arXiv subjects

Matthew R Whiteway

Publications and source records attributed to Matthew R Whiteway.

4 recordsLinked to original sources

arXiv2026

BEAST3D: Animal behavioral analysis and neural encoding from multi-view video via Gaussian splatting

Multi-view video recordings are increasingly used to capture the 3D movements of animals in experimental settings, yet extracting rich 3D representations from these recordings remains challenging. Supervised pose estimation requires extensive manual annotation, while general-purpose 3D reconstruction models trained on generic scene datasets fail on the specialized imagery and sparse-view setting of laboratory experiments. We address these limitations with BEAST3D, a self-supervised pretraining framework that learns 3D visual representations from unlabeled, calibrated multi-view video. BEAST3D uses a vision transformer to predict 3D Gaussian splats that reconstruct held-out views through differentiable rendering, while simultaneously segmenting the animal from the background. BEAST3D reconstructs 3D structure with as few as four views by conditioning directly on known camera parameters--unlike general-purpose models, which must estimate camera geometry from dense overlapping viewpoints that are seldom available in lab settings. Through comprehensive evaluation across four species, we demonstrate that BEAST3D produces rich, viewpoint-invariant features that transfer effectively to three downstream tasks: novel view synthesis, which validates the quality of the learned 3D representations; multi-view pose estimation, which provides the sparse keypoint trajectories widely used in behavioral analysis; and neural encoding, which relates 3D behavioral features to simultaneously recorded neural activity. BEAST3D thus establishes a versatile framework for behavioral analysis that leverages 3D structure in modern multi-view laboratory recordings.

q-bio.NC↗

arXiv2025

An uncertainty-aware framework for data-efficient multi-view animal pose estimation

Multi-view pose estimation is essential for quantifying animal behavior in scientific research, yet current methods struggle to achieve accurate tracking with limited labeled data and suffer from poor uncertainty estimates. We address these challenges with a comprehensive framework combining novel training and post-processing techniques, and a model distillation procedure that leverages the strengths of these techniques to produce a more efficient and effective pose estimator. Our multi-view transformer (MVT) utilizes pretrained backbones and enables simultaneous processing of information across all views, while a novel patch masking scheme learns robust cross-view correspondences without camera calibration. For calibrated setups, we incorporate geometric consistency through 3D augmentation and a triangulation loss. We extend the existing Ensemble Kalman Smoother (EKS) post-processor to the nonlinear case and enhance uncertainty quantification via a variance inflation technique. Finally, to leverage the scaling properties of the MVT, we design a distillation procedure that exploits improved EKS predictions and uncertainty estimates to generate high-quality pseudo-labels, thereby reducing dependence on manual labels. Our framework components consistently outperform existing methods across three diverse animal species (flies, mice, chickadees), with each component contributing complementary benefits. The result is a practical, uncertainty-aware system for reliable pose estimation that enables downstream behavioral analyses under real-world data constraints.

cs.CV↗

arXiv2024

A study of animal action segmentation algorithms across supervised, unsupervised, and semi-supervised learning paradigms

Action segmentation of behavioral videos is the process of labeling each frame as belonging to one or more discrete classes, and is a crucial component of many studies that investigate animal behavior. A wide range of algorithms exist to automatically parse discrete animal behavior, encompassing supervised, unsupervised, and semi-supervised learning paradigms. These algorithms -- which include tree-based models, deep neural networks, and graphical models -- differ widely in their structure and assumptions on the data. Using four datasets spanning multiple species -- fly, mouse, and human -- we systematically study how the outputs of these various algorithms align with manually annotated behaviors of interest. Along the way, we introduce a semi-supervised action segmentation model that bridges the gap between supervised deep neural networks and unsupervised graphical models. We find that fully supervised temporal convolutional networks with the addition of temporal information in the observations perform the best on our supervised metrics across all datasets.

cs.CV↗

arXiv2019

Characterizing the nonlinear structure of shared variability in cortical neuron populations using latent variable models

Sensory neurons often have variable responses to repeated presentations of the same stimulus, which can significantly degrade the stimulus information contained in those responses. This information can in principle be preserved if variability is shared across many neurons, but depends on the structure of the shared variability and its relationship to sensory encoding at the population level. The structure of this shared variability in neural activity can be characterized by latent variable models, although they have thus far typically been used under restrictive mathematical assumptions. Here we introduce two nonlinear latent variable models for analyzing large-scale neural recordings. We first present a general nonlinear latent variable model that is agnostic to the stimulus tuning properties of the individual neurons, and is hence well suited for exploring neural populations whose tuning properties are not well characterized. This motivates a second class of model, the Generalized Affine Model, which simultaneously determines each neuron's stimulus selectivity and a set of latent variables that modulate these stimulus-driven responses both additively and multiplicatively. While these approaches can detect very general nonlinear relationships in shared neural variability, we find that neural activity recorded in anesthetized primary visual cortex (V1) is best described by a single additive and single multiplicative latent variable, i.e. an `affine model'. In contrast, application of the same models to recordings in awake macaque prefrontal cortex discover more general nonlinearities to compactly describe the population response variability. These results thus demonstrate how nonlinear latent variable models can be used to describe population response variability, and suggest that a range of methods is necessary to study different brain regions under different experimental conditions.

q-bio.NC↗