{"id":"https://openalex.org/W7124749310","doi":"https://doi.org/10.1145/3787204","title":"Atom-Motif Contrastive Transformer for Molecular Property Prediction","display_name":"Atom-Motif Contrastive Transformer for Molecular Property Prediction","publication_year":2026,"publication_date":"2026-01-19","ids":{"openalex":"https://openalex.org/W7124749310","doi":"https://doi.org/10.1145/3787204"},"language":"en","primary_location":{"id":"doi:10.1145/3787204","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3787204","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-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/A5033032757","display_name":"Wentao Yu","orcid":"https://orcid.org/0000-0003-1416-5255"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wentao Yu","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China"],"raw_orcid":"https://orcid.org/0000-0003-1416-5255","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology, Nanjing, China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123335247","display_name":"Shuo Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Shuo Chen","raw_affiliation_strings":["School of Intelligence Science and Technology, Nanjing University, Suzhou, China and RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan"],"raw_orcid":"https://orcid.org/0009-0006-0159-8851","affiliations":[{"raw_affiliation_string":"School of Intelligence Science and Technology, Nanjing University, Suzhou, China and RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan","institution_ids":["https://openalex.org/I4210126580"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123345948","display_name":"Chen Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Gong","raw_affiliation_strings":["School of Automation and Intelligent Sensing, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0002-1154-6194","affiliations":[{"raw_affiliation_string":"School of Automation and Intelligent Sensing, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123353443","display_name":"Bo Han","orcid":null},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]},{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]}],"countries":["HK","JP"],"is_corresponding":false,"raw_author_name":"Bo Han","raw_affiliation_strings":["Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China and RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan"],"raw_orcid":"https://orcid.org/0000-0002-6338-0958","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR, China and RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan","institution_ids":["https://openalex.org/I4210126580","https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Gang Niu","orcid":"https://orcid.org/0000-0002-7353-5079"},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Gang Niu","raw_affiliation_strings":["RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan"],"raw_orcid":"https://orcid.org/0000-0002-7353-5079","affiliations":[{"raw_affiliation_string":"RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan","institution_ids":["https://openalex.org/I4210126580"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072744508","display_name":"Masashi Sugiyama","orcid":"https://orcid.org/0000-0001-6658-6743"},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Masashi Sugiyama","raw_affiliation_strings":["RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan and Complexity Science and Engineering, The University of Tokyo, Bunkyo, Japan"],"raw_orcid":"https://orcid.org/0000-0001-6658-6743","affiliations":[{"raw_affiliation_string":"RIKEN Center for Advanced Intelligence Project, Chuo-ku, Japan and Complexity Science and Engineering, The University of Tokyo, Bunkyo, Japan","institution_ids":["https://openalex.org/I4210126580"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1077775,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":"2","first_page":"1","last_page":"20"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.484499990940094,"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":0.484499990940094,"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":0.2475000023841858,"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":0.210099995136261,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.6550999879837036},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.59170001745224},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.44269999861717224},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.41019999980926514},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.34689998626708984},{"id":"https://openalex.org/keywords/molecular-graph","display_name":"Molecular graph","score":0.3149999976158142}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8091999888420105},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6550999879837036},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.59170001745224},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5230000019073486},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4717999994754791},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.44269999861717224},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.41019999980926514},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3528999984264374},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.34689998626708984},{"id":"https://openalex.org/C2780022179","wikidata":"https://www.wikidata.org/wiki/Q1986794","display_name":"Molecular graph","level":3,"score":0.3149999976158142},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3070000112056732},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.296099990606308},{"id":"https://openalex.org/C132677234","wikidata":"https://www.wikidata.org/wiki/Q3273544","display_name":"Structural motif","level":2,"score":0.29330000281333923},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.2856999933719635},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2770000100135803},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.2752000093460083},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2648000121116638},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.26269999146461487},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.2515999972820282}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3787204","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3787204","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8044755327","display_name":null,"funder_award_id":"62506155","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8599105139","display_name":null,"funder_award_id":"62336003, 12371510","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1757990252","https://openalex.org/W1969081492","https://openalex.org/W1986352004","https://openalex.org/W1994346982","https://openalex.org/W2038702914","https://openalex.org/W2056562706","https://openalex.org/W2114162221","https://openalex.org/W2121817924","https://openalex.org/W2150067511","https://openalex.org/W2153624566","https://openalex.org/W2162122425","https://openalex.org/W2290847742","https://openalex.org/W2531113820","https://openalex.org/W2594183968","https://openalex.org/W2783855936","https://openalex.org/W3123901912","https://openalex.org/W3167683763","https://openalex.org/W3173985861","https://openalex.org/W3185909432","https://openalex.org/W3202884269","https://openalex.org/W4231932059","https://openalex.org/W4295774968","https://openalex.org/W4313889424","https://openalex.org/W4367051006","https://openalex.org/W4367680667","https://openalex.org/W4393191472","https://openalex.org/W4393981121"],"related_works":[],"abstract_inverted_index":{"Recently,":[0],"Graph":[1],"Transformer":[2,110],"(GT)":[3],"models":[4],"have":[5],"been":[6],"widely":[7],"used":[8],"in":[9,22,33,72,163,186,196],"the":[10,24,31,43,55,96,116,122,126,142,151,158,171,176,191,198,238],"task":[11],"of":[12,65,68,80,98,128,141,179,200],"Molecular":[13],"Property":[14],"Prediction":[15],"(MPP)":[16],"due":[17],"to":[18,53,149,174,188],"their":[19],"high":[20],"reliability":[21],"characterizing":[23],"latent":[25],"relationship":[26],"among":[27,58],"graph":[28],"nodes":[29],"(i.e.,":[30],"atoms":[32,129],"a":[34,73,106,133,206],"molecule).":[35],"However,":[36],"most":[37],"existing":[38],"GT-based":[39],"methods":[40],"usually":[41],"explore":[42],"basic":[44],"interactions":[45,57,93,118],"between":[46],"pairwise":[47],"atoms,":[48],"and":[49,89,130,166,225,228],"thus":[50],"they":[51,145],"fail":[52],"consider":[54],"important":[56],"critical":[59,195],"motifs":[60,71,131,181,192],"(e.g.,":[61,87],"functional":[62],"groups":[63],"consisted":[64],"several":[66],"atoms)":[67],"molecules.":[69,184],"As":[70],"molecule":[74,135],"are":[75,79,136,146,194],"significant":[76],"patterns":[77],"that":[78,193],"great":[81],"importance":[82],"for":[83,132,154],"determining":[84],"molecular":[85],"properties":[86,199],"toxicity":[88],"solubility),":[90],"overlooking":[91],"motif":[92,160],"inevitably":[94],"hinders":[95],"effectiveness":[97,234],"MPP.":[99],"To":[100],"address":[101],"this":[102],"issue,":[103],"we":[104,168,203],"propose":[105],"novel":[107],"Atom-Motif":[108],"Contrastive":[109],"(AMCT),":[111],"which":[112],"not":[113],"only":[114],"explores":[115],"atom-level":[117],"but":[119],"also":[120,169],"considers":[121],"motif-level":[123],"interactions.":[124],"Since":[125],"representations":[127],"given":[134],"actually":[137],"two":[138],"different":[139,164,183],"views":[140],"same":[143,159],"instance,":[144],"naturally":[147],"aligned":[148],"generate":[150],"self-supervisory":[152],"signals":[153],"model":[155],"training.":[156],"Meanwhile,":[157],"can":[161],"exist":[162],"molecules,":[165],"hence":[167],"employ":[170],"contrastive":[172],"loss":[173],"maximize":[175],"representation":[177],"agreement":[178],"identical":[180],"across":[182],"Finally,":[185],"order":[187],"clearly":[189],"identify":[190],"deciding":[197],"each":[201],"molecule,":[202],"further":[204],"construct":[205],"property-aware":[207],"attention":[208],"mechanism":[209],"into":[210],"our":[211],"learning":[212],"framework.":[213],"Our":[214],"proposed":[215],"AMCT":[216],"is":[217],"extensively":[218],"evaluated":[219],"on":[220],"10":[221],"popular":[222],"benchmark":[223],"datasets,":[224],"both":[226],"quantitative":[227],"qualitative":[229],"results":[230],"firmly":[231],"demonstrate":[232],"its":[233],"when":[235],"compared":[236],"with":[237],"state-of-the-art":[239],"methods.":[240]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2026-01-20T00:00:00"}
