{"id":"https://openalex.org/W2953360940","doi":"https://doi.org/10.1109/bibm.2018.8621532","title":"Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge","display_name":"Learning Protein Structural Fingerprints under the Label-Free Supervision of Domain Knowledge","publication_year":2018,"publication_date":"2018-12-01","ids":{"openalex":"https://openalex.org/W2953360940","doi":"https://doi.org/10.1109/bibm.2018.8621532","mag":"2953360940"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2018.8621532","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621532","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089495153","display_name":"Yaosen Min","orcid":"https://orcid.org/0000-0003-4741-6188"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yaosen Min","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736011","display_name":"Shang Liu","orcid":"https://orcid.org/0000-0001-8050-7968"},"institutions":[{"id":"https://openalex.org/I139759216","display_name":"Beijing University of Posts and Telecommunications","ror":"https://ror.org/04w9fbh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I139759216"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shang Liu","raw_affiliation_strings":["E-Commerce Engineering with Law Beijing University of Posts and Telecommunications, Beijing, China"],"affiliations":[{"raw_affiliation_string":"E-Commerce Engineering with Law Beijing University of Posts and Telecommunications, Beijing, China","institution_ids":["https://openalex.org/I139759216"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021089898","display_name":"Chenyao Lou","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenyao Lou","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Institute for Interdisciplinary Information Sciences (IIIS), Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5089495153"],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":null,"apc_paid":null,"fwci":0.1838,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.54421897,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"69","last_page":"74"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976999759674072,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9976999759674072,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9927999973297119,"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":0.6173902750015259},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5112409591674805},{"id":"https://openalex.org/keywords/fingerprint","display_name":"Fingerprint (computing)","score":0.4432852864265442},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2896074950695038}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6173902750015259},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5112409591674805},{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.4432852864265442},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2896074950695038},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2018.8621532","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2018.8621532","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1493324970","https://openalex.org/W1608341719","https://openalex.org/W1916412816","https://openalex.org/W2022058405","https://openalex.org/W2032410720","https://openalex.org/W2058731099","https://openalex.org/W2071037669","https://openalex.org/W2081771568","https://openalex.org/W2102245393","https://openalex.org/W2106433904","https://openalex.org/W2130479394","https://openalex.org/W2131571251","https://openalex.org/W2137146016","https://openalex.org/W2144998676","https://openalex.org/W2147043108","https://openalex.org/W2149866421","https://openalex.org/W2152326664","https://openalex.org/W2153153865","https://openalex.org/W2157365507","https://openalex.org/W2157825442","https://openalex.org/W2157965775","https://openalex.org/W2158714788","https://openalex.org/W2163016858","https://openalex.org/W2170002939","https://openalex.org/W2187089797","https://openalex.org/W2243910093","https://openalex.org/W2311607323","https://openalex.org/W2526647724","https://openalex.org/W2540069603","https://openalex.org/W2600704321","https://openalex.org/W2747370968","https://openalex.org/W2917640756","https://openalex.org/W2919115771","https://openalex.org/W2949867299","https://openalex.org/W2963019788","https://openalex.org/W2963457143","https://openalex.org/W3023058184","https://openalex.org/W4298082496","https://openalex.org/W6636233635","https://openalex.org/W6698064614","https://openalex.org/W6727266034"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Finding":[0],"homologous":[1,91,117,131],"proteins":[2,92],"is":[3,22,46,136,183,230],"the":[4,60,71,102,149,152,158,162,165,174,177,189,194,206,213,236],"indispensable":[5],"first":[6],"step":[7],"in":[8,27,41],"many":[9],"protein":[10,20,28,39],"biology":[11],"studies.":[12],"Thus,":[13],"building":[14],"highly":[15,24],"efficient":[16],"\u201csearch":[17],"engines\u201d":[18],"for":[19,58,101,111,116,130,141],"databases":[21,115,129],"a":[23,51,55,121,220,226,231],"desired":[25],"function":[26],"bioinformatics.":[29],"As":[30],"of":[31,210,222],"August":[32],"2018,":[33],"there":[34],"are":[35,84,109,154],"more":[36],"than":[37],"140,000":[38],"structures":[40],"PDB,":[42],"and":[43,67,79,143],"this":[44],"number":[45,53],"still":[47],"increasing":[48],"rapidly.":[49],"Such":[50],"big":[52,56],"introduces":[54],"challenge":[57],"scanning":[59,113],"whole":[61],"structure":[62,81,114,128,139],"database":[63],"with":[64,148],"high":[65,68],"speeds":[66],"sensitivities":[69],"at":[70],"same":[72],"time.":[73],"Unfortunately,":[74],"classic":[75],"sequence":[76,95],"alignment":[77,82],"tools":[78,83],"pairwise":[80],"either":[85],"not":[86,98],"sensitive":[87],"enough":[88,100],"to":[89,125,137,144,192,201,224],"remote":[90],"(with":[93],"low":[94],"identities)":[96],"or":[97],"fast":[99],"task.":[103],"Therefore,":[104],"specifically":[105],"designed":[106],"computational":[107],"methods":[108],"required":[110],"quickly":[112,126],"proteins.Here,":[118],"we":[119],"propose":[120],"novel":[122],"ContactLib-DNN":[123,204,218],"method":[124],"scan":[127],"proteins.":[132,163],"The":[133],"core":[134],"idea":[135],"build":[138],"fingerprints":[140,153],"proteins,":[142],"perform":[145],"alignment-free":[146],"comparisons":[147],"fingerprints.":[150],"Specifically,":[151],"low-dimensional":[155],"vectors":[156,171],"representing":[157],"contact":[159,180],"groups":[160],"within":[161],"Notably,":[164],"Cartesian":[166],"distance":[167],"between":[168,176],"two":[169,178],"fingerprint":[170],"well":[172],"matches":[173],"RMSD":[175,187],"corresponding":[179],"groups.":[181],"This":[182,229],"done":[184],"by":[185,217,240],"using":[186],"as":[188],"domain":[190],"knowledge":[191],"supervise":[193],"deep":[195],"neural":[196],"network":[197],"learning.":[198],"When":[199],"comparing":[200],"existing":[202,241],"methods,":[203],"achieves":[205],"highest":[207],"average":[208],"AUROC":[209],"0.959.":[211],"Moreover,":[212],"best":[214,237],"candidate":[215],"found":[216],"has":[219],"probability":[221],"70.0%":[223],"be":[225],"true":[227],"positive.":[228],"significant":[232],"improvement":[233],"over":[234],"56.2%,":[235],"result":[238],"produced":[239],"methods.GitHub:":[242],"https://github.com/Chenyao2333/contactlib/":[243]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
