[Submitted on 7 Oct 2026 (v1), last revised 14 Oct 2026 (this version, v2)]
Authors:Jiheng Li, Michael E. Kim, Trent M. Schwartz, Yuhan Cui, Gaurav Rudravaram, Derek B. Archer, Timothy J. Hohman, Lori L. Beason-Held, Victoria L. Morgan, Dario J. Englot, Angela L. Jefferson, for the Alzheimer’s Disease Neuroimaging Initiative, for the BIOCARD Study team, for the Health, Aging Brain Study: Health Disparities (HABS-HD)Study Team, Lianrui Zuo, Guray Erus, Christos Davatzikos, Bennett A. Landman
Abstract:National-scale magnetic resonance imaging (MRI) repositories increasingly integrate data from different studies and institutions. However, subject identifiers assigned to study participants are typically specific to individual datasets, so the same person may appear under different identifiers when these datasets are aggregated, a problem we define as identity duplication. Such duplication can create leakage between training and test data and inflate apparent performance in downstream biomedical studies. Existing methods do not provide an end-to-end, image-based workflow to address this problem. In this work, we present HAPPEN, a human-in-the-loop pipeline for auditing identity duplication in T1-weighted brain MRI repositories. It combines SHA-256 fingerprinting for exact-duplicate detection with embeddings learned through supervised contrastive learning to retrieve near-duplicate candidates: pairs of non-identical scans that may originate from the same person. Retrieved pairs are reviewed as candidates in a locally hosted interface rather than automatically classified as duplicates. We deployed the workflow in a national-scale aggregated repository containing 95,129 scans and assessed end-to-end recovery of 54 pairs of subject records identified as duplicates using genome-wide genotype data. Transferability was assessed by locally deploying the same workflow on 22,386 scans at an independent institution without model retraining or image transfer. Deployment in the study repository identified 1,316 exact-duplicate scan groups and 1,275 near-duplicate groups of subject records supported by human review. Of these groups, 56% and 82%, respectively, crossed dataset boundaries. All 54 genetic-reference pairs were recovered. The external team independently completed the full workflow using a locally selected operating threshold and review standard.
Submission history
From: Jiheng Li [view email]
[v1] Wed, 7 Oct 2026 07:57:11 UTC (1,148 KB)
[v2] Wed, 14 Oct 2026 00:15:22 UTC (3,182 KB)
