{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T07:19:52Z","timestamp":1776496792002,"version":"3.51.2"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1013762","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,1,14]],"date-time":"2026-01-14T00:00:00Z","timestamp":1768348800000}}],"reference-count":55,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T00:00:00Z","timestamp":1767571200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009517","name":"Universit\u00e9 PSL","doi-asserted-by":"crossref","award":["Ecole Doctorale Fronti\u00e8re de l\u2019Innovation en Recherche et Education"],"award-info":[{"award-number":["Ecole Doctorale Fronti\u00e8re de l\u2019Innovation en Recherche et Education"]}],"id":[{"id":"10.13039\/501100009517","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100009517","name":"Universit\u00e9 PSL","doi-asserted-by":"crossref","award":["AI Junior Fellow program"],"award-info":[{"award-number":["AI Junior Fellow program"]}],"id":[{"id":"10.13039\/501100009517","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100010661","name":"Horizon 2020 Framework Programme","doi-asserted-by":"publisher","award":["H2020 MSCA ITN Project SmartNets GA-860949"],"award-info":[{"award-number":["H2020 MSCA ITN Project SmartNets GA-860949"]}],"id":[{"id":"10.13039\/100010661","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100019180","name":"HORIZON EUROPE European Research Council","doi-asserted-by":"publisher","award":["15980"],"award-info":[{"award-number":["15980"]}],"id":[{"id":"10.13039\/100019180","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Research Council","award":["715980"],"award-info":[{"award-number":["715980"]}]},{"DOI":"10.13039\/501100001665","name":"Agence Nationale de la Recherche","doi-asserted-by":"publisher","award":["Locomat ANR-21-CE16-0037"],"award-info":[{"award-number":["Locomat ANR-21-CE16-0037"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Understanding how collective neuronal activity in the brain orchestrates behavior is a central question in integrative neuroscience. Addressing this question requires models that can offer a unified interpretation of multimodal data. In this study, we jointly examine video-recordings of zebrafish larvae freely exploring their environment and calcium imaging of the Anterior Rhombencephalic Turning Region (ARTR) circuit, which is known to control swimming orientation, recorded\n                    <jats:italic>in vivo<\/jats:italic>\n                    under tethered conditions. We show that both behavioral and neural data can be accurately modeled using a Hidden Markov Model (HMM) with three hidden states. In the context of behavior, the hidden states correspond to leftward, rightward, and forward swimming. The HMM robustly captures the key statistical features of the swimming motion, including bout-type persistence and its dependence on bath temperature, while also revealing inter-individual phenotypic variability. For neural data, the three states are found to correspond to left- and right-lateral activation of the ARTR circuit, known to govern the selection of left vs. right reorientation, and a balanced state, which likely corresponds to the behavioral forward state. To further unify the two analyses, we exploit the generative nature of the HMM, using neural sequences to generate synthetic swimming trajectories, whose statistical properties are similar to the behavioral data. Overall, this work demonstrates how state-space models can be used to link neuronal and behavioral data, providing insights into the mechanisms of self-generated action.\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1013762","type":"journal-article","created":{"date-parts":[[2026,1,5]],"date-time":"2026-01-05T19:37:56Z","timestamp":1767641876000},"page":"e1013762","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":2,"title":["Linking brain and behavior states in Zebrafish Larvae locomotion using hidden Markov models"],"prefix":"10.1371","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-9407-3061","authenticated-orcid":true,"given":"Matt\u00e9o","family":"Dommanget-Kott","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4476-805X","authenticated-orcid":true,"given":"Jorge","family":"Fernandez-de-Cossio-Diaz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0004-2091-3592","authenticated-orcid":true,"given":"Monica","family":"Coraggioso","sequence":"additional","affiliation":[]},{"given":"Volker","family":"Bormuth","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4459-0204","authenticated-orcid":true,"given":"R\u00e9mi","family":"Monasson","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3698-4497","authenticated-orcid":true,"given":"Georges","family":"Debr\u00e9geas","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1852-7789","authenticated-orcid":true,"given":"Simona","family":"Cocco","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2026,1,5]]},"reference":[{"key":"pcbi.1013762.ref001","volume-title":"The study of instinct","author":"N Tinbergen","year":"2020"},{"issue":"6","key":"pcbi.1013762.ref002","doi-asserted-by":"crossref","first-page":"1121","DOI":"10.1016\/j.neuron.2015.11.031","article-title":"Mapping sub-second structure in mouse behavior","volume":"88","author":"AB Wiltschko","year":"2015","journal-title":"Neuron."},{"issue":"6","key":"pcbi.1013762.ref003","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007105","article-title":"Drosophila melanogaster grooming possesses syntax with distinct rules at different temporal scales","volume":"15","author":"JM Mueller","year":"2019","journal-title":"PLoS Comput Biol."},{"issue":"3","key":"pcbi.1013762.ref004","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0059865","article-title":"The geometry of locomotive behavioral states in C. elegans","volume":"8","author":"T Gallagher","year":"2013","journal-title":"PLoS One."},{"key":"pcbi.1013762.ref005","article-title":"Statistical structure of locomotion and its modulation by odors","volume":"8","author":"L Tao","year":"2019","journal-title":"Elife."},{"issue":"1","key":"pcbi.1013762.ref006","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2019.11.022","article-title":"Deconstructing hunting behavior reveals a tightly coupled stimulus-response loop","volume":"30","author":"DS Mearns","year":"2020","journal-title":"Curr Biol."},{"key":"pcbi.1013762.ref007","doi-asserted-by":"crossref","DOI":"10.1101\/621540","volume-title":"Hierarchical recurrent state space models reveal discrete and continuous dynamics of neural activity in C. elegans","author":"S Linderman","year":"2019"},{"issue":"42","key":"pcbi.1013762.ref008","doi-asserted-by":"crossref","first-page":"11943","DOI":"10.1073\/pnas.1607601113","article-title":"Predictability and hierarchy in Drosophila behavior","volume":"113","author":"GJ Berman","year":"2016","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"1","key":"pcbi.1013762.ref009","doi-asserted-by":"crossref","DOI":"10.1016\/j.cub.2019.11.026","article-title":"Probabilistic models of Larval Zebrafish behavior reveal structure on many scales","volume":"30","author":"RE Johnson","year":"2020","journal-title":"Curr Biol."},{"issue":"3","key":"pcbi.1013762.ref010","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nn.4497","article-title":"Dynamic models of large-scale brain activity","volume":"20","author":"M Breakspear","year":"2017","journal-title":"Nat Neurosci."},{"issue":"21","key":"pcbi.1013762.ref011","doi-asserted-by":"crossref","first-page":"8214","DOI":"10.1523\/JNEUROSCI.4819-14.2015","article-title":"Dynamics of multistable states during ongoing and evoked cortical activity","volume":"35","author":"L Mazzucato","year":"2015","journal-title":"J Neurosci."},{"key":"pcbi.1013762.ref012","doi-asserted-by":"crossref","first-page":"603","DOI":"10.3389\/fnins.2018.00603","article-title":"Task-evoked dynamic network analysis through hidden Markov modeling","volume":"12","author":"AJ Quinn","year":"2018","journal-title":"Front Neurosci."},{"key":"pcbi.1013762.ref013","doi-asserted-by":"crossref","unstructured":"Zhang Y, Saxena S. 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