{"id":"https://openalex.org/W3195991557","doi":"https://doi.org/10.1093/bioinformatics/btab580","title":"A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype","display_name":"A cross-level information transmission network for hierarchical omics data integration and phenotype prediction from a new genotype","publication_year":2021,"publication_date":"2021-08-12","ids":{"openalex":"https://openalex.org/W3195991557","doi":"https://doi.org/10.1093/bioinformatics/btab580","mag":"3195991557","pmid":"https://pubmed.ncbi.nlm.nih.gov/34390577"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/204/41891246/btab580.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/204/41891246/btab580.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100739031","display_name":"Di He","orcid":"https://orcid.org/0000-0002-0908-9123"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Di He","raw_affiliation_strings":["PhD Program in Computer Science, Graduate Center, City University of New York , New York, NY 10016, USA"],"raw_orcid":"https://orcid.org/0000-0002-0908-9123","affiliations":[{"raw_affiliation_string":"PhD Program in Computer Science, Graduate Center, City University of New York , New York, NY 10016, USA","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066245750","display_name":"Lei Xie","orcid":"https://orcid.org/0000-0001-9051-2111"},"institutions":[{"id":"https://openalex.org/I121847817","display_name":"The Graduate Center, CUNY","ror":"https://ror.org/00awd9g61","country_code":"US","type":"education","lineage":["https://openalex.org/I121847817"]},{"id":"https://openalex.org/I174216632","display_name":"City University of New York","ror":"https://ror.org/00453a208","country_code":"US","type":"education","lineage":["https://openalex.org/I174216632"]},{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]},{"id":"https://openalex.org/I39694355","display_name":"Hunter College","ror":"https://ror.org/00g2xk477","country_code":"US","type":"education","lineage":["https://openalex.org/I39694355"]},{"id":"https://openalex.org/I4210097825","display_name":"MIND Research Institute","ror":"https://ror.org/00we1gw23","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210097825"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lei Xie","raw_affiliation_strings":["Department of Computer Science, Hunter College, City University of New York , New York, NY 10065, USA","Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University , New York, NY 10021, USA","PhD Program in Computer Science, Graduate Center, City University of New York , New York, NY 10016, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hunter College, City University of New York , New York, NY 10065, USA","institution_ids":["https://openalex.org/I174216632","https://openalex.org/I39694355"]},{"raw_affiliation_string":"Feil Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University , New York, NY 10021, USA","institution_ids":["https://openalex.org/I205783295","https://openalex.org/I4210097825"]},{"raw_affiliation_string":"PhD Program in Computer Science, Graduate Center, City University of New York , New York, NY 10016, USA","institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066245750"],"corresponding_institution_ids":["https://openalex.org/I121847817","https://openalex.org/I174216632","https://openalex.org/I205783295","https://openalex.org/I39694355","https://openalex.org/I4210097825"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":{"value":3478,"currency":"USD","value_usd":3478},"fwci":0.9697,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.7402758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":98},"biblio":{"volume":"38","issue":"1","first_page":"204","last_page":"210"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4555000066757202,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4555000066757202,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.1746000051498413,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.13439999520778656,"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/computer-science","display_name":"Computer science","score":0.6619017124176025},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.5205267667770386},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.4482109248638153},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4431374669075012},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4223536252975464},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4214669466018677},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3599042296409607},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3249672055244446},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22155949473381042}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6619017124176025},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5205267667770386},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.4482109248638153},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4431374669075012},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4223536252975464},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4214669466018677},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3599042296409607},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3249672055244446},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22155949473381042},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/204/41891246/btab580.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34390577","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34390577","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8696111","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8696111","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab580","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab580","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/1/204/41891246/btab580.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Reduced inequalities","score":0.6800000071525574,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G2310007953","display_name":null,"funder_award_id":"R01 GM122845","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4636237231","display_name":null,"funder_award_id":"R01 AG057555","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"}],"funders":[{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3195991557.pdf","grobid_xml":"https://content.openalex.org/works/W3195991557.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1731081199","https://openalex.org/W2102409316","https://openalex.org/W2108068107","https://openalex.org/W2108933868","https://openalex.org/W2210006295","https://openalex.org/W2212660284","https://openalex.org/W2315556365","https://openalex.org/W2395579298","https://openalex.org/W2795345500","https://openalex.org/W2802321540","https://openalex.org/W2804291108","https://openalex.org/W2900569176","https://openalex.org/W2941444700","https://openalex.org/W2944664266","https://openalex.org/W2944727022","https://openalex.org/W2947189704","https://openalex.org/W2950457484","https://openalex.org/W2951449549","https://openalex.org/W2953127297","https://openalex.org/W2955502047","https://openalex.org/W2963046727","https://openalex.org/W3003739490","https://openalex.org/W3035604179","https://openalex.org/W3127930610","https://openalex.org/W4295521014","https://openalex.org/W4320013936","https://openalex.org/W6637618735","https://openalex.org/W6675401909","https://openalex.org/W6688325169","https://openalex.org/W6725448924","https://openalex.org/W6735913928","https://openalex.org/W6780725546"],"related_works":["https://openalex.org/W2965546495","https://openalex.org/W4389116644","https://openalex.org/W2153315159","https://openalex.org/W3103844505","https://openalex.org/W259157601","https://openalex.org/W4205463238","https://openalex.org/W2761785940","https://openalex.org/W2110523656","https://openalex.org/W1482209366","https://openalex.org/W2521627374"],"abstract_inverted_index":{"MOTIVATION:":[0],"An":[1],"unsolved":[2],"fundamental":[3],"problem":[4],"in":[5,31,177,210,242],"biology":[6],"is":[7,62,251],"to":[8,64,83,120,127,144,168,192,234],"predict":[9],"phenotypes":[10],"from":[11,69,81,215],"a":[12,112,231,243],"new":[13,25],"genotype":[14],"under":[15],"environmental":[16],"perturbations.":[17],"The":[18,248],"emergence":[19],"of":[20,35,41,47,133,149,158,173,180,196,208,221],"multiple":[21,87,139],"omics":[22,67,141,190],"data":[23,43,50,68,142,191,241,259],"provides":[24,230],"opportunities":[26],"but":[27],"imposes":[28],"great":[29],"challenges":[30],"the":[32,39,45,53,78,122,129,134,146,155,159,170,174,178,187,194,197,202,219],"predictive":[33,198],"modeling":[34],"genotype-phenotype":[36],"associations.":[37],"Firstly,":[38],"high-dimensionality":[40],"genomics":[42],"and":[44,100,143,204,238],"lack":[46],"coherent":[48],"labeled":[49],"often":[51],"make":[52],"existing":[54],"supervised":[55],"learning":[56,172],"techniques":[57],"less":[58],"successful.":[59],"Secondly,":[60],"it":[61,164],"challenging":[63],"integrate":[65,239],"heterogeneous":[66,189],"different":[70],"resources.":[71],"Finally,":[72],"few":[73],"works":[74],"have":[75,97],"explicitly":[76],"modeled":[77],"information":[79,236],"transmission":[80],"DNA":[82],"phenotype,":[84],"which":[85],"involves":[86],"intermediate":[88],"molecular":[89],"types.":[90],"Higher-level":[91],"features":[92,105],"(e.g.":[93,106],"gene":[94,222],"expression)":[95],"usually":[96],"stronger":[98],"discriminative":[99],"interpretable":[101],"power":[102,148],"than":[103],"lower-level":[104],"somatic":[107,216],"mutation).":[108],"RESULTS:":[109],"We":[110,200],"propose":[111],"novel":[113],"Cross-LEvel":[114],"Information":[115],"Transmission":[116],"(CLEIT)":[117],"network":[118],"framework":[119,233],"address":[121],"above":[123],"issues.":[124],"CLEIT":[125,152,184,209,229],"aims":[126],"represent":[128],"asymmetrical":[130],"multi-level":[131,244],"organization":[132],"biological":[135],"system":[136],"by":[137],"integrating":[138],"incoherent":[140],"improve":[145,169,193],"prediction":[147],"low-level":[150,175],"features.":[151],"first":[153],"learns":[154],"latent":[156],"representation":[157,171],"high-level":[160],"domain":[161,176],"then":[162],"uses":[163],"as":[165],"ground-truth":[166],"embedding":[167],"form":[179],"contrastive":[181],"loss.":[182],"Besides,":[183],"can":[185],"leverage":[186],"unlabeled":[188],"generalizability":[195],"model.":[199],"demonstrate":[201],"effectiveness":[203],"significant":[205],"performance":[206],"boost":[207],"predicting":[211],"anti-cancer":[212],"drug":[213],"sensitivity":[214],"mutations":[217],"via":[218],"assistance":[220],"expressions":[223],"when":[224],"compared":[225],"with":[226],"state-of-the-art":[227],"methods.":[228],"general":[232],"model":[235],"transmissions":[237],"multi-modal":[240],"system.":[245],"AVAILABILITYAND":[246],"IMPLEMENTATION:":[247],"source":[249],"code":[250],"freely":[252],"available":[253,261],"at":[254,262],"https://github.com/XieResearchGroup/CLEIT.":[255],"SUPPLEMENTARY":[256],"INFORMATION:":[257],"Supplementary":[258],"are":[260],"Bioinformatics":[263],"online.":[264]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
