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Recently, autoencoders (AEs) have gained interest for creating parametric and invertible projections of multidimensional data. Parametric projections make it possible to embed new, unseen samples without recalculating the entire projection,…

Variational auto-encoders (VAEs) are a popular and powerful deep generative model. Previous works on VAEs have assumed a factorized likelihood model, whereby the output uncertainty of each pixel is assumed to be independent. This…

Adaptability is central to autonomy. Intuitively, for high-dimensional learning problems such as navigating based on vision, internal models with higher complexity allow to accurately encode the information available. However, most learning…

We develop data-driven methods for incorporating physical information for priors to learn parsimonious representations of nonlinear systems arising from parameterized PDEs and mechanics. Our approach is based on Variational Autoencoders…

Sparse Autoencoders (SAEs) are widely used to interpret neural networks by identifying meaningful concepts from their representations. However, do SAEs truly uncover all concepts a model relies on, or are they inherently biased toward…

Variational autoencoders are powerful algorithms for identifying dominant latent structure in a single dataset. In many applications, however, we are interested in modeling latent structure and variation that are enriched in a target…

This paper addresses the challenges of detecting anomalies in cellular networks in an interpretable way and proposes a new approach using variational autoencoders (VAEs) that learn interpretable representations of the latent space for each…

This thesis is a proof of concept for the potential of Variational Auto-Encoder (VAE) on representation learning of real-world Knowledge Graphs (KG). Inspired by successful approaches to the generation of molecular graphs, we evaluate the…

Deep neural networks with discrete latent variables offer the promise of better symbolic reasoning, and learning abstractions that are more useful to new tasks. There has been a surge in interest in discrete latent variable models, however,…

We present VAEL, a neuro-symbolic generative model integrating variational autoencoders (VAE) with the reasoning capabilities of probabilistic logic (L) programming. Besides standard latent subsymbolic variables, our model exploits a…

We present PECMAE, an interpretable model for music audio classification based on prototype learning. Our model is based on a previous method, APNet, which jointly learns an autoencoder and a prototypical network. Instead, we propose to…

Deep generative models have demonstrated successful applications in learning non-linear data distributions through a number of latent variables and these models use a nonlinear function (generator) to map latent samples into the data space.…

Cancer is still one of the most devastating diseases of our time. One way of automatically classifying tumor samples is by analyzing its derived molecular information (i.e., its genes expression signatures). In this work, we aim to…

Healthcare models are transitioning from unimodal prediction toward multimodal reasoning over heterogeneous diagnostic inputs. In computational pathology, for complex tumor subtypes where morphology alone can be challenging to distinguish,…

Text variational autoencoders (VAEs) are notorious for posterior collapse, a phenomenon where the model's decoder learns to ignore signals from the encoder. Because posterior collapse is known to be exacerbated by expressive decoders,…

The integration of multi-modal data, such as pathological images and genomic data, is essential for understanding cancer heterogeneity and complexity for personalized treatments, as well as for enhancing survival predictions. Despite the…

This work presents StrAE: a Structured Autoencoder framework that through strict adherence to explicit structure, and use of a novel contrastive objective over tree-structured representations, enables effective learning of multi-level…

The de novo design of drug molecules is recognized as a time-consuming and costly process, and computational approaches have been applied in each stage of the drug discovery pipeline. Variational autoencoder is one of the computer-aided…

As an important problem in causal inference, we discuss the estimation of treatment effects (TEs). Representing the confounder as a latent variable, we propose Intact-VAE, a new variant of variational autoencoder (VAE), motivated by the…

Principal Component Analysis (PCA) minimizes the reconstruction error given a class of linear models of fixed component dimensionality. Probabilistic PCA adds a probabilistic structure by learning the probability distribution of the PCA…