Related papers: Explaining Deep Graph Networks with Molecular Coun…
Neural networks are prone to learning shortcuts -- they often model simple correlations, ignoring more complex ones that potentially generalize better. Prior works on image classification show that instead of learning a connection to object…
Graphs are fundamental data structures which concisely capture the relational structure in many important real-world domains, such as knowledge graphs, physical and social interactions, language, and chemistry. Here we introduce a powerful…
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…
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule…
Graph networks are a new machine learning (ML) paradigm that supports both relational reasoning and combinatorial generalization. Here, we develop universal MatErials Graph Network (MEGNet) models for accurate property prediction in both…
Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the…
Graph neural networks (GNNs) are deep learning architectures for machine learning problems on graphs. It has recently been shown that the expressiveness of GNNs can be characterised precisely by the combinatorial Weisfeiler-Leman algorithms…
Graph Machine Learning (GML) has numerous applications, such as node/graph classification and link prediction, in real-world domains. Providing human-understandable explanations for GML models is a challenging yet fundamental task to foster…
Counterfactual explanations offer an intuitive way to interpret graph neural networks (GNNs) by identifying minimal changes that alter a model's prediction, thereby answering "what must differ for a different outcome?". In this work, we…
Graph neural networks (GNNs) find applications in various domains such as computational biology, natural language processing, and computer security. Owing to their popularity, there is an increasing need to explain GNN predictions since…
Graph Neural Networks (GNNs) are effective for node classification in graph-structured data, but they lack explainability, especially at the global level. Current research mainly utilizes subgraphs of the input as local explanations or…
Predicating macroscopic influences of drugs on human body, like efficacy and toxicity, is a central problem of small-molecule based drug discovery. Molecules can be represented as an undirected graph, and we can utilize graph convolution…
Machine Learning (ML) systems are a building part of the modern tools which impact our daily life in several application domains. Due to their black-box nature, those systems are hardly adopted in application domains (e.g. health, finance)…
Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…
Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…
Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…
Deep generative models have achieved great success in areas such as image, speech, and natural language processing in the past few years. Thanks to the advances in graph-based deep learning, and in particular graph representation learning,…
Model interpretability has become an important problem in machine learning (ML) due to the increased effect that algorithmic decisions have on humans. Counterfactual explanations can help users understand not only why ML models make certain…
Graph Neural Networks (GNNs) have demonstrated great success in Knowledge Graph Completion (KGC) by modeling how entities and relations interact in recent years. However, most of them are designed to learn from the observed graph structure,…
Graph-structured data arise in many scenarios. A fundamental problem is to quantify the similarities of graphs for tasks such as classification. R-convolution graph kernels are positive-semidefinite functions that decompose graphs into…