{"id":"https://openalex.org/W4413816507","doi":"https://doi.org/10.1093/bioinformatics/btag193","title":"A cross-attentive multi-task graph learning framework for chemical reaction modeling","display_name":"A cross-attentive multi-task graph learning framework for chemical reaction modeling","publication_year":2026,"publication_date":"2026-04-18","ids":{"openalex":"https://openalex.org/W4413816507","doi":"https://doi.org/10.1093/bioinformatics/btag193","pmid":"https://pubmed.ncbi.nlm.nih.gov/42026905"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag193","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag193","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009424385","display_name":"Maryam Astero","orcid":"https://orcid.org/0000-0003-4829-7627"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Maryam Astero","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150,","Aalto University"],"raw_orcid":"https://orcid.org/0000-0003-4829-7627","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150,","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Aalto University","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060213945","display_name":"Anchen Li","orcid":"https://orcid.org/0000-0001-9828-6964"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Anchen Li","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150,","Aalto University"],"raw_orcid":"https://orcid.org/0000-0001-9828-6964","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150,","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Aalto University","institution_ids":["https://openalex.org/I9927081"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079939753","display_name":"Elena Casiraghi","orcid":"https://orcid.org/0000-0003-2024-7572"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","IT"],"is_corresponding":false,"raw_author_name":"Elena Casiraghi","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150,","Department of Computer Science, Universit\u00e0 degli Studi di Milano , Milan 20122,","University of Milan"],"raw_orcid":"https://orcid.org/0000-0003-2024-7572","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150,","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Department of Computer Science, Universit\u00e0 degli Studi di Milano , Milan 20122,","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"University of Milan","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091883185","display_name":"Juho Rousu","orcid":"https://orcid.org/0000-0002-0705-4314"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Juho Rousu","raw_affiliation_strings":["Department of Computer Science, Aalto University , Espoo 02150,","Department of Computer Science, University of Helsinki , Helsinki 00014,","Aalto University"],"raw_orcid":"https://orcid.org/0000-0002-0705-4314","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Aalto University , Espoo 02150,","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Department of Computer Science, University of Helsinki , Helsinki 00014,","institution_ids":["https://openalex.org/I133731052"]},{"raw_affiliation_string":"Aalto University","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00224329,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9858999848365784,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9858999848365784,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.0026000000070780516,"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/T10030","display_name":"Electrocatalysts for Energy Conversion","score":0.0013000000035390258,"subfield":{"id":"https://openalex.org/subfields/2105","display_name":"Renewable Energy, Sustainability and the Environment"},"field":{"id":"https://openalex.org/fields/21","display_name":"Energy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.639975368976593},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5652778744697571},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5513503551483154},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35630708932876587},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34162455797195435},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3389343023300171},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3215097188949585},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12020626664161682},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.055226296186447144}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.639975368976593},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5652778744697571},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5513503551483154},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35630708932876587},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34162455797195435},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3389343023300171},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3215097188949585},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12020626664161682},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.055226296186447144}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btag193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag193","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.21203/rs.3.rs-6977897/v2","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-6977897/v2","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},{"id":"pmid:42026905","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42026905","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/145470","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/067b98ed-2a58-4aa4-82d1-b6ce6d2b400a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401662","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13181183","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13181183/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag193","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag193","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1651447698","display_name":"AI technologies for interaction prediction in biomedicine","funder_award_id":"345802","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G757968218","display_name":"Machine Learning for Systems Pharmacology","funder_award_id":"339421","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F1744609432","display_name":"Helsinki Institute for Information Technology","ror":"https://ror.org/05kph4940"},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320322282","display_name":"Jane ja Aatos Erkon S\u00e4\u00e4ti\u00f6","ror":"https://ror.org/03vxy9y38"},{"id":"https://openalex.org/F4320332050","display_name":"Finnish Center for Artificial Intelligence","ror":null},{"id":"https://openalex.org/F7311471023","display_name":"NextGenerationEU","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W2003447360","https://openalex.org/W2060586571","https://openalex.org/W2061892036","https://openalex.org/W2103626206","https://openalex.org/W2130244530","https://openalex.org/W2551217916","https://openalex.org/W2769756736","https://openalex.org/W3146384714","https://openalex.org/W4226145240","https://openalex.org/W4283836015","https://openalex.org/W4391826830","https://openalex.org/W4392752197","https://openalex.org/W4395012136","https://openalex.org/W4402543877","https://openalex.org/W4410900645"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4224009465","https://openalex.org/W4306674287","https://openalex.org/W4286629047","https://openalex.org/W4389443772","https://openalex.org/W4205958290","https://openalex.org/W4384212932","https://openalex.org/W2548721895","https://openalex.org/W2373456246","https://openalex.org/W4390590544"],"abstract_inverted_index":{"MOTIVATION:":[0],"Understanding":[1],"chemical":[2],"reactions":[3],"requires":[4],"bridging":[5],"fine-grained":[6],"molecular":[7],"edits":[8],"with":[9,126,213],"broader":[10],"semantic":[11],"context.":[12],"Reaction":[13,54],"mechanisms":[14],"are":[15,243],"determined":[16],"not":[17],"only":[18],"by":[19,25],"local":[20,94,181],"atom-bond":[21],"transformations":[22,229],"but":[23],"also":[24],"the":[26,117,148,162,200],"global":[27,113,184],"reaction":[28,68,71,114,143,194,206],"class.":[29],"However,":[30],"most":[31],"existing":[32],"approaches":[33],"treat":[34],"these":[35],"tasks":[36],"separately":[37],"or":[38],"rely":[39],"on":[40],"external":[41],"atom-mapping":[42],"tools,":[43],"introducing":[44],"noise":[45],"and":[46,56,70,91,107,129,141,167,175,183,190,210,217,230,240,247],"limiting":[47],"end-to-end":[48],"learnability.":[49],"We":[50],"introduce":[51],"MARCC":[52,78,120,151,186,198],"(Mapping-Assisted":[53],"Center":[55],"Classification),":[57],"a":[58,74,84,98,188],"multi-task":[59,168],"graph":[60],"neural":[61],"network":[62],"that":[63,88,101],"jointly":[64],"predicts":[65],"atom":[66,133],"mappings,":[67],"centers,":[69],"classes":[72],"within":[73],"unified":[75],"architecture.":[76],"RESULTS:":[77],"integrates":[79],"three":[80],"key":[81],"innovations:":[82],"(i)":[83],"mapping-guided":[85,165],"cross-attention":[86],"mechanism":[87,211],"aligns":[89],"reactants":[90,128],"products":[92],"for":[93,112,193],"edit":[95,138],"detection,":[96],"(ii)":[97],"dual-graph":[99],"design":[100],"explicitly":[102],"reasons":[103],"about":[104],"bond-level":[105],"transformations,":[106],"(iii)":[108],"pooled":[109],"product":[110],"embeddings":[111],"classification.":[115],"On":[116],"USPTO-50K":[118],"benchmark,":[119],"achieves":[121],"state-of-the-art":[122],"results":[123],"when":[124],"trained":[125],"both":[127,172],"products,":[130],"including":[131],"98.2%":[132],"mapping":[134],"accuracy,":[135,140],"99.1%":[136],"Top-1":[137],"localization":[139],"97.2%":[142],"classification":[144],"accuracy.":[145],"Even":[146],"under":[147],"products-only":[149],"setting,":[150],"delivers":[152],"competitive":[153],"performance":[154],"comparable":[155],"to":[156,202,223],"specialized":[157],"baselines.":[158],"Ablation":[159],"studies":[160],"confirm":[161],"value":[163],"of":[164],"attention":[166],"supervision,":[169],"which":[170],"enhance":[171],"predictive":[173],"accuracy":[174],"interpretability.":[176],"By":[177],"unifying":[178],"atom-level":[179],"alignment,":[180],"reactivity,":[182],"classification,":[185],"provides":[187],"structured":[189],"interpretable":[191],"framework":[192],"understanding.":[195],"Beyond":[196],"benchmarks,":[197],"has":[199],"potential":[201],"support":[203],"applications":[204],"in":[205],"annotation,":[207],"template":[208],"discovery,":[209],"inference;":[212],"additional":[214],"domain-specific":[215],"modeling":[216],"data,":[218],"it":[219],"could":[220],"be":[221],"extended":[222],"biochemical":[224],"domains":[225],"such":[226],"as":[227],"enzyme-catalyzed":[228],"metabolic":[231],"pathway":[232],"modeling.":[233],"AVAILABILITY":[234],"AND":[235],"IMPLEMENTATION:":[236],"The":[237],"source":[238],"code":[239],"implementation":[241],"details":[242],"available":[244],"at":[245,249],"https://github.com/maryamastero/MARCC":[246],"archived":[248],"https://doi.org/10.5281/zenodo.18500230.":[250]},"counts_by_year":[],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}