{"id":"https://openalex.org/W7153218757","doi":"https://doi.org/10.48550/arxiv.2604.07560","title":"Predicting Activity Cliffs for Autonomous Medicinal Chemistry","display_name":"Predicting Activity Cliffs for Autonomous Medicinal Chemistry","publication_year":2026,"publication_date":"2026-04-08","ids":{"openalex":"https://openalex.org/W7153218757","doi":"https://doi.org/10.48550/arxiv.2604.07560"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2604.07560","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.07560","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2604.07560","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086519300","display_name":"Michael F. Cuccarese","orcid":"https://orcid.org/0000-0001-7431-9573"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Cuccarese, Michael","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5086519300"],"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9085000157356262,"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":0.9085000157356262,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.03449999913573265,"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"}},{"id":"https://openalex.org/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.006300000008195639,"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/pharmacophore","display_name":"Pharmacophore","score":0.6901000142097473},{"id":"https://openalex.org/keywords/chembl","display_name":"chEMBL","score":0.6880000233650208},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5584999918937683},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.5112000107765198},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.3560999929904938},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.34279999136924744},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.32749998569488525},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.30959999561309814}],"concepts":[{"id":"https://openalex.org/C56173144","wikidata":"https://www.wikidata.org/wiki/Q1539893","display_name":"Pharmacophore","level":2,"score":0.6901000142097473},{"id":"https://openalex.org/C63222358","wikidata":"https://www.wikidata.org/wiki/Q6120337","display_name":"chEMBL","level":3,"score":0.6880000233650208},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5584999918937683},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5378000140190125},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.5112000107765198},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4722999930381775},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46369999647140503},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.37540000677108765},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.367000013589859},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.3560999929904938},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.34279999136924744},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.33570000529289246},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.32749998569488525},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.30959999561309814},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2962000072002411},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.29440000653266907},{"id":"https://openalex.org/C164126121","wikidata":"https://www.wikidata.org/wiki/Q766383","display_name":"Quantitative structure\u2013activity relationship","level":2,"score":0.2903999984264374},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C202264299","wikidata":"https://www.wikidata.org/wiki/Q905695","display_name":"UniProt","level":3,"score":0.26969999074935913},{"id":"https://openalex.org/C148220186","wikidata":"https://www.wikidata.org/wiki/Q7111912","display_name":"Outcome (game theory)","level":2,"score":0.2632000148296356},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.2623000144958496},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2500999867916107}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2604.07560","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.07560","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2604.07560","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2604.07560","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"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":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Activity":[0],"cliff":[1],"prediction":[2],"-":[3,14,93,106,148,161],"identifying":[4],"positions":[5,72,152],"where":[6,94],"small":[7,32,95],"structural":[8],"changes":[9],"cause":[10,97],"large":[11,99],"potency":[12],"shifts":[13],"has":[15],"been":[16],"a":[17,28,153,162],"persistent":[18],"challenge":[19],"in":[20,165],"computational":[21],"medicinal":[22],"chemistry.":[23],"This":[24],"work":[25],"focuses":[26],"on":[27,184],"parsimonious":[29],"definition:":[30],"which":[31,35,169],"modifications,":[33],"at":[34],"positions,":[36],"confer":[37],"the":[38,137,143],"highest":[39],"probability":[40],"of":[41,142],"an":[42,108,195],"outcome":[43],"change.":[44],"Position-level":[45],"sensitivity":[46],"is":[47,75,173,189],"calculated":[48],"using":[49],"25":[50],"million":[51],"matched":[52],"molecular":[53],"pairs":[54],"from":[55,157,176],"50":[56],"ChEMBL":[57],"targets":[58],"across":[59,122],"six":[60,124],"protein":[61,125],"families,":[62,126],"revealing":[63],"that":[64],"two":[65],"questions":[66],"have":[67],"fundamentally":[68],"different":[69],"answers.":[70],"\"Which":[71,88],"vary":[73],"most?\"":[74],"answered":[76],"by":[77,103],"scaffold":[78],"size":[79],"alone":[80,178],"(NDCG@3":[81,115],"=":[82,116],"0.966),":[83],"requiring":[84],"no":[85],"machine":[86],"learning.":[87],"are":[89],"true":[90],"activity":[91],"cliffs?\"":[92],"modifications":[96],"disproportionately":[98],"effects,":[100],"as":[101,191],"captured":[102],"SALI":[104],"normalization":[105],"requires":[107],"11-feature":[109],"model":[110,135],"with":[111],"3D":[112],"pharmacophore":[113],"context":[114],"0.910":[117],"vs.":[118],"0.839":[119],"random),":[120],"generalizing":[121],"all":[123],"novel":[127,185],"scaffolds":[128],"(0.913),":[129],"and":[130,194],"temporal":[131],"splits":[132],"(0.878).":[133],"The":[134,187],"identifies":[136],"cliff-prone":[138],"position":[139],"first":[140],"53%":[141],"time":[144],"(vs.":[145],"27%":[146],"random":[147],"2x":[149],"lift),":[150],"reducing":[151],"chemist":[154],"must":[155],"explore":[156],"3.1":[158],"to":[159,171,182],"2.1":[160],"31%":[163],"reduction":[164],"first-round":[166],"experiments.":[167],"Predicting":[168],"modification":[170],"make":[172],"not":[174],"tractable":[175],"structure":[177],"(Spearman":[179],"0.268,":[180],"collapsing":[181],"-0.31":[183],"scaffolds).":[186],"system":[188],"released":[190],"open-source":[192],"code":[193],"interactive":[196],"webapp.":[197]},"counts_by_year":[],"updated_date":"2026-04-11T06:19:08.300824","created_date":"2026-04-11T00:00:00"}
