University Hospitals Birmingham NHS Foundation Trust

Bulk mucosal RNA sequencing in inflammatory bowel disease has been analyzed one cohort at a time, so historical data accumulate without becoming a reusable reference. IBDex trained a tissue-aware conditional variational autoencoder on 3,168 biopsies from 1,680 patients across four cohorts and suppressed cohort identity adversarially, then froze the gene interface, encoder, decoder, pathway basis and phenotype directions. After freezing, dataset identity fell to balanced accuracy 0.307 against chance 0.250 while inflammation stayed recoverable (AUC 0.82); in 93 patients with concordant endoscopic and histological remission, inflammation approached controls (AUC 0.58) but disease state stayed displaced (AUC 0.725).

Bulk mucosal RNA sequencing in inflammatory bowel disease has been analyzed one cohort at a time, so historical data accumulate without becoming a reusable reference. IBDex trained a tissue-aware conditional variational autoencoder on 3,168 biopsies from 1,680 patients across four cohorts and suppressed cohort identity adversarially, then froze the gene interface, encoder, decoder, pathway basis and phenotype directions. After freezing, dataset identity fell to balanced accuracy 0.307 against chance 0.250 while inflammation stayed recoverable (AUC 0.82); in 93 patients with concordant endoscopic and histological remission, inflammation approached controls (AUC 0.58) but disease state stayed displaced (AUC 0.725).