@ARTICLE{Chaudhary2025-it,
  title     = "{AI}-based histopathology phenotyping reveals germline loci
               shaping breast cancer morphology",
  author    = "Chaudhary, Shubham and Voigts, Almut and Vilov, Sergey and
               Heinig, Matthias and Casale, Francesco Paolo",
  publisher = "PMLR",
  pages     = "199--212",
  month     =  "31~" # dec,
  year      =  2025,
  url       = "https://raw.githubusercontent.com/mlresearch/v311/main/assets/chaudhary25a/chaudhary25a.pdf",
  keywords  = "GEMCONT MICCAI 2025"
}

@ARTICLE{HistoGWAS,
  title     = "{HistoGWAS}: an {AI}-enabled framework for automated genetic
               analysis of tissue phenotypes in histology cohorts",
  author    = "Chaudhary, Shubham and Voigts, Almut and Bereket, Michael and
               Albert, Matthew L and Schwamborn, Kristina and Zeggini,
               Eleftheria and Casale, Francesco Paolo",
  journal   = "Genome Biology",
  publisher = "Springer Science and Business Media LLC",
  volume    =  27,
  number    =  1,
  month     =  "31~" # mar,
  year      =  2026,
  url       = "http://dx.doi.org/10.1186/s13059-026-04031-z",
  keywords  = "Colocalization; Generative models; Genome-wide association
               studies; Histology; Kernel methods; Semantic autoencoder;
               Variance component test;GEMCONT MICCAI 2025",
  doi       = "10.1186/s13059-026-04031-z",
  pmc       = "PMC13063728",
  pmid      =  41918129,
  issn      = "1474-7596,1474-760X",
  language  = "en"
}


@ARTICLE{geno_pheno_link_heart,
  title       = "Genetic and functional insights into the fractal structure of
                 the heart",
  author      = "Meyer, Hannah V and Dawes, Timothy J W and Serrani, Marta and
                 Bai, Wenjia and Tokarczuk, Pawe\l{} and Cai, Jiashen and de
                 Marvao, Antonio and Henry, Albert and Lumbers, R Thomas and
                 Gierten, Jakob and Thumberger, Thomas and Wittbrodt, Joachim
                 and Ware, James S and Rueckert, Daniel and Matthews, Paul M and
                 Prasad, Sanjay K and Costantino, Maria L and Cook, Stuart A and
                 Birney, Ewan and O'Regan, Declan P",
  affiliation = "Simons Center for Quantitative Biology, Cold Spring Harbor
                 Laboratory, Cold Spring Harbor, NY, USA. hmeyer@cshl.edu.;
                 European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Cambridge, UK. hmeyer@cshl.edu.; MRC
                 London Institute of Medical Sciences, Imperial College London,
                 London, UK.; National Heart and Lung Institute, Imperial
                 College London, London, UK.; Department of Chemical Engineering
                 and Biotechnology, University of Cambridge, Cambridge, UK.;
                 Department of Chemistry, Materials and Chemical Engineering,
                 Politecnico di Milano, Milan, Italy.; Department of Computing,
                 Imperial College London, London, UK.; MRC London Institute of
                 Medical Sciences, Imperial College London, London, UK.;
                 Duke-National University of Singapore, Singapore, Singapore.;
                 Department of Internal Medicine, Singapore Health Services,
                 Singapore, Singapore.; Institute of Health Informatics,
                 University College London, London, UK.; Institute of
                 Cardiovascular Science, University College London, London, UK.;
                 Institute of Cardiovascular Science, University College London,
                 London, UK.; Health Data Research UK, London, UK.; Barts Heart
                 Centre, St Bartholomew's Hospital, London, UK.; Department of
                 Pediatric Cardiology, University Hospital Heidelberg,
                 Heidelberg, Germany.; Centre for Organismal Studies, Heidelberg
                 University, Heidelberg, Germany.; Centre for Organismal
                 Studies, Heidelberg University, Heidelberg, Germany.; MRC
                 London Institute of Medical Sciences, Imperial College London,
                 London, UK.; National Heart and Lung Institute, Imperial
                 College London, London, UK.; Cardiovascular Research Centre,
                 Royal Brompton \& Harefield NHS Foundation Trust, London, UK.;
                 Department of Brain Sciences, Imperial College London, London,
                 UK.; UK Dementia Research Institute, Imperial College London,
                 London, UK.; National Heart and Lung Institute, Imperial
                 College London, London, UK.; Cardiovascular Research Centre,
                 Royal Brompton \& Harefield NHS Foundation Trust, London, UK.;
                 Department of Chemistry, Materials and Chemical Engineering,
                 Politecnico di Milano, Milan, Italy.; MRC London Institute of
                 Medical Sciences, Imperial College London, London, UK.;
                 National Heart and Lung Institute, Imperial College London,
                 London, UK.; Duke-National University of Singapore, Singapore,
                 Singapore.; National Heart Centre Singapore, Singapore,
                 Singapore.; European Molecular Biology Laboratory, European
                 Bioinformatics Institute (EMBL-EBI), Cambridge, UK.; MRC London
                 Institute of Medical Sciences, Imperial College London, London,
                 UK. declan.oregan@imperial.ac.uk.",
  journal     = "Nature",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  584,
  number      =  7822,
  pages       = "589--594",
  month       =  aug,
  year        =  2020,
  url         = "http://dx.doi.org/10.1038/s41586-020-2635-8",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41586-020-2635-8",
  pmc         = "PMC7116759",
  pmid        =  32814899,
  issn        = "0028-0836,1476-4687",
  language    = "en"
}

@ARTICLE{geno_peno_link_brain,
  title     = "Genome-wide association studies of brain imaging phenotypes in
               {UK} Biobank",
  author    = "Elliott, Lloyd T and Sharp, Kevin and Alfaro-Almagro, Fidel and
               Shi, Sinan and Miller, Karla L and Douaud, Gwena{\"{e}}lle and
               Marchini, Jonathan and Smith, Stephen M",
  journal   = "Nature",
  publisher = "Springer Science and Business Media LLC",
  volume    =  562,
  number    =  7726,
  pages     = "210--216",
  month     =  oct,
  year      =  2018,
  url       = "https://www.nature.com/articles/s41586-018-0571-7",
  doi       = "10.1038/s41586-018-0571-7",
  pmc       = "PMC6786974",
  pmid      =  30305740,
  issn      = "0028-0836,1476-4687",
  language  = "en"
}

@ARTICLE{regOut2,
  title       = "An atlas of genetic associations in {UK} Biobank",
  author      = "Canela-Xandri, Oriol and Rawlik, Konrad and Tenesa, Albert",
  affiliation = "The Roslin Institute, Royal (Dick) School of Veterinary
                 Studies, The University of Edinburgh, Midlothian, UK.; MRC
                 Human Genetics Unit at the MRC Institute of Genetics and
                 Molecular Medicine, University of Edinburgh, Western General
                 Hospital, Edinburgh, UK.; The Roslin Institute, Royal (Dick)
                 School of Veterinary Studies, The University of Edinburgh,
                 Midlothian, UK.; The Roslin Institute, Royal (Dick) School of
                 Veterinary Studies, The University of Edinburgh, Midlothian,
                 UK. albert.tenesa@ed.ac.uk.; MRC Human Genetics Unit at the MRC
                 Institute of Genetics and Molecular Medicine, University of
                 Edinburgh, Western General Hospital, Edinburgh, UK.
                 albert.tenesa@ed.ac.uk.",
  journal     = "Nature Genetics",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  50,
  number      =  11,
  pages       = "1593--1599",
  month       =  nov,
  year        =  2018,
  url         = "http://dx.doi.org/10.1038/s41588-018-0248-z",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41588-018-0248-z",
  pmc         = "PMC6707814",
  pmid        =  30349118,
  issn        = "1061-4036,1546-1718",
  language    = "en"
}

@ARTICLE{regOut1,
  title     = "The {UK} Biobank resource with deep phenotyping and genomic data",
  author    = "Bycroft, Clare and Freeman, Colin and Petkova, Desislava and
               Band, Gavin and Elliott, Lloyd T and Sharp, Kevin and Motyer,
               Allan and Vukcevic, Damjan and Delaneau, Olivier and O'Connell,
               Jared and Cortes, Adrian and Welsh, Samantha and Young, Alan and
               Effingham, Mark and McVean, Gil and Leslie, Stephen and Allen,
               Naomi and Donnelly, Peter and Marchini, Jonathan",
  journal   = "Nature",
  publisher = "Springer Science and Business Media LLC",
  volume    =  562,
  number    =  7726,
  pages     = "203--209",
  month     =  oct,
  year      =  2018,
  url       = "https://www.nature.com/articles/s41586-018-0579-z",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1038/s41586-018-0579-z",
  pmc       = "PMC6786975",
  pmid      =  30305743,
  issn      = "0028-0836,1476-4687",
  language  = "en"
}

@ARTICLE{MR_1,
  title       = "Mendelian randomization: genetic anchors for causal inference
                 in epidemiological studies",
  author      = "Davey Smith, George and Hemani, Gibran",
  affiliation = "MRC Integrative Epidemiology Unit (IEU) at the University of
                 Bristol, School of Social and Community Medicine, Bristol, UK
                 Julia.Mackay@bristol.ac.uk.; MRC Integrative Epidemiology Unit
                 (IEU) at the University of Bristol, School of Social and
                 Community Medicine, Bristol, UK.",
  journal     = "Human molecular genetics",
  publisher   = "Oxford University Press (OUP)",
  volume      =  23,
  number      = "R1",
  pages       = "R89--98",
  month       =  "15~" # sep,
  year        =  2014,
  url         = "http://dx.doi.org/10.1093/hmg/ddu328",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1093/hmg/ddu328",
  pmc         = "PMC4170722",
  pmid        =  25064373,
  issn        = "0964-6906,1460-2083",
  language    = "en"
}

@ARTICLE{MR_2,
  title       = "Association between gut microbiota and diabetic nephropathy: a
                 mendelian randomization study",
  author      = "Jin, Yongxiu and Han, Chenxi and Yang, Dongliang and Gao,
                 Shanlin",
  affiliation = "Department of Nephrology, Tangshan Gongren Hosiptal, Tangshan,
                 China.; Graduate School, Hebei Medical University,
                 Shijiazhuang, China.; Tangshan Maternal and Child Health
                 Hospital, Tangshan, China.; Cangzhou Medical College, Cangzhou,
                 China.",
  journal     = "Frontiers in microbiology",
  volume      =  15,
  pages       =  1309871,
  month       =  "27~" # mar,
  year        =  2024,
  url         = "http://dx.doi.org/10.3389/fmicb.2024.1309871",
  keywords    = "diabetic nephropathy; gut microbiota; insulin resistance;
                 mendelian randomization; short-chain fatty acids;GEMCONT MICCAI
                 2025",
  doi         = "10.3389/fmicb.2024.1309871",
  pmc         = "PMC11004376",
  pmid        =  38601939,
  issn        = "1664-302X",
  language    = "en"
}

@ARTICLE{Choi2020-PRS-tutorial,
  title       = "Tutorial: a guide to performing polygenic risk score analyses",
  author      = "Choi, Shing Wan and Mak, Timothy Shin-Heng and O'Reilly, Paul F",
  affiliation = "MRC Social, Genetic and Developmental Psychiatry Centre,
                 Institute of Psychiatry, Psychology and Neuroscience, King's
                 College London, London, UK.; Department of Genetics and Genomic
                 Sciences, Icahn School of Medicine, Mount Sinai, New York, NY,
                 USA.; Centre of Genomic Sciences, University of Hong Kong, Hong
                 Kong, China.; MRC Social, Genetic and Developmental Psychiatry
                 Centre, Institute of Psychiatry, Psychology and Neuroscience,
                 King's College London, London, UK. paul.oreilly@mssm.edu.;
                 Department of Genetics and Genomic Sciences, Icahn School of
                 Medicine, Mount Sinai, New York, NY, USA.
                 paul.oreilly@mssm.edu.",
  journal     = "Nature protocols",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  15,
  number      =  9,
  pages       = "2759--2772",
  month       =  "24~" # sep,
  year        =  2020,
  url         = "https://www.nature.com/articles/s41596-020-0353-1",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41596-020-0353-1",
  pmc         = "PMC7612115",
  pmid        =  32709988,
  issn        = "1754-2189,1750-2799",
  language    = "en"
}

@INPROCEEDINGS{MRM,
  title     = "{MRM}: Masked relation modeling for medical image pre-training
               with genetics",
  author    = "Yang, Qiushi and Li, Wuyang and Li, Baopu and Yuan, Yixuan",
  booktitle = "2023 IEEE/CVF International Conference on Computer Vision (ICCV)",
  publisher = "IEEE",
  pages     = "21395--21405",
  month     =  "1~" # oct,
  year      =  2023,
  url       = "http://dx.doi.org/10.1109/iccv51070.2023.01961",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1109/iccv51070.2023.01961"
}

@INPROCEEDINGS{ContIG,
  title     = "{ContIG}: Self-supervised multimodal contrastive learning for
               medical imaging with genetics",
  author    = "Taleb, Aiham and Kirchler, Matthias and Monti, Remo and Lippert,
               Christoph",
  booktitle = "2022 IEEE/CVF Conference on Computer Vision and Pattern
               Recognition (CVPR)",
  publisher = "IEEE",
  month     =  jun,
  year      =  2022,
  url       = "https://openaccess.thecvf.com/content/CVPR2022/papers/Taleb_ContIG_Self-Supervised_Multimodal_Contrastive_Learning_for_Medical_Imaging_With_Genetics_CVPR_2022_paper.pdf",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1109/cvpr52688.2022.02024"
}

@ARTICLE{Shilova2025-wa,
  title       = "{REECAP}: Contrastive learning of retinal aging reveals genetic
                 loci linking morphology to eye disease",
  author      = "Shilova, Liubov and Sens, Daniel and Aliyeva, Ayshan and
                 Chaudhary, Shubham and Xu, Qiaohan and Salin, Emmanuelle and
                 Schiefelbein, Johannes and Asani, Ben and Amarie, Oana Veronica
                 and Schneltzer, Elida and Segr\`{e}, Ayellet V and Schnabel,
                 Julia A and Cai, Na and Eskofier, Bjoern M and Casale,
                 Francesco Paolo",
  journal     = "medRxiv: the preprint server for health sciences",
  institution = "medRxiv",
  month       =  "27~" # nov,
  year        =  2025,
  url         = "http://dx.doi.org/10.1101/2025.11.19.25340555",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1101/2025.11.19.25340555",
  pmc         = "PMC12668118",
  pmid        =  41332846,
  language    = "en"
}

@ARTICLE{Tam2019-ln,
  title       = "Benefits and limitations of genome-wide association studies",
  author      = "Tam, Vivian and Patel, Nikunj and Turcotte, Michelle and
                 Boss\'{e}, Yohan and Par\'{e}, Guillaume and Meyre, David",
  affiliation = "Department of Health Research Methods, Evidence, and Impact,
                 McMaster University, Hamilton, Ontario, Canada.; Institut
                 Universitaire de Cardiologie et de Pneumologie de
                 Qu\'{e}bec-Universit\'{e} Laval, Qu\'{e}bec City, Qu\'{e}bec,
                 Canada.; Department of Molecular Medicine, Laval University,
                 Qu\'{e}bec City, Quebec, Canada.; Department of Health Research
                 Methods, Evidence, and Impact, McMaster University, Hamilton,
                 Ontario, Canada.; Department of Pathology and Molecular
                 Medicine, McMaster University, Hamilton, Ontario, Canada.;
                 Department of Health Research Methods, Evidence, and Impact,
                 McMaster University, Hamilton, Ontario, Canada.
                 meyred@mcmaster.ca.; Department of Pathology and Molecular
                 Medicine, McMaster University, Hamilton, Ontario, Canada.
                 meyred@mcmaster.ca.; Inserm UMRS 954 N-GERE
                 (Nutrition-Genetics-Environmental Risks), University of
                 Lorraine, Faculty of Medicine, Nancy, France.
                 meyred@mcmaster.ca.",
  journal     = "Nature reviews. Genetics",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  20,
  number      =  8,
  pages       = "467--484",
  month       =  aug,
  year        =  2019,
  url         = "http://dx.doi.org/10.1038/s41576-019-0127-1",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41576-019-0127-1",
  pmid        =  31068683,
  issn        = "1471-0056,1471-0064",
  language    = "en"
}

@ARTICLE{frozen_fe_2,
  title    = "Frozen large-scale pretrained vision-language models are the
              effective foundational backbone for multimodal breast cancer
              prediction",
  author   = "Vo, Hung Q and Wang, Lin and Wong, Kelvin K and Ezeana, Chika F
              and Yu, Xiaohui and Yang, Wei and Chang, Jenny and Nguyen, Hien V
              and Wong, Stephen T C",
  journal  = "IEEE journal of biomedical and health informatics",
  volume   =  29,
  number   =  5,
  pages    = "3234--3246",
  month    =  may,
  year     =  2025,
  url      = "http://dx.doi.org/10.1109/JBHI.2024.3507638",
  keywords = "GEMCONT MICCAI 2025",
  doi      = "10.1109/JBHI.2024.3507638",
  pmc      = "PMC12145120",
  pmid     =  40030302,
  issn     = "2168-2194,2168-2208",
  language = "en"
}

@INCOLLECTION{frozen_fe_1,
  title     = "Big transfer ({BiT}): General visual representation learning",
  author    = "Kolesnikov, Alexander and Beyer, Lucas and Zhai, Xiaohua and
               Puigcerver, Joan and Yung, Jessica and Gelly, Sylvain and
               Houlsby, Neil",
  booktitle = "Computer Vision -- ECCV 2020",
  publisher = "Springer International Publishing",
  address   = "Cham",
  pages     = "491--507",
  series    = "Lecture notes in computer science",
  year      =  2020,
  url       = "http://dx.doi.org/10.1007/978-3-030-58558-7_29",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1007/978-3-030-58558-7\_29",
  isbn      = "9783030585570,9783030585587",
  issn      = "0302-9743,1611-3349"
}


@INPROCEEDINGS{ABMIL,
  title     = "Attention-based Deep Multiple Instance Learning",
  author    = "Ilse, Maximilian and Tomczak, Jakub and Welling, Max",
  editor    = "Dy, Jennifer and Krause, Andreas",
  booktitle = "Proceedings of the 35th International Conference on Machine
               Learning",
  publisher = "PMLR",
  volume    =  80,
  pages     = "2127--2136",
  series    = "Proceedings of Machine Learning Research",
  year      =  2018,
  url       = "https://proceedings.mlr.press/v80/ilse18a.html",
  keywords  = "GEMCONT MICCAI 2025"
}

@ARTICLE{fun_excl_3,
  title       = "Effectiveness and safety of {VISULAS\textregistered{}} green
                 selective laser trabeculoplasty: a prospective, interventional
                 multicenter clinical investigation",
  author      = "Pillunat, Karin R and Kretz, Florian T A and Koinzer, Stefan
                 and Ehlken, Christoph and Pillunat, Lutz E and Klabe, Karsten",
  affiliation = "Department of Ophthalmology, Medical Faculty Carl Gustav Carus,
                 Technische Universit{\"{a}}t Dresden, Fetscherstrasse 74,
                 01307, Dresden, Germany.
                 karin.pillunat@uniklinikum-dresden.de.; Precise Vision
                 Augen{\"{a}}rzte, Augentagesklinik Rheine, Osnabr{\"{u}}cker
                 Str. 233-235, 48429, Rheine, Germany.; Augenarztpraxis Am
                 Dreiecksplatz/Kiel, Holtenauer Stra\ss{}e 1, 24103, Kiel,
                 Germany.; Department of Ophthalmology,
                 Universit{\"{a}}tsklinikum Schleswig-Holstein,
                 Arnold-Heller-Str. 3, 24105, Kiel, Germany.; Department of
                 Ophthalmology, Medical Faculty Carl Gustav Carus, Technische
                 Universit{\"{a}}t Dresden, Fetscherstrasse 74, 01307, Dresden,
                 Germany.; Internationale Innovative Ophthalmochirurgie GbR,
                 Martin-Luther-Platz 22/26, 40212, D{\"{u}}sseldorf, Germany.",
  journal     = "International ophthalmology",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  43,
  number      =  7,
  pages       = "2215--2224",
  month       =  jul,
  year        =  2023,
  url         = "http://dx.doi.org/10.1007/s10792-022-02617-7",
  keywords    = "Adjunctive IOP-lowering therapy; Adverse events; Intraocular
                 pressure (IOP) reduction; Primary open-angle glaucoma (POAG);
                 Selective laser trabeculoplasty (SLT); VISULAS\textregistered{}
                 green laser;GEMCONT MICCAI 2025",
  doi         = "10.1007/s10792-022-02617-7",
  pmc         = "PMC10313537",
  pmid        =  36572747,
  issn        = "0165-5701,1573-2630",
  language    = "en"
}

@ARTICLE{fun_excl_2,
  title       = "Effect of trabeculectomy on {RNFL} thickness and optic disc
                 parameters using optical coherence tomography",
  author      = "Raghu, N and Pandav, S S and Kaushik, S and Ichhpujani, P and
                 Gupta, A",
  affiliation = "Advanced Eye Centre, Postgraduate Institute of Medical
                 Education and Research, Chandigarh, India.",
  journal     = "Eye",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  26,
  number      =  8,
  pages       = "1131--1137",
  month       =  aug,
  year        =  2012,
  url         = "http://dx.doi.org/10.1038/eye.2012.115",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/eye.2012.115",
  pmc         = "PMC3420047",
  pmid        =  22722487,
  issn        = "0950-222X,1476-5454",
  language    = "en"
}

@ARTICLE{fun_excl_1,
  title     = "Reversal of optic disc cupping after glaucoma surgery, analysed
               with a scanning laser tomograph",
  author    = "Lesk, Mark R and Spaeth, George L and Azuara-Blanco, Augusto and
               Araujo, Silvana V and Katz, L Jay and Terebuli, Annette K and
               Wilson, Richard P and Moster, Marlene R and Schmidt, Courtland M",
  journal   = "Journal of glaucoma",
  publisher = "Ovid Technologies (Wolters Kluwer Health)",
  volume    =  8,
  number    = "Supplement 1",
  pages     = "S11",
  month     =  feb,
  year      =  1999,
  url       = "http://dx.doi.org/10.1097/00061198-199902001-00022",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1097/00061198-199902001-00022",
  issn      = "1057-0829,1536-481X",
  language  = "en"
}

@INCOLLECTION{MCF-Net,
  title     = "Evaluation of retinal image quality assessment networks in
               different color-spaces",
  author    = "Fu, Huazhu and Wang, Boyang and Shen, Jianbing and Cui, Shanshan
               and Xu, Yanwu and Liu, Jiang and Shao, Ling",
  booktitle = "Lecture Notes in Computer Science",
  publisher = "Springer International Publishing",
  address   = "Cham",
  pages     = "48--56",
  series    = "Lecture notes in computer science",
  year      =  2019,
  url       = "http://dx.doi.org/10.1007/978-3-030-32239-7_6",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1007/978-3-030-32239-7\_6",
  isbn      = "9783030322380,9783030322397",
  issn      = "0302-9743,1611-3349",
  language  = "en"
}

@ARTICLE{METAL,
  title     = "{METAL}: fast and efficient meta-analysis of genomewide
               association scans",
  author    = "Willer, Cristen J and Li, Yun and Abecasis, Gon\c{c}alo R",
  journal   = "Bioinformatics (Oxford, England)",
  publisher = "Oxford University Press (OUP)",
  volume    =  26,
  number    =  17,
  pages     = "2190--2191",
  month     =  "1~" # sep,
  year      =  2010,
  url       = "https://dx.doi.org/10.1093/bioinformatics/btq340",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1093/bioinformatics/btq340",
  pmc       = "PMC2922887",
  pmid      =  20616382,
  issn      = "1367-4803,1367-4811",
  language  = "en"
}

@ARTICLE{MVP,
  title       = "Diversity and scale: Genetic architecture of 2,068 traits in
                 the {VA} Million Veteran Program",
  author      = "Verma, Anurag and Huffman, Jennifer E and Rodriguez, Alex and
                 Conery, Mitchell and Liu, Molei and Ho, Yuk-Lam and Kim,
                 Youngdae and Heise, David A and Guare, Lindsay and Panickan,
                 Vidul Ayakulangara and Garcon, Helene and Linares, Franciel and
                 Costa, Lauren and Goethert, Ian and Tipton, Ryan and Honerlaw,
                 Jacqueline and Davies, Laura and Whitbourne, Stacey and Cohen,
                 Jeremy and Posner, Daniel C and Sangar, Rahul and Murray,
                 Michael and Wang, Xuan and Dochtermann, Daniel R and Devineni,
                 Poornima and Shi, Yunling and Nandi, Tarak Nath and Assimes,
                 Themistocles L and Brunette, Charles A and Carroll, Robert J
                 and Clifford, Royce and Duvall, Scott and Gelernter, Joel and
                 Hung, Adriana and Iyengar, Sudha K and Joseph, Jacob and
                 Kember, Rachel and Kranzler, Henry and Levey, Daniel and Luoh,
                 Shiuh-Wen and Merritt, Victoria C and Overstreet, Cassie and
                 Deak, Joseph D and Grant, Struan F A and Polimanti, Renato and
                 Roussos, Panos and Sun, Yan V and Venkatesh, Sanan and
                 Voloudakis, Georgios and Justice, Amy and Begoli, Edmon and
                 Ramoni, Rachel and Tourassi, Georgia and Pyarajan, Saiju and
                 Tsao, Philip S and O'Donnell, Christopher J and Muralidhar,
                 Sumitra and Moser, Jennifer and Casas, Juan P and Bick,
                 Alexander G and Zhou, Wei and Cai, Tianxi and Voight, Benjamin
                 F and Cho, Kelly and Gaziano, Michael J and Madduri, Ravi K and
                 Damrauer, Scott M and Liao, Katherine P",
  affiliation = "Corporal Michael Crescenz VA Medical Center, Philadelphia, PA,
                 19104, USA.; Department of Medicine, Division of Translational
                 Medicine and Human Genetics, University of Pennsylvania -
                 Perelman School of Medicine, Philadelphia, PA, 19104, USA.;
                 Institute for Biomedical Informatics, University of
                 Pennsylvania - Perelman School of Medicine, Philadelphia, PA,
                 19104, USA.; Massachusetts Veterans Epidemiology Research and
                 Information Center (MAVERIC), VA Boston Healthcare System,
                 Boston, MA, 02130, USA.; Palo Alto Veterans Institute for
                 Research (PAVIR), Palo Alto Health Care System, Palo Alto, CA,
                 94304, USA.; Department of Medicine, Harvard Medical School,
                 Boston, MA, 02115, USA.; Data Science and Learning, Argonne
                 National Laboratory, Lemont, IL, 60439, USA.; Department of
                 Systems Pharmacology and Translational Therapeutics, University
                 of Pennsylvania - Perelman School of Medicine, Philadelphia,
                 PA, 19104, USA.; Department of Biostatistics, Columbia
                 University's Mailman School of Public Health, New York, NY,
                 10032, USA.; Massachusetts Veterans Epidemiology Research and
                 Information Center (MAVERIC), VA Boston Healthcare System,
                 Boston, MA, 02130, USA.; Mathematics and Computer Science
                 Division, Argonne National Laboratory, Lemont, IL, 60439, USA.;
                 National Security Sciences Directorate, Cyber Resilience and
                 Intelligence Division, Oak Ridge National Laboratory, Dept of
                 Energy, Oak Ridge, TN, 37831, USA.; Department of Medicine,
                 Division of Translational Medicine and Human Genetics,
                 University of Pennsylvania - Perelman School of Medicine,
                 Philadelphia, PA, 19104, USA.; Department of Biomedical
                 Informatics, Harvard Medical School, Boston, MA, 02115, USA.;
                 R\&D Systems Engineering, Information Technology Services
                 Directorate, Oak Ridge National Laboratory, Dept of Energy, Oak
                 Ridge, TN, 37831, USA.; MVP Boston Coordinating Center, VA
                 Boston Healthcare System, Boston, MA, 02111, USA.; Data
                 Management and Engineering, Information Technology Services
                 Division, Oak Ridge National Laboratory, Dept of Energy, Oak
                 Ridge, TN, 37831, USA.; Knowledge Discovery Infrastructure,
                 Information Technology Services Division, Oak Ridge National
                 Laboratory, Dept of Energy, Oak Ridge, TN, 37831, USA.;
                 Computing and Computational Sciences Dir PMO, PMO, Oak Ridge
                 National Laboratory, Dept of Energy, Oak Ridge, TN, 37831,
                 USA.; Department of Medicine, Harvard Medical School, Boston,
                 MA, 02115, USA.; MVP Boston Coordinating Center, VA Boston
                 Healthcare System, Boston, MA, 02111, USA.; Department of
                 Medicine, Division of Aging, Brigham and Women's Hospital,
                 Boston, MA, 02115, USA.; VA Cooperative Studies Program, VA
                 Boston Healthcare System, Boston, MA, 02130, USA.; Medicine,
                 Cardiology, VA Palo Alto Healthcare System, Palo Alto, CA,
                 94304, USA.; Research Service, VA Boston Healthcare System,
                 Boston, MA, 02130, USA.; Department of Medicine, Harvard
                 Medical School, Boston, MA, 02115, USA.; Department of
                 Biomedical Informatics, Vanderbilt University Medical Center,
                 Nashville, TN, 37211, USA.; Research Department, VA San Diego
                 Healthcare System, San Diego, CA, 92161, USA.; Surgery,
                 Otolaryngology, UCSD San Diego, La Jolla, California, 92093,
                 USA.; VA Informatics and Computing Infrastructure, VA Salt Lake
                 City Health Care System, Salt Lake City, UT, 84148, USA.;
                 Internal Medicine, Epidemiology, University of Utah School of
                 Medicine, Salt Lake City, UT, 84132, USA.; Psychiatry, Human
                 Genetics, Yale University, New Haven, CT, 06520, USA.; VA
                 Connecticut Healthcare System West Haven, West Haven, CT,
                 06516, USA.; Medicine, Nephrology \& Hypertension, VA Tennessee
                 Valley Healthcare System \& Vanderbilt University, Nashville,
                 TN, 37232, USA.; Population and Quantitative Health Sciences,
                 Case Western Reserve University, School of Medicine, Cleveland,
                 OH, 44106, USA.; Medicine, Cardiology Section, VA Providence
                 Healthcare System, Providence, RI, 02908, USA.; Department of
                 Medicine, Brown University, Providence, RI, 02908, USA.; Mental
                 Illness Research, Education and Clinical Center, Corporal
                 Michael Crescenz VA Medical Center, Philadelphia, PA, 19104,
                 USA.; Department of Psychiatry, University of Pennsylvania -
                 Perelman School of Medicine, Philadelphia, PA, 19104, USA.;
                 Medicine, VA Connecticut Healthcare System West Haven, West
                 Haven, CT, 06516, USA.; Psychiatry, Human Genetics, Yale
                 University, New Haven, CT, 06520, USA.; VA Portland Health Care
                 System, Portland, OR, 97239, USA.; Division of Hematology and
                 Medical Oncology, Knight Cancer Institute, Oregon Health and
                 Science University, Portland, OR, 97239, USA.; Research
                 Department, VA San Diego Healthcare System, San Diego, CA,
                 92161, USA.; Psychiatry, Human Genetics, Yale University, New
                 Haven, CT, 06520, USA.; Psychiatry, Yale University, New Haven,
                 CT, 06520, USA.; Psychiatry, VA Connecticut Healthcare System
                 West Haven, West Haven, CT, 06516, USA.; Center for Spatial and
                 Functional Genomics, Children's Hospital of Philadelphia,
                 Philadelphia, PA, 19104, USA.; Department of Pediatrics,
                 University of Pennsylvania - Perelman School of Medicine,
                 Philadelphia, PA, 19104, USA.; Divisions of Human Genetics and
                 Endocrinology and Diabetes, Children's Hospital of
                 Philadelphia, Philadelphia, PA, 19104, USA.; Department of
                 Genetics, University of Pennsylvania - Perelman School of
                 Medicine, Philadelphia, PA, 19104, USA.; Psychiatry, Yale
                 University, New Haven, CT, 06520, USA.; Psychiatry, Mental
                 Illness Research, Education and Clinical Center, James J.
                 Peters VA Medical Center; Icahn School of Medicine at Mount
                 Sinai, Bronx, NY, 10468, USA.; Epidemiology, Emory University
                 Rollins School of Public Health, Atlanta, GA, 30322, USA.;
                 Medicine, VA Connecticut Healthcare System West Haven, West
                 Haven, CT, 06516, USA.; Internal Medicine, General Medicine,
                 Yale University, New Haven, CT, 06520, USA.; Health Policy,
                 Yale School of Public Health, New Haven, CT, 06520, USA.; Oak
                 Ridge National Laboratory, Dept of Energy, Oak Ridge, TN,
                 37831, USA.; Office of Research and Development, Department of
                 Veterans Affairs, Washington, DC, 20420, USA.; National Center
                 for Computational Sciences, Oak Ridge National Laboratory, Dept
                 of Energy, Oak Ridge, TN, 37831, USA.; Medicine, Cardiology, VA
                 Palo Alto Healthcare System, Palo Alto, CA, 94304, USA.;
                 Department of Medicine, Stanford University, Palo Alto, CA,
                 94304, USA.; Medicine, Cardiology, VA Boston Healthcare System,
                 Boston, MA, 02130, USA.; Department of Medicine, Division of
                 Genetic Medicine, Vanderbilt University, Nashville, TN, 37325,
                 USA.; Department of Medicine, Analytic and Translational
                 Genetics Unit, Massachusetts General Hospital, Boston, MA,
                 02114, USA.; Stanley Center for Psychiatric Research,
                 Cambridge, MA, 02142, USA.; Program in Medical and Population
                 Genetics, Cambridge, MA, 02142, USA.; Corporal Michael Crescenz
                 VA Medical Center, Philadelphia, PA, 19104, USA.; Department of
                 Systems Pharmacology and Translational Therapeutics, University
                 of Pennsylvania - Perelman School of Medicine, Philadelphia,
                 PA, 19104, USA.; Department of Genetics, University of
                 Pennsylvania - Perelman School of Medicine, Philadelphia, PA,
                 19104, USA.; Institute of Translational Medicine and
                 Therapeutics, University of Pennsylvania - Perelman School of
                 Medicine, Philadelphia, PA, 19104, USA.; Corporal Michael
                 Crescenz VA Medical Center, Philadelphia, PA, 19104, USA.;
                 Department of Genetics, University of Pennsylvania - Perelman
                 School of Medicine, Philadelphia, PA, 19104, USA.; Department
                 of Surgery, University of Pennsylvania - Perelman School of
                 Medicine, Philadelphia, PA, 19104, USA.; Cardiovascular
                 Institute, University of Pennsylvania - Perelman School of
                 Medicine, Philadelphia, PA, 19104, USA.; Medicine,
                 Rheumatology, VA Boston Healthcare System, Boston, MA, 02130,
                 USA.; Department of Medicine, Division of Rheumatology,
                 Inflammation, and Immunity, Brigham and Women's Hospital,
                 Boston, MA, 02115, USA.",
  journal     = "medRxiv: the preprint server for health sciences",
  month       =  "29~" # jun,
  year        =  2023,
  url         = "http://dx.doi.org/10.1101/2023.06.28.23291975",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1101/2023.06.28.23291975",
  pmc         = "PMC10327290",
  pmid        =  37425708,
  language    = "en"
}

@ARTICLE{FinnGen,
  title       = "{FinnGen} provides genetic insights from a well-phenotyped
                 isolated population",
  author      = "Kurki, Mitja I and Karjalainen, Juha and Palta, Priit and
                 Sipil{\"{a}}, Timo P and Kristiansson, Kati and Donner, Kati M
                 and Reeve, Mary P and Laivuori, Hannele and Aavikko, Mervi and
                 Kaunisto, Mari A and Loukola, Anu and Lahtela, Elisa and
                 Mattsson, Hannele and Laiho, P{\"{a}}ivi and Della Briotta
                 Parolo, Pietro and Lehisto, Arto A and Kanai, Masahiro and
                 Mars, Nina and R{\"{a}}m{\"{o}}, Joel and Kiiskinen, Tuomo and
                 Heyne, Henrike O and Veerapen, Kumar and R{\"{u}}eger, Sina and
                 Lemmel{\"{a}}, Susanna and Zhou, Wei and Ruotsalainen, Sanni
                 and P{\"{a}}rn, Kalle and Hiekkalinna, Tero and Koskelainen,
                 Sami and Paajanen, Teemu and Llorens, Vincent and
                 Gracia-Tabuenca, Javier and Siirtola, Harri and Reis, Kadri and
                 Elnahas, Abdelrahman G and Sun, Benjamin and Foley, Christopher
                 N and Aalto-Set{\"{a}}l{\"{a}}, Katriina and Alasoo, Kaur and
                 Arvas, Mikko and Auro, Kirsi and Biswas, Shameek and
                 Bizaki-Vallaskangas, Argyro and Carpen, Olli and Chen, Chia-Yen
                 and Dada, Oluwaseun A and Ding, Zhihao and Ehm, Margaret G and
                 Eklund, Kari and F{\"{a}}rkkil{\"{a}}, Martti and Finucane,
                 Hilary and Ganna, Andrea and Ghazal, Awaisa and Graham, Robert
                 R and Green, Eric M and Hakanen, Antti and Hautalahti, Marco
                 and Hedman, \AA{}sa K and Hiltunen, Mikko and Hinttala, Reetta
                 and Hovatta, Iiris and Hu, Xinli and Huertas-Vazquez, Adriana
                 and Huilaja, Laura and Hunkapiller, Julie and Jacob, Howard and
                 Jensen, Jan-Nygaard and Joensuu, Heikki and John, Sally and
                 Julkunen, Valtteri and Jung, Marc and Junttila, Juhani and
                 Kaarniranta, Kai and K{\"{a}}h{\"{o}}nen, Mika and Kajanne,
                 Risto and Kallio, Lila and K{\"{a}}lvi{\"{a}}inen, Reetta and
                 Kaprio, Jaakko and {FinnGen} and Kerimov, Nurlan and Kettunen,
                 Johannes and Kilpel{\"{a}}inen, Elina and Kilpi, Terhi and
                 Klinger, Katherine and Kosma, Veli-Matti and Kuopio, Teijo and
                 Kurra, Venla and Laisk, Triin and Laukkanen, Jari and Lawless,
                 Nathan and Liu, Aoxing and Longerich, Simonne and M{\"{a}}gi,
                 Reedik and M{\"{a}}kel{\"{a}}, Johanna and M{\"{a}}kitie, Antti
                 and Malarstig, Anders and Mannermaa, Arto and Maranville,
                 Joseph and Matakidou, Athena and Meretoja, Tuomo and Mozaffari,
                 Sahar V and Niemi, Mari E K and Niemi, Marianna and Niiranen,
                 Teemu and O Donnell, Christopher J and Obeidat, Ma En and
                 Okafo, George and Ollila, Hanna M and Palom{\"{a}}ki, Antti and
                 Palotie, Tuula and Partanen, Jukka and Paul, Dirk S and
                 Pelkonen, Margit and Pendergrass, Rion K and Petrovski,
                 Slav\'{e} and Pitk{\"{a}}ranta, Anne and Platt, Adam and
                 Pulford, David and Punkka, Eero and Pussinen, Pirkko and
                 Raghavan, Neha and Rahimov, Fedik and Rajpal, Deepak and
                 Renaud, Nicole A and Riley-Gillis, Bridget and Rodosthenous,
                 Rodosthenis and Saarentaus, Elmo and Salminen, Aino and
                 Salminen, Eveliina and Salomaa, Veikko and Schleutker, Johanna
                 and Serpi, Raisa and Shen, Huei-Yi and Siegel, Richard and
                 Silander, Kaisa and Siltanen, Sanna and Soini, Sirpa and
                 Soininen, Hilkka and Sul, Jae Hoon and Tachmazidou, Ioanna and
                 Tasanen, Kaisa and Tienari, Pentti and Toppila-Salmi, Sanna and
                 Tukiainen, Taru and Tuomi, Tiinamaija and Turunen, Joni A and
                 Ulirsch, Jacob C and Vaura, Felix and Virolainen, Petri and
                 Waring, Jeffrey and Waterworth, Dawn and Yang, Robert and
                 Nelis, Mari and Reigo, Anu and Metspalu, Andres and Milani,
                 Lili and Esko, T\~{o}nu and Fox, Caroline and Havulinna, Aki S
                 and Perola, Markus and Ripatti, Samuli and Jalanko, Anu and
                 Laitinen, Tarja and M{\"{a}}kel{\"{a}}, Tomi P and Plenge,
                 Robert and McCarthy, Mark and Runz, Heiko and Daly, Mark J and
                 Palotie, Aarno",
  affiliation = "Institute for Molecular Medicine Finland (FIMM), Helsinki
                 Institute of Life Science (HiLIFE), University of Helsinki,
                 Helsinki, Finland. Program in Medical and Population Genetics,
                 Broad Institute of Harvard and MIT, Cambridge, MA, USA. Stanley
                 Center for Psychiatric Research, Broad Institute of Harvard and
                 MIT, Cambridge, MA, USA. Analytic and Translational Genetics
                 Unit, Massachusetts General Hospital, Boston, MA, USA. Estonian
                 Genome Centre, Institute of Genomics, University of Tartu,
                 Tartu, Estonia. Finnish Institute for Health and Welfare (THL),
                 Helsinki, Finland. Medical and Clinical Genetics, University of
                 Helsinki and Helsinki University Hospital, Helsinki, Finland.
                 Department of Obstetrics and Gynecology, Tampere University
                 Hospital, Tampere, Finland. Faculty of Medicine and Health
                 Technology, Center for Child, Adolescent and Maternal Health,
                 University of Tampere, Tampere, Finland. Helsinki Biobank,
                 University of Helsinki and Hospital District of Helsinki and
                 Uusimaa, Helsinki, Finland. Department of Biomedical
                 Informatics, Harvard Medical School, Boston, MA, USA. Digital
                 Health Center, Hasso Plattner Institute for Digital
                 Engineering, University of Potsdam Potsdam, Potsdam, Germany.
                 Hasso Plattner Institute for Digital Health at Mount Sinai,
                 Department of Genetics and Genomic Sciences, Icahn School of
                 Medicine at Mount Sinai, New York, NY, USA. TAUCHI Research
                 Center, Faculty of Information Technology and Communication
                 Sciences, Tampere University, Tampere, Finland. Translational
                 Biology, Research and Development, Biogen, Cambridge, MA, USA.
                 BHF Cardiovascular Epidemiology Unit, Department of Public
                 Health and Primary Care, University of Cambridge, Cambridge,
                 UK. Optima Partners, Edinburgh, UK. MRC Biostatistics Unit,
                 School of Clinical Medicine, University of Cambridge,
                 Cambridge, UK. Faculty of Medicine and Health Technology,
                 Tampere University, Tampere, Finland. Institute of Computer
                 Science, University of Tartu, Tartu, Estonia. Finnish Red Cross
                 Blood Service, Helsinki, Finland. GlaxoSmithKline, Espoo,
                 Finland. Bristol Myers Squibb, New York, NY, USA. Tampere
                 University Hospital and Tampere University, Tampere, Finland.
                 Biogen, Cambridge, MA, USA. Boehringer Ingelheim, Ingelheim am
                 Rhein, Germany. GlaxoSmithKline, Collegeville, PA, USA.
                 Division of Rheumatology, Department of Medicine, Helsinki
                 University Central Hospital, Helsinki, Finland. Orton
                 Orthopedic Hospital, Helsinki, Finland. Abdominal Center,
                 Helsinki University Hospital, Helsinki University, Helsinki,
                 Finland. Maze Therapeutics, South San Francisco, CA, USA. Auria
                 Biobank, University of Turku and Turku University Hospital,
                 Turku, Finland. FINBB, Finnish Biobank Cooperative, Helsinki,
                 Finland. Pfizer, New York, NY, USA. Department of Medicine,
                 Karolinska Institute, Solna, Sweden. Clinical Biobank Tampere,
                 Tampere University and Tampere University Hospital, Tampere,
                 Finland. Medical Research Center Oulu and PEDEGO Research Unit,
                 University of Oulu, Oulu, Finland. Biocenter Oulu, University
                 of Oulu, Oulu, Finland. Oulu University Hospital, Oulu,
                 Finland. Department of Psychology and Logopedics, Faculty of
                 Medicine, University of Helsinki, Helsinki, Finland. SleepWell
                 Research Program, Faculty of Medicine, University of Helsinki,
                 Helsinki, Finland. Merck \& Co, Kenilworth, NJ, USA. PEDEGO
                 Research Unit, University of Oulu, Oulu, Finland. Department of
                 Dermatology and Medical Research Center Oulu, Oulu University
                 Hospital, Oulu, Finland. Genentech, San Francisco, CA, USA.
                 AbbVie, Chicago, IL, USA. Helsinki University Hospital and
                 University of Helsinki, Helsinki, Finland. Neuro Center,
                 Neurology, Kuopio University Hospital, Kuopio, Finland.
                 Institute of Clinical Medicine-Neurology, University of Eastern
                 Finland, Kuopio, Finland. Northern Finland Biobank Borealis,
                 University of Oulu, Northern Ostrobothnia Hospital District,
                 Oulu, Finland. Department of Ophthalmology, Kuopio University
                 Hospital, Kuopio, Finland. Department of Ophthalmology,
                 Institute of Clinical Medicine, University of Eastern Finland,
                 Kuopio, Finland. Department of Clinical Physiology, Tampere
                 University Hospital, Tampere, Finland. Epilepsy Center, Kuopio
                 University Hospital, Kuopio, Finland. Department of Neurology,
                 University of Eastern Finland, Kuopio, Finland. Department of
                 Public Health, University of Helsinki, Helsinki, Finland.
                 Computational Medicine, Center for Life Course Health Research,
                 Faculty of Medicine, University of Oulu, Oulu, Finland.
                 Translational Sciences, Sanofi R\&D, Framingham, MA, USA.
                 Biobank of Eastern Finland, University of Eastern Finland,
                 Kuopio, Finland. Kuopio University Hospital, Kuopio, Finland.
                 Central Finland Biobank, Central Finland Health Care District,
                 Jyv{\"{a}}skyl{\"{a}}, Finland. Department of Clinical
                 Genetics, Tampere University Hospital, Tampere, Finland.
                 Department of Clinical Genetics, Faculty of Medicine and Health
                 Technology, Tampere, Finland. Department of Medicine, Institute
                 of Clinical Medicine, University of Eastern Finland, Kuopio,
                 Finland. FINBB, Finnish Biobank Cooperative, Turku, Finland.
                 Department of Otorhinolaryngology-Head and Neck Surgery,
                 University of Helsinki, Helsinki, Finland. Helsinki University
                 Hospital, Helsinki, Finland. Pfizer, Cambridge, MA, USA.
                 Department of Medical Epidemiology and Biostatistics,
                 Karolinska Institute, Solna, Sweden. Centre for Genomics
                 Research, Discovery Sciences, BioPharmaceuticals R\&D,
                 AstraZeneca, Cambridge, UK. TAUCHI Research Center \& Faculty
                 of Medicine and Health Technology, Tampere University, Tampere,
                 Finland. Turku University Hospital and University of Turku,
                 Turku, Finland. Novartis Institutes for BioMedical Research,
                 Cambridge, MA, USA. Anesthesia, Critical Care, and Pain
                 Medicine, Massachusetts General Hospital, Boston, MA, USA.
                 Department of Oral and Maxillofacial Diseases, Helsinki
                 University Hospital, Helsinki, Finland. Department of Oral and
                 Maxillofacial Diseases, University of Helsinki, Helsinki,
                 Finland. Finnish Hematological Biobank, Helsinki, Finland.
                 Department of Pulmonary Diseases, Kuopio University Hospital,
                 Kuopio, Finland. Department of Otorhinolaryngology, Helsinki
                 University Hospital and University of Helsinki, Helsinki,
                 Finland. Translational Science and Experimental Medicine,
                 Research and Early Development, Respiratory and Immunology,
                 BioPharmaceuticals R\&D, AstraZeneca, Cambridge, UK.
                 GlaxoSmithKline, Stevenage, UK. Department of Clinical
                 Genetics, HUSLAB, HUS Diagnostic Center, University of
                 Helsinki, Helsinki, Finland. Novartis Institutes for BioMedical
                 Research, Basel, Switzerland. Finnish Clinical Biobank Tampere,
                 Tampere University and Tampere University Hospital, Tampere,
                 Finland. Department of Neurology, Institute of Clinical
                 Medicine, University of Eastern Finland, Kuopio, Finland.
                 Department of Neurology, Helsinki University Hospital,
                 Helsinki, Finland. Translational Immunology, Research Programs
                 Unit, University of Helsinki, Helsinki, Finland. Department of
                 Allergy, Helsinki University Hospital and University of
                 Helsinki, Helsinki, Finland. Abdominal Center, Endocrinology,
                 Helsinki University Hospital, Helsinki, Finland. Folkhalsan
                 Research Center, Helsinki, Finland. Research Program of
                 Clinical and Molecular Metabolism, University of Helsinki,
                 Helsinki, Finland. Eye Genetics Group, Folkh{\"{a}}lsan
                 Research Center, Helsinki, Finland. University of Turku, Turku,
                 Finland. Janssen Research \& Development, Spring House, PA,
                 USA. Janssen Biotech, Beerse, Belgium. Genomics Core Facility,
                 Institute of Genomics, University of Tartu, Tartu, Estonia.
                 Helsinki Institute of Life Science (HiLIFE), University of
                 Helsinki, Helsinki, Finland. Institute for Molecular Medicine
                 Finland (FIMM), Helsinki Institute of Life Science (HiLIFE),
                 University of Helsinki, Helsinki, Finland.
                 aarno.palotie@helsinki.fi. Program in Medical and Population
                 Genetics, Broad Institute of Harvard and MIT, Cambridge, MA,
                 USA. aarno.palotie@helsinki.fi. Stanley Center for Psychiatric
                 Research, Broad Institute of Harvard and MIT, Cambridge, MA,
                 USA. aarno.palotie@helsinki.fi. Analytic and Translational
                 Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
                 aarno.palotie@helsinki.fi.",
  journal     = "Nature",
  volume      =  613,
  number      =  7944,
  pages       = "508--518",
  month       =  jan,
  year        =  2023,
  url         = "http://dx.doi.org/10.1038/s41586-022-05473-8",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41586-022-05473-8",
  pmc         = "PMC9849126",
  pmid        =  36653562,
  issn        = "0028-0836,1476-4687",
  language    = "en"
}

@ARTICLE{SCARF,
  title         = "{SCARF}: Self-supervised contrastive learning using random
                   feature corruption",
  author        = "Bahri, Dara and Jiang, Heinrich and Tay, Yi and Metzler,
                   Donald",
  journal       = "arXiv [cs.LG]",
  month         =  "29~" # jun,
  year          =  2021,
  url           = "https://openreview.net/pdf?id=CuV_qYkmKb3",
  archivePrefix = "arXiv",
  primaryClass  = "cs.LG",
  eprint        = "2106.15147",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{RetFound-DINOv2,
  title       = "Revealing the impact of pre-training data on medical foundation
                 models",
  author      = "Zhou, Yukun and Wang, Zheyuan and Wu, Yilan and Ong, Ariel
                 Yuhan and Wagner, Siegfried and Ruffell, Eden and Chia, Mark
                 and Guan, Zhouyu and Ju, Lie and Engelmann, Justin and Merle,
                 David and Li, Tingyao and Shu, Jia and Nderitu, Paul and Zou,
                 Ke and Goh, Jocelyn Hui Lin and Hou, Qingshan and Liu, Xiaoxuan
                 and Wang, Yaxing and Tham, Yih Chung and Altmann, Andre and
                 Cheung, Carol and Alexander, Daniel and Topol, Eric and
                 Denniston, Alastair and Wong, Tien Yin and Sheng, Bin and
                 Keane, Pearse A",
  affiliation = "University College London; MoE Key Lab of Artificial
                 Intelligence, Artificial Intelligence Institute, Shanghai Jiao
                 Tong University, Shanghai, China.; Tsinghua University;
                 University College London Institute of Ophthalmology,
                 University College London; The Royal Victorian Eye and Ear
                 Hospital; Shanghai Jiao Tong University School of Medicine;
                 Moorfields Eye Hospital NHS Foundation Trust; National
                 University of Singapore; Singapore Eye Research Institute,
                 Singapore National Eye Centre, Singapore.; University of
                 Birmingham; Centre for Innovation and Precision Eye Health; The
                 Chinese University of Hong Kong; Centre for Medical Image
                 Computing, Department of Computer Science, University College
                 London; Executive VP, Scripps Research Professor, Molecular
                 Medicine, Scripps Research Director \& Founder, Scripps
                 Research Translational Institute Department of Molecular
                 Medicine; Shanghai Jiao Tong University; NIHR Biomedical
                 Research Centre at Moorfields Eye Hospital NHS Foundation
                 Trust,University College London",
  journal     = "Research Square",
  institution = "Research Square",
  month       =  "3~" # apr,
  year        =  2025,
  url         = "http://dx.doi.org/10.21203/rs.3.rs-6080254/v1",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.21203/rs.3.rs-6080254/v1"
}

@ARTICLE{RetFound-MAE,
  title       = "A foundation model for generalizable disease detection from
                 retinal images",
  author      = "Zhou, Yukun and Chia, Mark A and Wagner, Siegfried K and Ayhan,
                 Murat S and Williamson, Dominic J and Struyven, Robbert R and
                 Liu, Timing and Xu, Moucheng and Lozano, Mateo G and
                 Woodward-Court, Peter and Kihara, Yuka and {UK Biobank Eye \&
                 Vision Consortium} and Altmann, Andre and Lee, Aaron Y and
                 Topol, Eric J and Denniston, Alastair K and Alexander, Daniel C
                 and Keane, Pearse A",
  affiliation = "Centre for Medical Image Computing, University College London,
                 London, UK. yukun.zhou.19@ucl.ac.uk. NIHR Biomedical Research
                 Centre at Moorfields Eye Hospital NHS Foundation Trust, London,
                 UK. yukun.zhou.19@ucl.ac.uk. Department of Medical Physics and
                 Biomedical Engineering, University College London, London, UK.
                 yukun.zhou.19@ucl.ac.uk. NIHR Biomedical Research Centre at
                 Moorfields Eye Hospital NHS Foundation Trust, London, UK.
                 Institute of Ophthalmology, University College London, London,
                 UK. Centre for Medical Image Computing, University College
                 London, London, UK. Department of Medical Physics and
                 Biomedical Engineering, University College London, London, UK.
                 Department of Computer Science, University of Coru\~{n}a, A
                 Coru\~{n}a, Spain. Institute of Health Informatics, University
                 College London, London, UK. Department of Ophthalmology,
                 University of Washington, Seattle, WA, USA. Roger and Angie
                 Karalis Johnson Retina Center, University of Washington,
                 Seattle, WA, USA. Department of Molecular Medicine, Scripps
                 Research, La Jolla, CA, USA. Academic Unit of Ophthalmology,
                 University of Birmingham, Birmingham, UK. University Hospitals
                 Birmingham NHS Foundation Trust, Birmingham, UK. Department of
                 Computer Science, University College London, London, UK. NIHR
                 Biomedical Research Centre at Moorfields Eye Hospital NHS
                 Foundation Trust, London, UK. p.keane@ucl.ac.uk. Institute of
                 Ophthalmology, University College London, London, UK.
                 p.keane@ucl.ac.uk.",
  journal     = "Nature",
  volume      =  622,
  number      =  7981,
  pages       = "156--163",
  month       =  oct,
  year        =  2023,
  url         = "http://dx.doi.org/10.1038/s41586-023-06555-x",
  keywords    = "DMR-GenRes;GEMCONT MICCAI 2025",
  doi         = "10.1038/s41586-023-06555-x",
  pmc         = "PMC10550819",
  pmid        =  37704728,
  issn        = "0028-0836,1476-4687",
  language    = "en"
}

@ARTICLE{spiro_excl,
  title    = "Spirometry",
  author   = "Paraskeva, Miranda A and Borg, Brigitte M and Naughton, Matthew T",
  journal  = "Australian family physician",
  volume   =  40,
  number   =  4,
  pages    =  216,
  year     =  2011,
  url      = "https://www.racgp.org.au/getattachment/b2aef6c3-a6fb-46bf-9acf-f0215484f04c/Spirometry.aspx",
  keywords = "GEMCONT MICCAI 2025",
  issn     = "0300-8495",
  language = "en"
}

@ARTICLE{Wang2022-fm,
  title       = "Deep learning for spirometry quality assurance with spirometric
                 indices and curves",
  author      = "Wang, Yimin and Li, Yicong and Chen, Wenya and Zhang,
                 Changzheng and Liang, Lijuan and Huang, Ruibo and Liang,
                 Jianling and Tu, Dandan and Gao, Yi and Zheng, Jinping and
                 Zhong, Nanshan",
  affiliation = "National Center for Respiratory Medicine, State Key Laboratory
                 of Respiratory Disease, National Clinical Research Center for
                 Respiratory Disease, Guangzhou Institute of Respiratory Health,
                 First Affiliated Hospital of Guangzhou Medical University,
                 Yanjiang Road 151, Guangzhou, 510120, Guangdong, People's
                 Republic of China.; Tsinghua-Berkeley Shenzhen Institute,
                 Tsinghua University, Shenzhen, 518055, China.; Huawei Cloud BU
                 EI Innovation Laboratory, Huawei Technologies, Shenzhen,
                 518129, China.; Huawei Cloud BU EI Innovation Laboratory,
                 Huawei Technologies, Shenzhen, 518129, China.; National Center
                 for Respiratory Medicine, State Key Laboratory of Respiratory
                 Disease, National Clinical Research Center for Respiratory
                 Disease, Guangzhou Institute of Respiratory Health, First
                 Affiliated Hospital of Guangzhou Medical University, Yanjiang
                 Road 151, Guangzhou, 510120, Guangdong, People's Republic of
                 China. misstall2@163.com.; National Center for Respiratory
                 Medicine, State Key Laboratory of Respiratory Disease, National
                 Clinical Research Center for Respiratory Disease, Guangzhou
                 Institute of Respiratory Health, First Affiliated Hospital of
                 Guangzhou Medical University, Yanjiang Road 151, Guangzhou,
                 510120, Guangdong, People's Republic of China.
                 jpzhenggy@163.com.; National Center for Respiratory Medicine,
                 State Key Laboratory of Respiratory Disease, National Clinical
                 Research Center for Respiratory Disease, Guangzhou Institute of
                 Respiratory Health, First Affiliated Hospital of Guangzhou
                 Medical University, Yanjiang Road 151, Guangzhou, 510120,
                 Guangdong, People's Republic of China. nanshan@vip.163.com.",
  journal     = "Respiratory research",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  23,
  number      =  1,
  pages       =  98,
  month       =  "21~" # apr,
  year        =  2022,
  url         = "http://dx.doi.org/10.1186/s12931-022-02014-9",
  keywords    = "Artificial intelligence; Deep learning; General practitioner;
                 Quality control; Spirometry;GEMCONT MICCAI 2025",
  doi         = "10.1186/s12931-022-02014-9",
  pmc         = "PMC9028127",
  pmid        =  35448995,
  issn        = "1465-9921,1465-993X",
  language    = "en"
}

@ARTICLE{Martins2025-kr,
  title       = "Transfer learning in spirometry: {CNN} models for automated
                 flow-volume curve quality control in paediatric populations",
  author      = "Martins, Carla and Barros, Henrique and Moreira, Andr\'{e}",
  affiliation = "EPIUnit - Instituto de Sa\'{u}de P\'{u}blica da Universidade do
                 Porto, Laborat\'{o}rio para a Investiga\c{c}\~{a}o Integrativa
                 e Translacional em Sa\'{u}de Populacional (ITR), Porto,
                 Portugal; Servi\c{c}o de Imunoalergologia, Unidade Local de
                 Sa\'{u}de de S\~{a}o Jo\~{a}o, Porto, Portugal. Electronic
                 address: cdanielaam@gmail.com.; EPIUnit - Instituto de
                 Sa\'{u}de P\'{u}blica da Universidade do Porto, Laborat\'{o}rio
                 para a Investiga\c{c}\~{a}o Integrativa e Translacional em
                 Sa\'{u}de Populacional (ITR), Porto, Portugal.; EPIUnit -
                 Instituto de Sa\'{u}de P\'{u}blica da Universidade do Porto,
                 Laborat\'{o}rio para a Investiga\c{c}\~{a}o Integrativa e
                 Translacional em Sa\'{u}de Populacional (ITR), Porto, Portugal;
                 Servi\c{c}o de Imunoalergologia, Unidade Local de Sa\'{u}de de
                 S\~{a}o Jo\~{a}o, Porto, Portugal; Laborat\'{o}rio de
                 Imunologia B\'{a}sica e Cl\'{\i}nica, Departamento de
                 Patologia, Faculdade de Medicina da Universidade do Porto,
                 Portugal.",
  journal     = "Computers in biology and medicine",
  publisher   = "Elsevier BV",
  volume      =  184,
  number      =  109341,
  pages       =  109341,
  month       =  jan,
  year        =  2025,
  url         = "http://dx.doi.org/10.1016/j.compbiomed.2024.109341",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1016/j.compbiomed.2024.109341",
  pmid        =  39541898,
  issn        = "0010-4825,1879-0534",
  language    = "en"
}

@ARTICLE{VCDR_1,
  title     = "The Ocular Hypertension Treatment Study: baseline factors that
               predict the onset of primary open-angle glaucoma",
  author    = "Gordon, Mae O and Beiser, Julia A and Brandt, James D and Heuer,
               Dale K and Higginbotham, Eve J and Johnson, Chris A and Keltner,
               John L and Miller, J Philip and Parrish, 2nd, Richard K and
               Wilson, M Roy and Kass, Michael A",
  journal   = "Archives of ophthalmology",
  publisher = "American Medical Association",
  volume    =  120,
  number    =  6,
  pages     = "714--20; discussion 829--30",
  month     =  jun,
  year      =  2002,
  url       = "http://dx.doi.org/10.1001/archopht.120.6.714",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1001/archopht.120.6.714",
  pmid      =  12049575,
  issn      = "0003-9950,1538-3601",
  language  = "en"
}

@ARTICLE{VCDR_2,
  title     = "The definition and classification of glaucoma in prevalence
               surveys",
  author    = "Foster, Paul J and Buhrmann, Ralf and Quigley, Harry A and
               Johnson, Gordon J",
  journal   = "The British journal of ophthalmology",
  publisher = "BMJ",
  volume    =  86,
  number    =  2,
  pages     = "238--242",
  month     =  feb,
  year      =  2002,
  url       = "https://bjo.bmj.com/content/86/2/238.short",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1136/bjo.86.2.238",
  pmc       = "PMC1771026",
  pmid      =  11815354,
  issn      = "0007-1161,1468-2079",
  language  = "en"
}


@ARTICLE{cup-to-disk_ratio,
  title       = "{UK} Biobank retinal imaging grading: methodology, baseline
                 characteristics and findings for common ocular diseases",
  author      = "Warwick, Alasdair N and Curran, Katie and Hamill, Barbra and
                 Stuart, Kelsey and Khawaja, Anthony P and Foster, Paul J and
                 Lotery, Andrew J and Quinn, Michael and Madhusudhan, Savita and
                 Balaskas, Konstantinos and Peto, Tunde and {UKBB Eye and Vision
                 Consortium}",
  affiliation = "Institute of Cardiovascular Science, University College London,
                 London, UK.; Medical Retina Service, Moorfields Eye Hospital
                 NHS Foundation Trust, London, UK.; Centre for Public Health,
                 Queen's University Belfast, Faculty of Medicine Health and Life
                 Sciences, Belfast, UK.; Institute of Ophthalmology, University
                 College London, London, UK.; NIHR Biomedical Research Centre,
                 Moorfields Eye Hospital NHS Foundation Trust, London, UK.;
                 Faculty of Medicine, Clinical and Experimental Sciences,
                 University of Southampton, Southampton, UK.; Medical Retina
                 Service, University Hospital Southampton NHS Foundation Trust,
                 Southampton, UK.; St. Paul's Eye Unit, Liverpool University
                 Hospitals NHS Foundation Trust, Liverpool, UK.; Medical Retina
                 Service, Moorfields Eye Hospital NHS Foundation Trust, London,
                 UK.; Institute of Ophthalmology, University College London,
                 London, UK.; Centre for Public Health, Queen's University
                 Belfast, Faculty of Medicine Health and Life Sciences, Belfast,
                 UK. t.peto@qub.ac.uk.",
  journal     = "Eye",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  37,
  number      =  10,
  pages       = "2109--2116",
  month       =  "3~" # jul,
  year        =  2023,
  url         = "https://www.nature.com/articles/s41433-022-02298-7",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41433-022-02298-7",
  pmc         = "PMC10333328",
  pmid        =  36329166,
  issn        = "0950-222X,1476-5454",
  language    = "en"
}


@ARTICLE{fun_diag,
  title       = "A fast and fully automated system for glaucoma detection using
                 color fundus photographs",
  author      = "Saha, Sajib and Vignarajan, Janardhan and Frost, Shaun",
  affiliation = "Australian e-Health Research Centre, Commonwealth Scientific
                 and Industrial Research Organisation (CSIRO), Perth, Australia.
                 Sajib.Saha@csiro.au.; Australian e-Health Research Centre,
                 Commonwealth Scientific and Industrial Research Organisation
                 (CSIRO), Perth, Australia.",
  journal     = "Scientific reports",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  13,
  number      =  1,
  pages       =  18408,
  month       =  "27~" # oct,
  year        =  2023,
  url         = "http://dx.doi.org/10.1038/s41598-023-44473-0",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41598-023-44473-0",
  pmc         = "PMC10611813",
  pmid        =  37891238,
  issn        = "2045-2322",
  language    = "en"
}

@ARTICLE{spiro_diag,
  title       = "Clinical standards for the diagnosis and management of asthma
                 in low- and middle-income countries",
  author      = "Jayasooriya, S and Stolbrink, M and Khoo, E M and Sunte, I T
                 and Awuru, J I and Cohen, M and Lam, D C and Spanevello, A and
                 Visca, D and Centis, R and Migliori, G B and Ayuk, A C and
                 Buendia, J A and Awokola, B I and Del-Rio-Navarro, B E and
                 Muteti-Fana, S and Lao-Araya, M and Chiarella, P and Badellino,
                 H and Somwe, S W and Anand, M P and Garc\'{\i}-Corzo, J R and
                 Bekele, A and Soto-Martinez, M E and Ngahane, B H M and Florin,
                 M and Voyi, K and Tabbah, K and Bakki, B and Alexander, A and
                 Garba, B L and Salvador, E M and Fischer, G B and Falade, A G
                 and {\v{Z}}ivkovi\'{C}, Zorica and Romero-Tapia, S J and
                 Erhabor, G E and Zar, H and Gemicioglu, B and Brand\~{a}o, H V
                 and Kurhasani, X and El-Sharif, N and Singh, V and Ranasinghe,
                 J C and Kudagammana, S T and Masjedi, M R and Vel\'{a}squez, J
                 N and Jain, A and Cherrez-Ojeda, I and Valdeavellano, L F M and
                 G\'{o}mez, R M and Mesonjesi, E and Morfin-Maciel, B M and
                 Ndikum, A E and Mukiibi, G B and Reddy, B K and Yusuf, O and
                 Taright-Mahi, S and M\'{e}rida-Palacio, J V and Kabra, S K and
                 Nkhama, E and Filho, N R and Zhjegi, V B and Mortimer, K and
                 Rylance, S and Masekela, R R",
  affiliation = "Academic Unit of Primary Care, University of Sheffield,
                 Sheffield.; Department of Clinical Sciences, Liverpool School
                 of Tropical Medicine, Liverpool, UK, Faculty of Medicine and
                 Health Sciences, Stellenbosch University, Tygerberg, South
                 Africa.; Faculty of Medicine, Universiti Malaya, Kuala Lumpur,
                 Malaysia, International Primary Care Respiratory Group,
                 Edinburgh, Scotland, UK.; Global Allergy and Airways Patient
                 Platform, Vienna, Austria.; Hospital Centro M\'{e}dico,
                 Guatemala City, Guatemala, Mexico, Asociaci\'{o}n
                 Latinoamericana de T\'{o}rax, Montevideo, Uruguay.; Department
                 of Medicine, University of Hong Kong, Hong Kong, Asian Pacific
                 Society of Respirology, Hong Kong, China.; Division of
                 Pulmonary Rehabilitation, Istituti Clinici Scientifici Maugeri,
                 Istituto di Ricovero e Cura a Carattere Scientifico, Tradate,
                 Department of Medicine and Surgery, Respiratory Diseases,
                 University of Insubria, Varese-Como.; Asociaci\'{o}n
                 Latinoamericana de T\'{o}rax, Montevideo, Uruguay, Department
                 of Medicine, University of Hong Kong, Hong Kong.; Servizio di
                 Epidemiologia Clinica delle Malattie Respiratorie, Istituti
                 Clinici Scientifici Maugeri, Tradate, Italy.; College of
                 Medicine, University of Nigeria, Enugu, Nigeria.; Affiliation
                 Departamento de Farmacologia y T\'{o}xicologia, Facultad de
                 Medicina, Universidad de Antioquia, Medell\'{\i}n, Colombia.;
                 Medical Research Council, The Gambia at the London School of
                 Tropical Medicine, The Gambia.; Hospital Infantil de M\'{e}xico
                 Federico G\^{o}mez, Mexico D.F, Mexico.; Department of Primary
                 Care Sciences, University of Zimbabwe, Harare, Zimbabwe.;
                 Division of Allergy and Clinical Immunology, Chian Mai
                 University, Chiang Mai, Thailand.; Health Sciences School,
                 Universidad Peruana de Ciencias Aplicadas, Lima, Peru.; Head
                 Pediatric Respiratory Medicine Department, Clinica Regional del
                 Este, San Francisco, Argentina.; Paediatrics and Child Health,
                 University of Lusaka, Lusaka, Zambia.; Department of
                 Respiratory Medicine, JSS Medical College, Mysore, India.;
                 Department of Pediatrics, Universidad Industrial de Santander,
                 Santander, Colombia.; College of Health Sciences, Addis Ababa
                 University, Addis Ababa, Ethiopia.; Department of Pediatrics,
                 Universidad de Costa Rica, San Jose, Costa Rica.; Douala
                 General Hospital, University of Douala, Douala, Cameroon.;
                 Institute of Pneumology M. Nasta, Bucharest, Romania.; School
                 of Health Systems and Public Health, University of Pretoria,
                 Pretoria, South Africa.; College of Medicine, Ajman University,
                 Ajman, United Arab Emirates.; University of Maiduguri Teaching
                 Hospital, Maiduguri.; Deparment of Medicine, University of
                 Abuja, Abuja.; Department of Paediatrics, Usmanu Danfodiyo,
                 University Teaching Hospital, Sokoto, Nigeria.; Deparment of
                 Biological Sciences, Eduardo Mondlane University, Maputo,
                 Mozambique.; University of Medical Sciences, Porto Alegre, RS,
                 Brazil.; Department of Paediatrics, University of Ibadan,
                 Ibadan, Nigeria.; Dragi\v{s}a Mi\v{s}ovic, Childrens Hsopital
                 for Lung Disease and TB, Belgrade, Serbia.; Health Sciences,
                 Academic Division, Juarez Autononous, University of Tabasco,
                 Villahermosa, Mexico.; Department of Medicine, Obafemi Awolowo
                 University Teaching Hospital Complex, Ile-Ife, Nigeria.;
                 Department of Paediatrics \& Child Health \& SA MRC Unit on
                 Children \& Adolescent Health, Red Cross Childrens Hospital,
                 University of Cape Town, Cape Town, South Africa.; Department
                 of Pulmonary Diseases, Istanbul University, Cerrahpasa,
                 Turkey.; State University of Feira de Santana, Feira de
                 Santana, BA, Brazil.; UBT Higher Education Institution,
                 Prishtina, Kosovo.; Al-Quds University, Jerusalem, Palestine.;
                 MJ Rajasthan Hospital, Jaipur, India.; Paediatrics Unit,
                 Teaching Hospital Peradeniya, Kandy.; Faculty of Medicine,
                 University of Peradeniya, Kandy, Sri Lanka.; Shahid Beheshti
                 University of Medical Sciences, Tehran, Iran.; Medical School,
                 Santander Industrial, Bucaramanga, Colombia.; Department of
                 Community Medicine, Kasturba Medical College, Mangalore.;
                 Universudad Esp\'{\i}ritu Santo, Samborond\'{o}n, Ecuador.;
                 Asociaci\'{o}n Latinoamericana de T\'{o}rax, Montevideo,
                 Uruguay, Francisco Morrogu\'{\i}n University, Guatemala City,
                 Guatemala.; Faculty of Health Sciences, Catholic University of
                 Salta, Salta, Argentina.; Department of Allergy and Clinical
                 Immunology, University Hospital Centre ``Mother Teresa'',
                 Tirana, Albania.; Hospital San Angel Inn, Mexico DF, Mexico.;
                 The University of Yaounde 1, Yaounde, Cameroon.; Health Concern
                 Initiative, Wakiso, Uganda.; Shishuka Children's Speciality
                 Hospital, Bangalore, India.; The Allergy and Asthma Institute,
                 Islamabad, Pakistan.; Medecin Faculty, Mustapha Universitary
                 Hospital Algiers, Algeria.; Centrode Investigaci\'{o}n de
                 Enfermedades Al\'{e}rgicas y Respiratorias SC, Mexico DF,
                 Mexico.; Pediatrics, All India Institute of Medical Sciences,
                 New Delhi, India.; Levy Mwanawasa Medical University, School of
                 Public Health and Environmental Sciences, Lusaka, Zambia.;
                 Federal University of Parana, Curitiba, PA, Brazil.; Social
                 Medicine, Medical Faculty, University of Prishtina, Prishtina,
                 Kosovo.; University of Cambridge, Cambridge, Imperial College,
                 London, Liverpool University Hospitals NHS Foundation Trust,
                 Liverpool, UK, Department of Paediatrics and Child Health,
                 School of Clinical Medicine, University of KwaZulu Natal,
                 Durban, South Africa.; Department of Non-communicable Diseases,
                 World Health Organization, Geneva, Switzerland.; Department of
                 Paediatrics and Child Health, School of Clinical Medicine,
                 University of KwaZulu Natal, Durban, South Africa.",
  journal     = "The international journal of tuberculosis and lung disease: the
                 official journal of the International Union against
                 Tuberculosis and Lung Disease",
  volume      =  27,
  number      =  9,
  pages       = "658--667",
  month       =  "1~" # sep,
  year        =  2023,
  url         = "http://dx.doi.org/10.5588/ijtld.23.0203",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.5588/ijtld.23.0203",
  pmc         = "PMC10443788",
  pmid        =  37608484,
  issn        = "1027-3719,1815-7920",
  language    = "en"
}

@INPROCEEDINGS{Kingma2014-fw,
  title     = "Auto-Encoding Variational Bayes",
  author    = "Kingma, Diederik P and Welling, Max",
  editor    = "Bengio, Yoshua and LeCun, Yann",
  booktitle = "2nd International Conference on Learning Representations, ICLR
               2014, Banff, AB, Canada, April 14-16, 2014, Conference Track
               Proceedings",
  year      =  2014,
  url       = "http://arxiv.org/abs/1312.6114",
  keywords  = "GEMCONT MICCAI 2025"
}

@ARTICLE{Hill2005-iq,
  title     = "Data and theory point to mainly additive genetic variance for
               complex traits",
  author    = "Hill, William (bill) W G and Goddard, Michael E and Visscher,
               Peter M",
  journal   = "PLoS genetics",
  publisher = "Public Library of Science (PLoS)",
  volume    = "preprint",
  number    =  2008,
  pages     = "e8",
  year      =  2005,
  url       = "http://dx.doi.org/10.1371/journal.pgen.1000008.eor",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1371/journal.pgen.1000008.eor",
  issn      = "1553-7390,1553-7404",
  language  = "en"
}

@ARTICLE{Lambert2015-nd,
  title       = "Diagnostic accuracy of {FEV1}/forced vital capacity ratio z
                 scores in asthmatic patients",
  author      = "Lambert, Allison and Drummond, M Bradley and Wei, Christine and
                 Irvin, Charles and Kaminsky, David and McCormack, Meredith and
                 Wise, Robert",
  affiliation = "Department of Medicine, Division of Pulmonary and Critical
                 Care, Johns Hopkins University, Baltimore, Md. Electronic
                 address: alamber5@jhmi.edu.; Department of Medicine, Division
                 of Pulmonary and Critical Care, Johns Hopkins University,
                 Baltimore, Md.; Department of Medicine, Division of Pulmonary
                 and Critical Care, University of Vermont, Burlington, Vt.",
  journal     = "The journal of allergy and clinical immunology",
  publisher   = "Elsevier BV",
  volume      =  136,
  number      =  3,
  pages       = "649--653.e4",
  month       =  sep,
  year        =  2015,
  url         = "http://dx.doi.org/10.1016/j.jaci.2015.02.027",
  doi         = "10.1016/j.jaci.2015.02.027",
  pmc         = "PMC4562860",
  pmid        =  25863976,
  issn        = "0091-6749,1097-6825",
  language    = "en"
}

@ARTICLE{Koch2015-fd,
  title    = "Siamese neural networks for one-shot image recognition",
  author   = "Koch, Gregory R",
  journal  = "cs.utoronto.ca",
  year     =  2015,
  url      = "https://www.cs.utoronto.ca/~rsalakhu/papers/oneshot1.pdf",
}


@ARTICLE{Rakowski2024-yf,
  title       = "{TransferGWAS} of {T1}-weighted brain {MRI} data from {UK}
                 Biobank",
  author      = "Rakowski, Alexander and Monti, Remo and Lippert, Christoph",
  affiliation = "Digital Health Machine Learning, Hasso Plattner Institute for
                 Digital Engineering, University of Potsdam, Germany.; Digital
                 Health Machine Learning, Hasso Plattner Institute for Digital
                 Engineering, University of Potsdam, Germany.;
                 Max-Delbr{\"{u}}ck-Center for Molecular Medicine in the
                 Helmholtz Association, Berlin Institute for Medical Systems
                 Biology, Berlin, Germany.; Digital Health Machine Learning,
                 Hasso Plattner Institute for Digital Engineering, University of
                 Potsdam, Germany.; Hasso Plattner Institute for Digital Health
                 at Mount Sinai, New York, New York, United States of America.",
  journal     = "PLoS genetics",
  volume      =  20,
  number      =  12,
  pages       = "e1011332",
  month       =  dec,
  year        =  2024,
  url         = "http://dx.doi.org/10.1371/journal.pgen.1011332",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1371/journal.pgen.1011332",
  pmc         = "PMC11687923",
  pmid        =  39671448,
  issn        = "1553-7390,1553-7404",
  language    = "en"
}

@ARTICLE{Kirchler2022-ud,
  title       = "{transferGWAS}: {GWAS} of images using deep transfer learning",
  author      = "Kirchler, Matthias and Konigorski, Stefan and Norden, Matthias
                 and Meltendorf, Christian and Kloft, Marius and Schurmann,
                 Claudia and Lippert, Christoph",
  affiliation = "Digital Health-Machine Learning Research Group, Digital Health
                 Center, Hasso Plattner Institute, University of Potsdam, 14482
                 Potsdam, Germany.; Department of Computer Science, TU
                 Kaiserslautern, 67663 Kaiserslautern, Germany.; Digital
                 Health-Machine Learning Research Group, Digital Health Center,
                 Hasso Plattner Institute, University of Potsdam, 14482 Potsdam,
                 Germany.; Hasso Plattner Institute for Digital Health at Mount
                 Sinai, Icahn School of Medicine at Mount Sinai, New York, NY
                 10029, USA.; Digital Health \& Personalized Medicine Research
                 Group, Digital Health Center, Hasso Plattner Institute,
                 University of Potsdam, 14482 Potsdam, Germany.; Department of
                 Anesthesiology and Intensive Care Medicine,
                 Charit\'{e}-Universit{\"{a}}tsmedizin Berlin, 10117 Berlin,
                 Germany.; Department of Electrical Engineering - Mechatronics -
                 Optometry, Beuth University of Applied Sciences Berlin, 13353
                 Berlin, Germany.; Department of Computer Science, TU
                 Kaiserslautern, 67663 Kaiserslautern, Germany.; Hasso Plattner
                 Institute for Digital Health at Mount Sinai, Icahn School of
                 Medicine at Mount Sinai, New York, NY 10029, USA.; Digital
                 Health \& Personalized Medicine Research Group, Digital Health
                 Center, Hasso Plattner Institute, University of Potsdam, 14482
                 Potsdam, Germany.",
  journal     = "Bioinformatics (Oxford, England)",
  publisher   = "Oxford University Press (OUP)",
  volume      =  38,
  number      =  14,
  pages       = "3621--3628",
  month       =  "11~" # jul,
  year        =  2022,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btac369",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1093/bioinformatics/btac369",
  pmid        =  35640976,
  issn        = "1367-4803,1367-4811",
  language    = "en"
}

@ARTICLE{Zech2018-yj,
  title         = "Confounding variables can degrade generalization performance
                   of radiological deep learning models",
  author        = "Zech, John R and Badgeley, Marcus A and Liu, Manway and
                   Costa, Anthony B and Titano, Joseph J and Oermann, Eric K",
  journal       = "arXiv [cs.CV]",
  month         =  "1~" # jul,
  year          =  2018,
  url           = "http://arxiv.org/abs/1807.00431",
  archivePrefix = "arXiv",
  primaryClass  = "cs.CV",
  eprint        = "1807.00431",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{Xie2024-pf,
  title       = "{iGWAS}: Image-based genome-wide association of self-supervised
                 deep phenotyping of retina fundus images",
  author      = "Xie, Ziqian and Zhang, Tao and Kim, Sangbae and Lu, Jiaxiong
                 and Zhang, Wanheng and Lin, Cheng-Hui and Wu, Man-Ru and Davis,
                 Alexander and Channa, Roomasa and Giancardo, Luca and Chen, Han
                 and Wang, Sui and Chen, Rui and Zhi, Degui",
  affiliation = "Department of Molecular and Human Genetics, Baylor College of
                 Medicine, Houston, Texas, United States of America.; School of
                 Biomedical Informatics, The University of Texas Health Science
                 Center at Houston, Houston, Texas, United States of America.;
                 Department of Molecular and Human Genetics, Baylor College of
                 Medicine, Houston, Texas, United States of America.; School of
                 Public Health, The University of Texas Health Science Center at
                 Houston, Houston, Texas, United States of America.; Department
                 of Ophthalmology, Stanford University School of Medicine,
                 Stanford, California, United States of America.; Department of
                 Ophthalmology and Visual Sciences, University of Wisconsin,
                 Madison, Wisconsin, United States of America.; School of
                 Biomedical Informatics, The University of Texas Health Science
                 Center at Houston, Houston, Texas, United States of America.;
                 School of Biomedical Informatics, The University of Texas
                 Health Science Center at Houston, Houston, Texas, United States
                 of America.; School of Public Health, The University of Texas
                 Health Science Center at Houston, Houston, Texas, United States
                 of America.; Human Genetics Center, Department of Epidemiology,
                 Human Genetics and Environmental Sciences, School of Public
                 Health, The University of Texas Health Science Center at
                 Houston, Houston, Texas, United States of America.",
  journal     = "PLoS genetics",
  publisher   = "Public Library of Science (PLoS)",
  volume      =  20,
  number      =  5,
  pages       = "e1011273",
  month       =  may,
  year        =  2024,
  url         = "http://dx.doi.org/10.1371/journal.pgen.1011273",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1371/journal.pgen.1011273",
  pmc         = "PMC11111076",
  pmid        =  38728357,
  issn        = "1553-7390,1553-7404",
  language    = "en"
}

@ARTICLE{UKBB_dataset,
  title       = "{UK} biobank: an open access resource for identifying the
                 causes of a wide range of complex diseases of middle and old
                 age",
  author      = "Sudlow, Cathie and Gallacher, John and Allen, Naomi and Beral,
                 Valerie and Burton, Paul and Danesh, John and Downey, Paul and
                 Elliott, Paul and Green, Jane and Landray, Martin and Liu,
                 Bette and Matthews, Paul and Ong, Giok and Pell, Jill and
                 Silman, Alan and Young, Alan and Sprosen, Tim and Peakman, Tim
                 and Collins, Rory",
  affiliation = "University of Edinburgh, Edinburgh, United Kingdom; UK Biobank,
                 Stockport, United Kingdom. University of Cardiff, Cardiff,
                 United Kingdom. UK Biobank, Stockport, United Kingdom;
                 University of Oxford, Oxford, United Kingdom. University of
                 Oxford, Oxford, United Kingdom. University of Bristol, Bristol,
                 United Kingdom. University of Cambridge, Cambridge, United
                 Kingdom. Imperial College, London, United Kingdom. University
                 of New South Wales, Sydney, Australia. University of Warwick,
                 Warwick, United Kingdom. University of Glasgow, Glasgow, United
                 Kingdom. University of Manchester, Manchester, United Kingdom.
                 UK Biobank, Stockport, United Kingdom.",
  journal     = "PLoS medicine",
  volume      =  12,
  number      =  3,
  pages       = "e1001779",
  month       =  mar,
  year        =  2015,
  url         = "http://dx.doi.org/10.1371/journal.pmed.1001779",
  keywords    = "DMR-GenRes;GEMCONT MICCAI 2025",
  doi         = "10.1371/journal.pmed.1001779",
  pmc         = "PMC4380465",
  pmid        =  25826379,
  issn        = "1549-1277,1549-1676",
  language    = "en"
}

@ARTICLE{Manolio2009-pi,
  title       = "Finding the missing heritability of complex diseases",
  author      = "Manolio, Teri A and Collins, Francis S and Cox, Nancy J and
                 Goldstein, David B and Hindorff, Lucia A and Hunter, David J
                 and McCarthy, Mark I and Ramos, Erin M and Cardon, Lon R and
                 Chakravarti, Aravinda and Cho, Judy H and Guttmacher, Alan E
                 and Kong, Augustine and Kruglyak, Leonid and Mardis, Elaine and
                 Rotimi, Charles N and Slatkin, Montgomery and Valle, David and
                 Whittemore, Alice S and Boehnke, Michael and Clark, Andrew G
                 and Eichler, Evan E and Gibson, Greg and Haines, Jonathan L and
                 Mackay, Trudy F C and McCarroll, Steven A and Visscher, Peter M",
  affiliation = "National Human Genome Research Institute, Building 31, Room
                 4B09, 31 Center Drive, MSC 2152, Bethesda, Maryland 20892-2152,
                 USA. manoliot@mail.nih.gov",
  journal     = "Nature",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  461,
  number      =  7265,
  pages       = "747--753",
  month       =  "8~" # oct,
  year        =  2009,
  url         = "http://dx.doi.org/10.1038/nature08494",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/nature08494",
  pmc         = "PMC2831613",
  pmid        =  19812666,
  issn        = "0028-0836,1476-4687",
  language    = "en"
}

@ARTICLE{Visscher2017-fx,
  title     = "10 years of {GWAS} discovery: Biology, function, and translation",
  author    = "Visscher, Peter M and Wray, Naomi R and Zhang, Qian and Sklar,
               Pamela and McCarthy, Mark I and Brown, Matthew A and Yang, Jian",
  journal   = "The American Journal of Human Genetics",
  publisher = "Elsevier BV",
  volume    =  101,
  number    =  1,
  pages     = "5--22",
  month     =  jul,
  year      =  2017,
  url       = "http://dx.doi.org/10.1016/j.ajhg.2017.06.005",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1016/j.ajhg.2017.06.005",
  issn      = "0002-9297,1537-6605",
  language  = "en"
}

@ARTICLE{Liu2021-sy,
  title       = "Genetic architecture of 11 organ traits derived from abdominal
                 {MRI} using deep learning",
  author      = "Liu, Yi and Basty, Nicolas and Whitcher, Brandon and Bell,
                 Jimmy D and Sorokin, Elena P and van Bruggen, Nick and Thomas,
                 E Louise and Cule, Madeleine",
  affiliation = "Calico Life Sciences LLC, South San Francisco, United States.;
                 Research Centre for Optimal Health, School of Life Sciences,
                 University of Westminster, London, United Kingdom.",
  journal     = "eLife",
  publisher   = "eLife Sciences Publications, Ltd",
  volume      =  10,
  pages       = "e65554",
  month       =  "15~" # jun,
  year        =  2021,
  url         = "https://elifesciences.org/articles/65554",
  keywords    = "adiposity; genetics; genome-wide association study; genomics;
                 human; magnetic resonance imaging; medicine;GEMCONT MICCAI 2025",
  doi         = "10.7554/eLife.65554",
  pmc         = "PMC8205492",
  pmid        =  34128465,
  issn        = "2050-084X",
  language    = "en"
}

@ARTICLE{Guo2024-fy,
  title       = "Efficient multi-phenotype genome-wide analysis identifies
                 genetic associations for unsupervised deep-learning-derived
                 high-dimensional brain imaging phenotypes",
  author      = "Guo, Bohong and Xie, Ziqian and He, Wei and Islam, Sheikh
                 Muhammad Saiful and Gottlieb, Assaf and Chen, Han and Zhi,
                 Degui",
  affiliation = "Department of Biostatistics \& Data Science, School of Public
                 Health, University of Texas Health Science Center, Houston,
                 Texas 77030, USA.; Department of Bioinformatics and Systems
                 Medicine, McWilliams School of Biomedical Informatics,
                 University of Texas Health Science Center, Houston, Texas
                 77030, USA.; Human Genetics Center, Department of Epidemiology,
                 School of Public Health, The University of Texas Health Science
                 Center at Houston, Houston, Texas 77030, USA.",
  journal     = "medRxiv: the preprint server for health sciences",
  month       =  "8~" # dec,
  year        =  2024,
  url         = "http://dx.doi.org/10.1101/2024.12.06.24318618",
  keywords    = "Endophenotype; GWAS; Image-derived phenotypes; Imaging
                 genetics; Multivariate; Statistical genetics;GEMCONT MICCAI
                 2025",
  doi         = "10.1101/2024.12.06.24318618",
  pmc         = "PMC11643246",
  pmid        =  39677479,
  language    = "en"
}

@ARTICLE{Wright2021-zi,
  title       = "Science for the next century: Deep phenotyping",
  author      = "Wright, J T and Herzberg, M C",
  affiliation = "Adams School of Dentistry, University of North Carolina at
                 Chapel Hill, Chapel Hill, NC, USA.; Department of Diagnostic
                 and Biological Sciences, School of Dentistry, University of
                 Minnesota, Minneapolis, MN, USA.",
  journal     = "Journal of dental research",
  publisher   = "SAGE Publications",
  volume      =  100,
  number      =  8,
  pages       = "785--789",
  month       =  jul,
  year        =  2021,
  url         = "http://dx.doi.org/10.1177/00220345211001850",
  keywords    = "caries; craniofacial; genotype; microbiome; periodontal;
                 phenotype;GEMCONT MICCAI 2025",
  doi         = "10.1177/00220345211001850",
  pmc         = "PMC8258723",
  pmid        =  33749358,
  issn        = "0022-0345,1544-0591",
  language    = "en"
}

@ARTICLE{Tracy2008-zy,
  title       = "'Deep phenotyping': characterizing populations in the era of
                 genomics and systems biology",
  author      = "Tracy, Russell P",
  affiliation = "Pathology and Biochemistry, University of Vermont College of
                 Medicine, Burlington, Vermont 05446, USA. Russell.Tracy@uvm.edu",
  journal     = "Current opinion in lipidology",
  publisher   = "Ovid Technologies (Wolters Kluwer Health)",
  volume      =  19,
  number      =  2,
  pages       = "151--157",
  month       =  apr,
  year        =  2008,
  url         = "https://journals.lww.com/co-lipidology/fulltext/2008/04000/_deep_phenotyping___characterizing_populations_in.9.aspx",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1097/MOL.0b013e3282f73893",
  pmid        =  18388695,
  issn        = "0957-9672,1473-6535",
  language    = "en"
}

@ARTICLE{Robinson2012-ax,
  title       = "Deep phenotyping for precision medicine",
  author      = "Robinson, Peter N",
  affiliation = "Institut f{\"{u}}r Medizinische Genetik und Humangenetik,
                 Charit\'{e}-Universit{\"{a}}tsmedizin Berlin, Berlin, Germany.
                 peter.robinson@charite.de",
  journal     = "Human mutation",
  publisher   = "Hindawi Limited",
  volume      =  33,
  number      =  5,
  pages       = "777--780",
  month       =  may,
  year        =  2012,
  url         = "http://dx.doi.org/10.1002/humu.22080",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1002/humu.22080",
  pmid        =  22504886,
  issn        = "1059-7794,1098-1004",
  language    = "en"
}

@ARTICLE{Delude2015-bb,
  title     = "Deep phenotyping: The details of disease",
  author    = "Delude, Cathryn M",
  journal   = "Nature",
  publisher = "Springer Science and Business Media LLC",
  volume    =  527,
  number    =  7576,
  pages     = "S14--5",
  month     =  "5~" # nov,
  year      =  2015,
  url       = "https://www.nature.com/articles/527S14a",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1038/527S14a",
  pmid      =  26536218,
  issn      = "0028-0836,1476-4687",
  language  = "en"
}

@ARTICLE{Khodaee2025-vw,
  title       = "Multimodal learning for mapping genotype-phenotype dynamics",
  author      = "Khodaee, Farhan and Zandie, Rohola and Edelman, Elazer R",
  affiliation = "Institute for Medical Engineering and Science, Massachusetts
                 Institute of Technology, Cambridge, MA, USA. farhank@mit.edu.;
                 Institute for Medical Engineering and Science, Massachusetts
                 Institute of Technology, Cambridge, MA, USA.; Institute for
                 Medical Engineering and Science, Massachusetts Institute of
                 Technology, Cambridge, MA, USA.; Department of Medicine
                 (Cardiovascular Medicine), Brigham and Women's Hospital,
                 Boston, MA, USA.",
  journal     = "Nature computational science",
  publisher   = "Nature Publishing Group",
  pages       = "1--12",
  month       =  "28~" # jan,
  year        =  2025,
  url         = "https://www.nature.com/articles/s43588-024-00765-7",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s43588-024-00765-7",
  pmid        =  39875699,
  issn        = "2662-8457",
  language    = "en"
}

@ARTICLE{Pytorch_software,
  title         = "{PyTorch}: An imperative style, high-performance deep
                   learning library",
  author        = "Paszke, Adam and Gross, Sam and Massa, Francisco and Lerer,
                   Adam and Bradbury, James and Chanan, Gregory and Killeen,
                   Trevor and Lin, Zeming and Gimelshein, Natalia and Antiga,
                   Luca and Desmaison, Alban and K{\"{o}}pf, Andreas and Yang,
                   Edward and DeVito, Zach and Raison, Martin and Tejani,
                   Alykhan and Chilamkurthy, Sasank and Steiner, Benoit and
                   Fang, Lu and Bai, Junjie and Chintala, Soumith",
  journal       = "Advances in neural information processing systems",
  month         =  "3~" # dec,
  year          =  2019,
  url           = "https://proceedings.neurips.cc/paper_files/paper/2019/hash/bdbca288fee7f92f2bfa9f7012727740-Abstract.html",
  archivePrefix = "arXiv",
  primaryClass  = "cs.LG",
  eprint        = "1912.01703",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{AdamW,
  title         = "Decoupled weight decay regularization",
  author        = "Loshchilov, Ilya and Hutter, Frank",
  journal       = "arXiv [cs.LG]",
  month         =  "14~" # nov,
  year          =  2017,
  url           = "http://arxiv.org/abs/1711.05101",
  archivePrefix = "arXiv",
  primaryClass  = "cs.LG",
  eprint        = "1711.05101",
  keywords      = "GEMCONT MICCAI 2025"
}

@techreport{UKBB_geno,
  title    = "Genotyping and quality control of {UK} Biobank , a large-scale ,
              extensively phenotyped prospective resource",
  year     =  2015,
  url      = "https://biobank.ctsu.ox.ac.uk/crystal/crystal/docs/genotyping_qc.pdf",
  language = "en"
}

@ARTICLE{REGLE,
  title       = "Unsupervised representation learning on high-dimensional
                 clinical data improves genomic discovery and prediction",
  author      = "Yun, Taedong and Cosentino, Justin and Behsaz, Babak and McCaw,
                 Zachary R and Hill, Davin and Luben, Robert and Lai, Dongbing
                 and Bates, John and Yang, Howard and Schwantes-An, Tae-Hwi and
                 Zhou, Yuchen and Khawaja, Anthony P and Carroll, Andrew and
                 Hobbs, Brian D and Cho, Michael H and McLean, Cory Y and
                 Hormozdiari, Farhad",
  affiliation = "Google Research, Cambridge, MA, USA. tedyun@google.com.; Google
                 Research, Mountain View, CA, USA.; Google Research, Cambridge,
                 MA, USA.; Google Research, Mountain View, CA, USA.; Insitro,
                 South San Francisco, CA, USA.; Department of Electrical and
                 Computer Engineering, Northeastern University, Boston, MA,
                 USA.; Channing Division of Network Medicine, Brigham and
                 Women's Hospital, Boston, MA, USA.; NIHR Biomedical Research
                 Centre at Moorfields Eye Hospital and University College London
                 (UCL) Institute of Ophthalmology, London, UK.; MRC Epidemiology
                 Unit, University of Cambridge, Cambridge, UK.; Department of
                 Medical and Molecular Genetics, Indiana University School of
                 Medicine, Indianapolis, IN, USA.; Verily Life Sciences, South
                 San Francisco, CA, USA.; Department of Medical and Molecular
                 Genetics, Indiana University School of Medicine, Indianapolis,
                 IN, USA.; Division of Cardiology, Department of Medicine,
                 Indiana University School of Medicine, Indianapolis, IN, USA.;
                 Channing Division of Network Medicine, Brigham and Women's
                 Hospital, Boston, MA, USA.; Division of Pulmonary and Critical
                 Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.;
                 Harvard Medical School, Boston, MA, USA.; Google Research,
                 Cambridge, MA, USA. cym@google.com.; Google Research,
                 Cambridge, MA, USA. fhormoz@google.com.",
  journal     = "Nature genetics",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  56,
  number      =  8,
  pages       = "1604--1613",
  month       =  "8~" # aug,
  year        =  2024,
  url         = "https://www.nature.com/articles/s41588-024-01831-6",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/s41588-024-01831-6",
  pmc         = "PMC11319202",
  pmid        =  38977853,
  issn        = "1061-4036,1546-1718",
  language    = "en"
}


@ARTICLE{MTGWAS3,
  title       = "A mixed-model approach for genome-wide association studies of
                 correlated traits in structured populations",
  author      = "Korte, Arthur and Vilhj\'{a}lmsson, Bjarni J and Segura,
                 Vincent and Platt, Alexander and Long, Quan and Nordborg,
                 Magnus",
  affiliation = "Gregor Mendel Institute, Austrian Academy of Sciences, Vienna,
                 Austria.",
  journal     = "Nature genetics",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  44,
  number      =  9,
  pages       = "1066--1071",
  month       =  sep,
  year        =  2012,
  url         = "http://dx.doi.org/10.1038/ng.2376",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/ng.2376",
  pmc         = "PMC3432668",
  pmid        =  22902788,
  issn        = "1061-4036,1546-1718",
  language    = "en"
}

@ARTICLE{MTGWAS2,
  title       = "Efficient set tests for the genetic analysis of correlated
                 traits",
  author      = "Casale, Francesco Paolo and Rakitsch, Barbara and Lippert,
                 Christoph and Stegle, Oliver",
  affiliation = "European Molecular Biology Laboratory, European Bioinformatics
                 Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
                 UK.; 1] Microsoft Research, Los Angeles, California, USA. [2]
                 Human Longevity, Inc., Mountain View, California, USA.",
  journal     = "Nature methods",
  publisher   = "Springer Science and Business Media LLC",
  volume      =  12,
  number      =  8,
  pages       = "755--758",
  month       =  aug,
  year        =  2015,
  url         = "http://dx.doi.org/10.1038/nmeth.3439",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1038/nmeth.3439",
  pmid        =  26076425,
  issn        = "1548-7091,1548-7105",
  language    = "en"
}

@ARTICLE{MTGWAS1,
  title       = "{LIMIX}: genetic analysis of multiple traits",
  author      = "Lippert, Christoph and Casale, Franceso Paolo and Rakitsch,
                 Barbara and Stegle, Oliver",
  journal     = "bioRxiv",
  institution = "bioRxiv",
  month       =  "21~" # may,
  year        =  2014,
  url         = "http://dx.doi.org/10.1101/003905",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1101/003905"
}  title       = "{LIMIX}: genetic analysis of multiple traits",
  author      = "Lippert, Christoph and Casale, Franceso Paolo and Rakitsch,
                 Barbara and Stegle, Oliver",
  journal     = "bioRxiv",
  institution = "bioRxiv",
  month       =  "21~" # may,
  year        =  2014,
  url         = "http://dx.doi.org/10.1101/003905",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1101/003905"
}

@ARTICLE{CLIP,
  title         = "Learning transferable visual models from natural language
                   supervision",
  author        = "Radford, Alec and Kim, Jong Wook and Hallacy, Chris and
                   Ramesh, Aditya and Goh, Gabriel and Agarwal, Sandhini and
                   Sastry, Girish and Askell, Amanda and Mishkin, Pamela and
                   Clark, Jack and Krueger, Gretchen and Sutskever, Ilya",
  journal       = "arXiv [cs.CV]",
  month         =  "26~" # feb,
  year          =  2021,
  url           = "https://proceedings.mlr.press/v139/radford21a/radford21a.pdf",
  archivePrefix = "arXiv",
  primaryClass  = "cs.CV",
  eprint        = "2103.00020",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{SimCLR,
  title         = "A simple framework for contrastive learning of visual
                   representations",
  author        = "Chen, Ting and Kornblith, Simon and Norouzi, Mohammad and
                   Hinton, Geoffrey",
  journal       = "arXiv [cs.LG]",
  month         =  "13~" # feb,
  year          =  2020,
  url           = "http://proceedings.mlr.press/v119/chen20j/chen20j.pdf",
  archivePrefix = "arXiv",
  primaryClass  = "cs.LG",
  eprint        = "2002.05709",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{EMNIST,
  title         = "{EMNIST}: an extension of {MNIST} to handwritten letters",
  author        = "Cohen, Gregory and Afshar, Saeed and Tapson, Jonathan and van
                   Schaik, Andr\'{e}",
  journal       = "arXiv [cs.CV]",
  month         =  "17~" # feb,
  year          =  2017,
  url           = "http://arxiv.org/abs/1702.05373",
  archivePrefix = "arXiv",
  primaryClass  = "cs.CV",
  eprint        = "1702.05373",
  keywords      = "GEMCONT MICCAI 2025"
}

@ARTICLE{PLINK_software,
  title       = "{PLINK}: a tool set for whole-genome association and
                 population-based linkage analyses",
  author      = "Purcell, Shaun and Neale, Benjamin and Todd-Brown, Kathe and
                 Thomas, Lori and Ferreira, Manuel A R and Bender, David and
                 Maller, Julian and Sklar, Pamela and de Bakker, Paul I W and
                 Daly, Mark J and Sham, Pak C",
  affiliation = "Center for Human Genetic Research, Massachusetts General
                 Hospital, Boston, MA 02114, USA. shaun@pngu.mgh.harvard.edu",
  journal     = "American journal of human genetics",
  volume      =  81,
  number      =  3,
  pages       = "559--575",
  month       =  sep,
  year        =  2007,
  url         = "http://dx.doi.org/10.1086/519795",
  keywords    = "GEMCONT MICCAI 2025",
  doi         = "10.1086/519795",
  pmc         = "PMC1950838",
  pmid        =  17701901,
  issn        = "0002-9297",
  language    = "en"
}

@ARTICLE{primer,
  title     = "Genetics-driven risk predictions leveraging the Mendelian
               randomization framework",
  author    = "Sens, Daniel and Shilova, Liubov and Gr{\"{a}}f, Ludwig and
               Grebenshchikova, Maria and Eskofier, Bjoern M and Casale,
               Francesco Paolo",
  journal   = "Genome Research",
  publisher = "Cold Spring Harbor Laboratory",
  volume    =  34,
  number    =  9,
  pages     = "1276--1285",
  month     =  "11~" # oct,
  year      =  2024,
  url       = "http://dx.doi.org/10.1101/gr.279252.124",
  keywords  = "GEMCONT MICCAI 2025",
  doi       = "10.1101/gr.279252.124",
  pmc       = "PMC11529896",
  pmid      =  39332904,
  issn      = "1088-9051,1549-5469",
  language  = "en"
}
