Related papers: Are VAEs Bad at Reconstructing Molecular Graphs?

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…

Prediction of a molecule's 3D conformer ensemble from the molecular graph holds a key role in areas of cheminformatics and drug discovery. Existing generative models have several drawbacks including lack of modeling important molecular…

Image generative models can learn the distributions of the training data and consequently generate examples by sampling from these distributions. However, when the training dataset is corrupted with outliers, generative models will likely…

The ability of Variational Autoencoders (VAEs) to learn disentangled representations has made them popular for practical applications. However, their behaviour is not yet fully understood. For example, the questions of when they can provide…

Variational auto-encoders (VAEs) provide an attractive solution to image generation problem. However, they tend to produce blurred and over-smoothed images due to their dependence on pixel-wise reconstruction loss. This paper introduces a…

We claim that a source of severe failures for Variational Auto-Encoders is the choice of the distribution class used for the observation model.A first theoretical and experimental contribution of the paper is to establish that even in the…

Noninvasive reconstruction of cardiac transmembrane potential (TMP) from surface electrocardiograms (ECG) involves an ill-posed inverse problem. Model-constrained regularization is powerful for incorporating rich physiological knowledge…

Deep generative models provide powerful tools for distributions over complicated manifolds, such as those of natural images. But many of these methods, including generative adversarial networks (GANs), can be difficult to train, in part…

Variational autoencoders (VAEs) are one of the powerful likelihood-based generative models with applications in many domains. However, they struggle to generate high-quality images, especially when samples are obtained from the prior…

Variational Auto-encoders (VAEs) are deep generative latent variable models that are widely used for a number of downstream tasks. While it has been demonstrated that VAE training can suffer from a number of pathologies, existing literature…

Generative deep neural networks used in machine learning, like the Variational Auto-Encoders (VAE), and Generative Adversarial Networks (GANs) produce new objects each time when asked to do so with the constraint that the new objects remain…

Deep generative models of molecules have grown immensely in popularity, trained on relevant datasets, these models are used to search through chemical space. The downstream utility of generative models for the inverse design of novel…

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the…

The posterior collapse phenomenon in variational autoencoder (VAE), where the variational posterior distribution closely matches the prior distribution, can hinder the quality of the learned latent variables. As a consequence of posterior…

Variational autoencoders (VAEs), one of the most widely used generative models, are known to suffer from posterior collapse, a phenomenon that reduces the diversity of generated samples. To avoid posterior collapse, many prior works have…

Recent advances in image tokenizers, such as VQ-VAE, have enabled text-to-image generation using auto-regressive methods, similar to language modeling. However, these methods have yet to leverage pre-trained language models, despite their…

The variational autoencoder (VAE) framework remains a popular option for training unsupervised generative models, especially for discrete data where generative adversarial networks (GANs) require workaround to create gradient for the…

Graph Neural Networks (GNNs) have shown remarkable success in molecular tasks, yet their interpretability remains challenging. Traditional model-level explanation methods like XGNN and GNNInterpreter often fail to identify valid…

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular…

Masked Autoencoders (MAEs) achieve impressive performance in image classification tasks, yet the internal representations they learn remain less understood. This work started as an attempt to understand the strong downstream classification…