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Graphs play an important role in representing complex relationships in various domains like social networks, knowledge graphs, and molecular discovery. With the advent of deep learning, Graph Neural Networks (GNNs) have emerged as a…

Machine learning in drug discovery has been focused on virtual screening of molecular libraries using discriminative models. Generative models are an entirely different approach that learn to represent and optimize molecules in a continuous…

The graph structure is a commonly used data storage mode, and it turns out that the low-dimensional embedded representation of nodes in the graph is extremely useful in various typical tasks, such as node classification, link prediction ,…

Introduction: molecular geometry, the three-dimensional arrangement of atoms within a molecule, is fundamental to understanding chemical reactivity, physical properties, and biological activity. The prevailing models used to describe…

Graph colouring is a combinatorial optimisation problem with applications in several important domains, including sports scheduling, cartography, street map navigation, and timetabling. It is also of significant theoretical interest and a…

Graph embeddings play a critical role in graph representation learning, allowing machine learning models to explore and interpret graph-structured data. However, existing methods often rely on opaque, high-dimensional embeddings, limiting…

Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes…

Machine learning plays an increasingly important role in many areas of chemistry and materials science, e.g. to predict materials properties, to accelerate simulations, to design new materials, and to predict synthesis routes of new…

Molecules have seemed like a natural fit to deep learning's tendency to handle a complex structure through representation learning, given enough data. However, this often continuous representation is not natural for understanding chemical…

Research into deep learning models for molecular property prediction has primarily focused on the development of better Graph Neural Network (GNN) architectures. Though new GNN variants continue to improve performance, their modifications…

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…

Representation learning on graphs has been gaining attention due to its wide applicability in predicting missing links, and classifying and recommending nodes. Most embedding methods aim to preserve certain properties of the original graph…

Large Language Models (LLMs) have demonstrated remarkable generalization and instruction-following capabilities with instruction tuning. The advancements in LLMs and instruction tuning have led to the development of Large Vision-Language…

Modeling molecules as undirected graphs and chemical reactions as graph rewriting operations is a natural and convenient approach tom odeling chemistry. Graph grammar rules are most naturally employed to model elementary reactions like…

Recent years have witnessed rapid advances in graph representation learning, with the continuous embedding approach emerging as the dominant paradigm. However, such methods encounter issues regarding parameter efficiency, interpretability,…

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…

Nowadays the development of new functional materials/chemical compounds using machine learning (ML) techniques is a hot topic and includes several crucial steps, one of which is the choice of chemical structure representation. Classical…

Graphs are a widely used paradigm for representing non-Euclidean data, with applications ranging from social network analysis to biomolecular prediction. While graph learning has achieved remarkable progress, real-world graph data presents…

It is well known that Drug Design is often a costly process both in terms of time and economic effort. While good Quantitative Structure-Activity Relationship models (QSAR) can help predicting molecular properties without the need to…

Generative deep learning has become pivotal in molecular design for drug discovery, materials science, and chemical engineering. A widely used paradigm is to pretrain neural networks on string representations of molecules and fine-tune them…