Joseph D. Janizek

The paper introduces DeepProfile, a deep learning framework for analyzing gene expression in 18 cancers, revealing biological insights through latent space analysis and linking gene expression to clinical outcomes.

This paper introduces a novel unsupervised pathway attribution method that identifies major transcriptomic variation sources when combined with biologically-constrained models, applied to Alzheimer's disease brain samples.

The paper introduces AD-AE, an adversarial deconfounding autoencoder that generates gene expression embeddings free of confounders and capable of generalizing across domains.

The paper functionally classifies thousands of BRCA1 variants using saturation genome editing to determine their impact on cancer risk.