RDFace: A Benchmark Dataset for Rare Disease Facial Image Analysis under Extreme Data Scarcity and Phenotype-Aware Synthetic Generation

Children with rare genetic diseases often exhibit distinctive facial phenotypes, yet developing computer vision systems for early diagnosis remains challenging due to extreme data scarcity, privacy constraints, and limited data sharing in pediatric settings. These challenges not only hinder automated diagnosis but also restrict the availability of visual resources for clinical genetic counseling. While prior work has shown that synthetic data can augment real datasets and preserve phenotype-level semantics, it remains unclear whether synthetic data alone is sufficient for learning in ultra-low-resource pediatric settings. In this work, we study the synthetic-only regime for pediatric rare disease recognition. Under a controlled experimental setup, models are trained exclusively on phenotype-aware synthetic facial images at increasing scales. We find that synthetic-only training achieves performance comparable to real-data-only baselines at sufficient scale across multiple backbones, suggesting that high-fidelity synthetic data can approximate clinically meaningful distributions. These findings together further enable the use of synthetic pediatric facial images as privacy-preserving resources for genetic education and counseling, supporting clinician training and patient communication. Our results highlight the potential of computer vision to improve data efficiency and expand accessible visual tools in children's healthcare.

Many rare genetic diseases are associated with recognizable craniofacial features. However, traditional approaches for describing facial morphology rely largely on qualitative clinical observation and free-text descriptions, which are often subjective, non-standardized, and difficult to reproduce across observers and institutions. Although the Human Phenotype Ontology (HPO) provides controlled terms for describing facial features, these terms are typically categorical rather than quantitative and may vary depending on examiner experience and interpretation. Here, we present FaceKit, a computational framework for quantitative facial phenotyping from frontal facial photographs. FaceKit extracts standardized measurements of facial landmarks and derived 120 morphological features, then reports feature-level z-scores representing deviation from population reference distributions. The reference distributions are built from the FairFace dataset spanning diverse ancestral groups. We evaluated FaceKit on a curated subset of the GestaltMatcher Database covering 50 rare-disease cohorts. In addition to quantitative facial analysis, FaceKit includes synthetic facial image generation to support rare disease model development and data augmentation. We also performed privacy evaluation to assess whether synthetic images reveal identifiable information from real patient photographs and could compromise patient privacy. Across disease case studies, FaceKit-derived quantitative measurements captured known facial features associated with rare genetic disorders and provided objective support for clinical phenotyping. Together, these results establish FaceKit as a useful tool for quantitative phenotyping, and has the potential to improve rare disease diagnosis, support genotype-phenotype studies, and enable more reproducible clinical characterization across diverse patient populations.

Class imbalance is a persistent challenge in visual recognition, particularly in safety-critical domains where collecting positive examples is expensive and rare events are inherently underrepresented. We propose a lightweight synthetic data augmentation pipeline that fine-tunes a LoRA adapter on as few as 20-50 real images of a rare class and uses a pretrained diffusion model to generate synthetic samples for training. We systematically vary the synthetic-to-real ratio and evaluate the approach across two structurally different domains: chest X-ray pathology classification (NIH ChestX-ray14) and industrial surface crack detection (Magnetic Tile Defect dataset). All evaluations are performed on held-out sets of real images only. Across both domains, synthetic augmentation consistently improves rare-class recall and F1 compared to training with real data alone. Performance improves with moderate synthetic augmentation and shows diminishing returns as the synthetic ratio increases. These results suggest that LoRA-adapted diffusion models provide a simple and scalable mechanism for augmenting rare classes, enabling effective learning in data-scarce scenarios across heterogeneous visual domains.