Benchmarking the AI-based diagnostic potential of plasma proteomics for neurodegenerative disease in 17,170 people

Co-pathology is a common feature of neurodegenerative diseases that complicates diagnosis, treatment and clinical management. However, sensitive, specific and scalable biomarkers for in vivo pathological diagnosis are not available for most neurodegenerative neuropathologies. Here, we present ProtAIDe-Dx, a deep joint-learning model trained on 17,170 patients and controls that uses plasma proteomics to provide simultaneous probabilistic diagnosis across six conditions associated with dementia in aging. ProtAIDe-Dx achieves cross-validated balanced classification accuracy of 69%-96% and AUCs > 79% across all conditions. The model’s diagnostic probabilities highlighted subgroups of patients with co-pathologies, and were associated with pathology-specific biomarkers in an external sample, even among cognitively unimpaired people. Model interpretation revealed a suite of protein networks marking shared and specific biological processes across diseases, and identified novel and previously described proteins discriminating each diagnosis. ProtAIDe-Dx significantly improved biomarker-based differential diagnosis in a memory clinic sample, pinpointing proteins leading to diagnostic decisions at an individual level. Together, this work highlights the promise of plasma proteomics to improve patient-level diagnostic work-up with a single blood draw.