{"id":"https://openalex.org/W4401749561","doi":"https://doi.org/10.1109/isbi56570.2024.10635208","title":"In Silico Optimization of Tissue Microarray Design for Machine Learning Analysis","display_name":"In Silico Optimization of Tissue Microarray Design for Machine Learning Analysis","publication_year":2024,"publication_date":"2024-05-27","ids":{"openalex":"https://openalex.org/W4401749561","doi":"https://doi.org/10.1109/isbi56570.2024.10635208"},"language":"en","primary_location":{"id":"doi:10.1109/isbi56570.2024.10635208","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/isbi56570.2024.10635208","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Symposium on Biomedical Imaging (ISBI)","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":"https://openalex.org/A5021334101","display_name":"Addie Woicik","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Addie Woicik","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033010930","display_name":"Zachary R. McCaw","orcid":"https://orcid.org/0000-0002-2006-9828"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zachary R McCaw","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056037696","display_name":"Santiago Akle","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Santiago Akle","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053652323","display_name":"Benjamin Dulken","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Benjamin Dulken","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043144551","display_name":"Sanjana Narayanan","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sanjana Narayanan","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011522960","display_name":"C Probert","orcid":"https://orcid.org/0000-0003-4550-0239"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Christopher Probert","raw_affiliation_strings":["Insitro,South San Francisco,CA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Insitro,South San Francisco,CA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08250895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"17","issue":null,"first_page":"1","last_page":"5"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9991000294685364,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9980000257492065,"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/T10862","display_name":"AI in cancer detection","score":0.9943000078201294,"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/in-silico","display_name":"In silico","score":0.8217753767967224},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6745462417602539},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.41018998622894287},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40471237897872925},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.39869290590286255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14074909687042236}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8217753767967224},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6745462417602539},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.41018998622894287},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40471237897872925},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.39869290590286255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14074909687042236},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isbi56570.2024.10635208","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/isbi56570.2024.10635208","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Symposium on Biomedical Imaging (ISBI)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1968036595","https://openalex.org/W1990534247","https://openalex.org/W2042789810","https://openalex.org/W2056264529","https://openalex.org/W2087810003","https://openalex.org/W2120579447","https://openalex.org/W2158485828","https://openalex.org/W2168203442","https://openalex.org/W2489000876","https://openalex.org/W2753919178","https://openalex.org/W2963258365","https://openalex.org/W2963966702","https://openalex.org/W2996092187","https://openalex.org/W3005186462","https://openalex.org/W3033721673","https://openalex.org/W3044996171","https://openalex.org/W3083699157","https://openalex.org/W3104135675","https://openalex.org/W3135547872","https://openalex.org/W3159481202","https://openalex.org/W4225116060","https://openalex.org/W4293363567","https://openalex.org/W4297825594","https://openalex.org/W4320710102","https://openalex.org/W4367311217","https://openalex.org/W4401748985","https://openalex.org/W6696497002","https://openalex.org/W6784333009"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Machine":[0],"learning":[1],"(ML)":[2],"methods":[3],"based":[4],"on":[5,62],"histopathology":[6],"slides":[7],"are":[8,25,110],"increasingly":[9],"used":[10],"for":[11,47,93],"cancer":[12],"diagnosis":[13],"and":[14,100,124],"treatment.":[15],"Analyses":[16],"with":[17],"specialized":[18],"experimental":[19],"stains,":[20],"such":[21],"as":[22],"spatial":[23],"proteomics,":[24],"often":[26],"limited":[27],"to":[28,38,50,74],"tissue":[29,49],"microarrays":[30],"(TMAs)":[31],"rather":[32],"than":[33],"whole":[34],"slide":[35],"images":[36],"due":[37],"the":[39,56,59,84],"cost":[40],"of":[41,58,78,86],"data":[42],"generation.":[43],"While":[44],"different":[45],"approaches":[46],"selecting":[48],"include":[51],"in":[52,129],"a":[53,71,119],"TMA":[54,80,89,114,126],"exist,":[55],"impact":[57],"sampling":[60,127],"protocol":[61],"downstream":[63],"ML-model":[64],"performance":[65,77,85],"is":[66],"under-explored.":[67],"Here,":[68],"we":[69,117],"present":[70],"general-purpose":[72],"framework":[73],"evaluate":[75],"ML":[76],"synthetic":[79,88],"datasets.":[81],"We":[82,103],"compare":[83],"16":[87],"breast":[90],"carcinoma":[91],"datasets":[92],"predicting":[94],"patient":[95],"overall":[96],"survival,":[97],"immunohistochemistry":[98],"subtype,":[99],"mutation":[101],"status.":[102],"deduce":[104],"several":[105],"common":[106],"design":[107],"principles":[108],"that":[109],"broadly":[111],"applicable":[112],"across":[113],"applications.":[115],"Finally,":[116],"conduct":[118],"case":[120],"study":[121],"into":[122],"principled":[123],"task-specific":[125],"procedures":[128],"budget-constrained":[130],"scenarios.":[131]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}