Publications

2018

Amortized Bayesian Inference for Clustering Models

Pakman, A., Paninski, L.

Neural Classifiers with Limited Connectivity and Recurrent Readouts

Kushnir, L., Fusi, S.

The Markov Link Method: A Nonparametric Approach to Combine Observations from Multiple Experiments

Loper, J., Bakken, T., Sumbul, U., Murphy, G., Zeng, H., Blei, D., Paninski, L.

Complementary Networks of Cortical Somatostatin Interneurons Enforce Layer Specific Control

Naka, A., Veit, J., Shababo, B., Chance, R.K., Risso, D., Stafford, D., Snyder, B., Egladyous, A., Chu, D., Sridharan, S., Paninski, L., Ngai, J., Adesnik, H.

How Biological Attention Mechanisms Improve Task Performance in a Large-scale Visual System Model

Lindsay, G.W., Miller, K.D.

Inferring Single-trial Neural Population Dynamics Using Sequential Auto-encoders

Pandarinath, C., O’Shea, D.J., Collins, J., Jozefowicz, R., Stavisky, S.D., Kao, J.C., Trautmann, E.M., Kaufman, M.T., Ryu, S.I., Hochberg, L.R., Henderson, J.M., Shenoy, K.V., Abbott, L.F., Sussillo, D.

The Geometry of Abstraction in Hippocampus and Prefrontal Cortex

Bernardi, S., Benna, M., Rigotti, M., Munuera, J., Fusi, S., Salzman, D.

Conservation of Preparatory Neural Events in Monkey Motor Cortex Regardless of How Movement is Initiated

Lara, A.H., Elsayed, G.F., Zimnik, A.J., Cunningham, J.P., Churchland, M.M.

Different Population Dynamics in the Supplementary Motor Area and Motor Cortex During Reaching

Lara, A.H., Cunningham, J.P., Churchland, M.M.

Internally Generated Predictions Enhance Neural and Behavioral Detection of Sensory Stimuli in an Electric Fish

Enikolopov, A.G., Abbott, L.F., Sawtell, N.B.

Inhibitory and Excitatory Populations in Parietal Cortex Are Equally Selective for Decision Outcome in Both Novices and Experts

Najafi, F., Elsayed, G.F., Pnevmatikakis, E.A., Cunningham, J., Churchland, A.K.

New Heuristics for Parallel and Scalable Bayesian Optimization

Rubin, R.

Scalable Approximate Bayesian Inference for Particle Tracking Data

Sun, R., Paninski, L.

The Striatum Organizes 3D Behavior via Moment-to-Moment Action Selection

Markowitz, J.E., Gillis W.F., Beron C.C., Neufeld S.Q., Robertson K., Bhagat N.D., Peterson R.E., Peterson E., Hyun M., Linderman S.W., Sabatini B.L., Datta S.R.

CaImAn: An Open Source Tool for Scalable Calcium Imaging Data Analysis

Giovannucci, A., Friedrich, J., Gunn, P., Kalfon, J., Koay, S., Taxidis, J., Najafi, F., Gauthier, J.L., Zhou, P., Tank, D.W., Chklovskii, D.B.

Penalized Matrix Decomposition for Denoising, Compression, and Improved Demixing of Functional Imaging Data

Buchanan, E.K., Kinsella, I., Zhou, D., Zhu, R., Zhou, P., Gerhard, F., Ferrante, J., Ma, Y., Kim, S., Shaik, M., Liang, Y., Lu, R., Reimer, J., Fahey, P., Muhammad, T., Dempsey, G., Hillman, E., Ji, N., Tolias, A., Paninski, L.

Neural Data Science: Accelerating the Experiment-Analysis-Theory Cycle in Large-Scale Neuroscience

Paninski, L., Cunningham, J.

Calibrating Deep Convolutional Gaussian Processes

Tran, G., Bonilla, E.V., Cunningham, J.P., Michiardi, P., Filippone, M.

Bayesian Estimation for Large Scale Multivariate Ornstein-Uhlenbeck Model of Brain Connectivity

Insabato, A., Cunningham, J.P., Gilson, M.

Community-Based Benchmarking Improves Spike Inference from Two-Photon Calcium Imaging Data

Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke J, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Rogerson LE, Sofroniew NJ, Re

Changes in Effective Hippocampal Network Coupling Mediate Learning and Memory of Associations Between Temporally Discontiguous Stimuli

Ahmed, M., Priestley, J., Castro, A., Stefanini, F., Balough, E., Lavoie, E., Mazzucato, L., Fusi, S., Losonczy, A.

Neuronal Variability as a Proxy for Network State

Nogueira, R., Lawrie, S., Moreno-Bote, R.

Emergence of Grid-like Representations by Training Recurrent Neural Networks to Perform Spatial Localization

Cueva, C.J., Wei, X.

The Dynamical Regime of Sensory Cortex: Stable Dynamics Around a Single Stimulus-Tuned Attractor Account for Patterns of Noise Variability

Hennequin, G., Ahmadian, Y., Rubin, D.B., Lengyel, M., Miller, K.D.

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