Topological Data Analysis of C. elegans Locomotion and Behavior
We apply topological data analysis to the behavior of C. elegans, a widely studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data. Our methods allow us to distinguish and classify videos fro...
| الحاوية / القاعدة: | Frontiers in Artificial Intelligence |
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| المؤلفون الرئيسيون: | , , , , , |
| التنسيق: | مقال |
| اللغة: | الإنجليزية |
| منشور في: |
Frontiers Media S.A.
2021-06-01
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| الموضوعات: | |
| الوصول للمادة أونلاين: | https://www.frontiersin.org/articles/10.3389/frai.2021.668395/full |
| _version_ | 1852723786016620544 |
|---|---|
| author | Ashleigh Thomas Kathleen Bates Alex Elchesen Iryna Hartsock Hang Lu Peter Bubenik |
| author_facet | Ashleigh Thomas Kathleen Bates Alex Elchesen Iryna Hartsock Hang Lu Peter Bubenik |
| author_sort | Ashleigh Thomas |
| collection | DOAJ |
| container_title | Frontiers in Artificial Intelligence |
| description | We apply topological data analysis to the behavior of C. elegans, a widely studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data. Our methods allow us to distinguish and classify videos from various environmental conditions and we analyze the trade-off between accuracy and interpretability. Furthermore, we present a novel technique for visualizing the outputs of our analysis in terms of the input. Specifically, we use representative cycles of persistent homology to produce synthetic videos of stereotypical behaviors. |
| format | Article |
| id | doaj-art-ddf8d3e925d84f46a9d8bbc9595f5dea |
| institution | Directory of Open Access Journals |
| issn | 2624-8212 |
| language | English |
| publishDate | 2021-06-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| spelling | doaj-art-ddf8d3e925d84f46a9d8bbc9595f5dea2025-08-19T21:11:23ZengFrontiers Media S.A.Frontiers in Artificial Intelligence2624-82122021-06-01410.3389/frai.2021.668395668395Topological Data Analysis of C. elegans Locomotion and BehaviorAshleigh Thomas0Kathleen Bates1Alex Elchesen2Iryna Hartsock3Hang Lu4Peter Bubenik5School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United StatesSchool of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United StatesDepartment of Mathematics, University of Florida, Gainesville, FL, United StatesDepartment of Mathematics, University of Florida, Gainesville, FL, United StatesSchool of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, United StatesDepartment of Mathematics, University of Florida, Gainesville, FL, United StatesWe apply topological data analysis to the behavior of C. elegans, a widely studied model organism in biology. In particular, we use topology to produce a quantitative summary of complex behavior which may be applied to high-throughput data. Our methods allow us to distinguish and classify videos from various environmental conditions and we analyze the trade-off between accuracy and interpretability. Furthermore, we present a novel technique for visualizing the outputs of our analysis in terms of the input. Specifically, we use representative cycles of persistent homology to produce synthetic videos of stereotypical behaviors.https://www.frontiersin.org/articles/10.3389/frai.2021.668395/fullpersistent homologytopological data analysisdelay embeddingsliding window embeddingC. elegansbehavior phenotyping |
| spellingShingle | Ashleigh Thomas Kathleen Bates Alex Elchesen Iryna Hartsock Hang Lu Peter Bubenik Topological Data Analysis of C. elegans Locomotion and Behavior persistent homology topological data analysis delay embedding sliding window embedding C. elegans behavior phenotyping |
| title | Topological Data Analysis of C. elegans Locomotion and Behavior |
| title_full | Topological Data Analysis of C. elegans Locomotion and Behavior |
| title_fullStr | Topological Data Analysis of C. elegans Locomotion and Behavior |
| title_full_unstemmed | Topological Data Analysis of C. elegans Locomotion and Behavior |
| title_short | Topological Data Analysis of C. elegans Locomotion and Behavior |
| title_sort | topological data analysis of c elegans locomotion and behavior |
| topic | persistent homology topological data analysis delay embedding sliding window embedding C. elegans behavior phenotyping |
| url | https://www.frontiersin.org/articles/10.3389/frai.2021.668395/full |
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