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Variational autoencoder (VAE) is a popular method for drug discovery and there had been a great deal of architectures and pipelines proposed to improve its performance. But the VAE model itself suffers from deficiencies such as poor…
Collecting labeled data for many important tasks in chemoinformatics is time consuming and requires expensive experiments. In recent years, machine learning has been used to learn rich representations of molecules using large scale…
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…
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…
We propose a variational autoencoder (VAE) approach for parameter estimation in nonlinear mixed-effects models based on ordinary differential equations (NLME-ODEs) using longitudinal data from multiple subjects. In moderate dimensions,…
Although variational autoencoders (VAEs) represent a widely influential deep generative model, many aspects of the underlying energy function remain poorly understood. In particular, it is commonly believed that Gaussian encoder/decoder…
Although the variational autoencoder (VAE) and its conditional extension (CVAE) are capable of state-of-the-art results across multiple domains, their precise behavior is still not fully understood, particularly in the context of data (like…
Current deep learning-based manifold learning algorithms such as the variational autoencoder (VAE) require fully sampled data to learn the probability density of real-world datasets. Once learned, the density can be used for a variety of…
Variational Autoencoders are one of the most commonly used generative models, particularly for image data. A prominent difficulty in training VAEs is data that is supported on a lower-dimensional manifold. Recent work by Dai and Wipf (2020)…
Learning interpretable and disentangled representations of data is a key topic in machine learning research. Variational Autoencoder (VAE) is a scalable method for learning directed latent variable models of complex data. It employs a clear…
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…
The manifold hypothesis states that high-dimensional data can be modeled as lying on or near a low-dimensional, nonlinear manifold. Variational Autoencoders (VAEs) approximate this manifold by learning mappings from low-dimensional latent…
Materials informatics (MI), which uses artificial intelligence and data analysis techniques to improve the efficiency of materials development, is attracting increasing interest from industry. One of its main applications is the rapid…
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…
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…
Automatic molecule generation plays an important role on drug discovery and has received a great deal of attention in recent years thanks to deep learning successful use. Graph-based neural network represents state of the art methods on…
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…
Variational autoencoder (VAE) is one of the most common techniques in the field of medical image generation, where this architecture has shown advanced researchers in recent years and has developed into various architectures. VAE has…
For personalized medicines, very crucial intrinsic information is present in high dimensional omics data which is difficult to capture due to the large number of molecular features and small number of available samples. Different types of…
We develop Riemannian approaches to variational autoencoders (VAEs) for PDE-type ambient data with regularizing geometric latent dynamics, which we refer to as VAE-DLM, or VAEs with dynamical latent manifolds. We redevelop the VAE framework…