Related papers: Learning Graph Models for Retrosynthesis Predictio…

Graph neural networks (GNNs) have been used extensively for addressing problems in drug design and discovery. Both ligand and target molecules are represented as graphs with node and edge features encoding information about atomic elements…

Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity…

Various template-based and template-free approaches have been proposed for single-step retrosynthesis prediction in recent years. While these approaches demonstrate strong performance from a data-driven metrics standpoint, many model…

Molecular property prediction is essential in a variety of contemporary scientific fields, such as drug development and designing energy storage materials. Although there are many machine learning models available for this purpose, those…

Graph transformers have gained popularity in various graph-based tasks by addressing challenges faced by traditional Graph Neural Networks. However, the quadratic complexity of self-attention operations and the extensive layering in graph…

Transformers, adapted from natural language processing, are emerging as a leading approach for graph representation learning. Contemporary graph transformers often treat nodes or edges as separate tokens. This approach leads to…

We propose a kernel regression method to predict a target signal lying over a graph when an input observation is given. The input and the output could be two different physical quantities. In particular, the input may not be a graph signal…

Graph neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…

Recent work on Graph Neural Networks has demonstrated that self-supervised pretraining can further enhance performance on downstream graph, link, and node classification tasks. However, the efficacy of pretraining tasks has not been fully…

Chemical reaction prediction is pivotal for accelerating drug discovery and synthesis planning. Despite advances in data-driven models, current approaches are hindered by an overemphasis on parameter and dataset scaling. Some methods…

We present a new approach, the Topograph, which reconstructs underlying physics processes, including the intermediary particles, by leveraging underlying priors from the nature of particle physics decays and the flexibility of message…

Stepwise inference protocols, such as scratchpads and chain-of-thought, help language models solve complex problems by decomposing them into a sequence of simpler subproblems. Despite the significant gain in performance achieved via these…

Designing accurate deep learning models for molecular property prediction plays an increasingly essential role in drug and material discovery. Recently, due to the scarcity of labeled molecules, self-supervised learning methods for learning…

Retrosynthesis, of which the goal is to find a set of reactants for synthesizing a target product, is an emerging research area of deep learning. While the existing approaches have shown promising results, they currently lack the ability to…

Advances in deep learning models have revolutionized the study of biomolecule systems and their mechanisms. Graph representation learning, in particular, is important for accurately capturing the geometric information of biomolecules at…

Identification and verification of molecular properties such as side effects is one of the most important and time-consuming steps in the process of molecule synthesis. For example, failure to identify side effects before submission to…

Self-assembly of dilute sequence-defined macromolecules is a complex phenomenon in which the local arrangement of chemical moieties can lead to the formation of long-range structure. The dependence of this structure on the sequence…

Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…

Self-supervised learning has shown its promising capability in graph representation learning in recent work. Most existing pre-training strategies usually choose the popular Graph neural networks (GNNs), which can be seen as a special form…

Finding the main product of a chemical reaction is one of the important problems of organic chemistry. This paper describes a method of applying a neural machine translation model to the prediction of organic chemical reactions. In order to…