{"id":"https://openalex.org/W4408293683","doi":"https://doi.org/10.1186/s13321-025-00974-w","title":"Accelerating the inference of string generation-based chemical reaction models for industrial applications","display_name":"Accelerating the inference of string generation-based chemical reaction models for industrial applications","publication_year":2025,"publication_date":"2025-03-10","ids":{"openalex":"https://openalex.org/W4408293683","doi":"https://doi.org/10.1186/s13321-025-00974-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/40065398"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-00974-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00974-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00974-w","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-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 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/s13321-025-00974-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074736657","display_name":"Mikhail G. Andronov","orcid":"https://orcid.org/0000-0002-7980-4495"},"institutions":[{"id":"https://openalex.org/I2614128279","display_name":"Dalle Molle Institute for Artificial Intelligence Research","ror":"https://ror.org/013355g38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I15196421","https://openalex.org/I2614128279","https://openalex.org/I57201433"]},{"id":"https://openalex.org/I15196421","display_name":"University of Applied Sciences and Arts of Southern Switzerland","ror":"https://ror.org/05ep8g269","country_code":"CH","type":"education","lineage":["https://openalex.org/I15196421"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Mikhail Andronov","raw_affiliation_strings":["IDSIA, USI, SUPSI, Lugano, Switzerland. mikhail.andronov@idsia.ch","IDSIA, USI, SUPSI, Lugano, Switzerland"],"affiliations":[{"raw_affiliation_string":"IDSIA, USI, SUPSI, Lugano, Switzerland. mikhail.andronov@idsia.ch","institution_ids":[]},{"raw_affiliation_string":"IDSIA, USI, SUPSI, Lugano, Switzerland","institution_ids":["https://openalex.org/I2614128279","https://openalex.org/I15196421"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111543399","display_name":"Natalia Andronova","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Natalia Andronova","raw_affiliation_strings":[", Lugano, Switzerland","Lugano, Switzerland"],"affiliations":[{"raw_affiliation_string":", Lugano, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Lugano, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020719193","display_name":"Michael Wand","orcid":"https://orcid.org/0000-0003-0966-7824"},"institutions":[{"id":"https://openalex.org/I15196421","display_name":"University of Applied Sciences and Arts of Southern Switzerland","ror":"https://ror.org/05ep8g269","country_code":"CH","type":"education","lineage":["https://openalex.org/I15196421"]},{"id":"https://openalex.org/I2614128279","display_name":"Dalle Molle Institute for Artificial Intelligence Research","ror":"https://ror.org/013355g38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I15196421","https://openalex.org/I2614128279","https://openalex.org/I57201433"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Michael Wand","raw_affiliation_strings":["IDSIA, USI, SUPSI, Lugano, Switzerland","Institute for Digital Technologies for Personalized Healthcare, SUPSI, Lugano, Switzerland"],"affiliations":[{"raw_affiliation_string":"IDSIA, USI, SUPSI, Lugano, Switzerland","institution_ids":["https://openalex.org/I2614128279","https://openalex.org/I15196421"]},{"raw_affiliation_string":"Institute for Digital Technologies for Personalized Healthcare, SUPSI, Lugano, Switzerland","institution_ids":["https://openalex.org/I2614128279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071172037","display_name":"J\u00fcrgen Schmidhuber","orcid":null},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]},{"id":"https://openalex.org/I15196421","display_name":"University of Applied Sciences and Arts of Southern Switzerland","ror":"https://ror.org/05ep8g269","country_code":"CH","type":"education","lineage":["https://openalex.org/I15196421"]},{"id":"https://openalex.org/I2614128279","display_name":"Dalle Molle Institute for Artificial Intelligence Research","ror":"https://ror.org/013355g38","country_code":"CH","type":"facility","lineage":["https://openalex.org/I15196421","https://openalex.org/I2614128279","https://openalex.org/I57201433"]}],"countries":["CH","SA"],"is_corresponding":false,"raw_author_name":"J\u00fcrgen Schmidhuber","raw_affiliation_strings":["AI Initiative, KAUST, Thuwal, Saudi Arabia","IDSIA, USI, SUPSI, Lugano, Switzerland"],"affiliations":[{"raw_affiliation_string":"AI Initiative, KAUST, Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]},{"raw_affiliation_string":"IDSIA, USI, SUPSI, Lugano, Switzerland","institution_ids":["https://openalex.org/I2614128279","https://openalex.org/I15196421"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044662284","display_name":"Djork-Arn\u00e9 Clevert","orcid":"https://orcid.org/0000-0003-4191-2156"},"institutions":[{"id":"https://openalex.org/I4210100293","display_name":"Pfizer (Germany)","ror":"https://ror.org/00m8w3m39","country_code":"DE","type":"company","lineage":["https://openalex.org/I180857899","https://openalex.org/I4210100293"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Djork-Arn\u00e9 Clevert","raw_affiliation_strings":["Machine Learning Research, Pfizer Research and Development, Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Machine Learning Research, Pfizer Research and Development, Berlin, Germany","institution_ids":["https://openalex.org/I4210100293"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074736657"],"corresponding_institution_ids":["https://openalex.org/I15196421","https://openalex.org/I2614128279"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.5454,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.8067637,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"31","last_page":"31"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9768000245094299,"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":0.9768000245094299,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9616000056266785,"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"}},{"id":"https://openalex.org/T12016","display_name":"Web Data Mining and Analysis","score":0.9430000185966492,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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":0.7072175145149231},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6574864387512207},{"id":"https://openalex.org/keywords/string","display_name":"String (physics)","score":0.5805060267448425},{"id":"https://openalex.org/keywords/biochemical-engineering","display_name":"Biochemical engineering","score":0.42212632298469543},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35889357328414917},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.25199973583221436},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.12362700700759888},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08235970139503479}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7072175145149231},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6574864387512207},{"id":"https://openalex.org/C157486923","wikidata":"https://www.wikidata.org/wiki/Q1376436","display_name":"String (physics)","level":2,"score":0.5805060267448425},{"id":"https://openalex.org/C183696295","wikidata":"https://www.wikidata.org/wiki/Q2487696","display_name":"Biochemical engineering","level":1,"score":0.42212632298469543},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35889357328414917},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25199973583221436},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.12362700700759888},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08235970139503479},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-00974-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00974-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00974-w","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-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 Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40065398","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40065398","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:doaj.org/article:198136afc55f4deb97bf360c11208e10","is_oa":true,"landing_page_url":"https://doaj.org/article/198136afc55f4deb97bf360c11208e10","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 1-11 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11895308","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11895308","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-00974-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-00974-w","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-00974-w","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-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 Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408293683.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W29374554","https://openalex.org/W1981276685","https://openalex.org/W2008381136","https://openalex.org/W2089217417","https://openalex.org/W2477622860","https://openalex.org/W2498686521","https://openalex.org/W2747592475","https://openalex.org/W2947423323","https://openalex.org/W3085139254","https://openalex.org/W3088265803","https://openalex.org/W3094771832","https://openalex.org/W3101155908","https://openalex.org/W3103092523","https://openalex.org/W3181403764","https://openalex.org/W4226159083","https://openalex.org/W4229040393","https://openalex.org/W4251094204","https://openalex.org/W4385763890","https://openalex.org/W4407016240","https://openalex.org/W6600445788","https://openalex.org/W6603798796","https://openalex.org/W6609127548"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Transformer-based,":[0],"template-free":[1],"SMILES-to-SMILES":[2],"translation":[3],"models":[4],"for":[5,61,106],"reaction":[6,73],"prediction":[7,75],"and":[8,51,76,140],"single-step":[9,77,112],"retrosynthesis":[10,78],"are":[11],"of":[12,87,93,102,125],"interest":[13],"to":[14,54,135],"computer-aided":[15],"synthesis":[16,94,144],"planning":[17,95],"systems,":[18],"as":[19,90],"they":[20],"offer":[21],"state-of-the-art":[22],"accuracy.":[23],"However,":[24],"their":[25,30],"slow":[26],"inference":[27,71],"speed":[28],"limits":[29],"practical":[31],"utility":[32],"in":[33,72,82,111,143],"such":[34],"applications.":[35],"To":[36,97],"address":[37],"this":[38],"challenge,":[39],"we":[40,114],"propose":[41],"speculative":[42,130],"decoding":[43],"with":[44,79,129],"a":[45,107,119],"simple":[46],"chemically":[47],"specific":[48],"drafting":[49],"strategy":[50],"apply":[52],"it":[53],"the":[55,85,88,91,99,123],"Molecular":[56],"Transformer,":[57],"an":[58],"encoder-decoder":[59],"transformer":[60,89],"conditional":[62],"SMILES":[63,105,110],"generation.":[64],"Our":[65,132],"approach":[66],"achieves":[67],"over":[68],"3X":[69],"faster":[70],"product":[74],"no":[80],"loss":[81],"accuracy,":[83],"increasing":[84],"potential":[86],"backbone":[92],"systems.":[96],"accelerate":[98],"simultaneous":[100],"generation":[101],"multiple":[103],"precursor":[104],"given":[108],"query":[109],"retrosynthesis,":[113],"introduce":[115],"Speculative":[116],"Beam":[117],"Search,":[118],"novel":[120],"algorithm":[121],"tackling":[122],"challenge":[124],"beam":[126],"search":[127],"acceleration":[128],"decoding.":[131],"methods":[133],"aim":[134],"improve":[136],"transformer-based":[137],"models'":[138],"scalability":[139],"industrial":[141],"applicability":[142],"planning.":[145]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-31T07:56:22.981413","created_date":"2025-10-10T00:00:00"}