Related papers: A Graph to Graphs Framework for Retrosynthesis Pre…

This paper presents novel techniques for the synthesis of reversible networks of Toffoli gates, as well as improvements to previous methods. Gate count and technology oriented cost metrics are used. Our synthesis techniques are independent…

Large-scale pre-trained language models (PLMs) have advanced Graph-to-Text (G2T) generation by processing the linearised version of a graph. However, the linearisation is known to ignore the structural information. Additionally, PLMs are…

Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring…

As they carry great potential for modeling complex interactions, graph neural network (GNN)-based methods have been widely used to predict quantum mechanical properties of molecules. Most of the existing methods treat molecules as molecular…

Retrieval-augmented generation (RAG) is critical for reducing hallucinations and incorporating external knowledge into Large Language Models (LLMs). However, advanced RAG systems face a trade-off between performance and efficiency.…

This paper tackles the pressing challenge of mutagenicity prediction by introducing three ground-breaking approaches. First, it showcases the superior performance of 2D scattering coefficients extracted from molecular images, compared to…

Many machine learning techniques have been proposed in the last few years to process data represented in graph-structured form. Graphs can be used to model several scenarios, from molecules and materials to RNA secondary structures. Several…

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…

Graph Neural Networks (GNNs) have shown remarkable success across various scientific fields, yet their adoption in critical decision-making is often hindered by a lack of interpretability. Recently, intrinsically interpretable GNNs have…

Geometric Deep Learning has recently attracted significant interest in a wide range of machine learning fields, including document analysis. The application of Graph Neural Networks (GNNs) has become crucial in various document-related…

Deep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is possible to side-step expensive search procedures in…

Graph neural networks frequently encounter significant performance degradation when confronted with structural noise or non-homophilous topologies. To address these systemic vulnerabilities, we present AdvSynGNN, a comprehensive…

The objective of graph coarsening is to generate smaller, more manageable graphs while preserving key information of the original graph. Previous work were mainly based on the perspective of spectrum-preserving, using some predefined…

Subgraph matching plays an important role in electronic design automation (EDA) and circuit verification. Traditional rule-based methods have limitations in generalizing to arbitrary target circuits. Furthermore, node-to-node matching…

Prediction of molecular properties, including physico-chemical properties, is a challenging task in chemistry. Herein we present a new state-of-the-art multitask prediction method based on existing graph neural network models. We have used…

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…

We argue that Transformers are essentially graph-to-graph models, with sequences just being a special case. Attention weights are functionally equivalent to graph edges. Our Graph-to-Graph Transformer architecture makes this ability…

This paper presents reconstructions of homogeneous targets from the 2D and 3D Fresnel databases by one-step imaging methods based on the computation of topological derivative and topological energy fields. The electromagnetic inverse…

We propose a novel framework for modeling the interaction between graphical structures and the natural language text associated with their nodes and edges. Existing approaches typically fall into two categories. On group ignores the…

Generative Flow Networks (GFlowNets), a new family of probabilistic samplers, have demonstrated remarkable capabilities to generate diverse sets of high-reward candidates, in contrast to standard return maximization approaches (e.g.,…