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Generalized additive models (GAMs) have long been a powerful white-box tool for the intelligible analysis of tabular data, revealing the influence of each feature on the model predictions. Despite the success of neural networks (NNs) in…
Learning and reasoning about 3D molecular structures with varying size is an emerging and important challenge in machine learning and especially in drug discovery. Equivariant Graph Neural Networks (GNNs) can simultaneously leverage the…
Accurate prediction of molecular properties is essential in drug discovery and related fields. However, existing graph neural networks (GNNs) often struggle to simultaneously capture both local and global molecular structures. In this work,…
Graph Auto-Encoders (GAEs) are powerful tools for graph representation learning. In this paper, we develop a novel Hierarchical Cluster-based GAE (HC-GAE), that can learn effective structural characteristics for graph data analysis. To this…
Deep generative models have been praised for their ability to learn smooth latent representation of images, text, and audio, which can then be used to generate new, plausible data. However, current generative models are unable to work with…
Graphs can be used to effectively represent complex data structures. Learning these irregular data in graphs is challenging and still suffers from shallow learning. Applying deep learning on graphs has recently showed good performance in…
Many real-world phenomena can be modeled as a graph, making them extremely valuable due to their ubiquitous presence. GNNs excel at capturing those relationships and patterns within these graphs, enabling effective learning and prediction…
Image matching, which aims to identify corresponding pixel locations between images, is crucial in a wide range of scientific disciplines, aiding in image registration, fusion, and analysis. In recent years, deep learning-based image…
Structural data from Electronic Health Records as complementary information to imaging data for disease prediction. We incorporate novel weighting layer into the Graph Convolutional Networks, which weights every element of structural data…
Machine learning of atomic-scale properties is revolutionizing molecular modelling, making it possible to evaluate inter-atomic potentials with first-principles accuracy, at a fraction of the costs. The accuracy, speed and reliability of…
We introduce a family of multilayer graph kernels and establish new links between graph convolutional neural networks and kernel methods. Our approach generalizes convolutional kernel networks to graph-structured data, by representing…
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics systems, learning molecular fingerprints, predicting protein interface, and classifying diseases demand a model…
Graph is an usual representation of relational data, which are ubiquitous in manydomains such as molecules, biological and social networks. A popular approach to learningwith graph structured data is to make use of graph kernels, which…
Graph pre-training has been concentrated on graph-level tasks involving small graphs (e.g., molecular graphs) or learning node representations on a fixed graph. Extending graph pre-trained models to web-scale graphs with billions of nodes…
Graph neural networks (GNN) has been demonstrated to be effective in classifying graph structures. To further improve the graph representation learning ability, hierarchical GNN has been explored. It leverages the differentiable pooling to…
Representation learning for protein biochemical space faces a difficult trade-off: protein language models excel at capturing long-range biological semantics but often miss fine-grained chemical details. Conversely, chemical language models…
The rapid development of high-throughput technologies has enabled the generation of data from biological or disease processes that span multiple layers, like genomic, proteomic or metabolomic data, and further pertain to multiple sources,…
Modern Large Language Models, such as the LLaMA, Qwen and DeepSeek series, predominantly adopt the Pre-LayerNorm (Pre-LN) Transformer architecture. While being stable during pretraining and scalable to large model sizes, Pre-LN suffers from…
Electron cryo-microscopy (cryo-EM) produces three-dimensional (3D) maps of the electrostatic potential of biological macromolecules, including proteins. Along with knowledge about the imaged molecules, cryo-EM maps allow de novo atomic…
A limitation of the Graph Convolutional Networks (GCNs) is that it assumes at a particular $l^{th}$ layer of the neural network model only the $l^{th}$ order neighbourhood nodes of a social network are influential. Furthermore, the GCN has…