
{"id":1828,"date":"2026-09-15T09:24:58","date_gmt":"2026-09-15T09:24:58","guid":{"rendered":"https:\/\/prg.inf.unibe.ch\/?page_id=1828"},"modified":"2026-09-15T09:24:58","modified_gmt":"2026-09-15T09:24:58","slug":"thesis-fusing-icu-time-series-with-tabpfn-based-clinical-context","status":"publish","type":"page","link":"https:\/\/prg.inf.unibe.ch\/index.php\/education\/thesis-fusing-icu-time-series-with-tabpfn-based-clinical-context\/","title":{"rendered":"thesis-Fusing ICU Time Series with TabPFN-Based Clinical Context"},"content":{"rendered":"\n<div style=\"height:150px\" aria-hidden=\"true\" class=\"wp-block-spacer\"><\/div>\n\n\n\n<section class=\"wp-block-uagb-columns uagb-columns__wrap uagb-columns__background-none uagb-columns__stack-mobile uagb-columns__valign- uagb-columns__gap-10 align uagb-block-b3397370 uagb-columns__columns-1 uagb-columns__max_width-theme\"><div class=\"uagb-columns__overlay\"><\/div><div class=\"uagb-columns__inner-wrap uagb-columns__columns-1\">\n<div class=\"wp-block-uagb-column uagb-column__wrap uagb-column__background-undefined uagb-block-3e0cbd99\"><div class=\"uagb-column__overlay\"><\/div>\n<h1 class=\"wp-block-heading\">Fusing ICU Time Series with TabPFN-Based Clinical Context<\/h1>\n\n\n\n<p><strong>Co-Supervised by:<\/strong> Nico Bigler<\/p>\n\n\n\n<p>If you are interested in this topic or have further questions, do not hesitate to contact <a href=\"mailto:daniel.bigler@students.unibe.ch\"><u>daniel.bigler@students.unibe.ch<\/u><\/a>.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Background \/ Context<\/h3>\n\n\n\n<p>ICU risk prediction can combine evolving physiology with tabular clinical context. This project investigates whether a TabPFN-derived representation adds predictive value beyond a conventional context branch. HiRID contains more than 33,000 ICU admissions and longitudinal physiological, laboratory and treatment data. Its static context is limited: age and sex can be supplemented with explicitly defined early measurements, but a comprehensive comorbidity profile should not be assumed. The project builds on the HiRID-ICU-Benchmark and requires credentialed PhysioNet access.<\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Research Question(s) \/ Goals<\/h3>\n\n\n\n<p>The research aims to evaluate the incremental value of TabPFN-based context by:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Comparing temporal-only, tabular-only and combined prediction models<\/li>\n\n\n\n<li>Testing whether TabPFN improves fusion relative to an MLP context branch<\/li>\n\n\n\n<li>Examining the value of temporal history while keeping the prediction landmark fixed<\/li>\n\n\n\n<li>Evaluating discrimination, calibration and computational feasibility<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Approach \/ Methods<\/h3>\n\n\n\n<p>The student will:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Use HiRID v1.1.1 and a pinned benchmark pipeline; audit eligible admissions, events, missingness and compute requirements before modelling<\/li>\n\n\n\n<li>Initially predict circulatory failure in the next 12 hours at a 6-hour ICU landmark, excluding current failure and applying explicit rules for incomplete outcome observation<\/li>\n\n\n\n<li>Combine age, sex and selected first-2-hour laboratory\/treatment summaries with an LSTM physiological branch; exclude APACHE group unless its timely availability is established<\/li>\n\n\n\n<li>Compare logistic regression, LightGBM and TabPFN baselines with LSTM-only, LSTM + MLP and LSTM + TabPFN; include LightGBM on temporal summaries<\/li>\n\n\n\n<li>Generate local TabPFN training embeddings out of fold and restrict context to training data; keep all observations from each admission together and prevent future-information leakage<\/li>\n\n\n\n<li>Evaluate AUPRC, AUROC, Brier score and calibration with admission-level uncertainty estimates; document that repeated stays of one person cannot be linked in HiRID<\/li>\n\n\n\n<li>Use out-of-fold probability fusion as a stated alternative if embedding extraction exceeds the available compute budget<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Expected Contributions \/ Outcomes<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A reproducible comparison of tabular foundation-model representations and conventional clinical-context branches<\/li>\n\n\n\n<li>Evidence on whether fusion adds useful information, including a valid negative result<\/li>\n\n\n\n<li>A documented cohort, leakage controls and an analysis of performance versus computational cost<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Required Skills \/ Prerequisites<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Python and machine learning; PyTorch and basic sequence modelling for the full Master project<\/li>\n\n\n\n<li>Interest in clinical time series and careful evaluation; clinical supervision for label review<\/li>\n\n\n\n<li>For a Bachelor thesis, a prepared authorized landmark dataset and a reduced comparison of tabular models; neural fusion is outside the core scope<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Possible Extensions<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>A Transformer temporal encoder or an additional prediction landmark<\/li>\n\n\n\n<li>Respiratory-failure prediction after completing the circulatory task<\/li>\n\n\n\n<li>External validation after confirming compatible variables and outcome definitions<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\">Further Reading \/ Starting Literature<\/h3>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Y\u00e8che, H., et al. (2021). \u201cHiRID-ICU-Benchmark \u2014 A Comprehensive Machine Learning Benchmark on High-resolution ICU Data.\u201d NeurIPS Datasets and Benchmarks. <a href=\"https:\/\/arxiv.org\/abs\/2111.08536\"><u>Link<\/u><\/a><\/li>\n\n\n\n<li>Hollmann, N., et al. (2025). \u201cAccurate predictions on small data with a tabular foundation model.\u201d Nature, 637, 319\u2013326. <a href=\"https:\/\/doi.org\/10.1038\/s41586-024-08328-6\"><u>Link<\/u><\/a><\/li>\n\n\n\n<li>HiRID documentation: data structure and schemas. <a href=\"https:\/\/hirid.intensivecare.ai\/structure-of-the-published-data\"><u>Link<\/u><\/a><\/li>\n\n\n\n<li>Prior Labs. TabPFN embedding documentation: out-of-fold extraction and local execution. <a href=\"https:\/\/docs.priorlabs.ai\/capabilities\/embeddings\"><u>Link<\/u><\/a><\/li>\n<\/ul>\n<\/div>\n<\/div><\/section>\n","protected":false},"excerpt":{"rendered":"<p>Fusing ICU Time Series with TabPFN-Based Clinical Context Co-Supervised by: Nico Bigler If you are interested in this topic or have further questions, do not hesitate to contact daniel.bigler@students.unibe.ch. Background \/ Context ICU risk prediction can combine evolving physiology with tabular clinical context. This project investigates whether a TabPFN-derived representation adds predictive value beyond a [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":731,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"no-sidebar","site-content-layout":"plain-container","ast-site-content-layout":"normal-width-container","site-content-style":"unboxed","site-sidebar-style":"unboxed","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"disabled","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"enabled","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"set","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":""},"class_list":["post-1828","page","type-page","status-publish","hentry"],"uagb_featured_image_src":{"full":false,"thumbnail":false,"medium":false,"medium_large":false,"large":false,"1536x1536":false,"2048x2048":false},"uagb_author_info":{"display_name":"prg-admin","author_link":"https:\/\/prg.inf.unibe.ch\/index.php\/author\/prg-admin\/"},"uagb_comment_info":0,"uagb_excerpt":"Fusing ICU Time Series with TabPFN-Based Clinical Context Co-Supervised by: Nico Bigler If you are interested in this topic or have further questions, do not hesitate to contact daniel.bigler@students.unibe.ch. Background \/ Context ICU risk prediction can combine evolving physiology with tabular clinical context. This project investigates whether a TabPFN-derived representation adds predictive value beyond a&hellip;","_links":{"self":[{"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/pages\/1828","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/comments?post=1828"}],"version-history":[{"count":1,"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/pages\/1828\/revisions"}],"predecessor-version":[{"id":1829,"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/pages\/1828\/revisions\/1829"}],"up":[{"embeddable":true,"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/pages\/731"}],"wp:attachment":[{"href":"https:\/\/prg.inf.unibe.ch\/index.php\/wp-json\/wp\/v2\/media?parent=1828"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}