{"id":"https://openalex.org/W7224803880","doi":"https://doi.org/10.64898/2026.10.29.762770","title":"Fox: Predicting rates of host-symbiont co-evolution events with association-aware attention","display_name":"Fox: Predicting rates of host-symbiont co-evolution events with association-aware attention","publication_year":2026,"publication_date":"2026-10-30","ids":{"openalex":"https://openalex.org/W7224803880","doi":"https://doi.org/10.64898/2026.10.29.762770"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.29.762770","doi":"https://doi.org/10.64898/2026.10.29.762770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762770","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.29.762770.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.29.762770.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083955819","display_name":"Gabriele Di Palma","orcid":"https://orcid.org/0009-0006-0928-5892","observed_orcids":["https://orcid.org/0009-0006-0928-5892"]},"institutions":[{"id":"https://openalex.org/I155125353","display_name":"Universit\u00e0 Campus Bio-Medico","ror":"https://ror.org/04gqx4x78","country_code":"IT","type":"education","lineage":["https://openalex.org/I155125353"]},{"id":"https://openalex.org/I56441308","display_name":"Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli","ror":"https://ror.org/01q8b6q23","country_code":"IT","type":"education","lineage":["https://openalex.org/I56441308"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Gabriele Di Palma","raw_affiliation_strings":["LUISS University, Rome, Italy","Universit\u00e0 Campus Bio-Medico di Roma, Rome, Italy"],"raw_orcid":"https://orcid.org/0009-0006-0928-5892","affiliations":[{"raw_affiliation_string":"LUISS University, Rome, Italy","institution_ids":["https://openalex.org/I56441308"]},{"raw_affiliation_string":"Universit\u00e0 Campus Bio-Medico di Roma, Rome, Italy","institution_ids":["https://openalex.org/I155125353"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059163151","display_name":"Laurent Jacob","orcid":"https://orcid.org/0000-0002-7826-2719","observed_orcids":["https://orcid.org/0000-0002-7826-2719"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laurent Jacob","raw_affiliation_strings":["Centre National de la Recherche Scientifique, France","Sorbonne Universit\u00e9, F-75005 Paris, France"],"raw_orcid":"https://orcid.org/0000-0002-7826-2719","affiliations":[{"raw_affiliation_string":"Centre National de la Recherche Scientifique, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Sorbonne Universit\u00e9, F-75005 Paris, France","institution_ids":["https://openalex.org/I39804081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082187550","display_name":"Catherine Matias","orcid":"https://orcid.org/0000-0001-6665-2421","observed_orcids":["https://orcid.org/0000-0001-6665-2421"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Catherine Matias","raw_affiliation_strings":["Centre National de la Recherche Scientifique, France","Sorbonne Universit\u00e9, F-75005 Paris, France","Universit\u00e9 Paris Cit\u00e9, Paris, France"],"raw_orcid":"https://orcid.org/0000-0001-6665-2421","affiliations":[{"raw_affiliation_string":"Centre National de la Recherche Scientifique, France","institution_ids":["https://openalex.org/I1294671590"]},{"raw_affiliation_string":"Sorbonne Universit\u00e9, F-75005 Paris, France","institution_ids":["https://openalex.org/I39804081"]},{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, Paris, France","institution_ids":["https://openalex.org/I204730241"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027309652","display_name":"Blerina Sinaimeri","orcid":"https://orcid.org/0000-0002-9797-7592","observed_orcids":["https://orcid.org/0000-0002-9797-7592"]},"institutions":[{"id":"https://openalex.org/I56441308","display_name":"Libera Universit\u00e0 Internazionale degli Studi Sociali Guido Carli","ror":"https://ror.org/01q8b6q23","country_code":"IT","type":"education","lineage":["https://openalex.org/I56441308"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Blerina Sinaimeri","raw_affiliation_strings":["LUISS University, Rome, Italy"],"raw_orcid":"https://orcid.org/0000-0002-9797-7592","affiliations":[{"raw_affiliation_string":"LUISS University, Rome, Italy","institution_ids":["https://openalex.org/I56441308"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083955819"],"corresponding_institution_ids":["https://openalex.org/I155125353","https://openalex.org/I56441308"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8574000000953674,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8574000000953674,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12134","display_name":"Insect symbiosis and bacterial influences","score":0.07180000096559525,"subfield":{"id":"https://openalex.org/subfields/1109","display_name":"Insect Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10815","display_name":"Parasite Biology and Host Interactions","score":0.012400000356137753,"subfield":{"id":"https://openalex.org/subfields/2405","display_name":"Parasitology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/host-symbiont-coevolution","display_name":"host-symbiont coevolution","score":0.9549999833106995},{"id":"https://openalex.org/keywords/cospeciation","display_name":"cospeciation","score":0.8659999966621399},{"id":"https://openalex.org/keywords/host-switching","display_name":"host switching","score":0.9179999828338623},{"id":"https://openalex.org/keywords/symbiont-loss","display_name":"symbiont loss","score":0.9909999966621399},{"id":"https://openalex.org/keywords/transformer","display_name":"transformer models","score":0.7160000205039978},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"multiple sequence alignment","score":0.7110000252723694},{"id":"https://openalex.org/keywords/blattabacterium","display_name":"Blattabacterium","score":0.8309999704360962},{"id":"https://openalex.org/keywords/simulation-based-inference","display_name":"simulation-based inference","score":0.671999990940094}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6646000146865845},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.638700008392334},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5317000150680542},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.5217000246047974},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.47940000891685486},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.460999995470047},{"id":"https://openalex.org/C2779377595","wikidata":"https://www.wikidata.org/wiki/Q21045424","display_name":"Approximate Bayesian computation","level":3,"score":0.45350000262260437},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4528000056743622},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.447299987077713},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.40540000796318054},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3952000141143799},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.3928999900817871},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.390500009059906},{"id":"https://openalex.org/C2777472644","wikidata":"https://www.wikidata.org/wiki/Q16968992","display_name":"Approximate inference","level":3,"score":0.37599998712539673},{"id":"https://openalex.org/C99844830","wikidata":"https://www.wikidata.org/wiki/Q102441924","display_name":"Scaling","level":2,"score":0.3666999936103821},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.3352999985218048},{"id":"https://openalex.org/C122383733","wikidata":"https://www.wikidata.org/wiki/Q865920","display_name":"Approximation error","level":2,"score":0.3255000114440918},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.32330000400543213},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30640000104904175},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2921000123023987},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.2881999909877777},{"id":"https://openalex.org/C33009525","wikidata":"https://www.wikidata.org/wiki/Q208841","display_name":"Coevolution","level":2,"score":0.2757999897003174},{"id":"https://openalex.org/C2777317252","wikidata":"https://www.wikidata.org/wiki/Q18393516","display_name":"Rare events","level":2,"score":0.27239999175071716},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.26010000705718994},{"id":"https://openalex.org/C82142266","wikidata":"https://www.wikidata.org/wiki/Q3456604","display_name":"Dynamic Bayesian network","level":3,"score":0.2572999894618988},{"id":"https://openalex.org/C40969351","wikidata":"https://www.wikidata.org/wiki/Q3516228","display_name":"Word error rate","level":2,"score":0.2565000057220459}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.64898/2026.10.29.762770","doi":"https://doi.org/10.64898/2026.10.29.762770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762770","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.29.762770.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:HAL:hal-05846167v1","doi":null,"is_oa":false,"landing_page_url":"https://hal.science/hal-05846167","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I4405252976","host_organization_name":"Centre pour la Communication Scientifique Directe","host_organization_lineage":["https://openalex.org/I4405252976"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2026","raw_type":"info:eu-repo/semantics/preprint"}],"best_oa_location":{"id":"doi:10.64898/2026.10.29.762770","doi":"https://doi.org/10.64898/2026.10.29.762770","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.29.762770","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/30/2026.10.29.762770.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320326256","display_name":"Grand \u00c9quipement National De Calcul Intensif","ror":"https://ror.org/0010d1q40"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7224803880.pdf","grobid_xml":"https://content.openalex.org/works/W7224803880.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1992274351","https://openalex.org/W2008252897","https://openalex.org/W2058069729","https://openalex.org/W2094002760","https://openalex.org/W2102109244","https://openalex.org/W2120145798","https://openalex.org/W2134255028","https://openalex.org/W2138798117","https://openalex.org/W2144454528","https://openalex.org/W2151070329","https://openalex.org/W2171695241","https://openalex.org/W2730073597","https://openalex.org/W2884761632","https://openalex.org/W2999997893","https://openalex.org/W3036622457","https://openalex.org/W3157478955","https://openalex.org/W3177828909","https://openalex.org/W4229066198","https://openalex.org/W4281387890","https://openalex.org/W4408339719","https://openalex.org/W4415274161","https://openalex.org/W4417514206","https://openalex.org/W7118545112","https://openalex.org/W7161978902"],"related_works":["https://openalex.org/W4281387890","https://openalex.org/W7097542056","https://openalex.org/W2134255028","https://openalex.org/W4410487051","https://openalex.org/W7095856077","https://openalex.org/W6966935794","https://openalex.org/W7151120961","https://openalex.org/W4393303805","https://openalex.org/W7213507260","https://openalex.org/W4220893675"],"abstract_inverted_index":{"Abstract":[0],"Motivation":[1],"Hosts":[2],"and":[3,58,91,97,135,158,215,217,272,303,306,323,352,364],"their":[4,98,307],"symbionts":[5],"share":[6],"a":[7,30,40,49,70,87,112,124,141],"history":[8],"of":[9,25,33,80,89,229,294],"associations":[10],"in":[11,140,274],"which":[12],"lineages":[13],"cospeciate,":[14],"switch":[15],"hosts,":[16],"duplicate,":[17],"or":[18,104],"are":[19],"lost.":[20],"Quantifying":[21],"the":[22,56,77,81,183,191,234,241,260,275,291,295,356,370],"relative":[23,78,292],"frequencies":[24,79,119,156,293],"these":[26,202],"four":[27,82,296],"events":[28,84,298],"is":[29,109,176,324,349],"central":[31],"goal":[32],"cophylogenetics,":[34],"but":[35,175],"existing":[36],"tools":[37],"typically":[38],"require":[39],"fully":[41],"resolved,":[42],"correctly":[43],"rooted":[44],"host":[45,90,213,302],"tree,":[46,51],"often":[47],"alongside":[48],"symbiont":[50,92,304,330],"propagating":[52],"tree-inference":[53],"errors":[54],"into":[55],"reconciliation":[57,105],"scaling":[59],"poorly":[60],"to":[61,181,190,233,253,326,328],"large":[62,329],"systems.":[63],"Results":[64],"We":[65],"introduce":[66],"F":[67,107,152,238,279,288,313,347],"ox":[68,108,153,239,280,289,314,348],",":[69,363],"transformer":[71],"neural":[72],"network":[73],"architecture":[74],"that":[75,246,259,332],"infers":[76,290],"cophylogenetic":[83,297],"directly":[85,299],"from":[86,120,148,166,265,284,300,343],"pair":[88],"multiple":[93],"sequence":[94,99],"alignments":[95,121,276],"(MSAs)":[96],"mapping,":[100,308],"with":[101,159,309],"no":[102,310],"tree-reconstruction":[103,311],"step.":[106,312],"trained":[110],"under":[111],"simulation-based":[113],"inference":[114],"scheme:":[115],"it":[116,204,368],"learns":[117],"event":[118,155],"generated":[122],"by":[123,209],"coevolutionary":[125,261],"process,":[126],"paying":[127],"its":[128,149,171],"computational":[129],"cost":[130],"once":[131],"at":[132],"training":[133,150],"time":[134],"processing":[136],"any":[137],"new":[138],"system":[139],"single":[142],"forward":[143],"pass.":[144],"On":[145,162,340],"held-out":[146],"data":[147,165,251,342,367],"simulator,":[151,170,346],"recovers":[154,240,369],"accurately":[157],"near-zero":[160],"bias.":[161],"additional":[163],"synthetic":[164],"an":[167,344],"independent":[168,345],"cophylogeny":[169],"error":[172,208,220],"roughly":[173],"doubled,":[174],"still":[177],"very":[178],"low":[179],"allowing":[180],"track":[182],"true":[184],"frequencies.":[185],"Most":[186],"importantly,":[187],"when":[188],"compared":[189],"Approximate":[192],"Bayesian":[193],"Computation":[194],"(ABC)-based":[195],"method":[196],"A":[197,319,333,359],"mo":[198,320,334,360],"C":[199,321,335,361],"oala":[200,322,336,362],"on":[201,249,365],"data,":[203],"reduces":[205],"mean":[206],"absolute":[207],"45-76%":[210],"for":[211,221],"cospeciations,":[212],"switches":[214],"duplications":[216],"shows":[218],"similar":[219],"losses,":[222],"while":[223],"running":[224],"more":[225,350],"than":[226,318,355],"three":[227],"orders":[228],"magnitude":[230],"faster.":[231],"Applied":[232],"empirical":[235,366],"cockroach-Blattabacterium":[236],"system,":[237],"expected":[242,371],"cospeciation-dominated":[243,372],"profile,":[244],"showing":[245],"behaviour":[247],"learned":[248],"simulated":[250,341],"transfers":[252],"real":[254],"sequences.":[255],"These":[256],"results":[257],"confirm":[258],"signal":[262],"usually":[263],"extracted":[264],"trees":[266,331],"can":[267,281],"be":[268,282],"read":[269],"directly,":[270],"accurately,":[271],"fast":[273],"themselves.":[277],"Availability":[278],"downloaded":[283],"https://github.com/Gabbo240900/Fox":[285],"Key":[286],"Messages":[287],"paired":[301],"MSAs":[305],"produces":[315],"inferences":[316],"faster":[317],"able":[325],"scale":[327],"could":[337],"not":[338],"complete.":[339],"accurate":[351],"less":[353],"biased":[354],"ABC":[357],"baseline":[358],"profile.":[373]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-10-31T00:00:00"}
