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We present two deep generative models based on Variational Autoencoders to improve the accuracy of drug response prediction. Our models, Perturbation Variational Autoencoder and its semi-supervised extension, Drug Response Variational…

This paper introduces the Descriptive Variational Autoencoder (DVAE), an unsupervised and end-to-end trainable neural network for predicting vehicle trajectories that provides partial interpretability. The novel approach is based on the…

The need for interpretable models has fostered the development of self-explainable classifiers. Prior approaches are either based on multi-stage optimization schemes, impacting the predictive performance of the model, or produce…

Cancer is a heterogeneous disease with diverse molecular etiologies and outcomes. The Cancer Genome Atlas (TCGA) has released a large compendium of over 10,000 tumors with RNA-seq gene expression measurements. Gene expression captures the…

Variational autoencoders (VAE) represent a popular, flexible form of deep generative model that can be stochastically fit to samples from a given random process using an information-theoretic variational bound on the true underlying…

Transformer models have become state-of-the-art in decoding stimuli and behavior from neural activity, significantly advancing neuroscience research. Yet greater transparency in their decision-making processes would substantially enhance…

Variational autoencoders (VAEs) employ Bayesian inference to interpret sensory inputs, mirroring processes that occur in primate vision across both ventral (Higgins et al., 2021) and dorsal (Vafaii et al., 2023) pathways. Despite their…

As in many fields of medical research, survival analysis has witnessed a growing interest in the application of deep learning techniques to model complex, high-dimensional, heterogeneous, incomplete, and censored medical data. Current…

Data-driven fault diagnostics of safety-critical systems often faces the challenge of a complete lack of labeled data associated with faulty system conditions (i.e., fault types) at training time. Since an unknown number and nature of fault…

In this thesis, we develop methods to enhance the interpretability of recent representation learning techniques in natural language processing (NLP) while accounting for the unavailability of annotated data. We choose to leverage…

Finding an interpretable non-redundant representation of real-world data is one of the key problems in Machine Learning. Biological neural networks are known to solve this problem quite well in unsupervised manner, yet unsupervised…

Recently there has been an increased interest in unsupervised learning of disentangled representations using the Variational Autoencoder (VAE) framework. Most of the existing work has focused largely on modifying the variational cost…

In this tutorial, we explore Variational Autoencoders (VAEs), an essential framework for unsupervised learning, particularly suited for high-dimensional datasets such as neuroimaging. By integrating deep learning with Bayesian inference,…

In the following short article we adapt a new and popular machine learning model for inference on medical data sets. Our method is based on the Variational AutoEncoder (VAE) framework that we adapt to survival analysis on small data sets…

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior…

Pan-cancer classification using transcriptomic (RNA-Seq) data can inform tumor subtyping and therapy selection, but is challenging due to extremely high dimensionality and limited sample sizes. In this study, we propose a novel deep…

Pathology plays an important role in disease diagnosis, treatment decision-making and drug development. Previous works on interpretability for machine learning models on pathology images have revolved around methods such as attention value…

Optimal computations under uncertainty require an adequate probabilistic representation about beliefs. Deep generative models, and specifically Variational Autoencoders (VAEs), have the potential to meet this demand by building latent…

Often the analysis of time-dependent chemical and biophysical systems produces high-dimensional time-series data for which it can be difficult to interpret which individual features are most salient. While recent work from our group and…

High-dimensional clinical data have become invaluable resources for genetic studies, due to their accessibility in biobank-scale datasets and the development of high performance modeling techniques especially using deep learning. Recent…