{"id":"https://openalex.org/W4414804602","doi":"https://doi.org/10.48550/arxiv.2510.00087","title":"Revealing the temporal dynamics of antibiotic anomalies in the infant gut microbiome with neural jump ODEs","display_name":"Revealing the temporal dynamics of antibiotic anomalies in the infant gut microbiome with neural jump ODEs","publication_year":2025,"publication_date":"2025-09-30","ids":{"openalex":"https://openalex.org/W4414804602","doi":"https://doi.org/10.48550/arxiv.2510.00087"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2510.00087","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2510.00087","pdf_url":"https://arxiv.org/pdf/2510.00087","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2510.00087","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082470569","display_name":"A. K. Adamov","orcid":"https://orcid.org/0000-0002-7506-1583"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adamov, Anja","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119839251","display_name":"Markus Chardonnet","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Chardonnet, Markus","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049192596","display_name":"Florian Krach","orcid":"https://orcid.org/0000-0002-4506-8792"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Krach, Florian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010858034","display_name":"Jakob Heiss","orcid":"https://orcid.org/0000-0003-1447-6782"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Heiss, Jakob","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084818994","display_name":"Josef Teichmann","orcid":"https://orcid.org/0000-0003-0125-7484"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Teichmann, Josef","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5000165682","display_name":"Nicholas A. Bokulich","orcid":"https://orcid.org/0000-0002-1784-8935"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bokulich, Nicholas A.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13289","display_name":"Infant Health and Development","score":0.9096999764442444,"subfield":{"id":"https://openalex.org/subfields/3611","display_name":"Pharmacy"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T13289","display_name":"Infant Health and Development","score":0.9096999764442444,"subfield":{"id":"https://openalex.org/subfields/3611","display_name":"Pharmacy"},"field":{"id":"https://openalex.org/fields/36","display_name":"Health Professions"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/anomaly","display_name":"Anomaly (physics)","score":0.6969000101089478},{"id":"https://openalex.org/keywords/jump","display_name":"Jump","score":0.626800000667572},{"id":"https://openalex.org/keywords/ode","display_name":"Ode","score":0.6129000186920166},{"id":"https://openalex.org/keywords/anomaly-detection","display_name":"Anomaly detection","score":0.5051000118255615},{"id":"https://openalex.org/keywords/replicate","display_name":"Replicate","score":0.5002999901771545},{"id":"https://openalex.org/keywords/microbiome","display_name":"Microbiome","score":0.48100000619888306},{"id":"https://openalex.org/keywords/noise","display_name":"Noise (video)","score":0.38830000162124634},{"id":"https://openalex.org/keywords/path","display_name":"Path (computing)","score":0.3481000065803528}],"concepts":[{"id":"https://openalex.org/C12997251","wikidata":"https://www.wikidata.org/wiki/Q567560","display_name":"Anomaly (physics)","level":2,"score":0.6969000101089478},{"id":"https://openalex.org/C2780695682","wikidata":"https://www.wikidata.org/wiki/Q4005959","display_name":"Jump","level":2,"score":0.626800000667572},{"id":"https://openalex.org/C34862557","wikidata":"https://www.wikidata.org/wiki/Q178985","display_name":"Ode","level":2,"score":0.6129000186920166},{"id":"https://openalex.org/C739882","wikidata":"https://www.wikidata.org/wiki/Q3560506","display_name":"Anomaly detection","level":2,"score":0.5051000118255615},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.5002999901771545},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.48100000619888306},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4269999861717224},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4097999930381775},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.38830000162124634},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37139999866485596},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.3481000065803528},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.33980000019073486},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.336899995803833},{"id":"https://openalex.org/C112758219","wikidata":"https://www.wikidata.org/wiki/Q16038819","display_name":"Duration (music)","level":2,"score":0.3312000036239624},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.33009999990463257},{"id":"https://openalex.org/C501593827","wikidata":"https://www.wikidata.org/wiki/Q12187","display_name":"Antibiotics","level":2,"score":0.32659998536109924},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3221000134944916},{"id":"https://openalex.org/C196083921","wikidata":"https://www.wikidata.org/wiki/Q7915758","display_name":"Variance (accounting)","level":2,"score":0.3215999901294708},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3197999894618988},{"id":"https://openalex.org/C145912823","wikidata":"https://www.wikidata.org/wiki/Q113558","display_name":"Dynamics (music)","level":2,"score":0.2953999936580658},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.275299996137619},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.272599995136261},{"id":"https://openalex.org/C93226319","wikidata":"https://www.wikidata.org/wiki/Q193137","display_name":"Differential (mechanical device)","level":2,"score":0.27070000767707825},{"id":"https://openalex.org/C2778067643","wikidata":"https://www.wikidata.org/wiki/Q166507","display_name":"Interval (graph theory)","level":2,"score":0.25119999051094055}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2510.00087","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2510.00087","pdf_url":"https://arxiv.org/pdf/2510.00087","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2510.00087","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2510.00087","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2510.00087","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2510.00087","pdf_url":"https://arxiv.org/pdf/2510.00087","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Detecting":[0],"anomalies":[1,83,139],"in":[2,10,40,110],"irregularly":[3,21],"sampled":[4,22],"multi-variate":[5],"time-series":[6,23],"is":[7],"challenging,":[8],"especially":[9],"data-scarce":[11],"settings.":[12],"Here":[13],"we":[14],"introduce":[15],"an":[16],"anomaly":[17,48,108],"detection":[18],"framework":[19,61],"for":[20,127,136],"that":[24],"leverages":[25],"neural":[26],"jump":[27],"ordinary":[28],"differential":[29],"equations":[30],"(NJODEs).":[31],"The":[32],"method":[33],"infers":[34],"conditional":[35],"mean":[36],"and":[37,46,57,76,91,115,129,132],"variance":[38],"trajectories":[39],"a":[41,134,144],"fully":[42],"path":[43],"dependent":[44],"way":[45],"computes":[47],"scores.":[49],"On":[50],"synthetic":[51],"data":[52],"containing":[53],"jump,":[54],"drift,":[55],"diffusion,":[56],"noise":[58],"anomalies,":[59],"the":[60,74,94,102,106],"accurately":[62,111],"identifies":[63],"diverse":[64],"deviations.":[65],"Applied":[66],"to":[67,147],"infant":[68],"gut":[69],"microbiome":[70],"trajectories,":[71],"it":[72],"delineates":[73],"magnitude":[75],"persistence":[77],"of":[78,97,105],"antibiotic-induced":[79],"disruptions:":[80],"revealing":[81],"prolonged":[82],"after":[84],"second":[85,95],"antibiotic":[86,113],"courses,":[87],"extended":[88],"duration":[89],"treatments,":[90],"exposures":[92],"during":[93],"year":[96],"life.":[98],"We":[99],"further":[100],"demonstrate":[101],"predictive":[103],"capabilities":[104],"inferred":[107],"scores":[109],"predicting":[112],"events":[114],"outperforming":[116],"diversity-based":[117],"baselines.":[118],"Our":[119],"approach":[120],"accommodates":[121],"unevenly":[122],"spaced":[123],"longitudinal":[124],"observations,":[125],"adjusts":[126],"static":[128],"dynamic":[130],"covariates,":[131],"provides":[133],"foundation":[135],"inferring":[137],"microbial":[138,153],"induced":[140],"by":[141,151],"perturbations,":[142],"offering":[143],"translational":[145],"opportunity":[146],"optimize":[148],"intervention":[149],"regimens":[150],"minimizing":[152],"disruptions.":[154]},"counts_by_year":[],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}
