{"id":"https://openalex.org/W7164942212","doi":"https://doi.org/10.48550/arxiv.2606.16540","title":"MultiMolecule: a modular ecosystem for biomolecular sequence-model workflows","display_name":"MultiMolecule: a modular ecosystem for biomolecular sequence-model workflows","publication_year":2026,"publication_date":"2026-06-15","ids":{"openalex":"https://openalex.org/W7164942212","doi":"https://doi.org/10.48550/arxiv.2606.16540"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2606.16540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.16540","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":null,"license_id":null,"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.2606.16540","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5138699994","display_name":"Zhiyuan Chen","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Chen, Zhiyuan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5138699994"],"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/T11986","display_name":"Scientific Computing and Data Management","score":0.34310001134872437,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.34310001134872437,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.2012999951839447,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.06830000132322311,"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/workflow","display_name":"Workflow","score":0.8087000250816345},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.7239000201225281},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6873000264167786},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6733999848365784},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.660099983215332},{"id":"https://openalex.org/keywords/reuse","display_name":"Reuse","score":0.5648000240325928},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.551800012588501},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.511900007724762},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4526999890804291}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8087000250816345},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7689999938011169},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.7239000201225281},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6873000264167786},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6733999848365784},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.660099983215332},{"id":"https://openalex.org/C206588197","wikidata":"https://www.wikidata.org/wiki/Q846574","display_name":"Reuse","level":2,"score":0.5648000240325928},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.551800012588501},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5371000170707703},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.511900007724762},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4526999890804291},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.42809998989105225},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.40380001068115234},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.36899998784065247},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3578999936580658},{"id":"https://openalex.org/C51929080","wikidata":"https://www.wikidata.org/wiki/Q2425187","display_name":"Codebase","level":3,"score":0.35519999265670776},{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.3334999978542328},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.32989999651908875},{"id":"https://openalex.org/C32833848","wikidata":"https://www.wikidata.org/wiki/Q4115054","display_name":"Extensibility","level":2,"score":0.30469998717308044},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.30219998955726624},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.29789999127388},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.29679998755455017},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.29600000381469727},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.29109999537467957},{"id":"https://openalex.org/C198140048","wikidata":"https://www.wikidata.org/wiki/Q10859422","display_name":"Software versioning","level":3,"score":0.28999999165534973},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.2784999907016754},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2784999907016754},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.2583000063896179},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.25440001487731934},{"id":"https://openalex.org/C2780615836","wikidata":"https://www.wikidata.org/wiki/Q2471869","display_name":"USable","level":2,"score":0.251800000667572}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2606.16540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.16540","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2606.16540","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2606.16540","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.5218756198883057}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Biomolecular":[0],"sequence":[1],"models":[2,28,33,172],"are":[3,103],"increasingly":[4],"reused":[5],"outside":[6],"the":[7,19],"studies":[8],"in":[9],"which":[10],"they":[11],"were":[12],"introduced,":[13],"but":[14],"public":[15,93,118],"checkpoints":[16,146],"rarely":[17],"preserve":[18],"execution":[20],"context":[21],"needed":[22],"to":[23,29,105,122,147,151,173],"inspect":[24,123],"source-defined":[25,168],"behavior,":[26,170],"adapt":[27],"new":[30,174],"assays,":[31,175],"compare":[32],"under":[34],"shared":[35,63],"task":[36],"definitions":[37],"or":[38,109,139],"deploy":[39],"biological":[40,159],"predictions.":[41,182],"MultiMolecule":[42,162],"is":[43],"an":[44],"open-source":[45],"Python":[46],"ecosystem":[47],"that":[48],"turns":[49],"heterogeneous":[50],"RNA,":[51],"DNA":[52],"and":[53,66,96,117,131,158,179],"protein":[54],"sequence-model":[55],"releases":[56],"into":[57],"complete,":[58],"source-checked":[59],"model-family":[60,77],"implementations":[61,78,149],"with":[62,79,85],"loading,":[64],"workflow":[65],"prediction":[67,99,160],"interfaces.":[68],"The":[69],"Resource":[70],"state":[71],"reported":[72],"here":[73],"includes":[74],"53":[75],"complete":[76],"112":[80],"standardized":[81,152],"model":[82,169],"checkpoints,":[83,153],"together":[84],"16":[86],"curated":[87,154],"dataset":[88,94],"resources":[89],"released":[90],"through":[91],"39":[92],"repositories":[95],"10":[97],"user-facing":[98],"pipelines.":[100],"Standardized":[101],"components":[102],"linked":[104],"source":[106],"provenance,":[107],"conversion":[108],"preparation":[110],"code,":[111],"source-reference":[112],"checks,":[113],"Extended":[114],"Data":[115],"summaries":[116],"documentation,":[119],"allowing":[120],"users":[121],"what":[124,127],"was":[125,129],"standardized,":[126],"behavior":[128],"checked":[130],"how":[132],"each":[133],"component":[134],"enters":[135],"training,":[136],"evaluation,":[137],"inference":[138],"deployment.":[140],"By":[141],"shifting":[142],"reuse":[143],"from":[144],"repository-specific":[145],"executable":[148],"connected":[150],"datasets,":[155],"Runner":[156],"workflows":[157],"pipelines,":[161],"provides":[163],"common":[164],"infrastructure":[165],"for":[166],"preserving":[167],"adapting":[171],"enabling":[176],"controlled":[177],"evaluation":[178],"deploying":[180],"biomolecular":[181]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-06-17T00:00:00"}
