Related papers: Are VAEs Bad at Reconstructing Molecular Graphs?

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…

Multimodal variational autoencoders (VAEs) have shown promise as efficient generative models for weakly-supervised data. Yet, despite their advantage of weak supervision, they exhibit a gap in generative quality compared to unimodal VAEs,…

Objective: This paper investigates how generative models, trained on ground-truth images, can be used \changes{as} priors for inverse problems, penalizing reconstructions far from images the generator can produce. The aim is that learned…

Deep generative models are attracting great attention as a new promising approach for molecular design. All models reported so far are based on either variational autoencoder (VAE) or generative adversarial network (GAN). Here we propose a…

Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…

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…

A range of methods with suitable inductive biases exist to learn interpretable object-centric representations of images without supervision. However, these are largely restricted to visually simple images; robust object discovery in…

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…

We consider the problem of learning Variational Autoencoders (VAEs), i.e., a type of deep generative model, from data with missing values. Such data is omnipresent in real-world applications of machine learning because complete data is…

Molecular Representation Learning (MRL) has proven impactful in numerous biochemical applications such as drug discovery and enzyme design. While Graph Neural Networks (GNNs) are effective at learning molecular representations from a 2D…

Graph neural networks (GNNs) demonstrate great performance in compound property and activity prediction due to their capability to efficiently learn complex molecular graph structures. However, two main limitations persist including…

Recent work leverages Vision Foundation Models as image encoders to boost the generative performance of latent diffusion models (LDMs), as their semantic feature distributions are easy to learn. However, such semantic features often lack…

We introduce a version of a variational auto-encoder (VAE), which can generate good perturbations of images, when trained on a complex dataset (in our experiments, CIFAR-10). The net is using only two latent generative dimensions per class,…

Molecular Machine Learning (ML) bears promise for efficient molecule property prediction and drug discovery. However, labeled molecule data can be expensive and time-consuming to acquire. Due to the limited labeled data, it is a great…

Variational Autoencoder (VAE) and its variations are classic generative models by learning a low-dimensional latent representation to satisfy some prior distribution (e.g., Gaussian distribution). Their advantages over GAN are that they can…

In data-driven drug discovery, designing molecular descriptors is a very important task. Deep generative models such as variational autoencoders (VAEs) offer a potential solution by designing descriptors as probabilistic latent vectors…

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…

Deep generative models are increasingly becoming integral parts of the in silico molecule design pipeline and have dual goals of learning the chemical and structural features that render candidate molecules viable while also being flexible…

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…

Graph autoencoders (GAEs), as a kind of generative self-supervised learning approach, have shown great potential in recent years. GAEs typically rely on distance-based criteria, such as mean-square-error (MSE), to reconstruct the input…