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.04.24.720703 · Cited by 1

Coordinated Representational Drift Across the Mouse CortexPreprint

Kodandaramaiah, S. B., Peters, R., Hope, J., Feldkamp, M., Beckerle, T., Oladepo, I., Hryb, I., Saxena, K., & Redish, A. D. (2026) · Research Square · doi:10.21203/rs.3.rs-9933652/v1 · Cited by 1

Explorative Analysis and Data Mining in Big Neural Data

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Investigation of Methods for Assessing Sensorimotor Performance in Humans and Monkeys

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Prefrontal-thalamo-hippocampal circuit contributions to spatial working memory

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Modelling Low Dimensional Neural Activity

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Low-Rank Correlations in Heterogeneous Neural CircuitsPreprint

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Towards population coding principles in the primate premotor and parietal grasping network

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Characterizing and interpreting the influence of internal variables on sensory activityPreprint

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Inferring the brain's internal model from sensory responses in a

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Latent variable models for uncovering motor cortical ensemble dynamics

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The Viterbi process, decay-convexity and parallelized maximum a-posteriori estimation.Preprint

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The Coordination of Movement from Motor Units to Muscle Synergies

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 1

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Spatial and temporal structure of choice representations in primate prefrontal cortexPreprint

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Optimal Fisher Decoding of Neural Activity Near Criticality

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Neural Dynamics and the Geometry of Population Activity

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Shrinkage Classification for Overlapping Time Series: An interpretable method for mapping stimulus-differentiated evoked responsePreprint

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Representation of individual finger movements in macaque areas AIP, F5 and M1

Sheng, W.-A. (2019) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-7457

Why do we foster and grant wrong innovative scientific methods? The Neuroscientific Challenge

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A FEAST variant incorporated with a power iterationPreprint

Yeung, M.-C., & Lee, L. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1912.01642

Shared Neuronal Bases of Inhibition And Economic Choice in Orbitofrontal CortexPreprint

Balasubramani, P. P., Yadav, P., & Hayden, B. Y. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.23.057455

An approach for analyzing spike train data using dimensionality reduction.

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Enhanced representation of space by prefrontal neuronal ensembles and its dependence on cognitive statesPreprint

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Extracting single-trial neural interaction using latent dynamical systems model

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Incorporating Task-Related Information in Dimensionality Reduction of Neural Population Using Autoencoders

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Flexible Corticospinal Control of Muscles

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Bayesian Inference in High-Dimensional Time-Serieswith the Orthogonal Stochastic Linear Mixing ModelPreprint

Meng, R., & Bouchard, K. E. (2021) · arXiv (Cornell University) · doi:10.48550/arxiv.2106.13379 · Cited by 1

Activity recognition and bioinspired approaches for robotics in intelligent environments

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Resting-state functional MRI-based connectivity

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The effect of synaptic weight initialization in feature-based successor representation learning.Preprint

Lee, H. (2021) · arXiv (Cornell University)

Introduction

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Neural population dynamics and frontal-parietal circuit for context-dependent sensorimotor computations

Guo, H. (2020) · eDiss (Georg-August-Universität Göttingen) · doi:10.53846/goediss-7990

Electrophysiology

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Introduction

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Faculty Opinions recommendation of Different population dynamics in the supplementary motor area and motor cortex during reaching.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733650771.793560111

Faculty Opinions recommendation of Voltage imaging and optogenetics reveal behaviour-dependent changes in hippocampal dynamics.

Knöpfel, T. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.735645689.793560868

Faculty Opinions recommendation of Corticoamygdala transfer of socially derived information gates observational learning.

Miczek, K. A., & Covington, H. E. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733162596.793561606

Faculty Opinions recommendation of Long-term stability of cortical population dynamics underlying consistent behavior.

Schoenbaum, G. M., & Zhou, J. (2020) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.737164238.793571683

Closed-Loop Deep Brain Stimulation for Refractory Chronic Pain

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Faculty Opinions recommendation of Learning by neural reassociation.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.732828264.793560117

Faculty Opinions recommendation of Neural constraints on learning.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.718546237.793560114

Faculty Opinions recommendation of Neurophysiology of rule switching in the corticostriatal circuit.

Hayden, B. Y. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726127312.793565481

Faculty Opinions recommendation of Reorganization between preparatory and movement population responses in motor cortex.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.726917517.793560108

Faculty Opinions recommendation of Condition-Dependent Neural Dimensions Progressively Shift during Reach to Grasp.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.734621941.793560109

Faculty Opinions recommendation of Super-wide-field two-photon imaging with a micro-optical device moving in post-objective space.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733934910.793560134

Faculty Opinions recommendation of Neural Dynamics of Variable Grasp-Movement Preparation in the Macaque Frontoparietal Network.

Kalaska, J. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733308657.793560113

Investigação de correlatos neurais de estratégias de enfrentamento ao estresse na atividade oscilatória da rede mesolímbica-hipocampo-frontocortical

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Improving Latent Factor Analysis via Self-supervised Signal Extracting

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Brain-Machine Interfaces: From Restoring Sensorimotor Control to Augmenting Cognition

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Archetypal Analysis for neuronal clique detection in low-rate calcium fluorescence imaging

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Simulation of fronto-parietal neural population activity to probe dimensionality reduction methods.

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Algebraic approach for subspace decomposition and clustering of neural activity

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The cost of multiplexing: PFC integrates multiple sources of information in non-orthogonal components accounting for behavioral variabilityPreprint

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Decision letter: Population codes enable learning from few examples by shaping inductive bias

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eLife Assessment: Neuroelectrophysiology-Compatible Electrolytic Lesioning

Behrens, T. E. J. (2023) · eLife · doi:10.7554/elife.84385.1.sa3

Neural-Population-ActivityPreprint

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Dimensionality reduction for neural population decodingPreprint

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Scaling Properties of Dimensionality Reduction for Neural Populations and Network Models

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Bridging large-scale neuronal recordings and large-scale network models using dimensionality reductionPreprint

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Targeted dimensionality reduction enables reliable estimation of neural population coding accuracy from trial-limited data

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