{"id":"https://openalex.org/W7225638146","doi":"https://doi.org/10.64898/2026.11.07.765023","title":"A Three-View System for CRISPR-Cas12a crRNA Activity Ranking: When to Ensemble, When Context Matters More","display_name":"A Three-View System for CRISPR-Cas12a crRNA Activity Ranking: When to Ensemble, When Context Matters More","publication_year":2026,"publication_date":"2026-11-09","ids":{"openalex":"https://openalex.org/W7225638146","doi":"https://doi.org/10.64898/2026.11.07.765023"},"language":"en","primary_location":{"id":"doi:10.64898/2026.11.07.765023","doi":"https://doi.org/10.64898/2026.11.07.765023","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.07.765023","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.07.765023.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/2026/11/09/2026.11.07.765023.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5161359696","display_name":"Tianze Deng","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Tianze Deng","raw_affiliation_strings":["University of Washington;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Washington;","institution_ids":["https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143898268","display_name":"Zibo Lin","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zibo Lin","raw_affiliation_strings":["Central South University;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central South University;","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5147143891","display_name":"Hoyan Lam","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Hoyan Lam","raw_affiliation_strings":["The Chinese University of Hong Kong;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Chinese University of Hong Kong;","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5161306222","display_name":"Shirui Xu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27781120","display_name":"Wenzhou Medical University","ror":"https://ror.org/00rd5t069","country_code":"CN","type":"education","lineage":["https://openalex.org/I27781120"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shirui Xu","raw_affiliation_strings":["Wenzhou Medical University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wenzhou Medical University","institution_ids":["https://openalex.org/I27781120"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5161359696"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9990000128746033,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9990000128746033,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":9.999999747378752e-05,"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/T10211","display_name":"Computational Drug Discovery Methods","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/crispr-cas12a","display_name":"CRISPR/Cas12a","score":0.9990000128746033},{"id":"https://openalex.org/keywords/crrna-design","display_name":"crRNA design","score":0.7250000238418579},{"id":"https://openalex.org/keywords/sequence-features","display_name":"sequence features","score":0.546999990940094},{"id":"https://openalex.org/keywords/reference-mapping","display_name":"reference mapping","score":0.6480000019073486},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"ensemble learning","score":0.5590000152587891},{"id":"https://openalex.org/keywords/xgboost","display_name":"XGBoost","score":0.7639999985694885},{"id":"https://openalex.org/keywords/information-leakage","display_name":"information leakage","score":0.722000002861023},{"id":"https://openalex.org/keywords/perturbation-analysis","display_name":"perturbation analysis","score":0.5910000205039978}],"concepts":[{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6183000206947327},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5906000137329102},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5590000152587891},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5042999982833862},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5016000270843506},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.4481000006198883},{"id":"https://openalex.org/C159744936","wikidata":"https://www.wikidata.org/wiki/Q1126730","display_name":"Spearman's rank correlation coefficient","level":2,"score":0.4189999997615814},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.4020000100135803},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4002000093460083},{"id":"https://openalex.org/C150921843","wikidata":"https://www.wikidata.org/wiki/Q1170431","display_name":"Resampling","level":2,"score":0.34630000591278076},{"id":"https://openalex.org/C119898033","wikidata":"https://www.wikidata.org/wiki/Q3433888","display_name":"Ensemble forecasting","level":2,"score":0.34549999237060547},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32580000162124634},{"id":"https://openalex.org/C3019719930","wikidata":"https://www.wikidata.org/wiki/Q3910099","display_name":"Predictive value","level":2,"score":0.3142000138759613},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.29330000281333923},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.28769999742507935},{"id":"https://openalex.org/C2776291640","wikidata":"https://www.wikidata.org/wiki/Q2912517","display_name":"Value (mathematics)","level":2,"score":0.28700000047683716},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28139999508857727},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.25929999351501465},{"id":"https://openalex.org/C25343380","wikidata":"https://www.wikidata.org/wiki/Q277521","display_name":"Relation (database)","level":2,"score":0.2542000114917755},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.25279998779296875}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.11.07.765023","doi":"https://doi.org/10.64898/2026.11.07.765023","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.07.765023","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.07.765023.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:10.64898/2026.11.07.765023","doi":"https://doi.org/10.64898/2026.11.07.765023","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.11.07.765023","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/11/09/2026.11.07.765023.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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225638146.pdf","grobid_xml":"https://content.openalex.org/works/W7225638146.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1989020100","https://openalex.org/W2010759469","https://openalex.org/W2079135485","https://openalex.org/W2086561953","https://openalex.org/W2295598076","https://openalex.org/W2560136348","https://openalex.org/W2787024379","https://openalex.org/W3020992444","https://openalex.org/W3109609494","https://openalex.org/W4233056867","https://openalex.org/W4392120809","https://openalex.org/W4399702097","https://openalex.org/W4401455507"],"related_works":["https://openalex.org/W4410267784","https://openalex.org/W7162857298","https://openalex.org/W2801867656","https://openalex.org/W4404235119","https://openalex.org/W4387707751","https://openalex.org/W7162295190","https://openalex.org/W4415068222","https://openalex.org/W4292291423","https://openalex.org/W4290729342","https://openalex.org/W4362582590"],"abstract_inverted_index":{"CRISPR-Cas12a":[0],"assays":[1],"require":[2],"effective":[3],"crRNA":[4],"selection,":[5],"but":[6,166],"experimentally":[7],"screening":[8],"all":[9],"possible":[10],"candidates":[11,160],"is":[12,173],"costly.":[13],"We":[14],"developed":[15],"TriCasRank,":[16],"a":[17,85],"ranking":[18,159],"model":[19,89,126],"that":[20,83],"combines":[21],"sequence":[22],"features":[23],"with":[24],"EasyDesign":[25],"reference":[26],"mapping":[27,108],"and":[28,109,151],"activity":[29,137],"summaries":[30,36],"from":[31,59],"related":[32],"training":[33,41,150],"records.":[34],"Historical":[35],"were":[37,116,122,147],"calculated":[38],"within":[39,162],"each":[40],"fold":[42],"to":[43,65,75,82,98],"avoid":[44],"information":[45],"leakage.":[46],"In":[47],"five-fold":[48],"target-grouped":[49],"cross-validation":[50],"using":[51,124],"out-of-fold":[52],"predictions,":[53],"TriCasRank":[54,153],"improved":[55],"the":[56,62,104,133,136,163],"Spearman":[57],"correlation":[58],"0.741":[60],"for":[61,158],"sequence-only":[63],"ensemble":[64],"0.821":[66],"(paired":[67],"difference,":[68,93],"0.080;":[69],"95%":[70,95],"target-group":[71],"bootstrap":[72],"interval,":[73,96],"0.072":[74],"0.090).":[76],"However,":[77],"its":[78],"performance":[79],"was":[80],"comparable":[81,119],"of":[84,107,135],"strong":[86],"sequence-plus-mapping":[87],"XGBoost":[88],"(SCC,":[90],"0.822;":[91],"paired":[92],"-0.001;":[94],"-0.007":[97],"0.005).":[99],"Separate":[100],"perturbation":[101],"analyses":[102],"supported":[103],"predictive":[105],"value":[106],"historical":[110],"features,":[111],"although":[112],"their":[113],"effect":[114],"sizes":[115],"not":[117],"directly":[118],"because":[120],"they":[121],"evaluated":[123],"different":[125],"configurations.":[127],"Prediction":[128],"errors":[129],"remained":[130],"larger":[131],"at":[132],"extremes":[134],"distribution.":[138],"Performance":[139],"also":[140],"became":[141],"less":[142],"stable":[143],"when":[144],"template":[145],"identities":[146],"separated":[148],"between":[149],"evaluation.":[152],"may":[154],"therefore":[155],"be":[156],"useful":[157],"represented":[161],"EasyDesign-derived":[164],"domain,":[165],"evaluation":[167],"on":[168],"an":[169],"independent":[170],"experimental":[171],"cohort":[172],"still":[174],"needed.":[175]},"counts_by_year":[],"updated_date":"2026-11-11T12:16:26.678958","created_date":"2026-11-10T00:00:00"}
