{"id":"https://openalex.org/W4402345346","doi":"https://doi.org/10.1109/access.2024.3509714","title":"Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer\u2019s Disease","display_name":"Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer\u2019s Disease","publication_year":2024,"publication_date":"2024-01-01","ids":{"openalex":"https://openalex.org/W4402345346","doi":"https://doi.org/10.1109/access.2024.3509714"},"language":"en","primary_location":{"id":"doi:10.1109/access.2024.3509714","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2024.3509714","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2024.3509714","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000312847","display_name":"Christos Theodoropoulos","orcid":"https://orcid.org/0000-0002-2810-7817"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Christos Theodoropoulos","raw_affiliation_strings":["Department of Computer Science, LIIR, KU Leuven, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, LIIR, KU Leuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010412227","display_name":"Andrei Catalin Coman","orcid":null},"institutions":[{"id":"https://openalex.org/I7495430","display_name":"Idiap Research Institute","ror":"https://ror.org/05932h694","country_code":"CH","type":"facility","lineage":["https://openalex.org/I7495430"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Andrei Catalin Coman","raw_affiliation_strings":["Idiap Research Institute, Martigny, Switzerland"],"affiliations":[{"raw_affiliation_string":"Idiap Research Institute, Martigny, Switzerland","institution_ids":["https://openalex.org/I7495430"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084321238","display_name":"James Henderson","orcid":"https://orcid.org/0000-0003-3714-4799"},"institutions":[{"id":"https://openalex.org/I7495430","display_name":"Idiap Research Institute","ror":"https://ror.org/05932h694","country_code":"CH","type":"facility","lineage":["https://openalex.org/I7495430"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"James Henderson","raw_affiliation_strings":["Idiap Research Institute, Martigny, Switzerland"],"affiliations":[{"raw_affiliation_string":"Idiap Research Institute, Martigny, Switzerland","institution_ids":["https://openalex.org/I7495430"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075796989","display_name":"Marie\u2010Francine Moens","orcid":"https://orcid.org/0000-0002-3732-9323"},"institutions":[{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Marie-Francine Moens","raw_affiliation_strings":["Department of Computer Science, LIIR, KU Leuven, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, LIIR, KU Leuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000312847"],"corresponding_institution_ids":["https://openalex.org/I99464096"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.6813,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.75259467,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"12","issue":null,"first_page":"180652","last_page":"180673"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9836000204086304,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9836000204086304,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.965399980545044,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9470999836921692,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.672514021396637},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5314007997512817},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.49880146980285645},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.42177602648735046},{"id":"https://openalex.org/keywords/knowledge-management","display_name":"Knowledge management","score":0.3834649920463562},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2837877869606018}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.672514021396637},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5314007997512817},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.49880146980285645},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.42177602648735046},{"id":"https://openalex.org/C56739046","wikidata":"https://www.wikidata.org/wiki/Q192060","display_name":"Knowledge management","level":1,"score":0.3834649920463562},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2837877869606018},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/access.2024.3509714","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2024.3509714","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2407.13492","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2407.13492","pdf_url":"https://arxiv.org/pdf/2407.13492","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:infoscience.epfl.ch:20.500.14299/242521","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/242521","pdf_url":"https://infoscience.epfl.ch/bitstreams/dbb7c765-18f4-4566-b886-a3ae4421d3c9/download","source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"research article"},{"id":"pmh:oai:lirias2repo.kuleuven.be:20.500.12942/755409","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/755409","pdf_url":"https://lirias.kuleuven.be/retrieve/37073a03-ab5d-4cf1-a1bb-ead31109e701","source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"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":"Ieee Access, vol. 12, (180652-180673)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:doaj.org/article:bb8ea465f0d94a8d8e94ae6cdf42616a","is_oa":true,"landing_page_url":"https://doaj.org/article/bb8ea465f0d94a8d8e94ae6cdf42616a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 12, Pp 180652-180673 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2024.3509714","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2024.3509714","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7200000286102295,"id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G4600610186","display_name":null,"funder_award_id":"G094020N","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G4836148144","display_name":null,"funder_award_id":"20002","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G5388806002","display_name":null,"funder_award_id":"unknown","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G7858199836","display_name":"Deep Learning Models for Continual Extraction of Knowledge from Text","funder_award_id":"189458","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7895516993","display_name":null,"funder_award_id":"Belgium","funder_id":"https://openalex.org/F4320322308","funder_display_name":"KU Leuven"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G993971353","display_name":null,"funder_award_id":"200021","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320322308","display_name":"KU Leuven","ror":"https://ror.org/05f950310"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":97,"referenced_works":["https://openalex.org/W1527927437","https://openalex.org/W1850865022","https://openalex.org/W1934602670","https://openalex.org/W2040298461","https://openalex.org/W2040325458","https://openalex.org/W2048028417","https://openalex.org/W2064030835","https://openalex.org/W2094289721","https://openalex.org/W2113072832","https://openalex.org/W2114850508","https://openalex.org/W2127978399","https://openalex.org/W2129767020","https://openalex.org/W2129842875","https://openalex.org/W2136437513","https://openalex.org/W2155518941","https://openalex.org/W2159583324","https://openalex.org/W2164777277","https://openalex.org/W2166474856","https://openalex.org/W2170189740","https://openalex.org/W2346452181","https://openalex.org/W2582146834","https://openalex.org/W2746012317","https://openalex.org/W2888645935","https://openalex.org/W2921377602","https://openalex.org/W2961517618","https://openalex.org/W2963020213","https://openalex.org/W2967166693","https://openalex.org/W2979250794","https://openalex.org/W3011575855","https://openalex.org/W3026298482","https://openalex.org/W3028004046","https://openalex.org/W3033896008","https://openalex.org/W3041133507","https://openalex.org/W3042324527","https://openalex.org/W3046375318","https://openalex.org/W3048090444","https://openalex.org/W3093891978","https://openalex.org/W3106811464","https://openalex.org/W3131198033","https://openalex.org/W3131782536","https://openalex.org/W3131957723","https://openalex.org/W3158665049","https://openalex.org/W3178755335","https://openalex.org/W3211267063","https://openalex.org/W4206046172","https://openalex.org/W4211123915","https://openalex.org/W4221047109","https://openalex.org/W4221154868","https://openalex.org/W4226167522","https://openalex.org/W4228997258","https://openalex.org/W4283318325","https://openalex.org/W4285604902","https://openalex.org/W4294214983","https://openalex.org/W4297253404","https://openalex.org/W4307814854","https://openalex.org/W4310136297","https://openalex.org/W4316345124","https://openalex.org/W4318328370","https://openalex.org/W4365511667","https://openalex.org/W4377820139","https://openalex.org/W4379743587","https://openalex.org/W4381587418","https://openalex.org/W4382069925","https://openalex.org/W4384071683","https://openalex.org/W4384914609","https://openalex.org/W4385245566","https://openalex.org/W4385490607","https://openalex.org/W4386014872","https://openalex.org/W4386120650","https://openalex.org/W4388139915","https://openalex.org/W4388467895","https://openalex.org/W4388615774","https://openalex.org/W4389109084","https://openalex.org/W4390843754","https://openalex.org/W4394789579","https://openalex.org/W4396560090","https://openalex.org/W4401054437","https://openalex.org/W4401110069","https://openalex.org/W6601325530","https://openalex.org/W6603694148","https://openalex.org/W6606243021","https://openalex.org/W6628888145","https://openalex.org/W6631190155","https://openalex.org/W6632766574","https://openalex.org/W6638641193","https://openalex.org/W6658704000","https://openalex.org/W6662590293","https://openalex.org/W6674330103","https://openalex.org/W6691209883","https://openalex.org/W6713154993","https://openalex.org/W6763541153","https://openalex.org/W6769243733","https://openalex.org/W6785847369","https://openalex.org/W6801102277","https://openalex.org/W6802841870","https://openalex.org/W6809711173","https://openalex.org/W6852589961"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W93075631","https://openalex.org/W3005434123","https://openalex.org/W2599205313","https://openalex.org/W2076251662","https://openalex.org/W4231842067"],"abstract_inverted_index":{"The":[0],"rapidly":[1],"increasing":[2],"number":[3],"of":[4,62,105,109],"biomedical":[5,67,153],"publications":[6],"presents":[7],"a":[8,102],"significant":[9],"challenge":[10],"for":[11,77,88],"efficient":[12],"knowledge":[13,30,43,98,154],"discovery.":[14,99,155],"To":[15,38,100],"address":[16],"this,":[17],"we":[18,45,112],"introduce":[19],"an":[20],"open-source,":[21],"end-to-end":[22],"framework":[23],"designed":[24],"to":[25,73,124,128],"automatically":[26],"extract":[27],"and":[28,55,80,92,121,138],"construct":[29],"about":[31],"specific":[32],"diseases":[33],"directly":[34],"from":[35],"unstructured":[36],"text.":[37,134],"facilitate":[39],"research":[40,151],"in":[41,97,152],"disease-related":[42],"discovery,":[44],"create":[46],"two":[47],"annotated":[48],"datasets":[49,140],"focused":[50],"on":[51],"Rett":[52],"syndrome":[53],"(RS)":[54],"Alzheimer\u2019s":[56],"disease":[57],"(AD),":[58],"enabling":[59],"the":[60,106,133,136,139],"identification":[61],"semantic":[63,89,130],"relations":[64,79,131],"between":[65],"various":[66],"entities.":[68],"We":[69],"perform":[70],"extensive":[71],"benchmarking":[72],"evaluate":[74],"different":[75,118],"approaches":[76],"representing":[78],"entities,":[81],"providing":[82],"insights":[83],"into":[84],"optimal":[85],"modeling":[86],"strategies":[87],"relation":[90],"detection":[91],"highlighting":[93],"language":[94],"models\u2019":[95],"competence":[96],"gain":[101],"deeper":[103],"understanding":[104],"internal":[107],"mechanisms":[108],"transformer":[110],"models,":[111],"also":[113],"conduct":[114],"probing":[115],"experiments,":[116],"analyzing":[117],"layer":[119],"representations":[120],"attention":[122],"scores,":[123],"explore":[125],"transformers\u2019":[126],"ability":[127],"capture":[129],"within":[132],"Both":[135],"code":[137],"will":[141],"be":[142],"publicly":[143],"available":[144],"at":[145],"<uri":[146],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[147],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">https://github.com/christos42/Enhancing-Biomedical-Knowledge-Discovery-for-Diseases</uri>,":[148],"encouraging":[149],"further":[150]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
