Related papers: Are VAEs Bad at Reconstructing Molecular Graphs?

Text variational autoencoders (VAEs) are notorious for posterior collapse, a phenomenon where the model's decoder learns to ignore signals from the encoder. Because posterior collapse is known to be exacerbated by expressive decoders,…

Variational autoencoders (VAEs) are used for transfer learning across various research domains such as music generation or medical image analysis. However, there is no principled way to assess before transfer which components to retrain or…

Generative models of graphs are well-known, but many existing models are limited in scalability and expressivity. We present a novel sequential graphical variational autoencoder operating directly on graphical representations of data. In…

Limited-angle X-ray tomography reconstruction is an ill-conditioned inverse problem in general. Especially when the projection angles are limited and the measurements are taken in a photon-limited condition, reconstructions from classical…

Recent work (Bengio et al., 2013) has shown howDenoising Auto-Encoders(DAE) become gener-ative models as a density estimator. However,in practice, the framework suffers from a mixingproblem in the MCMC sampling process and nodirect method…

Molecular representation is a critical element in our understanding of the physical world and the foundation for modern molecular machine learning. Previous molecular machine learning models have employed strings, fingerprints, global…

Constructing appropriate representations of molecules lies at the core of numerous tasks such as material science, chemistry and drug designs. Recent researches abstract molecules as attributed graphs and employ graph neural networks (GNN)…

Design of new drug compounds with target properties is a key area of research in generative modeling. We present a small drug molecule design pipeline based on graph-generative models and a comparison study of two state-of-the-art graph…

Building a scalable machine learning system for unsupervised anomaly detection via representation learning is highly desirable. One of the prevalent methods is using a reconstruction error from variational autoencoder (VAE) via maximizing…

Autoregressive models (ARMs) have become the workhorse for sequence generation tasks, since many problems can be modeled as next-token prediction. While there appears to be a natural ordering for text (i.e., left-to-right), for many data…

Although Retrieval-Augmented Large Language Models (RALMs) demonstrate their superiority in terms of factuality, they do not consistently outperform the original retrieval-free Language Models (LMs). Our experiments reveal that this…

Invertible transformation of large graphs into fixed dimensional vectors (embeddings) remains a challenge. Its overcoming would reduce any operation on graphs to an operation in a vector space. However, most existing methods are limited to…

Generative convolutional deep neural networks, e.g. popular GAN architectures, are relying on convolution based up-sampling methods to produce non-scalar outputs like images or video sequences. In this paper, we show that common up-sampling…

Graph neural networks (GNNs) have limited expressive power, failing to represent many graph classes correctly. While more expressive graph representation learning (GRL) alternatives can distinguish some of these classes, they are…

We investigate deep generative models that can exchange multiple modalities bi-directionally, e.g., generating images from corresponding texts and vice versa. A major approach to achieve this objective is to train a model that integrates…

Graph autoencoders (GAE) and variational graph autoencoders (VGAE) emerged as powerful methods for link prediction. Their performances are less impressive on community detection problems where, according to recent and concurring…

Generative autoencoders offer a promising approach for controllable text generation by leveraging their latent sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text…

Autoregressive graph generators define likelihoods via a sequential construction process, but these likelihoods are only meaningful if they are consistent across all linearizations of the same graph. Segmented Eulerian Neighborhood Trails…

Retrosynthesis prediction is a fundamental problem in organic synthesis, where the task is to identify precursor molecules that can be used to synthesize a target molecule. A key consideration in building neural models for this task is…

Variational autoencoder (VAE) is a widely used generative model for learning latent representations. Burda et al. in their seminal paper showed that learning capacity of VAE is limited by over-pruning. It is a phenomenon where a significant…