{"id":"https://openalex.org/W2098427571","doi":"https://doi.org/10.1093/bioinformatics/btu263","title":"New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence","display_name":"New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence","publication_year":2014,"publication_date":"2014-06-11","ids":{"openalex":"https://openalex.org/W2098427571","doi":"https://doi.org/10.1093/bioinformatics/btu263","mag":"2098427571"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/12/i219/48926989/bioinformatics_30_12_i219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/30/12/i219/48926989/bioinformatics_30_12_i219.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109210245","display_name":"Mengfei Cao","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mengfei Cao","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063679457","display_name":"Christopher Michael Pietras","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Christopher M. Pietras","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059566178","display_name":"Xian Zhang Feng","orcid":null},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xian Feng","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077250520","display_name":"Kathryn J Doroschak","orcid":"https://orcid.org/0000-0003-4806-5164"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kathryn J. Doroschak","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111654874","display_name":"Thomas Schaffner","orcid":null},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Schaffner","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100779613","display_name":"Jisoo Park","orcid":"https://orcid.org/0000-0002-3077-1979"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jisoo Park","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100396872","display_name":"Hao Zhang","orcid":"https://orcid.org/0000-0002-2058-7123"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hao Zhang","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026411021","display_name":"Lenore Cowen","orcid":"https://orcid.org/0000-0001-6698-6413"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]},{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lenore J. Cowen","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073101130","display_name":"Benjamin Hescott","orcid":"https://orcid.org/0000-0002-8179-9496"},"institutions":[{"id":"https://openalex.org/I121934306","display_name":"Tufts University","ror":"https://ror.org/05wvpxv85","country_code":"US","type":"education","lineage":["https://openalex.org/I121934306"]},{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin J. Hescott","raw_affiliation_strings":["1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA"],"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science, Tufts University, Medford, MA 02155, USA and 2Department of Computer Science, University of Minnesota, Minneapolis, MN 55455, USA","institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5109210245"],"corresponding_institution_ids":["https://openalex.org/I121934306","https://openalex.org/I130238516"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.8502,"has_fulltext":true,"cited_by_count":130,"citation_normalized_percentile":{"value":0.94301364,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"30","issue":"12","first_page":"i219","last_page":"i227"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10064","display_name":"Complex Network Analysis Techniques","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10241","display_name":"Functional Brain Connectivity Studies","score":0.9854999780654907,"subfield":{"id":"https://openalex.org/subfields/2805","display_name":"Cognitive Neuroscience"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7497532367706299},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.6241333484649658},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6115759015083313},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5260051488876343},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5066609978675842},{"id":"https://openalex.org/keywords/probabilistic-logic","display_name":"Probabilistic logic","score":0.5059310793876648},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.45854854583740234},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.45034003257751465},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4242938756942749},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40519198775291443},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3575565814971924},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.33791154623031616}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7497532367706299},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.6241333484649658},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6115759015083313},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5260051488876343},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5066609978675842},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.5059310793876648},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.45854854583740234},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.45034003257751465},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4242938756942749},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40519198775291443},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3575565814971924},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33791154623031616},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btu263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/12/i219/48926989/bioinformatics_30_12_i219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:4058952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4058952","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu263","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu263","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/30/12/i219/48926989/bioinformatics_30_12_i219.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.47999998927116394,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[{"id":"https://openalex.org/G935226081","display_name":null,"funder_award_id":"R01 HD076140","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2098427571.pdf","grobid_xml":"https://content.openalex.org/works/W2098427571.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1486817521","https://openalex.org/W1942404831","https://openalex.org/W1990223774","https://openalex.org/W2011986160","https://openalex.org/W2027439534","https://openalex.org/W2037442572","https://openalex.org/W2038122249","https://openalex.org/W2074549773","https://openalex.org/W2077047516","https://openalex.org/W2090766471","https://openalex.org/W2095867585","https://openalex.org/W2097636810","https://openalex.org/W2099438806","https://openalex.org/W2099656145","https://openalex.org/W2102814386","https://openalex.org/W2103017472","https://openalex.org/W2105924489","https://openalex.org/W2113654464","https://openalex.org/W2119220491","https://openalex.org/W2123280311","https://openalex.org/W2132582966","https://openalex.org/W2134711219","https://openalex.org/W2136316164","https://openalex.org/W2137804845","https://openalex.org/W2137917513","https://openalex.org/W2138582694","https://openalex.org/W2143962926","https://openalex.org/W2144563318","https://openalex.org/W2150381702","https://openalex.org/W2152336513","https://openalex.org/W2153929049","https://openalex.org/W2159482845","https://openalex.org/W2163485494","https://openalex.org/W2166468869","https://openalex.org/W2170958240","https://openalex.org/W2171403830","https://openalex.org/W4255855797","https://openalex.org/W4294216483","https://openalex.org/W6657524342","https://openalex.org/W6675414248"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2894446834"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"It":[2],"has":[3,44,65],"long":[4],"been":[5,46],"hypothesized":[6],"that":[7,50,68,201],"incorporating":[8,213],"models":[9],"of":[10,25,91,114,119,126,174,184,195],"network":[11,156],"noise":[12],"as":[13,15,205],"well":[14],"edge":[16],"directions":[17,71],"and":[18,72,98,109,144,236,242],"known":[19,106],"pathway":[20,214,230],"information":[21,231],"into":[22,111,217],"the":[23,101,112,124,127,152,172,189,203,218,226,239],"representation":[24],"protein\u2013protein":[26],"interaction":[27],"(PPI)":[28],"networks":[29],"might":[30],"improve":[31],"their":[32],"utility":[33],"for":[34,59,224,228,237],"functional":[35,145],"inference.":[36],"However,":[37],"a":[38],"simple":[39],"way":[40],"to":[41,123],"do":[42],"this":[43,198],"not":[45],"obvious.":[47],"We":[48,86,130,169],"find":[49],"diffusion":[51],"state":[52],"distance":[53],"(DSD),":[54],"our":[55,175],"recent":[56],"diffusion-based":[57],"metric":[58],"measuring":[60],"dissimilarity":[61],"in":[62,157,197],"PPI":[63,128,155],"networks,":[64],"natural":[66],"extensions":[67],"incorporate":[69],"confidence,":[70,105],"can":[73],"even":[74],"express":[75],"coherent":[76],"pathways":[77,110,204],"by":[78],"calculating":[79,225,238],"DSD":[80,92,177],"on":[81,151,179],"an":[82,180],"augmented":[83,176],"graph.":[84],"Results:":[85],"define":[87],"three":[88],"incremental":[89],"versions":[90],"which":[93],"we":[94],"term":[95],"cDSD,":[96,240],"caDSD":[97,241],"capDSD,":[99],"where":[100],"capDSD":[102,196,243],"matrix":[103],"incorporates":[104],"directed":[107],"edges,":[108],"measure":[113],"how":[115],"similar":[116],"each":[117],"pair":[118],"nodes":[120],"is":[121,163,208],"according":[122],"structure":[125],"network.":[129,219],"test":[131,171],"four":[132],"popular":[133],"function":[134],"prediction":[135],"methods":[136,178],"(majority":[137],"vote,":[138,141],"weighted":[139,164],"majority":[140,165],"multi-way":[142],"cut":[143],"flow)":[146],"using":[147,167],"these":[148],"different":[149],"matrices":[150,244],"Baker\u2019s":[153],"yeast":[154],"cross-validation.":[158],"The":[159,192],"best":[160],"performing":[161],"method":[162],"vote":[166],"capDSD.":[168],"then":[170],"performance":[173,194],"integrated":[181],"heterogeneous":[182],"set":[183],"protein":[185],"association":[186],"edges":[187,215],"from":[188,232,247],"STRING":[190],"database.":[191],"superior":[193],"context":[199],"confirms":[200],"treating":[202],"probabilistic":[206],"units":[207],"more":[209],"powerful":[210],"than":[211],"simply":[212],"independently":[216],"Availability:":[220],"All":[221],"source":[222],"code":[223],"confidences,":[227],"extracting":[229],"KEGG":[233],"XML":[234],"files,":[235],"are":[245,257],"available":[246,258],"http://dsd.cs.tufts.edu/capdsd":[248],"Contact:":[249],"lenore.cowen@tufts.edu":[250],"or":[251],"benjamin.hescott@tufts.edu":[252],"Supplementary":[253,255],"information:":[254],"data":[256],"at":[259],"Bioinformatics":[260],"online.":[261]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":13},{"year":2021,"cited_by_count":22},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":18},{"year":2018,"cited_by_count":11},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":11}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}