{"id":"https://openalex.org/W4386081153","doi":"https://doi.org/10.48550/arxiv.2308.10166","title":"Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures","display_name":"Cell Spatial Analysis in Crohn's Disease: Unveiling Local Cell Arrangement Pattern with Graph-based Signatures","publication_year":2023,"publication_date":"2023-08-20","ids":{"openalex":"https://openalex.org/W4386081153","doi":"https://doi.org/10.48550/arxiv.2308.10166"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2308.10166","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2308.10166","pdf_url":"https://arxiv.org/pdf/2308.10166","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2308.10166","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048972725","display_name":"Shunxing Bao","orcid":"https://orcid.org/0000-0001-6376-4292"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Bao, Shunxing","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102487041","display_name":"Si-Chen Zhu","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhu, Sichen","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022498498","display_name":"Vasantha L. Kolachala","orcid":"https://orcid.org/0009-0005-6919-3765"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kolachala, Vasantha L","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058681839","display_name":"Lucas W. Remedios","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Remedios, Lucas W.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065498389","display_name":"Yeonjoo Hwang","orcid":"https://orcid.org/0000-0002-3000-4710"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hwang, Yeonjoo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100587792","display_name":"Yutong Sun","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sun, Yutong","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037133367","display_name":"Ruining Deng","orcid":"https://orcid.org/0000-0001-6300-8518"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Deng, Ruining","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103187104","display_name":"Can Cui","orcid":"https://orcid.org/0000-0002-6226-5747"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Cui, Can","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101537780","display_name":"Yike Li","orcid":"https://orcid.org/0009-0008-4300-6732"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Yike","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024517475","display_name":"Jia Li","orcid":"https://orcid.org/0000-0002-4969-7158"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Li, Jia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038262486","display_name":"Joseph T. Roland","orcid":"https://orcid.org/0000-0001-9977-0520"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Roland, Joseph T.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101757038","display_name":"Qi Liu","orcid":"https://orcid.org/0000-0002-6113-856X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Liu, Qi","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060368492","display_name":"Ken S. Lau","orcid":"https://orcid.org/0000-0001-8438-0319"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lau, Ken S.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006249166","display_name":"Subra Kugathasan","orcid":"https://orcid.org/0000-0002-8686-4189"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kugathasan, Subra","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101449039","display_name":"Peng Qiu","orcid":"https://orcid.org/0000-0002-2509-3683"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Qiu, Peng","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036231550","display_name":"Keith T. Wilson","orcid":"https://orcid.org/0000-0003-4421-1830"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wilson, Keith T.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073353188","display_name":"Lori A. Coburn","orcid":"https://orcid.org/0000-0003-3249-9806"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Coburn, Lori A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075735203","display_name":"Bennett A. Landman","orcid":"https://orcid.org/0000-0001-5733-2127"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Landman, Bennett A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5067191302","display_name":"Yuankai Huo","orcid":"https://orcid.org/0000-0002-2096-8065"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Huo, Yuankai","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":19,"corresponding_author_ids":["https://openalex.org/A5048972725"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T10134","display_name":"Inflammatory Bowel Disease","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}},"topics":[{"id":"https://openalex.org/T10134","display_name":"Inflammatory Bowel Disease","score":0.9757999777793884,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9228000044822693,"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/crohns-disease","display_name":"Crohn's disease","score":0.5983499884605408},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5648318529129028},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3654332756996155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3262324631214142},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.3247249722480774},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.30812984704971313},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2884187698364258},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.2649160623550415},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24743670225143433},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.21727880835533142},{"id":"https://openalex.org/keywords/pathology","display_name":"Pathology","score":0.14766690135002136}],"concepts":[{"id":"https://openalex.org/C2779280984","wikidata":"https://www.wikidata.org/wiki/Q1472","display_name":"Crohn's disease","level":3,"score":0.5983499884605408},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5648318529129028},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3654332756996155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3262324631214142},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.3247249722480774},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30812984704971313},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2884187698364258},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.2649160623550415},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24743670225143433},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.21727880835533142},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.14766690135002136}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2308.10166","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2308.10166","pdf_url":"https://arxiv.org/pdf/2308.10166","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2308.10166","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2308.10166","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":"pmh:oai:arXiv.org:2308.10166","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2308.10166","pdf_url":"https://arxiv.org/pdf/2308.10166","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386081153.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4383420693","https://openalex.org/W2025062623","https://openalex.org/W2147907790","https://openalex.org/W4380486554","https://openalex.org/W2383105242","https://openalex.org/W2019430989","https://openalex.org/W4381193501","https://openalex.org/W2094862489","https://openalex.org/W2224940988","https://openalex.org/W3123423932"],"abstract_inverted_index":{"Crohn's":[0],"disease":[1],"(CD)":[2],"is":[3,19,134],"a":[4,68,82,157],"chronic":[5],"and":[6,32,42,49,66,102,129],"relapsing":[7],"inflammatory":[8],"condition":[9],"that":[10],"affects":[11],"segments":[12],"of":[13,27,76,112,123,153,169,192],"the":[14,25,39,72,115,120,140,161,167,180,185,190],"gastrointestinal":[15],"tract.":[16],"CD":[17,128,177],"activity":[18],"determined":[20],"by":[21],"histological":[22],"findings,":[23],"particularly":[24],"density":[26],"neutrophils":[28],"observed":[29],"on":[30,136,160,172],"Hematoxylin":[31],"Eosin":[33],"stains":[34],"(H&amp;E)":[35],"imaging.":[36],"However,":[37],"understanding":[38],"broader":[40],"morphometry":[41],"local":[43,73],"cell":[44,47,61,88,154,173],"arrangement":[45],"beyond":[46],"counting":[48],"tissue":[50],"morphology":[51],"remains":[52],"challenging.":[53],"To":[54],"address":[55],"this,":[56],"we":[57,80],"characterize":[58],"six":[59],"distinct":[60,151],"types":[62],"from":[63],"H&amp;E":[64],"images":[65],"develop":[67],"novel":[69],"approach":[70],"for":[71,90,96],"spatial":[74,98,124,174,181],"signature":[75],"each":[77,91],"cell.":[78,93],"Specifically,":[79],"create":[81],"10-cell":[83],"neighborhood":[84],"matrix,":[85],"representing":[86],"neighboring":[87],"arrangements":[89,175],"individual":[92],"Utilizing":[94],"t-SNE":[95],"non-linear":[97],"projection":[99],"in":[100,114,176],"scatter-plot":[101],"Kernel":[103],"Density":[104],"Estimation":[105],"contour-plot":[106],"formats,":[107],"our":[108],"study":[109],"examines":[110],"patterns":[111,125],"differences":[113],"cellular":[116],"environment":[117],"associated":[118],"with":[119,156],"odds":[121],"ratio":[122],"between":[126,184],"active":[127],"control":[130],"groups.":[131],"This":[132],"analysis":[133,200],"based":[135],"data":[137,170],"collected":[138],"at":[139,205],"two":[141,186],"research":[142,187,199],"institutes.":[143],"The":[144],"findings":[145],"reveal":[146],"heterogeneous":[147],"nearest-neighbor":[148],"patterns,":[149],"signifying":[150],"tendencies":[152],"clustering,":[155],"particular":[158],"focus":[159],"rectum":[162],"region.":[163],"These":[164],"variations":[165],"underscore":[166],"impact":[168],"heterogeneity":[171],"patients.":[178],"Moreover,":[179],"distribution":[182],"disparities":[183],"sites":[188],"highlight":[189],"significance":[191],"collaborative":[193],"efforts":[194],"among":[195],"healthcare":[196],"organizations.":[197],"All":[198],"pipeline":[201],"tools":[202],"are":[203],"available":[204],"https://github.com/MASILab/cellNN.":[206]},"counts_by_year":[],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
