{"id":"https://openalex.org/W4416250204","doi":"https://doi.org/10.1109/ijcnn64981.2025.11227921","title":"Biologically Informed procedure for Feature Summarization in Spatial Transcriptomics","display_name":"Biologically Informed procedure for Feature Summarization in Spatial Transcriptomics","publication_year":2025,"publication_date":"2025-06-30","ids":{"openalex":"https://openalex.org/W4416250204","doi":"https://doi.org/10.1109/ijcnn64981.2025.11227921"},"language":"en","primary_location":{"id":"doi:10.1109/ijcnn64981.2025.11227921","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn64981.2025.11227921","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Matteo Baldan","orcid":null},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Matteo Baldan","raw_affiliation_strings":["University of Padova,Dept. of Information Engineering,Padova,Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova,Dept. of Information Engineering,Padova,Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039145389","display_name":"Giulia Cesaro","orcid":"https://orcid.org/0000-0001-7971-963X"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giulia Cesaro","raw_affiliation_strings":["University of Padova,Dept. of Information Engineering,Padova,Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova,Dept. of Information Engineering,Padova,Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010617664","display_name":"Giacomo Baruzzo","orcid":"https://orcid.org/0000-0001-6129-5007"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Giacomo Baruzzo","raw_affiliation_strings":["University of Padova,Dept. of Information Engineering,Padova,Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova,Dept. of Information Engineering,Padova,Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077821068","display_name":"Barbara Di Camillo","orcid":"https://orcid.org/0000-0001-8415-4688"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Barbara Di Camillo","raw_affiliation_strings":["University of Padova,Dept. of Information Engineering,Padova,Italy"],"affiliations":[{"raw_affiliation_string":"University of Padova,Dept. of Information Engineering,Padova,Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29399614,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987000226974487,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987000226974487,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":9.999999747378752e-05,"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/interpretability","display_name":"Interpretability","score":0.8866000175476074},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.682699978351593},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.57669997215271},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.5756999850273132},{"id":"https://openalex.org/keywords/curse-of-dimensionality","display_name":"Curse of dimensionality","score":0.5055000185966492},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4943999946117401},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4871000051498413},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.46320000290870667}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8866000175476074},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.682699978351593},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6739000082015991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6585000157356262},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.57669997215271},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.5756999850273132},{"id":"https://openalex.org/C111030470","wikidata":"https://www.wikidata.org/wiki/Q1430460","display_name":"Curse of dimensionality","level":2,"score":0.5055000185966492},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4943999946117401},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4871000051498413},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4650000035762787},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.46320000290870667},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.43700000643730164},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.3986999988555908},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.364300012588501},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.3605000078678131},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.3294999897480011},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.32280001044273376},{"id":"https://openalex.org/C2779304628","wikidata":"https://www.wikidata.org/wiki/Q3503480","display_name":"Face (sociological concept)","level":2,"score":0.314300000667572},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.29840001463890076},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.267300009727478},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2660999894142151}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/ijcnn64981.2025.11227921","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn64981.2025.11227921","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"},{"id":"pmh:oai:www.research.unipd.it:11577/3566042","is_oa":false,"landing_page_url":"https://hdl.handle.net/11577/3566042","pdf_url":null,"source":{"id":"https://openalex.org/S4377196283","display_name":"Research Padua  Archive (University of Padua)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:www.research.unipd.it:11577/3566042","is_oa":false,"landing_page_url":"https://ieeexplore.ieee.org/abstract/document/11227921","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":18,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2069089843","https://openalex.org/W2540833380","https://openalex.org/W2594042184","https://openalex.org/W2817838603","https://openalex.org/W3021105102","https://openalex.org/W3081332038","https://openalex.org/W3171692328","https://openalex.org/W3202498768","https://openalex.org/W3203364159","https://openalex.org/W3208940117","https://openalex.org/W4220765701","https://openalex.org/W4247110653","https://openalex.org/W4280533477","https://openalex.org/W4362692446","https://openalex.org/W4387661643","https://openalex.org/W4405231264","https://openalex.org/W4407053453"],"related_works":[],"abstract_inverted_index":{"Modern":[0],"machine":[1],"learning":[2],"approaches":[3],"have":[4],"shown":[5],"remarkable":[6],"success":[7],"in":[8],"extracting":[9],"patterns":[10],"from":[11,87],"high-dimensional":[12],"biological":[13],"data.":[14],"However,":[15],"when":[16],"applied":[17],"to":[18,27,91],"spatial":[19,53,106],"transcriptomics,":[20],"these":[21,43],"methods":[22],"face":[23],"significant":[24],"challenges":[25],"due":[26],"the":[28,35],"sparsity":[29],"of":[30,95],"spatially":[31],"resolved":[32],"measurements":[33],"and":[34,52,78,101],"complex,":[36],"nonlinear":[37],"relationships":[38],"between":[39],"molecular":[40],"features.To":[41],"address":[42],"challenges,":[44],"we":[45],"propose":[46],"a":[47,92,99],"procedure":[48],"that":[49,72],"integrates":[50],"single-cell":[51],"transcriptomics":[54],"by":[55,85],"considering":[56],"biologically":[57,102],"meaningful":[58],"regulatory":[59,96],"factors":[60,67],"as":[61,69],"an":[62],"interpretable":[63,103],"feature":[64],"space.":[65],"These":[66],"act":[68],"latent":[70],"variables":[71],"encode":[73],"transcriptional":[74],"programmes,":[75],"reducing":[76],"dimensionality":[77],"preserving":[79],"mechanistic":[80],"relevance.This":[81],"approach":[82],"improves":[83],"interpretability":[84],"shifting":[86],"raw":[88],"gene":[89],"expression":[90],"structured":[93],"representation":[94],"activity,":[97],"providing":[98],"scalable":[100],"framework":[104],"for":[105],"transcriptomic":[107],"analysis.":[108]},"counts_by_year":[],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-11-14T00:00:00"}