{"id":"https://openalex.org/W4388042006","doi":"https://doi.org/10.1007/s10994-023-06369-y","title":"Explainable AI in drug discovery: self-interpretable graph neural network for molecular property prediction using concept whitening","display_name":"Explainable AI in drug discovery: self-interpretable graph neural network for molecular property prediction using concept whitening","publication_year":2023,"publication_date":"2023-10-31","ids":{"openalex":"https://openalex.org/W4388042006","doi":"https://doi.org/10.1007/s10994-023-06369-y"},"language":"en","primary_location":{"id":"doi:10.1007/s10994-023-06369-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-023-06369-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-023-06369-y.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10994-023-06369-y.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011791362","display_name":"Michela Proietti","orcid":"https://orcid.org/0000-0002-1469-3253"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michela Proietti","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015848532","display_name":"Alessio Ragno","orcid":"https://orcid.org/0000-0002-8477-2088"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Alessio Ragno","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012880794","display_name":"Biagio La Rosa","orcid":"https://orcid.org/0000-0002-4071-170X"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Biagio La Rosa","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \"Antonio Ruberti\", Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003256018","display_name":"Rino Ragno","orcid":"https://orcid.org/0000-0001-5399-975X"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Rino Ragno","raw_affiliation_strings":["Rome Center for Molecular Design, Department of Drug Chemistry and Technologies, Sapienza University, Rome, Italy"],"affiliations":[{"raw_affiliation_string":"Rome Center for Molecular Design, Department of Drug Chemistry and Technologies, Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016238183","display_name":"Roberto Capobianco","orcid":"https://orcid.org/0000-0002-2219-215X"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Roberto Capobianco","raw_affiliation_strings":["Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","Sony AI, Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Computer, Control and Management Engineering \u201cAntonio Ruberti\u201d, Sapienza University, Rome, Italy","institution_ids":["https://openalex.org/I861853513"]},{"raw_affiliation_string":"Sony AI, Zurich, Switzerland","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011791362"],"corresponding_institution_ids":["https://openalex.org/I861853513"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":5.6074,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.96707573,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"113","issue":"4","first_page":"2013","last_page":"2044"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9966999888420105,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9921000003814697,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.9335035085678101},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7150362730026245},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.6981301307678223},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6627305746078491},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5984817743301392},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5802008509635925},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5540640354156494},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4866248071193695},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.47062018513679504},{"id":"https://openalex.org/keywords/power-graph-analysis","display_name":"Power graph analysis","score":0.42581063508987427},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32793959975242615},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.22277164459228516}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9335035085678101},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7150362730026245},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.6981301307678223},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6627305746078491},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5984817743301392},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5802008509635925},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5540640354156494},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4866248071193695},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.47062018513679504},{"id":"https://openalex.org/C106937863","wikidata":"https://www.wikidata.org/wiki/Q7236518","display_name":"Power graph analysis","level":3,"score":0.42581063508987427},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32793959975242615},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.22277164459228516},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/s10994-023-06369-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-023-06369-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-023-06369-y.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"},{"id":"pmh:oai:iris.uniroma1.it:11573/1691190","is_oa":true,"landing_page_url":"https://hdl.handle.net/11573/1691190","pdf_url":"https://iris.uniroma1.it/bitstream/11573/1691190/3/Proietti_Explainable_2024.pdf","source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","issn_l":null,"issn":null,"is_oa":false,"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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1007/s10994-023-06369-y","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10994-023-06369-y","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10994-023-06369-y.pdf","source":{"id":"https://openalex.org/S62148650","display_name":"Machine Learning","issn_l":"0885-6125","issn":["0885-6125","1573-0565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Machine Learning","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","score":0.5400000214576721,"display_name":"Peace, Justice and strong institutions"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4388042006.pdf"},"referenced_works_count":77,"referenced_works":["https://openalex.org/W1662382123","https://openalex.org/W1836465849","https://openalex.org/W2034549041","https://openalex.org/W2066273100","https://openalex.org/W2070072705","https://openalex.org/W2080447388","https://openalex.org/W2086953401","https://openalex.org/W2103599338","https://openalex.org/W2108798400","https://openalex.org/W2110039716","https://openalex.org/W2116341502","https://openalex.org/W2135732933","https://openalex.org/W2150120952","https://openalex.org/W2150625809","https://openalex.org/W2295107390","https://openalex.org/W2406943157","https://openalex.org/W2461470610","https://openalex.org/W2468907370","https://openalex.org/W2502312327","https://openalex.org/W2519887557","https://openalex.org/W2594183968","https://openalex.org/W2610646689","https://openalex.org/W2616247523","https://openalex.org/W2618851150","https://openalex.org/W2624431344","https://openalex.org/W2740946158","https://openalex.org/W2759764766","https://openalex.org/W2776207810","https://openalex.org/W2786016794","https://openalex.org/W2796885425","https://openalex.org/W2918342466","https://openalex.org/W2943714799","https://openalex.org/W2946617578","https://openalex.org/W2947950688","https://openalex.org/W2951157442","https://openalex.org/W2951384661","https://openalex.org/W2963743626","https://openalex.org/W2969457089","https://openalex.org/W2970119293","https://openalex.org/W2970971581","https://openalex.org/W2973049920","https://openalex.org/W2979481854","https://openalex.org/W2979943691","https://openalex.org/W2983721890","https://openalex.org/W2992072991","https://openalex.org/W3000478925","https://openalex.org/W3004725381","https://openalex.org/W3022298391","https://openalex.org/W3083504878","https://openalex.org/W3085084733","https://openalex.org/W3092798752","https://openalex.org/W3093687066","https://openalex.org/W3102564565","https://openalex.org/W3108823960","https://openalex.org/W3110901318","https://openalex.org/W3110933132","https://openalex.org/W3113107791","https://openalex.org/W3116637551","https://openalex.org/W3134426364","https://openalex.org/W3152893301","https://openalex.org/W3198474015","https://openalex.org/W3201055938","https://openalex.org/W3207981989","https://openalex.org/W4200146763","https://openalex.org/W4212774754","https://openalex.org/W4223618280","https://openalex.org/W4235673248","https://openalex.org/W4252355329","https://openalex.org/W4280570233","https://openalex.org/W4295312788","https://openalex.org/W4312307693","https://openalex.org/W4390224413","https://openalex.org/W6734194636","https://openalex.org/W6736685754","https://openalex.org/W6748556633","https://openalex.org/W6757634740","https://openalex.org/W6772452955"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W4390569940","https://openalex.org/W2888392564","https://openalex.org/W4361193272","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W2806259446","https://openalex.org/W2963326959","https://openalex.org/W4247136043","https://openalex.org/W4312407344"],"abstract_inverted_index":{"Abstract":[0],"Molecular":[1],"property":[2],"prediction":[3],"is":[4,39,55],"a":[5,32],"fundamental":[6],"task":[7],"in":[8,31,127],"the":[9,69,73,77,83,102,118,142],"field":[10],"of":[11,34,76,120],"drug":[12],"discovery.":[13],"Several":[14],"works":[15],"use":[16],"graph":[17,23,50],"neural":[18,51],"networks":[19],"to":[20,49,60,107,112],"leverage":[21],"molecular":[22,105],"representations.":[24],"Although":[25],"they":[26],"have":[27],"been":[28],"successfully":[29],"applied":[30],"variety":[33],"applications,":[35],"their":[36],"decision":[37],"process":[38],"not":[40],"transparent.":[41],"In":[42],"this":[43],"work,":[44,99],"we":[45,100,134],"adapt":[46],"concept":[47,121],"whitening":[48,122],"networks.":[52],"This":[53],"approach":[54],"an":[56,62,125],"explainability":[57],"method":[58],"used":[59,109],"build":[61],"inherently":[63],"interpretable":[64],"model,":[65],"which":[66],"allows":[67],"identifying":[68],"concepts":[70,111],"and":[71,131,138],"consequently":[72],"structural":[74,137],"parts":[75],"molecules":[78],"that":[79,117],"are":[80],"relevant":[81],"for":[82,141],"output":[84],"predictions.":[85,143],"We":[86,115],"test":[87],"popular":[88],"models":[89],"on":[90],"several":[91,136],"benchmark":[92],"datasets":[93],"from":[94,97],"MoleculeNet.":[95],"Starting":[96],"previous":[98],"identify":[101],"most":[103],"significant":[104],"properties":[106],"be":[108],"as":[110],"perform":[113],"classification.":[114],"show":[116],"addition":[119],"layers":[123],"brings":[124],"improvement":[126],"both":[128],"classification":[129],"performance":[130],"interpretability.":[132],"Finally,":[133],"provide":[135],"conceptual":[139],"explanations":[140]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
