Quantifying behavior to understand the brain

TD Pereira, JW Shaevitz, M Murthy - Nature neuroscience, 2020 - nature.com
Over the past years, numerous methods have emerged to automate the quantification of
animal behavior at a resolution not previously imaginable. This has opened up a new field of …

The emergence and influence of internal states

SW Flavell, N Gogolla, M Lovett-Barron, M Zelikowsky - Neuron, 2022 - cell.com
Animal behavior is shaped by a variety of" internal states"—partially hidden variables that
profoundly shape perception, cognition, and action. The neural basis of internal states, such …

Keypoint-MoSeq: parsing behavior by linking point tracking to pose dynamics

C Weinreb, JE Pearl, S Lin, MAM Osman, L Zhang… - Nature …, 2024 - nature.com
Keypoint tracking algorithms can flexibly quantify animal movement from videos obtained in
a wide variety of settings. However, it remains unclear how to parse continuous keypoint …

A primer on motion capture with deep learning: principles, pitfalls, and perspectives

A Mathis, S Schneider, J Lauer, MW Mathis - Neuron, 2020 - cell.com
Extracting behavioral measurements non-invasively from video is stymied by the fact that it is
a hard computational problem. Recent advances in deep learning have tremendously …

The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice

C Segalin, J Williams, T Karigo, M Hui, M Zelikowsky… - Elife, 2021 - elifesciences.org
The study of naturalistic social behavior requires quantification of animals' interactions. This
is generally done through manual annotation—a highly time-consuming and tedious …

Deep time-series clustering: A review

A Alqahtani, M Ali, X Xie, MW Jones - Electronics, 2021 - mdpi.com
We present a comprehensive, detailed review of time-series data analysis, with emphasis on
deep time-series clustering (DTSC), and a case study in the context of movement behavior …

Toward the explainability, transparency, and universality of machine learning for behavioral classification in neuroscience

NL Goodwin, SRO Nilsson, JJ Choong… - Current opinion in …, 2022 - Elsevier
The use of rigorous ethological observation via machine learning techniques to understand
brain function (computational neuroethology) is a rapidly growing approach that is poised to …

AmadeusGPT: a natural language interface for interactive animal behavioral analysis

S Ye, J Lauer, M Zhou, A Mathis… - Advances in neural …, 2024 - proceedings.neurips.cc
The process of quantifying and analyzing animal behavior involves translating the naturally
occurring descriptive language of their actions into machine-readable code. Yet, codifying …

Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling and cloud-native open-source tools

D Biderman, MR Whiteway, C Hurwitz, N Greenspan… - Nature …, 2024 - nature.com
Contemporary pose estimation methods enable precise measurements of behavior via
supervised deep learning with hand-labeled video frames. Although effective in many cases …

Open-source tools for behavioral video analysis: Setup, methods, and best practices

K Luxem, JJ Sun, SP Bradley, K Krishnan, E Yttri… - Elife, 2023 - elifesciences.org
Recently developed methods for video analysis, especially models for pose estimation and
behavior classification, are transforming behavioral quantification to be more precise …