{"id":"https://openalex.org/W7147104452","doi":"https://doi.org/10.48550/arxiv.2603.27113","title":"Hierarchy-Guided Topology Latent Flow for Molecular Graph Generation","display_name":"Hierarchy-Guided Topology Latent Flow for Molecular Graph Generation","publication_year":2026,"publication_date":"2026-03-28","ids":{"openalex":"https://openalex.org/W7147104452","doi":"https://doi.org/10.48550/arxiv.2603.27113"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2603.27113","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.27113","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":null,"license_id":null,"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.2603.27113","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5132594709","display_name":"Urvi Awasthi","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Awasthi, Urvi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132720767","display_name":"Alexander Arjun Lobo","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lobo, Alexander Arjun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5004770347","display_name":"Leonid Zhukov","orcid":"https://orcid.org/0000-0003-2604-1057"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhukov, Leonid","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.3921000063419342,"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":0.3921000063419342,"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":0.27079999446868896,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.09449999779462814,"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/topology","display_name":"Topology (electrical circuits)","score":0.7336999773979187},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6279000043869019},{"id":"https://openalex.org/keywords/bond-graph","display_name":"Bond graph","score":0.45489999651908875},{"id":"https://openalex.org/keywords/flow","display_name":"Flow (mathematics)","score":0.45159998536109924},{"id":"https://openalex.org/keywords/stability","display_name":"Stability (learning theory)","score":0.41190001368522644},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3968999981880188}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.7336999773979187},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6279000043869019},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5073999762535095},{"id":"https://openalex.org/C187593909","wikidata":"https://www.wikidata.org/wiki/Q838024","display_name":"Bond graph","level":2,"score":0.45489999651908875},{"id":"https://openalex.org/C38349280","wikidata":"https://www.wikidata.org/wiki/Q1434290","display_name":"Flow (mathematics)","level":2,"score":0.45159998536109924},{"id":"https://openalex.org/C112972136","wikidata":"https://www.wikidata.org/wiki/Q7595718","display_name":"Stability (learning theory)","level":2,"score":0.41190001368522644},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3968999981880188},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.3650999963283539},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3578000068664551},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35100001096725464},{"id":"https://openalex.org/C69738904","wikidata":"https://www.wikidata.org/wiki/Q11693","display_name":"Bond","level":2,"score":0.32190001010894775},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.3172999918460846},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3073999881744385},{"id":"https://openalex.org/C129089157","wikidata":"https://www.wikidata.org/wiki/Q621550","display_name":"General topology","level":3,"score":0.27079999446868896},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.25519999861717224},{"id":"https://openalex.org/C58312451","wikidata":"https://www.wikidata.org/wiki/Q4817200","display_name":"Atom (system on chip)","level":2,"score":0.2540000081062317}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2603.27113","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.27113","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2603.27113","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2603.27113","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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/16","display_name":"Peace, Justice and strong institutions","score":0.5124773979187012}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Generating":[0],"chemically":[1],"valid":[2],"3D":[3,33,65],"molecules":[4,27],"is":[5],"hindered":[6],"by":[7],"discrete":[8],"bond":[9,13,62],"topology:":[10],"small":[11],"local":[12],"errors":[14],"can":[15],"cause":[16],"global":[17,73],"failures":[18],"(valence":[19],"violations,":[20],"disconnections,":[21],"implausible":[22],"rings),":[23],"especially":[24],"for":[25,72],"drug-like":[26],"with":[28,64],"long-range":[29],"constraints.":[30],"Many":[31],"unconditional":[32],"generators":[34],"emphasize":[35],"coordinates":[36],"and":[37,75,90,112],"then":[38],"infer":[39],"bonds":[40],"or":[41],"rely":[42],"on":[43],"post-processing,":[44],"leaving":[45],"topology":[46,126],"feasibility":[47],"weakly":[48],"controlled.":[49],"We":[50],"propose":[51],"Hierarchy-Guided":[52],"Latent":[53],"Topology":[54],"Flow":[55],"(HLTF),":[56],"a":[57,68,76],"planner-executor":[58],"model":[59],"that":[60,132],"generates":[61],"graphs":[63],"coordinates,":[66],"using":[67],"latent":[69],"multi-scale":[70],"plan":[71],"context":[74],"constraint-aware":[77],"sampler":[78],"to":[79,96],"suppress":[80],"topology-driven":[81],"failures.":[82],"On":[83,104],"QM9,":[84],"HLTF":[85,106],"achieves":[86],"98.8%":[87],"atom":[88],"stability":[89],"92.9%":[91],"valid-and-unique,":[92],"improving":[93],"PoseBusters":[94],"validity":[95],"94.0%":[97],"(+0.9":[98],"over":[99],"the":[100,121],"strongest":[101],"reported":[102],"baseline).":[103],"GEOM-DRUGS,":[105],"attains":[107],"85.5%/85.0%":[108],"validity/valid-unique-novel":[109],"without":[110],"post-processing":[111],"92.2%/91.2%":[113],"after":[114],"standardized":[115],"relaxation,":[116],"within":[117],"0.9":[118],"points":[119],"of":[120],"best":[122],"post-processed":[123],"baseline.":[124],"Explicit":[125],"generation":[127],"also":[128],"reduces":[129],"\"false-valid\"":[130],"samples":[131],"pass":[133],"RDKit":[134],"sanitization":[135],"but":[136],"fail":[137],"stricter":[138],"checks.":[139]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-04-02T00:00:00"}
