Navigating Chemical Space with Latent Flows Article Swipe

PDF

Guanghao Wei , Yining Huang , Chenru Duan , Yue Song , Yuanqi Du ·

YOU? · · 2024 · Open Access · · DOI: https://doi.org/10.48550/arxiv.2405.03987

Recent progress of deep generative models in the vision and language domain has stimulated significant interest in more structured data generation such as molecules. However, beyond generating new random molecules, efficient exploration and a comprehensive understanding of the vast chemical space are of great importance to molecular science and applications in drug design and materials discovery. In this paper, we propose a new framework, ChemFlow, to traverse chemical space through navigating the latent space learned by molecule generative models through flows. We introduce a dynamical system perspective that formulates the problem as learning a vector field that transports the mass of the molecular distribution to the region with desired molecular properties or structure diversity. Under this framework, we unify previous approaches on molecule latent space traversal and optimization and propose alternative competing methods incorporating different physical priors. We validate the efficacy of ChemFlow on molecule manipulation and single- and multi-objective molecule optimization tasks under both supervised and unsupervised molecular discovery settings. Codes and demos are publicly available on GitHub at https://github.com/garywei944/ChemFlow.

Related Topics

Concepts

Space (punctuation) Chemical space Computer science Chemistry Drug discovery Operating system Biochemistry

Metadata

Type: preprint
Language: en
Landing Page: http://arxiv.org/abs/2405.03987
PDF: https://arxiv.org/pdf/2405.03987
OA Status: green
Related Works: 10
OpenAlex ID: https://openalex.org/W4396813982

All OpenAlex metadata

Raw OpenAlex JSON

OpenAlex ID: https://openalex.org/W4396813982

Canonical identifier for this work in OpenAlex
DOI: https://doi.org/10.48550/arxiv.2405.03987

Digital Object Identifier
Title: Navigating Chemical Space with Latent Flows

Work title
Type: preprint

OpenAlex work type
Language: en

Primary language
Publication year: 2024

Year of publication
Publication date: 2024-05-07

Full publication date if available
Authors: Guanghao Wei, Yining Huang, Chenru Duan, Yue Song, Yuanqi Du

List of authors in order
Landing page: https://arxiv.org/abs/2405.03987

Publisher landing page
PDF URL: https://arxiv.org/pdf/2405.03987

Direct link to full text PDF
Open access: Yes

Whether a free full text is available
OA status: green

Open access status per OpenAlex
OA URL: https://arxiv.org/pdf/2405.03987

Direct OA link when available
Concepts: Space (punctuation), Chemical space, Computer science, Chemistry, Drug discovery, Operating system, Biochemistry

Top concepts (fields/topics) attached by OpenAlex
Cited by: 0

Total citation count in OpenAlex
Related works (count): 10

Other works algorithmically related by OpenAlex

Full payload

id	https://openalex.org/W4396813982
doi	https://doi.org/10.48550/arxiv.2405.03987
ids.doi	https://doi.org/10.48550/arxiv.2405.03987
ids.openalex	https://openalex.org/W4396813982
fwci
type	preprint
title	Navigating Chemical Space with Latent Flows
biblio.issue
biblio.volume
biblio.last_page
biblio.first_page
topics[0].id	https://openalex.org/T11986
topics[0].field.id	https://openalex.org/fields/18
topics[0].field.display_name	Decision Sciences
topics[0].score	0.6685000061988831
topics[0].domain.id	https://openalex.org/domains/2
topics[0].domain.display_name	Social Sciences
topics[0].subfield.id	https://openalex.org/subfields/1802
topics[0].subfield.display_name	Information Systems and Management
topics[0].display_name	Scientific Computing and Data Management
is_xpac	False
apc_list
apc_paid
concepts[0].id	https://openalex.org/C2778572836
concepts[0].level	2
concepts[0].score	0.6433004140853882
concepts[0].wikidata	https://www.wikidata.org/wiki/Q380933
concepts[0].display_name	Space (punctuation)
concepts[1].id	https://openalex.org/C99726746
concepts[1].level	3
concepts[1].score	0.4547445476055145
concepts[1].wikidata	https://www.wikidata.org/wiki/Q906396
concepts[1].display_name	Chemical space
concepts[2].id	https://openalex.org/C41008148
concepts[2].level	0
concepts[2].score	0.3369606137275696
concepts[2].wikidata	https://www.wikidata.org/wiki/Q21198
concepts[2].display_name	Computer science
concepts[3].id	https://openalex.org/C185592680
concepts[3].level	0
concepts[3].score	0.1185663640499115
concepts[3].wikidata	https://www.wikidata.org/wiki/Q2329
concepts[3].display_name	Chemistry
concepts[4].id	https://openalex.org/C74187038
concepts[4].level	2
concepts[4].score	0.0
concepts[4].wikidata	https://www.wikidata.org/wiki/Q1418791
concepts[4].display_name	Drug discovery
concepts[5].id	https://openalex.org/C111919701
concepts[5].level	1
concepts[5].score	0.0
concepts[5].wikidata	https://www.wikidata.org/wiki/Q9135
concepts[5].display_name	Operating system
concepts[6].id	https://openalex.org/C55493867
concepts[6].level	1
concepts[6].score	0.0
concepts[6].wikidata	https://www.wikidata.org/wiki/Q7094
concepts[6].display_name	Biochemistry
keywords[0].id	https://openalex.org/keywords/space
keywords[0].score	0.6433004140853882
keywords[0].display_name	Space (punctuation)
keywords[1].id	https://openalex.org/keywords/chemical-space
keywords[1].score	0.4547445476055145
keywords[1].display_name	Chemical space
keywords[2].id	https://openalex.org/keywords/computer-science
keywords[2].score	0.3369606137275696
keywords[2].display_name	Computer science
keywords[3].id	https://openalex.org/keywords/chemistry
keywords[3].score	0.1185663640499115
keywords[3].display_name	Chemistry
language	en
locations[0].id	pmh:oai:arXiv.org:2405.03987
locations[0].is_oa	True
locations[0].source.id	https://openalex.org/S4306400194
locations[0].source.issn
locations[0].source.type	repository
locations[0].source.is_oa	True
locations[0].source.issn_l
locations[0].source.is_core	False
locations[0].source.is_in_doaj	False
locations[0].source.display_name	arXiv (Cornell University)
locations[0].source.host_organization	https://openalex.org/I205783295
locations[0].source.host_organization_name	Cornell University
locations[0].source.host_organization_lineage	https://openalex.org/I205783295
locations[0].license
locations[0].pdf_url	https://arxiv.org/pdf/2405.03987
locations[0].version	submittedVersion
locations[0].raw_type	text
locations[0].license_id
locations[0].is_accepted	False
locations[0].is_published	False
locations[0].raw_source_name
locations[0].landing_page_url	http://arxiv.org/abs/2405.03987
locations[1].id	doi:10.48550/arxiv.2405.03987
locations[1].is_oa	True
locations[1].source.id	https://openalex.org/S4306400194
locations[1].source.issn
locations[1].source.type	repository
locations[1].source.is_oa	True
locations[1].source.issn_l
locations[1].source.is_core	False
locations[1].source.is_in_doaj	False
locations[1].source.display_name	arXiv (Cornell University)
locations[1].source.host_organization	https://openalex.org/I205783295
locations[1].source.host_organization_name	Cornell University
locations[1].source.host_organization_lineage	https://openalex.org/I205783295
locations[1].license
locations[1].pdf_url
locations[1].version
locations[1].raw_type	article
locations[1].license_id
locations[1].is_accepted	False
locations[1].is_published
locations[1].raw_source_name
locations[1].landing_page_url	https://doi.org/10.48550/arxiv.2405.03987
indexed_in	arxiv, datacite
authorships[0].author.id	https://openalex.org/A5104169948
authorships[0].author.orcid	https://orcid.org/0009-0009-3477-1894
authorships[0].author.display_name	Guanghao Wei
authorships[0].author_position	first
authorships[0].raw_author_name	Wei, Guanghao
authorships[0].is_corresponding	False
authorships[1].author.id	https://openalex.org/A5008557264
authorships[1].author.orcid	https://orcid.org/0000-0001-9265-5896
authorships[1].author.display_name	Yining Huang
authorships[1].author_position	middle
authorships[1].raw_author_name	Huang, Yining
authorships[1].is_corresponding	False
authorships[2].author.id	https://openalex.org/A5029457626
authorships[2].author.orcid	https://orcid.org/0000-0003-2592-4237
authorships[2].author.display_name	Chenru Duan
authorships[2].author_position	middle
authorships[2].raw_author_name	Duan, Chenru
authorships[2].is_corresponding	False
authorships[3].author.id	https://openalex.org/A5075379587
authorships[3].author.orcid	https://orcid.org/0000-0003-1920-740X
authorships[3].author.display_name	Yue Song
authorships[3].author_position	middle
authorships[3].raw_author_name	Song, Yue
authorships[3].is_corresponding	False
authorships[4].author.id	https://openalex.org/A5006709853
authorships[4].author.orcid	https://orcid.org/0000-0003-2988-0374
authorships[4].author.display_name	Yuanqi Du
authorships[4].author_position	last
authorships[4].raw_author_name	Du, Yuanqi
authorships[4].is_corresponding	False
has_content.pdf	False
has_content.grobid_xml	False
is_paratext	False
open_access.is_oa	True
open_access.oa_url	https://arxiv.org/pdf/2405.03987
open_access.oa_status	green
open_access.any_repository_has_fulltext	False
created_date	2025-10-10T00:00:00
display_name	Navigating Chemical Space with Latent Flows
has_fulltext	False
is_retracted	False
updated_date	2025-11-06T06:51:31.235846
primary_topic.id	https://openalex.org/T11986
primary_topic.field.id	https://openalex.org/fields/18
primary_topic.field.display_name	Decision Sciences
primary_topic.score	0.6685000061988831
primary_topic.domain.id	https://openalex.org/domains/2
primary_topic.domain.display_name	Social Sciences
primary_topic.subfield.id	https://openalex.org/subfields/1802
primary_topic.subfield.display_name	Information Systems and Management
primary_topic.display_name	Scientific Computing and Data Management
related_works	https://openalex.org/W4391375266, https://openalex.org/W2748952813, https://openalex.org/W2902857455, https://openalex.org/W2161782568, https://openalex.org/W4212982662, https://openalex.org/W4226062292, https://openalex.org/W4281772408, https://openalex.org/W2078293348, https://openalex.org/W4254684673, https://openalex.org/W2345388732
cited_by_count	0
locations_count	2
best_oa_location.id	pmh:oai:arXiv.org:2405.03987
best_oa_location.is_oa	True
best_oa_location.source.id	https://openalex.org/S4306400194
best_oa_location.source.issn
best_oa_location.source.type	repository
best_oa_location.source.is_oa	True
best_oa_location.source.issn_l
best_oa_location.source.is_core	False
best_oa_location.source.is_in_doaj	False
best_oa_location.source.display_name	arXiv (Cornell University)
best_oa_location.source.host_organization	https://openalex.org/I205783295
best_oa_location.source.host_organization_name	Cornell University
best_oa_location.source.host_organization_lineage	https://openalex.org/I205783295
best_oa_location.license
best_oa_location.pdf_url	https://arxiv.org/pdf/2405.03987
best_oa_location.version	submittedVersion
best_oa_location.raw_type	text
best_oa_location.license_id
best_oa_location.is_accepted	False
best_oa_location.is_published	False
best_oa_location.raw_source_name
best_oa_location.landing_page_url	http://arxiv.org/abs/2405.03987
primary_location.id	pmh:oai:arXiv.org:2405.03987
primary_location.is_oa	True
primary_location.source.id	https://openalex.org/S4306400194
primary_location.source.issn
primary_location.source.type	repository
primary_location.source.is_oa	True
primary_location.source.issn_l
primary_location.source.is_core	False
primary_location.source.is_in_doaj	False
primary_location.source.display_name	arXiv (Cornell University)
primary_location.source.host_organization	https://openalex.org/I205783295
primary_location.source.host_organization_name	Cornell University
primary_location.source.host_organization_lineage	https://openalex.org/I205783295
primary_location.license
primary_location.pdf_url	https://arxiv.org/pdf/2405.03987
primary_location.version	submittedVersion
primary_location.raw_type	text
primary_location.license_id
primary_location.is_accepted	False
primary_location.is_published	False
primary_location.raw_source_name
primary_location.landing_page_url	http://arxiv.org/abs/2405.03987
publication_date	2024-05-07
publication_year	2024
referenced_works_count	0
abstract_inverted_index.a	33, 61, 83, 93
abstract_inverted_index.In	56
abstract_inverted_index.We	81, 137
abstract_inverted_index.as	22, 91
abstract_inverted_index.at	169
abstract_inverted_index.by	75
abstract_inverted_index.in	6, 16, 50
abstract_inverted_index.of	2, 36, 42, 100, 141
abstract_inverted_index.on	121, 143, 167
abstract_inverted_index.or	111
abstract_inverted_index.to	45, 65, 104
abstract_inverted_index.we	59, 117
abstract_inverted_index.and	9, 32, 48, 53, 126, 128, 146, 148, 156, 162
abstract_inverted_index.are	41, 164
abstract_inverted_index.has	12
abstract_inverted_index.new	27, 62
abstract_inverted_index.the	7, 37, 71, 89, 98, 101, 105, 139
abstract_inverted_index.both	154
abstract_inverted_index.data	19
abstract_inverted_index.deep	3
abstract_inverted_index.drug	51
abstract_inverted_index.mass	99
abstract_inverted_index.more	17
abstract_inverted_index.such	21
abstract_inverted_index.that	87, 96
abstract_inverted_index.this	57, 115
abstract_inverted_index.vast	38
abstract_inverted_index.with	107
abstract_inverted_index.Codes	161
abstract_inverted_index.Under	114
abstract_inverted_index.demos	163
abstract_inverted_index.field	95
abstract_inverted_index.great	43
abstract_inverted_index.space	40, 68, 73, 124
abstract_inverted_index.tasks	152
abstract_inverted_index.under	153
abstract_inverted_index.unify	118
abstract_inverted_index.GitHub	168
abstract_inverted_index.Recent	0
abstract_inverted_index.beyond	25
abstract_inverted_index.design	52
abstract_inverted_index.domain	11
abstract_inverted_index.flows.	80
abstract_inverted_index.latent	72, 123
abstract_inverted_index.models	5, 78
abstract_inverted_index.paper,	58
abstract_inverted_index.random	28
abstract_inverted_index.region	106
abstract_inverted_index.system	85
abstract_inverted_index.vector	94
abstract_inverted_index.vision	8
abstract_inverted_index.desired	108
abstract_inverted_index.learned	74
abstract_inverted_index.methods	132
abstract_inverted_index.priors.	136
abstract_inverted_index.problem	90
abstract_inverted_index.propose	60, 129
abstract_inverted_index.science	47
abstract_inverted_index.single-	147
abstract_inverted_index.through	69, 79
abstract_inverted_index.ChemFlow	142
abstract_inverted_index.However,	24
abstract_inverted_index.chemical	39, 67
abstract_inverted_index.efficacy	140
abstract_inverted_index.interest	15
abstract_inverted_index.language	10
abstract_inverted_index.learning	92
abstract_inverted_index.molecule	76, 122, 144, 150
abstract_inverted_index.physical	135
abstract_inverted_index.previous	119
abstract_inverted_index.progress	1
abstract_inverted_index.publicly	165
abstract_inverted_index.traverse	66
abstract_inverted_index.validate	138
abstract_inverted_index.ChemFlow,	64
abstract_inverted_index.available	166
abstract_inverted_index.competing	131
abstract_inverted_index.different	134
abstract_inverted_index.discovery	159
abstract_inverted_index.dynamical	84
abstract_inverted_index.efficient	30
abstract_inverted_index.introduce	82
abstract_inverted_index.materials	54
abstract_inverted_index.molecular	46, 102, 109, 158
abstract_inverted_index.settings.	160
abstract_inverted_index.structure	112
abstract_inverted_index.traversal	125
abstract_inverted_index.approaches	120
abstract_inverted_index.discovery.	55
abstract_inverted_index.diversity.	113
abstract_inverted_index.formulates	88
abstract_inverted_index.framework,	63, 116
abstract_inverted_index.generating	26
abstract_inverted_index.generation	20
abstract_inverted_index.generative	4, 77
abstract_inverted_index.importance	44
abstract_inverted_index.molecules,	29
abstract_inverted_index.molecules.	23
abstract_inverted_index.navigating	70
abstract_inverted_index.properties	110
abstract_inverted_index.stimulated	13
abstract_inverted_index.structured	18
abstract_inverted_index.supervised	155
abstract_inverted_index.transports	97
abstract_inverted_index.alternative	130
abstract_inverted_index.exploration	31
abstract_inverted_index.perspective	86
abstract_inverted_index.significant	14
abstract_inverted_index.applications	49
abstract_inverted_index.distribution	103
abstract_inverted_index.manipulation	145
abstract_inverted_index.optimization	127, 151
abstract_inverted_index.unsupervised	157
abstract_inverted_index.comprehensive	34
abstract_inverted_index.incorporating	133
abstract_inverted_index.understanding	35
abstract_inverted_index.multi-objective	149
abstract_inverted_index.https://github.com/garywei944/ChemFlow.	170
cited_by_percentile_year
countries_distinct_count	0
institutions_distinct_count	5
citation_normalized_percentile