Flora Jay

Burak Yelmen, Maris Alver, Merve Nur Güler et al.

Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands of variants for multiple complex traits, conventional statistical approaches can be limited by simplified assumptions such as linearity and lack of epistasis in models. In this work, we trained artificial neural networks to predict complex traits using both simulated and real genotype-phenotype datasets. We extracted feature importance scores via different post hoc interpretability methods to identify potentially associated loci (PAL) for the target phenotype and devised an approach for obtaining p-values for the detected PAL. Simulations with various parameters demonstrated that associated loci can be detected with good precision using strict selection criteria. By applying our approach to the schizophrenia cohort in the Estonian Biobank, we detected multiple loci associated with this highly polygenic and heritable disorder. There was significant concordance between PAL and loci previously associated with schizophrenia and bipolar disorder, with enrichment analyses of genes within the identified PAL predominantly highlighting terms related to brain morphology and function. With advancements in model optimization and uncertainty quantification, artificial neural networks have the potential to enhance the identification of genomic loci associated with complex diseases, offering a more comprehensive approach for GWAS and serving as initial screening tools for subsequent functional studies.

Antoine Szatkownik, Aurélien Decelle, Beatriz Seoane et al.

Deep generative models are often trained on sensitive data, such as genetic sequences, health data, or more broadly, any copyrighted, licensed or protected content. This raises critical concerns around privacy-preserving synthetic data, and more specifically around privacy leakage, an issue closely tied to overfitting. Existing methods almost exclusively rely on global criteria to estimate the risk of privacy failure associated to a model, offering only quantitative non interpretable insights. The absence of rigorous evaluation methods for data privacy at the sample-level may hinder the practical deployment of synthetic data in real-world applications. Using extreme value statistics on nearest-neighbor distances, we propose PRIVET, a generic sample-based, modality-agnostic algorithm that assigns an individual privacy leak score to each synthetic sample. We empirically demonstrate that PRIVET reliably detects instances of memorization and privacy leakage across diverse data modalities, including settings with very high dimensionality, limited sample sizes such as genetic data and even under underfitting regimes. We compare our method to existing approaches under controlled settings and show its advantage in providing both dataset level and sample level assessments through qualitative and quantitative outputs. Additionally, our analysis reveals limitations in existing computer vision embeddings to yield perceptually meaningful distances when identifying near-duplicate samples.