{"id":"https://openalex.org/W7165671876","doi":"https://doi.org/10.48550/arxiv.2606.23443","title":"What Does a Chemical Language Model Know About Molecules?","display_name":"What Does a Chemical Language Model Know About Molecules?","publication_year":2026,"publication_date":"2026-06-22","ids":{"openalex":"https://openalex.org/W7165671876","doi":"https://doi.org/10.48550/arxiv.2606.23443"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.23443","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.23443","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2606.23443","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5114674224","display_name":"Christian Kenneth","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kenneth, Christian","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137562131","display_name":"Etowah Adams","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Adams, Etowah","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139134039","display_name":"Liam Bai","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bai, Liam","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5018833948","display_name":"Gerard Jp van Westen","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"van Westen, Gerard JP","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.8686000108718872,"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":0.8686000108718872,"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":0.01940000057220459,"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/T10028","display_name":"Topic Modeling","score":0.010400000028312206,"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/representation","display_name":"Representation (politics)","score":0.6444000005722046},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.6363999843597412},{"id":"https://openalex.org/keywords/parsing","display_name":"Parsing","score":0.555899977684021},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.3716000020503998},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.33230000734329224},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.30660000443458557}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7228999733924866},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6800000071525574},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6444000005722046},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6363999843597412},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5940999984741211},{"id":"https://openalex.org/C186644900","wikidata":"https://www.wikidata.org/wiki/Q194152","display_name":"Parsing","level":2,"score":0.555899977684021},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3716000020503998},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.33230000734329224},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.30660000443458557},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.30250000953674316},{"id":"https://openalex.org/C188147891","wikidata":"https://www.wikidata.org/wiki/Q147638","display_name":"Cognitive science","level":1,"score":0.28700000047683716},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2824999988079071},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.2639000117778778},{"id":"https://openalex.org/C2993724205","wikidata":"https://www.wikidata.org/wiki/Q315","display_name":"Human language","level":2,"score":0.26190000772476196},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.23443","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.23443","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.23443","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.23443","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"score":0.6655694246292114,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Chemical":[0],"language":[1],"models":[2],"(cLMs)":[3],"are":[4,35],"widely":[5],"assumed":[6],"to":[7,24,29,48],"learn":[8],"surface-level":[9],"syntactic":[10],"patterns":[11],"rather":[12],"than":[13,72],"learning":[14],"meaningful":[15],"molecular":[16,33,50,96],"semantics.":[17],"Here,":[18],"we":[19,62,86],"apply":[20],"sparse":[21],"autoencoders":[22],"(SAEs)":[23],"MolFormer,":[25],"an":[26,89],"encoder-only":[27],"cLM,":[28],"mechanistically":[30],"examine":[31],"how":[32],"representations":[34],"built":[36],"across":[37,80],"layers.":[38,81],"We":[39],"discover":[40],"that":[41,64],"early":[42],"layers":[43,54],"rely":[44],"on":[45,95],"position-tracking":[46],"latents":[47],"parse":[49],"grammar,":[51],"while":[52],"later":[53],"encode":[55],"atom-in-substructure":[56],"and":[57,98],"pharmacologically":[58],"relevant":[59],"features.":[60],"Additionally,":[61],"show":[63],"non-canonical":[65],"SMILES":[66],"produce":[67],"more":[68],"disruptive":[69],"representation":[70],"shifts":[71],"invalid":[73],"SMILES,":[74],"driven":[75],"by":[76],"position-latent":[77],"disruption":[78],"propagating":[79],"To":[82],"support":[83],"further":[84],"exploration,":[85],"develop":[87],"InterMol,":[88],"interactive":[90],"visualizer":[91],"for":[92],"SAE":[93],"activations":[94],"strings":[97],"structures.":[99]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-06-24T00:00:00"}