2024
Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration.
PLoS Comput. Biol., 2024
Removing direct photocurrent artifacts in optogenetic connectivity mapping data via constrained matrix factorization.
PLoS Comput. Biol., 2024
A study of animal action segmentation algorithms across supervised, unsupervised, and semi-supervised learning paradigms.
CoRR, 2024
Towards a "universal translator" for neural dynamics at single-cell, single-spike resolution.
,
,
,
,
,
,
,
,
,
,
CoRR, 2024
Towards a "Universal Translator" for Neural Dynamics at Single-Cell, Single-Spike Resolution.
,
,
,
,
,
,
,
,
,
,
,
Proceedings of the Advances in Neural Information Processing Systems 38: Annual Conference on Neural Information Processing Systems 2024, 2024
2023
Bypassing spike sorting: Density-based decoding using spike localization from dense multielectrode probes.
,
,
,
,
,
,
,
,
,
,
,
,
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Towards robust and generalizable representations of extracellular data using contrastive learning.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Bayesian target optimisation for high-precision holographic optogenetics.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023
Learning Probabilistic Piecewise Rigid Atlases of Model Organisms via Generative Deep Networks.
Proceedings of the Information Processing in Medical Imaging, 2023
Robust Online Multiband Drift Estimation in Electrophysiology Data.
,
,
,
,
,
,
,
,
,
,
,
,
Proceedings of the IEEE International Conference on Acoustics, 2023
Multimodal Microscopy Image Alignment Using Spatial and Shape Information and a Branch-and-Bound Algorithm.
Proceedings of the IEEE International Conference on Acoustics, 2023
2022
Blind demixing methods for recovering dense neuronal morphology from barcode imaging data.
PLoS Comput. Biol., 2022
SemiMultiPose: A Semi-supervised Multi-animal Pose Estimation Framework.
CoRR, 2022
2021
Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders.
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
PLoS Comput. Biol., 2021
BARcode DEmixing through Non-negative Spatial Regression (BarDensr).
PLoS Comput. Biol., 2021
Nonlinear Decoding of Natural Images From Large-Scale Primate Retinal Ganglion Recordings.
Neural Comput., 2021
A general linear-time inference method for Gaussian Processes on one dimension.
J. Mach. Learn. Res., 2021
Three-dimensional spike localization and improved motion correction for Neuropixels recordings.
Proceedings of the Advances in Neural Information Processing Systems 34: Annual Conference on Neural Information Processing Systems 2021, 2021
Non-parametric Vignetting Correction for Sparse Spatial Transcriptomics Images.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2021 - 24th International Conference, Strasbourg, France, September 27, 2021
Decentralized Motion Inference and Registration of Neuropixel Data.
Proceedings of the IEEE International Conference on Acoustics, 2021
2020
Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.
,
,
,
,
,
,
,
,
,
,
PLoS Comput. Biol., 2020
Attentive Clustering Processes.
CoRR, 2020
General linear-time inference for Gaussian Processes on one dimension.
CoRR, 2020
Disentangled Sticky Hierarchical Dirichlet Process Hidden Markov Model.
Proceedings of the Machine Learning and Knowledge Discovery in Databases, 2020
Deep Graph Pose: a semi-supervised deep graphical model for improved animal pose tracking.
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020
Recurrent Switching Dynamical Systems Models for Multiple Interacting Neural Populations.
Proceedings of the Advances in Neural Information Processing Systems 33: Annual Conference on Neural Information Processing Systems 2020, 2020
Statistical Atlas of C. elegans Neurons.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020
Demixing Calcium Imaging Data in C. elegans via Deformable Non-negative Matrix Factorization.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020
Probabilistic Joint Segmentation and Labeling of C. elegans Neurons.
Proceedings of the Medical Image Computing and Computer Assisted Intervention - MICCAI 2020, 2020
Neural Clustering Processes.
Proceedings of the 37th International Conference on Machine Learning, 2020
2019
Discrete Neural Processes.
CoRR, 2019
Scalable Bayesian inference of dendritic voltage via spatiotemporal recurrent state space models.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Efficient characterization of electrically evoked responses for neural interfaces.
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
BehaveNet: nonlinear embedding and Bayesian neural decoding of behavioral videos.
,
,
,
,
,
,
,
,
,
,
,
,
Proceedings of the Advances in Neural Information Processing Systems 32: Annual Conference on Neural Information Processing Systems 2019, 2019
Neural Permutation Processes.
Proceedings of the Symposium on Advances in Approximate Bayesian Inference, 2019
Sinkhorn Permutation Variational Marginal Inference.
Proceedings of the Symposium on Advances in Approximate Bayesian Inference, 2019
2018
Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
PLoS Comput. Biol., 2018
Amortized Bayesian inference for clustering models.
CoRR, 2018
A Novel Variational Family for Hidden Nonlinear Markov Models.
CoRR, 2018
Scalable Approximate Bayesian Inference for Particle Tracking Data.
Proceedings of the 35th International Conference on Machine Learning, 2018
Reparameterizing the Birkhoff Polytope for Variational Permutation Inference.
Proceedings of the International Conference on Artificial Intelligence and Statistics, 2018
2017
Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays.
PLoS Comput. Biol., 2017
Fast online deconvolution of calcium imaging data.
PLoS Comput. Biol., 2017
Multi-scale approaches for high-speed imaging and analysis of large neural populations.
PLoS Comput. Biol., 2017
Neural Networks for Efficient Bayesian Decoding of Natural Images from Retinal Neurons.
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
YASS: Yet Another Spike Sorter.
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
OnACID: Online Analysis of Calcium Imaging Data in Real Time.
Proceedings of the Advances in Neural Information Processing Systems 30: Annual Conference on Neural Information Processing Systems 2017, 2017
Stochastic Bouncy Particle Sampler.
Proceedings of the 34th International Conference on Machine Learning, 2017
Multilayer Recurrent Network Models of Primate Retinal Ganglion Cell Responses.
Proceedings of the 5th International Conference on Learning Representations, 2017
Scalable Variational Inference for Super Resolution Microscopy.
Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 2017
Bayesian Learning and Inference in Recurrent Switching Linear Dynamical Systems.
Proceedings of the 20th International Conference on Artificial Intelligence and Statistics, 2017
2016
Neuroprosthetic Decoder Training as Imitation Learning.
PLoS Comput. Biol., 2016
Automated scalable segmentation of neurons from multispectral images.
Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016
Linear dynamical neural population models through nonlinear embeddings.
Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016
Fast Active Set Methods for Online Spike Inference from Calcium Imaging.
Proceedings of the Advances in Neural Information Processing Systems 29: Annual Conference on Neural Information Processing Systems 2016, 2016
Partition Functions from Rao-Blackwellized Tempered Sampling.
Proceedings of the 33nd International Conference on Machine Learning, 2016
2015
Efficient "Shotgun" Inference of Neural Connectivity from Highly Sub-sampled Activity Data.
PLoS Comput. Biol., 2015
Encoder-Decoder Optimization for Brain-Computer Interfaces.
PLoS Comput. Biol., 2015
2014
On Quadrature Methods for Refractory Point Process Likelihoods.
Neural Comput., 2014
Fast inference in generalized linear models via expected log-likelihoods.
J. Comput. Neurosci., 2014
Fast state-space methods for inferring dendritic synaptic connectivity.
J. Comput. Neurosci., 2014
Clustered factor analysis of multineuronal spike data.
Proceedings of the Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, 2014
2013
Bayesian Inference and Online Experimental Design for Mapping Neural Microcircuits.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
Sparse nonnegative deconvolution for compressive calcium imaging: algorithms and phase transitions.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
Robust learning of low-dimensional dynamics from large neural ensembles.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
Auxiliary-variable Exact Hamiltonian Monte Carlo Samplers for Binary Distributions.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
A multi-agent control framework for co-adaptation in brain-computer interfaces.
Proceedings of the Advances in Neural Information Processing Systems 26: 27th Annual Conference on Neural Information Processing Systems 2013. Proceedings of a meeting held December 5-8, 2013
Bayesian spike inference from calcium imaging data.
Proceedings of the 2013 Asilomar Conference on Signals, 2013
2012
EMG Prediction From Motor Cortical Recordings via a Nonnegative Point-Process Filter.
IEEE Trans. Biomed. Eng., 2012
Fast Spatiotemporal Smoothing of Calcium Measurements in Dendritic Trees.
PLoS Comput. Biol., 2012
Low rank continuous-space graphical models.
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012
Fast interior-point inference in high-dimensional sparse, penalized state-space models.
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, 2012
Modeling the impact of common noise inputs on the network activity of retinal ganglion cells.
J. Comput. Neurosci., 2012
Inferring synaptic inputs given a noisy voltage trace via sequential Monte Carlo methods.
J. Comput. Neurosci., 2012
A Bayesian compressed-sensing approach for reconstructing neural connectivity from subsampled anatomical data.
J. Comput. Neurosci., 2012
Optimal experimental design for sampling voltage on dendritic trees in the low-SNR regime.
J. Comput. Neurosci., 2012
Decoding arm and hand movements across layers of the macaque frontal cortices.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012
Robust particle filters via sequential pairwise reparameterized Gibbs sampling.
Proceedings of the 46th Annual Conference on Information Sciences and Systems, 2012
2011
Model-Based Decoding, Information Estimation, and Change-Point Detection Techniques for Multineuron Spike Trains.
Neural Comput., 2011
Hidden Markov Models for the Stimulus-Response Relationships of Multistate Neural Systems.
Neural Comput., 2011
Efficient Markov Chain Monte Carlo Methods for Decoding Neural Spike Trains.
Neural Comput., 2011
Automating the design of informative sequences of sensory stimuli.
J. Comput. Neurosci., 2011
Information Rates and Optimal Decoding in Large Neural Populations.
Proceedings of the Advances in Neural Information Processing Systems 24: 25th Annual Conference on Neural Information Processing Systems 2011. Proceedings of a meeting held 12-14 December 2011, 2011
2010
A new look at state-space models for neural data.
J. Comput. Neurosci., 2010
Fast Kalman filtering on quasilinear dendritic trees.
J. Comput. Neurosci., 2010
Efficient computation of the maximum a posteriori path and parameter estimation in integrate-and-fire and more general state-space models.
J. Comput. Neurosci., 2010
2009
Bayesian Image Recovery for Dendritic Structures Under Low Signal-to-Noise Conditions.
IEEE Trans. Image Process., 2009
Smoothing of, and Parameter Estimation from, Noisy Biophysical Recordings.
PLoS Comput. Biol., 2009
Mean-Field Approximations for Coupled Populations of Generalized Linear Model Spiking Neurons with Markov Refractoriness.
Neural Comput., 2009
Sequential Optimal Design of Neurophysiology Experiments.
Neural Comput., 2009
Maximally Reliable Markov Chains Under Energy Constraints.
Neural Comput., 2009
2008
Undersmoothed Kernel Entropy Estimators.
IEEE Trans. Inf. Theory, 2008
A Coincidence-Based Test for Uniformity Given Very Sparsely Sampled Discrete Data.
IEEE Trans. Inf. Theory, 2008
State-Space Decoding of Goal-Directed Movements.
IEEE Signal Process. Mag., 2008
Integral equation methods for computing likelihoods and their derivatives in the stochastic integrate-and-fire model.
J. Comput. Neurosci., 2008
Designing neurophysiology experiments to optimally constrain receptive field models along parametric submanifolds.
Proceedings of the Advances in Neural Information Processing Systems 21, 2008
2007
Efficient active learning with generalized linear models.
Proceedings of the Eleventh International Conference on Artificial Intelligence and Statistics, 2007
2006
The Spike-Triggered Average of the Integrate-and-Fire Cell Driven by Gaussian White Noise.
Neural Comput., 2006
The most likely voltage path and large deviations approximations for integrate-and-fire neurons.
J. Comput. Neurosci., 2006
Real-time adaptive information-theoretic optimization of neurophysiology experiments.
Proceedings of the Advances in Neural Information Processing Systems 19, 2006
Efficient model-based design of neurophysiological experiments.
Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006
2005
Statistical encoding model for a primary motor cortical brain-machine interface.
IEEE Trans. Biomed. Eng., 2005
Asymptotic Theory of Information-Theoretic Experimental Design.
Neural Comput., 2005
Comparing integrate-and-fire models estimated using intracellular and extracellular data.
Neurocomputing, 2005
Nonparametric inference of prior probabilities from Bayes-optimal behavior.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005
Large-scale biophysical parameter estimation in single neurons via constrained linear regression.
Proceedings of the Advances in Neural Information Processing Systems 18 [Neural Information Processing Systems, 2005
2004
Estimating Entropy on m Bins Given Fewer than m Samples.
IEEE Trans. Inf. Theory, 2004
Maximum Likelihood Estimation of a Stochastic Integrate-and-Fire Neural Encoding Model.
Neural Comput., 2004
Variational Minimax Estimation of Discrete Distributions under KL Loss.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
Log-concavity Results on Gaussian Process Methods for Supervised and Unsupervised Learning.
Proceedings of the Advances in Neural Information Processing Systems 17 [Neural Information Processing Systems, 2004
2003
Estimation of Entropy and Mutual Information.
Neural Comput., 2003
Noise-driven adaptation: in vitro and mathematical analysis.
Neurocomputing, 2003
Robustness of neuroprosthetic decoding algorithms.
Biol. Cybern., 2003
Maximum Likelihood Estimation of a Stochastic Integrate-and-Fire Neural Model.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003
Design of Experiments via Information Theory.
Proceedings of the Advances in Neural Information Processing Systems 16 [Neural Information Processing Systems, 2003
2002
Convergence Properties of Some Spike-Triggered Analysis Techniques.
Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002
2001
Stochastic optimal control and the human oculomotor system.
Neurocomputing, 2001