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Goodwin NL, Choong JJ, Hwang S, Pitts K, Bloom L, Islam A, Zhang YY, Szelenyi ER, Tong X, Newman EL, Miczek K, Wright HR, McLaughlin RJ, Norville ZC, Eshel N, Heshmati M, Nilsson SRO, Golden SA. Simple Behavioral Analysis (SimBA) as a platform for explainable machine learning in behavioral neuroscience. Nat Neurosci 2024; 27:1411-1424. [PMID: 38778146 DOI: 10.1038/s41593-024-01649-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
The study of complex behaviors is often challenging when using manual annotation due to the absence of quantifiable behavioral definitions and the subjective nature of behavioral annotation. Integration of supervised machine learning approaches mitigates some of these issues through the inclusion of accessible and explainable model interpretation. To decrease barriers to access, and with an emphasis on accessible model explainability, we developed the open-source Simple Behavioral Analysis (SimBA) platform for behavioral neuroscientists. SimBA introduces several machine learning interpretability tools, including SHapley Additive exPlanation (SHAP) scores, that aid in creating explainable and transparent behavioral classifiers. Here we show how the addition of explainability metrics allows for quantifiable comparisons of aggressive social behavior across research groups and species, reconceptualizing behavior as a sharable reagent and providing an open-source framework. We provide an open-source, graphical user interface (GUI)-driven, well-documented package to facilitate the movement toward improved automation and sharing of behavioral classification tools across laboratories.
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Affiliation(s)
- Nastacia L Goodwin
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Jia J Choong
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Sophia Hwang
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Kayla Pitts
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Liana Bloom
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Aasiya Islam
- Department of Biological Structure, University of Washington, Seattle, WA, USA
| | - Yizhe Y Zhang
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Eric R Szelenyi
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
| | - Xiaoyu Tong
- New York University Neuroscience Institute, New York, NY, USA
| | - Emily L Newman
- Department of Psychiatry, Harvard Medical School McLean Hospital, Belmont, MA, USA
| | - Klaus Miczek
- Department of Psychology, Tufts University, Medford, MA, USA
| | - Hayden R Wright
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
- Graduate Program in Neuroscience, Washington State University, Pullman, WA, USA
| | - Ryan J McLaughlin
- Department of Integrative Physiology and Neuroscience, Washington State University, Pullman, WA, USA
- Graduate Program in Neuroscience, Washington State University, Pullman, WA, USA
| | | | - Neir Eshel
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Mitra Heshmati
- Department of Biological Structure, University of Washington, Seattle, WA, USA
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA, USA
| | - Simon R O Nilsson
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
| | - Sam A Golden
- Department of Biological Structure, University of Washington, Seattle, WA, USA.
- Graduate Program in Neuroscience, University of Washington, Seattle, WA, USA.
- Center of Excellence in Neurobiology of Addiction, Pain and Emotion (NAPE), University of Washington, Seattle, WA, USA.
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Howard SR, Dyer AG. Quantity misperception by hymenopteran insects observing the solitaire illusion. iScience 2024; 27:108697. [PMID: 38288356 PMCID: PMC10823103 DOI: 10.1016/j.isci.2023.108697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/31/2024] Open
Abstract
Visual illusions are errors in signal perception and inform us about the visual and cognitive processes of different animals. Invertebrates are relatively less studied for their illusionary perception, despite the insight that comparative data provides on the evolution of common perceptual mechanisms. The Solitaire Illusion is a numerosity illusion where a viewer typically misperceives the relative quantities of two items of different colors consisting of identical quantity, with more centrally clustered items appearing more numerous. We trained European honeybees (Apis mellifera) and European wasps (Vespula vulgaris) to select stimuli containing a higher quantity of yellow dots in arrays of blue and yellow dots and then presented them with the Solitaire Illusion. Insects learnt to discriminate between dot quantities and showed evidence of perceiving the Solitaire Illusion. Further work should determine whether the illusion is caused by numerical cues only or by both quantity and non-numerical spatial cues.
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Affiliation(s)
- Scarlett R. Howard
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Adrian G. Dyer
- Department of Physiology, Monash University, Clayton, VIC, Australia
- Institute of Developmental Biology and Neurobiology (iDN), Johannes Gutenberg University, 55122 Mainz, Germany
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