{"id":"https://openalex.org/W4406917942","doi":"https://doi.org/10.1021/acs.jcim.4c01901","title":"Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction","display_name":"Chemically Informed Deep Learning for Interpretable Radical Reaction Prediction","publication_year":2025,"publication_date":"2025-01-28","ids":{"openalex":"https://openalex.org/W4406917942","doi":"https://doi.org/10.1021/acs.jcim.4c01901","pmid":"https://pubmed.ncbi.nlm.nih.gov/39871741"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.4c01901","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01901","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1021/acs.jcim.4c01901","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051408309","display_name":"Mohammadamin Tavakoli","orcid":"https://orcid.org/0000-0002-8833-3891"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammadamin Tavakoli","raw_affiliation_strings":["Department of Computer Science","University of California, Irvine","Department of Computer Science, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]},{"raw_affiliation_string":"University of California, Irvine","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054501273","display_name":"Yin Ting T. Chiu","orcid":"https://orcid.org/0000-0001-5449-8391"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yin Ting T. Chiu","raw_affiliation_strings":["Department of Chemistry","University of California, Irvine","Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0001-5449-8391","affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of California, Irvine","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068803389","display_name":"Annmarie G. Carlton","orcid":"https://orcid.org/0000-0002-8574-1507"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ann Marie Carlton","raw_affiliation_strings":["Department of Chemistry","University of California, Irvine","Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0002-8574-1507","affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of California, Irvine","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081882130","display_name":"David L. Van Vranken","orcid":"https://orcid.org/0000-0001-5964-7042"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"David Van Vranken","raw_affiliation_strings":["Department of Chemistry","University of California, Irvine","Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0001-5964-7042","affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"University of California, Irvine","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Chemistry, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088813478","display_name":"Pierre Baldi","orcid":"https://orcid.org/0000-0001-8752-4664"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pierre Baldi","raw_affiliation_strings":["Department of Computer Science","University of California, Irvine","Department of Computer Science, University of California, Irvine, Irvine, California 92697, United States"],"raw_orcid":"https://orcid.org/0000-0001-8752-4664","affiliations":[{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]},{"raw_affiliation_string":"University of California, Irvine","institution_ids":["https://openalex.org/I204250578"]},{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, Irvine, California 92697, United States","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5081882130","https://openalex.org/A5088813478"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":null,"apc_paid":null,"fwci":1.1439,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.7387058,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"65","issue":"3","first_page":"1228","last_page":"1242"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9993000030517578,"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/T13180","display_name":"Chemistry and Chemical Engineering","score":0.9776999950408936,"subfield":{"id":"https://openalex.org/subfields/2304","display_name":"Environmental Chemistry"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4779339134693146},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.417294442653656},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.397038996219635},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.3731837868690491},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3659013509750366}],"concepts":[{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4779339134693146},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.417294442653656},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.397038996219635},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3731837868690491},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3659013509750366}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D005609","descriptor_name":"Free Radicals","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","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":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1021/acs.jcim.4c01901","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01901","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:39871741","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39871741","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":"Journal of chemical information and modeling","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6b55p7j6","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/6b55p7j6","pdf_url":"https://escholarship.org/content/qt6b55p7j6/qt6b55p7j6.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Journal of chemical information and computer sciences, vol 65, iss 3","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11815866","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11815866","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11815866/pdf/ci4c01901.pdf","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},{"id":"pmh:ark:/13030/qt6b55p7j6","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.4c01901","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.4c01901","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G775384628","display_name":null,"funder_award_id":"W911NF1810349","funder_id":"https://openalex.org/F4320338281","funder_display_name":"Army Research Office"},{"id":"https://openalex.org/G8937981919","display_name":null,"funder_award_id":"195811","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1548551133","https://openalex.org/W1757990252","https://openalex.org/W1969596950","https://openalex.org/W1973166400","https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W2015532490","https://openalex.org/W2028054907","https://openalex.org/W2040010296","https://openalex.org/W2046589863","https://openalex.org/W2064535969","https://openalex.org/W2064675550","https://openalex.org/W2066412916","https://openalex.org/W2089431002","https://openalex.org/W2093205000","https://openalex.org/W2093264248","https://openalex.org/W2098614082","https://openalex.org/W2109759383","https://openalex.org/W2153580689","https://openalex.org/W2171590421","https://openalex.org/W2296508036","https://openalex.org/W2324964582","https://openalex.org/W2331727781","https://openalex.org/W2529996553","https://openalex.org/W2538573120","https://openalex.org/W2580919858","https://openalex.org/W2606363443","https://openalex.org/W2612690371","https://openalex.org/W2621742623","https://openalex.org/W2775684663","https://openalex.org/W2782636657","https://openalex.org/W2784918212","https://openalex.org/W2785942661","https://openalex.org/W2790847493","https://openalex.org/W2903262661","https://openalex.org/W2947423323","https://openalex.org/W2950955377","https://openalex.org/W2955601895","https://openalex.org/W2970764640","https://openalex.org/W2972608805","https://openalex.org/W2990138404","https://openalex.org/W3004164548","https://openalex.org/W3009202547","https://openalex.org/W3103092523","https://openalex.org/W3126568646","https://openalex.org/W3147020900","https://openalex.org/W3175633940","https://openalex.org/W3181403764","https://openalex.org/W3189262114","https://openalex.org/W3213485948","https://openalex.org/W4223537994","https://openalex.org/W4226159083","https://openalex.org/W4243148237","https://openalex.org/W4286901673","https://openalex.org/W4321165952","https://openalex.org/W4323660312","https://openalex.org/W4392800579","https://openalex.org/W4394485229"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2731899572","https://openalex.org/W2961085424","https://openalex.org/W3215138031","https://openalex.org/W4306674287","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4321369474"],"abstract_inverted_index":{"Organic":[0],"radical":[1,32,58,96],"reactions":[2,75],"are":[3,40,49],"crucial":[4],"in":[5,76,108],"many":[6],"areas":[7],"of":[8,25,45,57,72,88,94,106],"chemistry,":[9],"including":[10],"synthetic,":[11],"biological,":[12],"and":[13,51,68,92,110],"atmospheric":[14,109],"chemistry.":[15,112],"We":[16,98],"develop":[17],"a":[18,84,95],"predictive":[19],"framework":[20],"based":[21],"on":[22,30,103],"the":[23,54,64,73,100],"interaction":[24,67],"molecular":[26],"orbitals":[27],"that":[28],"operates":[29],"mechanistic-level":[31],"reactions.":[33],"Given":[34],"our":[35],"chemistry-aware":[36],"model,":[37],"all":[38,90],"predictions":[39],"provided":[41],"with":[42],"different":[43],"levels":[44],"interpretability.":[46],"Our":[47,61],"models":[48],"trained":[50],"evaluated":[52],"using":[53],"RMechDB":[55],"database":[56],"reaction":[59],"steps.":[60],"model":[62],"predicts":[63],"correct":[65],"orbital":[66],"products":[69],"for":[70],"96%":[71],"test":[74,99],"RMechDB.":[77],"By":[78],"chaining":[79],"these":[80],"predictions,":[81],"we":[82],"perform":[83],"pathway":[85,101],"search":[86,102],"capable":[87],"identifying":[89],"intermediates":[91],"byproducts":[93],"reaction.":[97],"two":[104],"classes":[105],"problems":[107],"polymerization":[111],"RMechRP":[113],"is":[114],"publicly":[115],"available":[116],"online":[117],"at":[118],"https://deeprxn.ics.uci.edu/rmechrp/.":[119]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-07T08:38:57.713557","created_date":"2025-10-10T00:00:00"}