{"id":"https://openalex.org/W7225646559","doi":"https://doi.org/10.64898/2026.11.06.764882","title":"HERACLES for fast and accurate likelihood-based reconstruction of massive lineages","display_name":"HERACLES for fast and accurate likelihood-based reconstruction of massive lineages","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225646559","doi":"https://doi.org/10.64898/2026.11.06.764882"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.06.764882","doi":"https://doi.org/10.64898/2026.11.06.764882","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764882","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764882.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":"submittedVersion","is_accepted":false,"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/2026/11/09/2026.11.06.764882.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025881742","display_name":"Sitara Persad","orcid":"https://orcid.org/0009-0009-0422-3280","observed_orcids":["https://orcid.org/0009-0009-0422-3280"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sitara C Persad","raw_affiliation_strings":["Memorial Sloan Kettering Cancer Centre;"],"raw_orcid":"https://orcid.org/0009-0009-0422-3280","affiliations":[{"raw_affiliation_string":"Memorial Sloan Kettering Cancer Centre;","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035010657","display_name":"Quaid Morris","orcid":"https://orcid.org/0000-0002-2760-6999","observed_orcids":["https://orcid.org/0000-0002-2760-6999"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Quaid Morris","raw_affiliation_strings":["Memorial Sloan Kettering Cancer Center"],"raw_orcid":"https://orcid.org/0000-0002-2760-6999","affiliations":[{"raw_affiliation_string":"Memorial Sloan Kettering Cancer Center","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5035010657"],"corresponding_institution_ids":["https://openalex.org/I1334819555"],"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5443999767303467,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.5443999767303467,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2793000042438507,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.07100000232458115,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-reconstruction","display_name":"phylogenetic inference","score":0.8169999718666077},{"id":"https://openalex.org/keywords/heracles","display_name":"Heracles","score":0.7929999828338623},{"id":"https://openalex.org/keywords/hyperbolic-space-embedding","display_name":"hyperbolic space embedding","score":0.8629999756813049},{"id":"https://openalex.org/keywords/continuous-optimization","display_name":"continuous optimization","score":0.30799999833106995}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6575000286102295},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6564000248908997},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5673999786376953},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.525600016117096},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.5051000118255615},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.45019999146461487},{"id":"https://openalex.org/C75291252","wikidata":"https://www.wikidata.org/wiki/Q1315756","display_name":"TRACE (psycholinguistics)","level":2,"score":0.41260001063346863},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4018999934196472},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3668999969959259},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.366100013256073},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3312000036239624},{"id":"https://openalex.org/C206175624","wikidata":"https://www.wikidata.org/wiki/Q595731","display_name":"Branching (polymer chemistry)","level":2,"score":0.30550000071525574},{"id":"https://openalex.org/C137836250","wikidata":"https://www.wikidata.org/wiki/Q984063","display_name":"Optimization problem","level":2,"score":0.28870001435279846},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.25130000710487366},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.250900000333786}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.06.764882","doi":"https://doi.org/10.64898/2026.11.06.764882","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764882","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764882.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.11.06.764882","doi":"https://doi.org/10.64898/2026.11.06.764882","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.06.764882","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.06.764882.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225646559.pdf","grobid_xml":"https://content.openalex.org/works/W7225646559.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W2060425093","https://openalex.org/W2065973977","https://openalex.org/W2097706568","https://openalex.org/W2102424972","https://openalex.org/W2129816388","https://openalex.org/W2406991867","https://openalex.org/W2794829817","https://openalex.org/W2949490462","https://openalex.org/W3014807564","https://openalex.org/W3015748341","https://openalex.org/W3023439819","https://openalex.org/W3024554698","https://openalex.org/W3123518732","https://openalex.org/W3159107339","https://openalex.org/W4229016240","https://openalex.org/W4389992940","https://openalex.org/W4399871727","https://openalex.org/W4403096184","https://openalex.org/W4411924941","https://openalex.org/W4412623163","https://openalex.org/W4417498256","https://openalex.org/W7117292375","https://openalex.org/W7133202814"],"related_works":["https://openalex.org/W7124525945","https://openalex.org/W4327566754","https://openalex.org/W4205239247","https://openalex.org/W7163887041","https://openalex.org/W4403096184","https://openalex.org/W3015748341","https://openalex.org/W4409739068","https://openalex.org/W4415655683","https://openalex.org/W6967536073","https://openalex.org/W7161165356"],"abstract_inverted_index":{"CRISPR-based":[0],"lineage":[1,155,194],"recording":[2,164],"technologies":[3],"can":[4],"trace":[5],"the":[6,59],"ancestry":[7],"of":[8,10,12,30,86,171,182],"hundreds":[9],"thousands":[11],"cells,":[13],"yet":[14],"reconstructing":[15],"accurate":[16],"phylogenies":[17,147],"at":[18],"this":[19],"scale":[20,48],"remains":[21],"computationally":[22,39],"challenging.":[23],"Likelihood-based":[24],"methods":[25,123],"employ":[26],"explicit":[27,104],"evolutionary":[28,105,184],"models":[29],"CRISPR":[31,87],"editing":[32,60,168],"that":[33,54],"improve":[34],"tree":[35,43],"accuracy":[36,120],"but":[37,50],"require":[38],"expensive":[40],"searches":[41],"over":[42,121],"topologies,":[44],"whereas":[45],"distance-based":[46],"alternatives":[47],"efficiently":[49],"rely":[51],"on":[52,135],"distances":[53],"may":[55],"not":[56],"faithfully":[57],"represent":[58],"process,":[61],"introducing":[62],"biases":[63],"whose":[64],"magnitude":[65],"and":[66,110,124,142,153,189],"direction":[67],"are":[68],"unknown.":[69],"Here,":[70],"we":[71],"introduce":[72],"HERACLES,":[73],"which":[74],"optimizes":[75],"cell":[76],"coordinates":[77],"in":[78,131],"hyperbolic":[79],"space":[80],"under":[81],"a":[82,136,187],"quartet-based":[83],"composite":[84],"likelihood":[85,159],"editing.":[88],"By":[89],"recovering":[90],"local":[91,183],"branching":[92],"structures":[93],"directly":[94],"from":[95],"embedded":[96],"distances,":[97],"HERACLES":[98,117,145],"guides":[99],"continuous":[100,180],"optimization":[101,181],"with":[102,149],"an":[103],"model":[106],"without":[107],"repeatedly":[108],"constructing":[109],"evaluating":[111],"complete":[112],"phylogenies.":[113],"Across":[114],"simulated":[115,172],"benchmarks,":[116],"improves":[118,169],"reconstruction":[119,170],"existing":[122],"scales":[125],"to":[126,192],"lineages":[127],"containing":[128],"150,000":[129],"cells":[130],"about":[132],"four":[133],"hours":[134],"single":[137],"GPU.":[138],"On":[139],"experimental":[140],"KP-tracer":[141],"PEtracer":[143],"datasets,":[144],"reconstructs":[146],"consistent":[148],"independent":[150],"anatomical":[151],"annotations":[152],"temporal":[154],"markers.":[156],"Its":[157],"flexible":[158,190],"framework":[160],"also":[161],"accommodates":[162],"different":[163],"mechanisms:":[165],"incorporating":[166],"sequential":[167],"DNA":[173],"Typewriter":[174],"lineages.":[175],"Together,":[176],"these":[177],"results":[178],"establish":[179],"relationships":[185],"as":[186],"scalable":[188],"approach":[191],"probabilistic":[193],"reconstruction.":[195]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}
