Abstract: Methods, devices, and systems for detecting inflammatory bowel disease are described herein. The method includes obtaining a biological sample of a subject, determining sequencing data from the biological sample, and preprocessing the sequencing data. The preprocessing includes filtering the sequencing data to remove rare features, normalizing the filtered sequencing data to remove sequencing coverage variability, and batch effect reducing the filtered and normalized sequencing data. The method further includes calculating a likelihood of inflammatory bowel disease with a machine learning model using the preprocessed data as inputs.