{"id":"https://openalex.org/W4407633510","doi":"https://doi.org/10.1186/s13321-025-00969-7","title":"Predictive modeling of biodegradation pathways using transformer architectures","display_name":"Predictive modeling of biodegradation pathways using transformer architectures","publication_year":2025,"publication_date":"2025-02-17","ids":{"openalex":"https://openalex.org/W4407633510","doi":"https://doi.org/10.1186/s13321-025-00969-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/39962584"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00969-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00969-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00969-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00969-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5083529271","display_name":"Liam Brydon","orcid":null},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]},{"id":"https://openalex.org/I39854758","display_name":"Auckland University of Technology","ror":"https://ror.org/01zvqw119","country_code":"NZ","type":"education","lineage":["https://openalex.org/I39854758"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Liam Brydon","raw_affiliation_strings":["School of Computer Science, University of Auckland, Auckland, New Zealand. lbry121@aucklanduni.ac.nz","School of Computer Science, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Auckland, Auckland, New Zealand. lbry121@aucklanduni.ac.nz","institution_ids":["https://openalex.org/I154130895","https://openalex.org/I39854758"]},{"raw_affiliation_string":"School of Computer Science, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053302519","display_name":"Kunyang Zhang","orcid":"https://orcid.org/0009-0008-4588-9487"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I63664421","display_name":"Swiss Federal Institute of Aquatic Science and Technology","ror":"https://ror.org/00pc48d59","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2799323385","https://openalex.org/I63664421"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Kunyang Zhang","raw_affiliation_strings":["Eawag-Swiss Federal Institute of Aquatic Science and Technology, D\u00fcbendorf, Switzerland","University of Z\u00fcrich, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Eawag-Swiss Federal Institute of Aquatic Science and Technology, D\u00fcbendorf, Switzerland","institution_ids":["https://openalex.org/I63664421"]},{"raw_affiliation_string":"University of Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016115576","display_name":"Gillian Dobbie","orcid":"https://orcid.org/0000-0001-7245-0367"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Gillian Dobbie","raw_affiliation_strings":["School of Computer Science, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039842961","display_name":"Katerina Ta\u0161kova","orcid":"https://orcid.org/0000-0002-3217-7877"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Katerina Ta\u0161kova","raw_affiliation_strings":["School of Computer Science, University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079908211","display_name":"J\u00f6rg Wicker","orcid":"https://orcid.org/0000-0003-0533-3368"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"J\u00f6rg Simon Wicker","raw_affiliation_strings":["School of Computer Science, University of Auckland, Auckland, New Zealand","enviPath UG & Co. KG, Ockenheim, Germany"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"enviPath UG & Co. KG, Ockenheim, Germany","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5083529271"],"corresponding_institution_ids":["https://openalex.org/I154130895","https://openalex.org/I39854758"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":15.6742,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.98621526,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"21","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T14351","display_name":"Statistical and Computational Modeling","score":0.9325000047683716,"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"}},"topics":[{"id":"https://openalex.org/T14351","display_name":"Statistical and Computational Modeling","score":0.9325000047683716,"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/computer-science","display_name":"Computer science","score":0.6342400312423706},{"id":"https://openalex.org/keywords/biodegradation","display_name":"Biodegradation","score":0.5318355560302734},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.5189071297645569},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.18528205156326294},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.1425667405128479},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.07790875434875488}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6342400312423706},{"id":"https://openalex.org/C157021035","wikidata":"https://www.wikidata.org/wiki/Q696715","display_name":"Biodegradation","level":2,"score":0.5318355560302734},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.5189071297645569},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.18528205156326294},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.1425667405128479},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.07790875434875488},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-025-00969-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00969-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00969-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:39962584","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39962584","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 cheminformatics","raw_type":null},{"id":"pmh:oai:dora:eawag_34066","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400127","display_name":"DORA Eawag (Swiss Federal Institute of Aquatic Science and Technology (Eawag))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I63664421","host_organization_name":"Swiss Federal Institute of Aquatic Science and Technology","host_organization_lineage":["https://openalex.org/I63664421"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:aaf790bd57e74b7281cba6f5bd8c31d5","is_oa":true,"landing_page_url":"https://doaj.org/article/aaf790bd57e74b7281cba6f5bd8c31d5","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-16 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11834682","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11834682","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00969-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00969-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00969-7","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407633510.pdf","grobid_xml":"https://content.openalex.org/works/W4407633510.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W2121249519","https://openalex.org/W2131623463","https://openalex.org/W2132468877","https://openalex.org/W2145679532","https://openalex.org/W2149948001","https://openalex.org/W2155806188","https://openalex.org/W2174759676","https://openalex.org/W2468778456","https://openalex.org/W2591456708","https://openalex.org/W2769423117","https://openalex.org/W2888680235","https://openalex.org/W2947423323","https://openalex.org/W3038856956","https://openalex.org/W3041133507","https://openalex.org/W3103092523","https://openalex.org/W3105895642","https://openalex.org/W3117879109","https://openalex.org/W3133194039","https://openalex.org/W3140809986","https://openalex.org/W4226159083","https://openalex.org/W4280607179","https://openalex.org/W4295312788","https://openalex.org/W4296686673","https://openalex.org/W4381852030","https://openalex.org/W4385563817","https://openalex.org/W4401357524","https://openalex.org/W6930426830","https://openalex.org/W6949198368"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W3150851457","https://openalex.org/W3006534613","https://openalex.org/W2972590550","https://openalex.org/W2077174545","https://openalex.org/W2413403697","https://openalex.org/W2127573273","https://openalex.org/W2031529581"],"abstract_inverted_index":{"In":[0,116],"recent":[1],"years,":[2],"the":[3,22,35,42,47,76,95,121,124],"integration":[4],"of":[5,24,41,51,80,128],"machine":[6],"learning":[7],"techniques":[8],"into":[9],"chemical":[10,25,52],"reaction":[11,113],"product":[12,96],"prediction":[13,56,97,114],"has":[14],"opened":[15],"new":[16],"avenues":[17],"for":[18,29,123],"understanding":[19],"and":[20,38,49,78,104,111],"predicting":[21],"behaviour":[23],"substances.":[26],"The":[27],"necessity":[28],"such":[30],"predictive":[31],"methods":[32,57,85],"stems":[33],"from":[34,107],"growing":[36],"regulatory":[37],"social":[39],"awareness":[40],"environmental":[43],"consequences":[44],"associated":[45],"with":[46],"persistence":[48],"accumulation":[50],"residues.":[53],"Traditional":[54],"biodegradation":[55],"rely":[58],"on":[59,90],"expert":[60,68],"knowledge":[61,69],"to":[62,75,87],"perform":[63,88],"predictions.":[64],"However,":[65],"creating":[66],"this":[67],"is":[70],"becoming":[71],"increasingly":[72],"prohibitive":[73],"due":[74],"complexity":[77],"diversity":[79],"newer":[81],"datasets,":[82],"leaving":[83],"existing":[84],"unable":[86],"predictions":[89],"these":[91],"datasets.":[92],"We":[93],"formulate":[94],"problem":[98],"as":[99],"a":[100],"sequence-to-sequence":[101],"generation":[102],"task":[103],"take":[105],"inspiration":[106],"natural":[108],"language":[109],"processing":[110],"other":[112],"tasks.":[115],"doing":[117],"so,":[118],"we":[119],"reduce":[120],"need":[122],"expensive":[125],"manual":[126],"creation":[127],"expert-based":[129],"rules.":[130]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
