Related papers: Interpretable Embeddings From Molecular Simulation…

Integrating physics models within machine learning models holds considerable promise toward learning robust models with improved interpretability and abilities to extrapolate. In this work, we focus on the integration of incomplete physics…

The rising use of machine learning in various fields requires robust methods to create synthetic tabular data. Data should preserve key characteristics while addressing data scarcity challenges. Current approaches based on Generative…

Gaussian Process (GP) Variational Autoencoders (VAEs) extend standard VAEs by replacing the fully factorised Gaussian prior with a GP prior, thereby capturing richer correlations among latent variables. However, performing exact GP…

Variational auto-encoders (VAEs) have proven to be a well suited tool for performing dimensionality reduction by extracting latent variables lying in a potentially much smaller dimensional space than the data. Their ability to capture…

Microscopy techniques generate vast amounts of complex image data that in principle can be used to discover simpler, interpretable, and parsimonious forms to reveal the underlying physical structures, such as elementary building blocks in…

Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box…

The estimation of patient-specific tissue properties in the form of model parameters is important for personalized physiological models. However, these tissue properties are spatially varying across the underlying anatomical model,…

Variational autoencoders (VAEs) are widely used deep generative models capable of learning unsupervised latent representations of data. Such representations are often difficult to interpret or control. We consider the problem of…

The variational autoencoder (VAE) is a generative model with continuous latent variables where a pair of probabilistic encoder (bottom-up) and decoder (top-down) is jointly learned by stochastic gradient variational Bayes. We first…

Macromolecular and biomolecular folding landscapes typically contain high free energy barriers that impede efficient sampling of configurational space by standard molecular dynamics simulation. Biased sampling can artificially drive the…

Deep generative models are commonly used for generating images and text. Interpretability of these models is one important pursuit, other than the generation quality. Variational auto-encoder (VAE) with Gaussian distribution as prior has…

Variational Autoencoders (VAEs) provide a theoretically-backed and popular framework for deep generative models. However, learning a VAE from data poses still unanswered theoretical questions and considerable practical challenges. In this…

Modelling longitudinal data is an important yet challenging task. These datasets can be high-dimensional, contain non-linear effects and time-varying covariates. Gaussian process (GP) prior-based variational autoencoders (VAEs) have emerged…

Mini-proteins and peptides manifest dynamic conformational fluctuation and involve mutual interconversion among metastable states. A robust mapping of the conformational landscape underlying mini-proteins and peptides often requires…

Longitudinal datasets measured repeatedly over time from individual subjects, arise in many biomedical, psychological, social, and other studies. A common approach to analyse high-dimensional data that contains missing values is to learn a…

Dimensionality reduction represents a crucial step in extracting meaningful insights from Molecular Dynamics (MD) simulations. Conventional approaches, including linear methods such as principal component analysis as well as various…

We present a new method to visualize data ensembles by constructing structured probabilistic representations in latent spaces, i.e., lower-dimensional representations of spatial data features. Our approach transforms the spatial features of…

Multi-View Clustering (MVC) has gained significant attention for its ability to leverage complementary information across diverse views. However, existing deep MVC methods often struggle with view-distribution entanglement during cross-view…

We consider the problem of encoding pairwise correlations between coupled dynamical systems in a low-dimensional latent space based on few distinct observations. We used variational autoencoders (VAE) to embed temporal correlations between…

We introduce MGP-VAE (Multi-disentangled-features Gaussian Processes Variational AutoEncoder), a variational autoencoder which uses Gaussian processes (GP) to model the latent space for the unsupervised learning of disentangled…