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Graphs serve as fundamental descriptors for systems composed of interacting elements, capturing a wide array of data types, from molecular interactions to social networks and knowledge graphs. In this paper, we present an exhaustive review…

As opposed to natural languages, source code understanding is influenced by grammatical relationships between tokens regardless of their identifier name. Graph representations of source code such as Abstract Syntax Tree (AST) can capture…

Understanding molecular structure and related knowledge is crucial for scientific research. Recent studies integrate molecular graphs with their textual descriptions to enhance molecular representation learning. However, they focus on the…

Can we use machine learning to compress graph data? The absence of ordering in graphs poses a significant challenge to conventional compression algorithms, limiting their attainable gains as well as their ability to discover relevant…

Recently, a novel two-phase framework named mol-infer for inference of chemical compounds with prescribed abstract structures and desired property values has been proposed. The framework mol-infer is primarily based on using mixed integer…

Low-rank approximation models of data matrices have become important machine learning and data mining tools in many fields including computer vision, text mining, bioinformatics and many others. They allow for embedding high-dimensional…

Graph clustering, aiming to partition nodes of a graph into various groups via an unsupervised approach, is an attractive topic in recent years. To improve the representative ability, several graph auto-encoder (GAE) models, which are based…

Generative modeling and representation learning are two key tasks in computer vision. However, these models are typically trained independently, which ignores the potential for each task to help the other, and leads to training and model…

Molecule generation is central to a variety of applications. Current attention has been paid to approaching the generation task as subgraph prediction and assembling. Nevertheless, these methods usually rely on hand-crafted or external…

Encoder-decoder architectures are prominent building blocks of state-of-the-art solutions for tasks across multiple fields where deep learning (DL) or foundation models play a key role. Although there is a growing community working on the…

Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top…

The graph neural network (GNN) has been a powerful deep-learning tool in chemistry domain, due to its close connection with molecular graphs. Most GNN models collect and update atom and molecule features from the fed atom (and, in some…

Deep neural networks have been widely used in medical image analysis and medical image segmentation is one of the most important tasks. U-shaped neural networks with encoder-decoder are prevailing and have succeeded greatly in various…

Graph Transformers, which incorporate self-attention and positional encoding, have recently emerged as a powerful architecture for various graph learning tasks. Despite their impressive performance, the complex non-convex interactions…

Geometric representation-conditioned molecule generation provides an effective paradigm that decouples molecule representation modeling from structure generation. By decoupling molecule generation into two stages-first generating a…

Graph and hypergraph representation learning has attracted increasing attention from various research fields. Despite the decent performance and fruitful applications of Graph Neural Networks (GNNs), Hypergraph Neural Networks (HGNNs), and…

The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however,…

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used.…

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Molecular language modeling tasks such as molecule captioning have been recognized for their potential to further understand molecular properties that can aid drug discovery or material synthesis based on chemical reactions. Unlike the…