{"id":"https://openalex.org/W4403488076","doi":"https://doi.org/10.3233/faia240663","title":"Molecular Topological Profile (MOLTOP) - Simple and Strong Baseline for Molecular Graph Classification","display_name":"Molecular Topological Profile (MOLTOP) - Simple and Strong Baseline for Molecular Graph Classification","publication_year":2024,"publication_date":"2024-10-16","ids":{"openalex":"https://openalex.org/W4403488076","doi":"https://doi.org/10.3233/faia240663"},"language":"en","primary_location":{"id":"doi:10.3233/faia240663","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240663","pdf_url":null,"source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.3233/faia240663","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077243404","display_name":"Jakub Adamczyk","orcid":"https://orcid.org/0000-0003-4336-4288"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]},{"id":"https://openalex.org/I686019","display_name":"AGH University of Krakow","ror":"https://ror.org/00bas1c41","country_code":"PL","type":"education","lineage":["https://openalex.org/I686019"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Jakub Adamczyk","raw_affiliation_strings":["Faculty of Computer Science, AGH University of Krakow, Krakow, Poland"],"raw_orcid":"https://orcid.org/0000-0003-4336-4288","affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, AGH University of Krakow, Krakow, Poland","institution_ids":["https://openalex.org/I686019","https://openalex.org/I126596746"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055999742","display_name":"Wojciech Czech","orcid":"https://orcid.org/0000-0002-1903-8098"},"institutions":[{"id":"https://openalex.org/I126596746","display_name":"Jagiellonian University","ror":"https://ror.org/03bqmcz70","country_code":"PL","type":"education","lineage":["https://openalex.org/I126596746"]},{"id":"https://openalex.org/I686019","display_name":"AGH University of Krakow","ror":"https://ror.org/00bas1c41","country_code":"PL","type":"education","lineage":["https://openalex.org/I686019"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Wojciech Czech","raw_affiliation_strings":["Faculty of Computer Science, AGH University of Krakow, Krakow, Poland"],"raw_orcid":"https://orcid.org/0000-0002-1903-8098","affiliations":[{"raw_affiliation_string":"Faculty of Computer Science, AGH University of Krakow, Krakow, Poland","institution_ids":["https://openalex.org/I686019","https://openalex.org/I126596746"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077243404"],"corresponding_institution_ids":["https://openalex.org/I126596746","https://openalex.org/I686019"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.50576399,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9972000122070312,"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":0.9972000122070312,"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/T12327","display_name":"Various Chemistry Research Topics","score":0.9452999830245972,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.914900004863739,"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/baseline","display_name":"Baseline (sea)","score":0.6905478239059448},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.6173477172851562},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.42950695753097534},{"id":"https://openalex.org/keywords/topology","display_name":"Topology (electrical circuits)","score":0.3900723457336426},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3666364550590515},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3529661297798157},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.31316515803337097},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1378249228000641},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.07855403423309326},{"id":"https://openalex.org/keywords/epistemology","display_name":"Epistemology","score":0.05468115210533142}],"concepts":[{"id":"https://openalex.org/C12725497","wikidata":"https://www.wikidata.org/wiki/Q810247","display_name":"Baseline (sea)","level":2,"score":0.6905478239059448},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.6173477172851562},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42950695753097534},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.3900723457336426},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3666364550590515},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3529661297798157},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.31316515803337097},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1378249228000641},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.07855403423309326},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.05468115210533142},{"id":"https://openalex.org/C505870484","wikidata":"https://www.wikidata.org/wiki/Q180538","display_name":"Fishery","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/faia240663","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240663","pdf_url":null,"source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"}],"best_oa_location":{"id":"doi:10.3233/faia240663","is_oa":true,"landing_page_url":"https://doi.org/10.3233/faia240663","pdf_url":null,"source":{"id":"https://openalex.org/S4210201731","display_name":"Frontiers in artificial intelligence and applications","issn_l":"0922-6389","issn":["0922-6389","1879-8314"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"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":"Frontiers in Artificial Intelligence and Applications","raw_type":"book-chapter"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2383111961","https://openalex.org/W2365952365","https://openalex.org/W2352448290","https://openalex.org/W2380820513","https://openalex.org/W2913146933","https://openalex.org/W2372385138","https://openalex.org/W4296359239","https://openalex.org/W2101155126","https://openalex.org/W2043093291"],"abstract_inverted_index":{"We":[0,18,117],"revisit":[1],"the":[2,144,164,176],"effectiveness":[3],"of":[4,31,154],"topological":[5],"descriptors":[6,33],"for":[7,37,56,151,171],"molecular":[8],"graph":[9],"classification":[10,125],"and":[11,34,40,75,98,147],"design":[12],"a":[13,21,47,53],"simple,":[14,95],"yet":[15],"strong":[16,54,140],"baseline.":[17],"demonstrate":[19],"that":[20,159],"simple":[22],"approach":[23,81,101],"to":[24,83,89],"feature":[25],"engineering":[26],"-":[27,43],"employing":[28],"histogram":[29],"aggregation":[30],"edge":[32],"one-hot":[35],"encoding":[36],"atomic":[38],"numbers":[39],"bond":[41],"types":[42],"when":[44,87],"combined":[45],"with":[46],"Random":[48],"Forest":[49],"classifier,":[50],"can":[51],"establish":[52],"baseline":[55],"Graph":[57,115,130],"Neural":[58],"Networks":[59],"(GNNs).":[60],"The":[61,132],"novel":[62],"algorithm,":[63],"Molecular":[64],"Topological":[65],"Profile":[66],"(MOLTOP),":[67],"integrates":[68],"Edge":[69],"Betweenness":[70],"Centrality,":[71],"Adjusted":[72],"Rand":[73],"Index":[74],"SCAN":[76],"Structural":[77],"Similarity":[78],"score.":[79],"This":[80],"proves":[82],"be":[84],"remarkably":[85],"competitive":[86],"compared":[88],"modern":[90],"GNNs,":[91],"while":[92],"also":[93],"being":[94],"fast,":[96],"low-variance":[97],"hyperparameter-free.":[99],"Our":[100,156],"is":[102,158],"rigorously":[103],"tested":[104],"on":[105,123],"MoleculeNet":[106],"datasets":[107,137],"using":[108],"fair":[109],"evaluation":[110],"protocol":[111],"provided":[112],"by":[113],"Open":[114],"Benchmark.":[116,131],"additionally":[118],"show":[119],"out-of-domain":[120],"generation":[121],"capabilities":[122],"peptide":[124],"task":[126],"from":[127],"Long":[128],"Range":[129],"evaluations":[133],"across":[134],"eleven":[135],"benchmark":[136],"reveal":[138],"MOLTOP\u2019s":[139],"discriminative":[141],"capabilities,":[142],"surpassing":[143],"1-WL":[145],"test":[146,150],"even":[148],"3-WL":[149],"some":[152],"classes":[153],"graphs.":[155],"conclusion":[157],"descriptor-based":[160],"baselines,":[161],"such":[162],"as":[163],"one":[165],"we":[166],"propose,":[167],"are":[168],"still":[169],"crucial":[170],"accurately":[172],"assessing":[173],"advancements":[174],"in":[175],"GNN":[177],"domain.":[178]},"counts_by_year":[],"updated_date":"2025-12-21T01:58:51.020947","created_date":"2025-10-10T00:00:00"}
