{"id":"https://openalex.org/W7171527945","doi":"https://doi.org/10.1145/3807503.3819478","title":"Beyond Binning: Resolution-Preserving MS1 Pretraining for Clinical Proteomics Classification","display_name":"Beyond Binning: Resolution-Preserving MS1 Pretraining for Clinical Proteomics Classification","publication_year":2026,"publication_date":"2026-06-30","ids":{"openalex":"https://openalex.org/W7171527945","doi":"https://doi.org/10.1145/3807503.3819478"},"language":null,"primary_location":{"id":"doi:10.1145/3807503.3819478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819478","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3807503.3819478","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103208367","display_name":"Yu Zhou","orcid":"https://orcid.org/0009-0002-3914-1102"},"institutions":[{"id":"https://openalex.org/I4210121365","display_name":"Leibniz Institute for Analytical Sciences - ISAS","ror":"https://ror.org/02jhqqg57","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210121365"]},{"id":"https://openalex.org/I904495901","display_name":"Ruhr University Bochum","ror":"https://ror.org/04tsk2644","country_code":"DE","type":"education","lineage":["https://openalex.org/I904495901"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yu Zhou","raw_affiliation_strings":["Ruhr University Bochum, Bochum, Germany and Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany"],"raw_orcid":"https://orcid.org/0009-0002-3914-1102","affiliations":[{"raw_affiliation_string":"Ruhr University Bochum, Bochum, Germany and Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany","institution_ids":["https://openalex.org/I4210121365","https://openalex.org/I904495901"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047993355","display_name":"Vladimir Vutov","orcid":"https://orcid.org/0000-0002-4758-5822"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Vladimir Vutov","raw_affiliation_strings":["Heidelberg University Hospital, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4758-5822","affiliations":[{"raw_affiliation_string":"Heidelberg University Hospital, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101988471","display_name":"Susmita Ghosh","orcid":"https://orcid.org/0000-0001-9798-0989"},"institutions":[{"id":"https://openalex.org/I4210121365","display_name":"Leibniz Institute for Analytical Sciences - ISAS","ror":"https://ror.org/02jhqqg57","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210121365"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Susmita Ghosh","raw_affiliation_strings":["Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany"],"raw_orcid":"https://orcid.org/0000-0001-9798-0989","affiliations":[{"raw_affiliation_string":"Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany","institution_ids":["https://openalex.org/I4210121365"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091108485","display_name":"Fabienne Meier\u2010Abt","orcid":"https://orcid.org/0000-0001-5337-6210"},"institutions":[{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Fabienne Meier-Abt","raw_affiliation_strings":["University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-5337-6210","affiliations":[{"raw_affiliation_string":"University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041096726","display_name":"Sibylle Pfammatter","orcid":"https://orcid.org/0000-0002-3024-7560"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sibylle Pfammatter","raw_affiliation_strings":["Functional Genomics Center Zurich (FGCZ), University of Zurich, Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0002-3024-7560","affiliations":[{"raw_affiliation_string":"Functional Genomics Center Zurich (FGCZ), University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065374551","display_name":"Sandra Kummer","orcid":null},"institutions":[{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Sandra Kummer","raw_affiliation_strings":["University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0009-0005-0779-6958","affiliations":[{"raw_affiliation_string":"University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004992368","display_name":"Odit Gutwein","orcid":"https://orcid.org/0000-0003-0204-099X"},"institutions":[{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Odit Gutwein","raw_affiliation_strings":["University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-0204-099X","affiliations":[{"raw_affiliation_string":"University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5143805811","display_name":"Rosary Yao","orcid":"https://orcid.org/0009-0002-4226-5480"},"institutions":[{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Rosary Yao","raw_affiliation_strings":["University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0009-0002-4226-5480","affiliations":[{"raw_affiliation_string":"University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000098098","display_name":"Thorsten Zenz","orcid":"https://orcid.org/0000-0001-7890-9845"},"institutions":[{"id":"https://openalex.org/I4210100468","display_name":"University Hospital of Zurich","ror":"https://ror.org/01462r250","country_code":"CH","type":"funder","lineage":["https://openalex.org/I4210100468"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Thorsten Zenz","raw_affiliation_strings":["University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-7890-9845","affiliations":[{"raw_affiliation_string":"University Hospital Zurich and University of Zurich (UZH), Zurich, Switzerland","institution_ids":["https://openalex.org/I4210100468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020520632","display_name":"Matthias Gunzer","orcid":"https://orcid.org/0000-0002-5534-6055"},"institutions":[{"id":"https://openalex.org/I62318514","display_name":"University of Duisburg-Essen","ror":"https://ror.org/04mz5ra38","country_code":"DE","type":"education","lineage":["https://openalex.org/I62318514"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Gunzer","raw_affiliation_strings":["University of Duisburg-Essen, Essen, Germany and Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany"],"raw_orcid":"https://orcid.org/0000-0002-5534-6055","affiliations":[{"raw_affiliation_string":"University of Duisburg-Essen, Essen, Germany and Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany","institution_ids":["https://openalex.org/I62318514"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077710470","display_name":"Junyan Lu","orcid":"https://orcid.org/0000-0002-9211-0746"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Junyan Lu","raw_affiliation_strings":["Heidelberg University Hospital, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0002-9211-0746","affiliations":[{"raw_affiliation_string":"Heidelberg University Hospital, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052870302","display_name":"Jianxu Chen","orcid":"https://orcid.org/0000-0002-8500-1357"},"institutions":[{"id":"https://openalex.org/I4210121365","display_name":"Leibniz Institute for Analytical Sciences - ISAS","ror":"https://ror.org/02jhqqg57","country_code":"DE","type":"facility","lineage":["https://openalex.org/I315704651","https://openalex.org/I4210121365"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Jianxu Chen","raw_affiliation_strings":["Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany"],"raw_orcid":"https://orcid.org/0000-0002-8500-1357","affiliations":[{"raw_affiliation_string":"Leibniz-Institut f\u00fcr Analytische Wissenschaften \u2013 ISAS \u2013 e.V., Dortmund, Germany","institution_ids":["https://openalex.org/I4210121365"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.40119999647140503},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.31200000643730164},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.2711000144481659},{"id":"https://openalex.org/keywords/proteogenomics","display_name":"Proteogenomics","score":0.2538999915122986}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41019999980926514},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.40119999647140503},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35030001401901245},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3465000092983246},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3292999863624573},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.31949999928474426},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.31200000643730164},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.2711000144481659},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2549999952316284},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.2538999915122986}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3807503.3819478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819478","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3807503.3819478","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3807503.3819478","pdf_url":null,"source":null,"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1980793852","https://openalex.org/W2023096047","https://openalex.org/W2947763854","https://openalex.org/W2991106430","https://openalex.org/W3006932683","https://openalex.org/W3171209108","https://openalex.org/W3179183389","https://openalex.org/W4214546240","https://openalex.org/W4296664038","https://openalex.org/W4311940838","https://openalex.org/W4386158194","https://openalex.org/W4391648678","https://openalex.org/W4400045958","https://openalex.org/W4401728772","https://openalex.org/W4404024625","https://openalex.org/W4404046121","https://openalex.org/W4404458588","https://openalex.org/W4405224584","https://openalex.org/W4409410549","https://openalex.org/W4410858407","https://openalex.org/W4417299611","https://openalex.org/W7124469645","https://openalex.org/W7133209653"],"related_works":[],"abstract_inverted_index":{"Liquid":[0],"chromatography\u2013mass":[1],"spectrometry":[2],"(LC\u2013MS)":[3],"proteomics":[4,160],"enables":[5,83],"large-scale":[6],"protein":[7],"profiling":[8],"for":[9,202],"biomarker":[10],"discovery":[11],"and":[12,22,31,145,177,205,211],"disease":[13],"stratification,":[14],"but":[15],"conventional":[16],"analysis":[17],"depends":[18],"on":[19,214],"complex":[20],"identification":[21],"quantification":[23],"pipelines.":[24],"Rapid":[25],"MS1-centric":[26,196],"acquisition":[27],"shortens":[28],"instrument":[29],"time":[30,54],"motivates":[32],"sample":[33,198],"classification":[34,199],"directly":[35,42],"from":[36,43,87,117,136,153],"MS1":[37,44,89,150,216],"precursor":[38,90,134,217],"signals.":[39,191],"However,":[40],"learning":[41,86,175],"peak":[45,67,91,115,151,218],"data":[46],"remains":[47],"challenging:":[48],"rasterizing":[49],"peaks":[50],"into":[51],"binned":[52],"retention":[53],"(RT)":[55],"\u00d7":[56],"mass-to-charge":[57],"ratio":[58],"(m/z)":[59],"images":[60],"sacrifices":[61],"resolution,":[62],"while":[63],"processing":[64],"full,":[65],"unbinned":[66,114],"sets":[68],"end-to-end":[69,169],"is":[70,222],"often":[71],"computationally":[72],"impractical.":[73],"Here,":[74],"we":[75],"present":[76],"MS1\u2013MPM,":[77],"a":[78,126],"self-supervised":[79],"pretraining":[80,163,210],"framework":[81],"that":[82,130],"scalable":[84,212],"representation":[85],"full-resolution":[88],"sets.":[92,219],"Our":[93,184],"model":[94,140],"uses":[95],"an":[96],"efficient":[97],"attention":[98],"mechanism":[99],"with":[100,180],"linear":[101],"scaling":[102],"in":[103],"the":[104,112,139,143,149],"number":[105],"of":[106,111,148],"precursors,":[107],"enabling":[108],"direct":[109],"ingestion":[110],"complete":[113],"set":[116],"each":[118],"run":[119],"without":[120],"aggressive":[121],"downsampling.":[122],"We":[123],"further":[124,187],"introduce":[125],"masked":[127,133],"point-reconstruction":[128],"objective":[129],"predicts":[131],"randomly":[132],"attributes":[135],"context,":[137],"encouraging":[138],"to":[141],"capture":[142],"geometric":[144],"contextual":[146],"structure":[147],"patterns":[152],"abundant":[154],"unlabeled":[155],"runs.":[156],"Across":[157],"multiple":[158],"clinical":[159,197],"datasets,":[161],"our":[162,193],"yields":[164],"strong":[165],"initializations":[166],"that,":[167],"after":[168],"fine-tuning,":[170],"consistently":[171],"outperform":[172],"specialized":[173],"deep":[174],"methods":[176],"remain":[178],"competitive":[179],"classical":[181],"machine-learning":[182],"baselines.":[183],"interpretability":[185],"analyses":[186],"highlight":[188],"biologically":[189],"meaningful":[190],"Overall,":[192],"approach":[194],"makes":[195],"more":[200],"practical":[201],"rapid":[203],"screening":[204],"large-cohort":[206],"studies":[207],"via":[208],"resolution-preserving":[209],"fine-tuning":[213],"full":[215],"The":[220],"code":[221],"released":[223],"at:":[224],"ms1mpm.":[225]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2026-07-29T00:00:00"}
