Literature DB >> 35487088

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

Nastacia L Goodwin1, Simon R O Nilsson2, Jia Jie Choong3, Sam A Golden4.   

Abstract

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 significantly change how behavioral neuroscience is commonly performed. With the development of open-source platforms for automated tracking and behavioral recognition, these approaches are now accessible to a wide array of neuroscientists despite variations in budget and computational experience. Importantly, this adoption has moved the field toward a common understanding of behavior and brain function through the removal of manual bias and the identification of previously unknown behavioral repertoires. Although less apparent, another consequence of this movement is the introduction of analytical tools that increase the explainabilty, transparency, and universality of the machine-based behavioral classifications both within and between research groups. Here, we focus on three main applications of such machine model explainabilty tools and metrics in the drive toward behavioral (i) standardization, (ii) specialization, and (iii) explainability. We provide a perspective on the use of explainability tools in computational neuroethology, and detail why this is a necessary next step in the expansion of the field. Specifically, as a possible solution in behavioral neuroscience, we propose the use of Shapley values via Shapley Additive Explanations (SHAP) as a diagnostic resource toward explainability of human annotation, as well as supervised and unsupervised behavioral machine learning analysis.
Copyright © 2022 Elsevier Ltd. All rights reserved.

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Year:  2022        PMID: 35487088      PMCID: PMC9464364          DOI: 10.1016/j.conb.2022.102544

Source DB:  PubMed          Journal:  Curr Opin Neurobiol        ISSN: 0959-4388            Impact factor:   7.070


  29 in total

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Authors:  John W Krakauer; Asif A Ghazanfar; Alex Gomez-Marin; Malcolm A MacIver; David Poeppel
Journal:  Neuron       Date:  2017-02-08       Impact factor: 17.173

Review 2.  Toward a science of computational ethology.

Authors:  David J Anderson; Pietro Perona
Journal:  Neuron       Date:  2014-10-01       Impact factor: 17.173

Review 3.  Computational Neuroethology: A Call to Action.

Authors:  Sandeep Robert Datta; David J Anderson; Kristin Branson; Pietro Perona; Andrew Leifer
Journal:  Neuron       Date:  2019-10-09       Impact factor: 17.173

4.  DeepLabCut: markerless pose estimation of user-defined body parts with deep learning.

Authors:  Alexander Mathis; Pranav Mamidanna; Kevin M Cury; Taiga Abe; Venkatesh N Murthy; Mackenzie Weygandt Mathis; Matthias Bethge
Journal:  Nat Neurosci       Date:  2018-08-20       Impact factor: 24.884

5.  A call for transparent reporting to optimize the predictive value of preclinical research.

Authors:  Story C Landis; Susan G Amara; Khusru Asadullah; Chris P Austin; Robi Blumenstein; Eileen W Bradley; Ronald G Crystal; Robert B Darnell; Robert J Ferrante; Howard Fillit; Robert Finkelstein; Marc Fisher; Howard E Gendelman; Robert M Golub; John L Goudreau; Robert A Gross; Amelie K Gubitz; Sharon E Hesterlee; David W Howells; John Huguenard; Katrina Kelner; Walter Koroshetz; Dimitri Krainc; Stanley E Lazic; Michael S Levine; Malcolm R Macleod; John M McCall; Richard T Moxley; Kalyani Narasimhan; Linda J Noble; Steve Perrin; John D Porter; Oswald Steward; Ellis Unger; Ursula Utz; Shai D Silberberg
Journal:  Nature       Date:  2012-10-11       Impact factor: 49.962

6.  Fast animal pose estimation using deep neural networks.

Authors:  Talmo D Pereira; Diego E Aldarondo; Lindsay Willmore; Mikhail Kislin; Samuel S-H Wang; Mala Murthy; Joshua W Shaevitz
Journal:  Nat Methods       Date:  2018-12-20       Impact factor: 28.547

7.  Geometric deep learning enables 3D kinematic profiling across species and environments.

Authors:  Timothy W Dunn; Jesse D Marshall; Kyle S Severson; Diego E Aldarondo; David G C Hildebrand; Selmaan N Chettih; William L Wang; Amanda J Gellis; David E Carlson; Dmitriy Aronov; Winrich A Freiwald; Fan Wang; Bence P Ölveczky
Journal:  Nat Methods       Date:  2021-04-19       Impact factor: 28.547

8.  DeepEthogram, a machine learning pipeline for supervised behavior classification from raw pixels.

Authors:  James P Bohnslav; Nivanthika K Wimalasena; Kelsey J Clausing; Yu Y Dai; David A Yarmolinsky; Tomás Cruz; Adam D Kashlan; M Eugenia Chiappe; Lauren L Orefice; Clifford J Woolf; Christopher D Harvey
Journal:  Elife       Date:  2021-09-02       Impact factor: 8.140

Review 9.  A Shared Vision for Machine Learning in Neuroscience.

Authors:  Mai-Anh T Vu; Tülay Adalı; Demba Ba; György Buzsáki; David Carlson; Katherine Heller; Conor Liston; Cynthia Rudin; Vikaas S Sohal; Alik S Widge; Helen S Mayberg; Guillermo Sapiro; Kafui Dzirasa
Journal:  J Neurosci       Date:  2018-01-26       Impact factor: 6.709

10.  Action detection using a neural network elucidates the genetics of mouse grooming behavior.

Authors:  Brian Q Geuther; Asaf Peer; Hao He; Gautam Sabnis; Vivek M Philip; Vivek Kumar
Journal:  Elife       Date:  2021-03-17       Impact factor: 8.140

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  2 in total

Review 1.  Neural circuits regulating prosocial behaviors.

Authors:  Jessica J Walsh; Daniel J Christoffel; Robert C Malenka
Journal:  Neuropsychopharmacology       Date:  2022-06-14       Impact factor: 7.853

2.  A machine learning model based on ultrasound image features to assess the risk of sentinel lymph node metastasis in breast cancer patients: Applications of scikit-learn and SHAP.

Authors:  Gaosen Zhang; Yan Shi; Peipei Yin; Feifei Liu; Yi Fang; Xiang Li; Qingyu Zhang; Zhen Zhang
Journal:  Front Oncol       Date:  2022-07-25       Impact factor: 5.738

  2 in total

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