Siamese network‐based vector embeddings of MRI scans for twin identification

Abstract

Monozygotic twins are identical twins that develop from a single fertilised egg that spontaneously splits, resulting in two individuals sharing 100% genetic material. Identifying monozygotic twins from brain MRI scans represents a frontier challenge in computational medical imaging with significant implications for understanding genetic influences on neuroanatomical structure through direct pattern recognition. While classical twin studies using ACE models decompose statistical variance to establish independent regional heritability estimates (60‐80%), this study introduces a fundamentally different computational framework that learns directly from MRI data to rank neuroanatomical regions by their collective discriminative capacity for genetic similarity detection, complementing traditional statistical approaches through data‐driven analysis. Adeep learning methodology employing Siamese networks with 3D CNN backbones is developed for automated twin identification using 138 genetically verified monozygotic twin pairs (276 subjects) from the Human Connectome Project S1200 dataset. Modified U‐Net, ResNet, and DenseNet architectures generate 128‐dimensional embeddings optimised via triplet loss with hard negative mining, forcing models to learn subtle genetic signatures by focusing on challenging discriminative examples that distinguish twins from their most similar morphological matches. U‐Net achieved superior computational performance with 92.0% F1‐score (σ = 2.5%), 95.2% AUC‐ROC, and 91.4% accuracy, while ResNet demonstrated competitive results (89.6% F1‐score) and DenseNet showed greater variability (88.5% F1‐score). Embedding analysis reveals clear bimodal separation between genetically related and unrelated individuals through learned morphological patterns. Layer‐Wise Relevance Propagation analysis provides the first data‐driven ranking of neuroanatomical regions by discriminative importance for genetic relatedness detection. Statistical analysis reveals pronounced subcortical dominance with large effect size (Cohen’s d = 2.80, p = 3.89e‐6), with six subcortical structures occupying top positions, including the thalamus (0.955), brainstem (0.875), and hypothalamus (0.707). This computational hierarchy contrasts with traditional ACE studies reporting highest heritability in cortical areas (frontal 78‐95%, temporal 77‐89%), demonstrating that direct pattern recognition from MRI data identifies different neuroanatomical signatures than statistical variance decomposition. Notably, models utilise practically all brain regions (most importance scores > 0.2), indicating distributed multivariate processing rather than selective regional dependence. Ablation studies confirm data augmentation’s critical role, with substantial i performance improvements across CNN architectures. Clinical integration through standard neuroimaging formats in Connectome Workbench demonstrates immediate practical utility, positioning this computational approach for adoption in research and clinical environments requiring direct analysis of genetic influences in brain structure. The framework advances precision neuroimaging by providing automated, quantitative genetic similarity detection through direct pattern recognition, revealing spatial insights that complement traditional heritability studies while offering methodological advances applicable to diverse medical imaging classification tasks requiring regional discriminative analysis