{"id":"https://openalex.org/W4388940266","doi":"https://doi.org/10.1186/s13321-023-00784-y","title":"An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification","display_name":"An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification","publication_year":2023,"publication_date":"2023-11-23","ids":{"openalex":"https://openalex.org/W4388940266","doi":"https://doi.org/10.1186/s13321-023-00784-y","pmid":"https://pubmed.ncbi.nlm.nih.gov/37996942"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00784-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00784-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00784-y","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/s13321-023-00784-y","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046410250","display_name":"Daniel Probst","orcid":"https://orcid.org/0000-0003-1737-4407"},"institutions":[{"id":"https://openalex.org/I5124864","display_name":"\u00c9cole Polytechnique F\u00e9d\u00e9rale de Lausanne","ror":"https://ror.org/02s376052","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I5124864"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Daniel Probst","raw_affiliation_strings":["Signal Processing Laboratory 2, Institute of Electrical and Micro Engineering, School of Engineering, EPFL, Rte Cantonale, 1015, Lausanne, Vaud, Switzerland. daniel.probst@epfl.ch","Signal Processing Laboratory 2, Institute of Electrical and Micro Engineering, School of Engineering, EPFL, Rte Cantonale, 1015, Lausanne, Vaud, Switzerland"],"affiliations":[{"raw_affiliation_string":"Signal Processing Laboratory 2, Institute of Electrical and Micro Engineering, School of Engineering, EPFL, Rte Cantonale, 1015, Lausanne, Vaud, Switzerland. daniel.probst@epfl.ch","institution_ids":[]},{"raw_affiliation_string":"Signal Processing Laboratory 2, Institute of Electrical and Micro Engineering, School of Engineering, EPFL, Rte Cantonale, 1015, Lausanne, Vaud, Switzerland","institution_ids":["https://openalex.org/I5124864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5046410250"],"corresponding_institution_ids":["https://openalex.org/I5124864"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":2.3351,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90547313,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"15","issue":"1","first_page":"113","last_page":"113"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9979000091552734,"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":0.9979000091552734,"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":0.9944000244140625,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9889000058174133,"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/biocatalysis","display_name":"Biocatalysis","score":0.7206747531890869},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6632726788520813},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.5183571577072144},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4624410569667816},{"id":"https://openalex.org/keywords/enzyme","display_name":"Enzyme","score":0.46045544743537903},{"id":"https://openalex.org/keywords/chemical-reaction","display_name":"Chemical reaction","score":0.43917202949523926},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.4181276559829712},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.378921777009964},{"id":"https://openalex.org/keywords/combinatorial-chemistry","display_name":"Combinatorial chemistry","score":0.3432621955871582},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34136033058166504},{"id":"https://openalex.org/keywords/catalysis","display_name":"Catalysis","score":0.33797746896743774},{"id":"https://openalex.org/keywords/reaction-mechanism","display_name":"Reaction mechanism","score":0.24682116508483887},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.2453264594078064},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.0844380259513855}],"concepts":[{"id":"https://openalex.org/C191503008","wikidata":"https://www.wikidata.org/wiki/Q16007026","display_name":"Biocatalysis","level":4,"score":0.7206747531890869},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6632726788520813},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.5183571577072144},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4624410569667816},{"id":"https://openalex.org/C181199279","wikidata":"https://www.wikidata.org/wiki/Q8047","display_name":"Enzyme","level":2,"score":0.46045544743537903},{"id":"https://openalex.org/C177801218","wikidata":"https://www.wikidata.org/wiki/Q36534","display_name":"Chemical reaction","level":2,"score":0.43917202949523926},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.4181276559829712},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.378921777009964},{"id":"https://openalex.org/C21951064","wikidata":"https://www.wikidata.org/wiki/Q899212","display_name":"Combinatorial chemistry","level":1,"score":0.3432621955871582},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34136033058166504},{"id":"https://openalex.org/C161790260","wikidata":"https://www.wikidata.org/wiki/Q82264","display_name":"Catalysis","level":2,"score":0.33797746896743774},{"id":"https://openalex.org/C65024703","wikidata":"https://www.wikidata.org/wiki/Q373406","display_name":"Reaction mechanism","level":3,"score":0.24682116508483887},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.2453264594078064},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0844380259513855}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13321-023-00784-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00784-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00784-y","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:37996942","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37996942","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:pubmedcentral.nih.gov:10668483","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10668483","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10668483/pdf/13321_2023_Article_784.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e4d5fb2e60cd4041af525717570cb3e5","is_oa":true,"landing_page_url":"https://doaj.org/article/e4d5fb2e60cd4041af525717570cb3e5","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 15, Iss 1, Pp 1-13 (2023)","raw_type":"article"},{"id":"pmh:oai:infoscience.epfl.ch:306652","is_oa":true,"landing_page_url":"https://infoscience.epfl.ch/handle/20.500.14299/202387","pdf_url":null,"source":{"id":"https://openalex.org/S4306400487","display_name":"Infoscience (Ecole Polytechnique F\u00e9d\u00e9rale de Lausanne)","issn_l":null,"issn":null,"is_oa":true,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"research article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00784-y","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00784-y","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00784-y","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":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.47999998927116394}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4388940266.pdf"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1996239184","https://openalex.org/W1996830618","https://openalex.org/W2010707723","https://openalex.org/W2034994407","https://openalex.org/W2070484508","https://openalex.org/W2095279025","https://openalex.org/W2096706242","https://openalex.org/W2110679449","https://openalex.org/W2111973517","https://openalex.org/W2171421143","https://openalex.org/W2559588208","https://openalex.org/W2605409611","https://openalex.org/W2751743037","https://openalex.org/W2757682641","https://openalex.org/W2779144909","https://openalex.org/W2782584560","https://openalex.org/W2809336338","https://openalex.org/W2892210937","https://openalex.org/W2905012389","https://openalex.org/W2908663744","https://openalex.org/W2910665987","https://openalex.org/W2924412896","https://openalex.org/W2949078105","https://openalex.org/W2949274932","https://openalex.org/W2953321375","https://openalex.org/W2962862931","https://openalex.org/W2963095307","https://openalex.org/W2965590414","https://openalex.org/W2979585142","https://openalex.org/W3035847987","https://openalex.org/W3095049046","https://openalex.org/W3105895642","https://openalex.org/W3111322479","https://openalex.org/W3136918052","https://openalex.org/W3160706794","https://openalex.org/W3164046276","https://openalex.org/W3173107846","https://openalex.org/W3211718555","https://openalex.org/W4213314063","https://openalex.org/W4220747243","https://openalex.org/W4220937616","https://openalex.org/W4225876201","https://openalex.org/W4226145240","https://openalex.org/W4280566055","https://openalex.org/W4280651558","https://openalex.org/W4293581802","https://openalex.org/W4297399257","https://openalex.org/W4300862723","https://openalex.org/W4313648381","https://openalex.org/W6969352860","https://openalex.org/W6977367121"],"related_works":["https://openalex.org/W4252713238","https://openalex.org/W91931185","https://openalex.org/W2125201894","https://openalex.org/W4233688127","https://openalex.org/W2373828514","https://openalex.org/W2751743037","https://openalex.org/W4251952782","https://openalex.org/W2489720830","https://openalex.org/W19842636","https://openalex.org/W4242663467"],"abstract_inverted_index":{"Assigning":[0],"or":[1,9],"proposing":[2],"a":[3,7,74,86,101,105],"catalysing":[4,102],"enzyme":[5,72,103],"given":[6,57,106],"chemical":[8,145],"biochemical":[10,107,147],"reaction":[11,53,75],"is":[12,114],"of":[13,26,32,46,60,67,100,116],"great":[14],"interest":[15],"to":[16,38,73,93,126,139],"life":[17],"sciences":[18],"and":[19,24,29,54,62,81,95,132,146],"chemistry":[20],"alike.":[21],"The":[22],"exploration":[23],"design":[25],"metabolic":[27],"pathways":[28],"the":[30,58,98,111,129],"challenge":[31],"finding":[33],"more":[34],"sustainable":[35],"enzyme-catalysed":[36,68],"alternatives":[37],"traditional":[39],"organic":[40,123],"reactions":[41,124],"are":[42],"just":[43],"two":[44],"examples":[45],"tasks":[47],"that":[48],"require":[49],"an":[50,71],"association":[51,99],"between":[52],"enzyme.":[55],"However,":[56],"lack":[59],"large":[61],"balanced":[63],"annotated":[64],"data":[65],"sets":[66],"reactions,":[69],"assigning":[70],"still":[76],"relies":[77],"on":[78],"expert-curated":[79],"rules":[80],"databases.":[82],"Here,":[83],"we":[84],"present":[85],"data-driven":[87],"explainable":[88],"human-in-the-loop":[89],"machine":[90],"learning":[91],"approach":[92],"support":[94,140],"ultimately":[96],"automate":[97],"with":[104],"reaction.":[108],"In":[109],"addition,":[110],"proposed":[112],"method":[113],"capable":[115],"predicting":[117],"enzymes":[118],"as":[119],"candidate":[120],"catalysts":[121],"for":[122],"amendable":[125],"biocatalysis.":[127],"Finally,":[128],"introduced":[130],"explainability":[131],"visualisation":[133],"methods":[134],"can":[135],"easily":[136],"be":[137],"generalised":[138],"other":[141],"machine-learning":[142],"approaches":[143],"involving":[144],"reactions.":[148]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
