Related papers: Continuous Representation of Molecules Using Graph…

Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

Generating novel drug molecules with desired biological properties is a time consuming and complex task. Conditional generative adversarial models have recently been proposed as promising approaches for de novo drug design. In this paper,…

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…

Molecular representation learning is vital for various downstream applications, including the analysis and prediction of molecular properties and side effects. While Graph Neural Networks (GNNs) have been a popular framework for modeling…

Generative networks have made it possible to generate meaningful signals such as images and texts from simple noise. Recently, generative methods based on GAN and VAE were developed for graphs and graph signals. However, the mathematical…

Variational AutoEncoders (VAEs) provide a means to generate representational latent embeddings. Previous research has highlighted the benefits of achieving representations that are disentangled, particularly for downstream tasks. However,…

In the last few years there have been important advancements in generative models with the two dominant approaches being Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs). However, standard Autoencoders (AEs) and…

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as two powerful groups of unsupervised node embedding methods, with various applications to graph-based machine learning problems such as link prediction and…

Variational autoencoders (VAE) often use Gaussian or category distribution to model the inference process. This puts a limit on variational learning because this simplified assumption does not match the true posterior distribution, which is…

3D geometric contents are becoming increasingly popular. In this paper, we study the problem of analyzing deforming 3D meshes using deep neural networks. Deforming 3D meshes are flexible to represent 3D animation sequences as well as…

While unsupervised variational autoencoders (VAE) have become a powerful tool in neuroimage analysis, their application to supervised learning is under-explored. We aim to close this gap by proposing a unified probabilistic model for…

The Variational Autoencoder (VAE) has proven to be an effective model for producing semantically meaningful latent representations for natural data. However, it has thus far seen limited application to sequential data, and, as we…

Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a…

Generative modeling aims to generate new data samples that resemble a given dataset, with diffusion models recently becoming the most popular generative model. One of the main challenges of diffusion models is solving the problem in the…

Electron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine…

By composing graphical models with deep learning architectures, we learn generative models with the strengths of both frameworks. The structured variational autoencoder (SVAE) inherits structure and interpretability from graphical models,…

In this paper, we propose the "adversarial autoencoder" (AAE), which is a probabilistic autoencoder that uses the recently proposed generative adversarial networks (GAN) to perform variational inference by matching the aggregated posterior…

Learning useful representations without supervision remains a key challenge in machine learning. In this paper, we propose a simple yet powerful generative model that learns such discrete representations. Our model, the Vector…

Variational auto-encoder (VAE) is a powerful unsupervised learning framework for image generation. One drawback of VAE is that it generates blurry images due to its Gaussianity assumption and thus L2 loss. To allow the generation of high…

In this paper, we present a general framework to scale graph autoencoders (AE) and graph variational autoencoders (VAE). This framework leverages graph degeneracy concepts to train models only from a dense subset of nodes instead of using…