Graph diffusion models have emerged as state-of-the-art techniques in graph generation; yet, integrating domain knowledge into these models remains challenging. Domain knowledge is particularly important in real-world scenarios, where invalid generated graphs hinder deployment in practical applications. Unconstrained and conditioned graph diffusion models fail to guarantee such domain-specific structural properties. We present ConStruct, a novel framework that enables graph diffusion models to incorporate hard constraints on specific properties, such as planarity or acyclicity. Our approach ensures that the sampled graphs remain within the domain of graphs that satisfy the specified property throughout the entire trajectory in both the forward and reverse processes. This is achieved by introducing an edge-absorbing noise model and a new projector operator. ConStruct demonstrates versatility across several structural and edge-deletion invariant constraints and achieves state-of-the-art performance for both synthetic benchmarks and attributed real-world datasets. For example, by incorporating planarity constraints in digital pathology graph datasets, the proposed method outperforms existing baselines, improving data validity by up to 71.1 percentage points.

This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly operates on both continuous (atom coordinates) and categorical features (atom types). In addition, we provide a probabilistic analysis which admits likelihood computation of molecules using our model. Experimentally, the proposed method significantly outperforms previous 3D molecular generative methods regarding the quality of generated samples and the efficiency at training time.

Current state of the art algorithms for recommender systems are mainly based on collaborative filtering, which exploits user ratings to discover latent factors in the data. These algorithms unfortunately do not make effective use of other features, which can help solve two well identified problems of collaborative filtering: cold start (not enough data is available for new users or products) and concept shift (the distribution of ratings changes over time). To address these problems, we propose Modurec: an autoencoder-based method that combines all available information using the feature-wise modulation mechanism, which has demonstrated its effectiveness in several fields. While time information helps mitigate the effects of concept shift, the combination of user and item features improve prediction performance when little data is available. We show on Movielens datasets that these modifications produce state-of-the-art results in most evaluated settings compared with standard autoencoder-based methods and other collaborative filtering approaches.

Seminal works on graph neural networks have primarily targeted semi-supervised node classification problems with few observed labels and high-dimensional signals. With the development of graph networks, this setup has become a de facto benchmark for a significant body of research. Interestingly, several works have recently shown that in this particular setting, graph neural networks do not perform much better than predefined low-pass filters followed by a linear classifier. However, when learning from little data in a high-dimensional space, it is not surprising that simple and heavily regularized methods are near-optimal. In this paper, we show empirically that in settings with fewer features and more training data, more complex graph networks significantly outperform simple models, and propose a few insights towards the proper choice of graph network architectures. We finally outline the importance of using sufficiently diverse benchmarks (including lower dimensional signals as well) when designing and studying new types of graph neural networks.

Message-passing has proved to be an effective way to design graph neural networks, as it is able to leverage both permutation equivariance and an inductive bias towards learning local structures in order to achieve good generalization. However, current message-passing architectures have a limited representation power and fail to learn basic topological properties of graphs. We address this problem and propose a powerful and equivariant message-passing framework based on two ideas: first, we propagate a one-hot encoding of the nodes, in addition to the features, in order to learn a local context matrix around each node. This matrix contains rich local information about both features and topology and can eventually be pooled to build node representations. Second, we propose methods for the parametrization of the message and update functions that ensure permutation equivariance. Having a representation that is independent of the specific choice of the one-hot encoding permits inductive reasoning and leads to better generalization properties. Experimentally, our model can predict various graph topological properties on synthetic data more accurately than previous methods and achieves state-of-the-art results on molecular graph regression on the ZINC dataset.