Related papers: Improving VAE based molecular representations for …

The use of machine learning is becoming increasingly common in computational materials science. To build effective models of the chemistry of materials, useful machine-based representations of atoms and their compounds are required. We…

Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…

Autoencoders are powerful machine learning models used to compress information from multiple data sources. However, autoencoders, like all artificial neural networks, are often unidentifiable and uninterpretable. This research focuses on…

Variational autoencoders (VAEs) are one class of generative probabilistic latent-variable models designed for inference based on known data. We develop three variations on VAEs by introducing a second parameterized encoder/decoder pair and,…

A feature learning task involves training models that are capable of inferring good representations (transformations of the original space) from input data alone. When working with limited or unlabelled data, and also when multiple visual…

The variational autoencoder (VAE; Kingma, Welling (2014)) is a recently proposed generative model pairing a top-down generative network with a bottom-up recognition network which approximates posterior inference. It typically makes strong…

Does a Variational AutoEncoder (VAE) consistently encode typical samples generated from its decoder? This paper shows that the perhaps surprising answer to this question is `No'; a (nominally trained) VAE does not necessarily amortize…

Molecular property prediction plays a fundamental role in drug discovery to identify candidate molecules with target properties. However, molecular property prediction is essentially a few-shot problem which makes it hard to use regular…

We combine conditional variational autoencoders (VAE) with adversarial censoring in order to learn invariant representations that are disentangled from nuisance/sensitive variations. In this method, an adversarial network attempts to…

Chemical representation learning has gained increasing interest due to the limited availability of supervised data in fields such as drug and materials design. This interest particularly extends to chemical language representation learning,…

We develop a framework for incorporating structured graphical models in the \emph{encoders} of variational autoencoders (VAEs) that allows us to induce interpretable representations through approximate variational inference. This allows us…

We demonstrate the application of machine learning for rapid and accurate extraction of plasmonic particles cluster geometries from hyperspectral image data via a dual variational autoencoder (dual-VAE). In this approach, the information is…

The representations of a compound, called "descriptors" or "features", play an essential role in constructing a machine-learning model of its physical properties. In this study, we adopt a procedure for generating a systematic set of…

Finding collective variables to describe some important coarse-grained information on physical systems, in particular metastable states, remains a key issue in molecular dynamics. Recently, machine learning techniques have been intensively…

Predicting drop coalescence based on process parameters is crucial for experiment design in chemical engineering. However, predictive models can suffer from the lack of training data and more importantly, the label imbalance problem. In…

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…

Optimization of rotating electrical machines is both time- and computationally expensive. Because of the different parametrization, design optimization is commonly executed separately for each machine technology. In this paper, we present…

Variational Auto-Encoders (VAEs) have been widely applied for learning compact, low-dimensional latent representations of high-dimensional data. When the correlation structure among data points is available, previous work proposed…

The prediction of absorption, distribution, metabolism, excretion, and toxicity (ADMET) of small molecules from their molecular structure is a central problem in medicinal chemistry with great practical importance in drug discovery.…

Variational autoencoder-based voice conversion (VAE-VC) has the advantage of requiring only pairs of speeches and speaker labels for training. Unlike the majority of the research in VAE-VC which focuses on utilizing auxiliary losses or…