Related papers: A Graph Feature Auto-Encoder for the Prediction of…

Unsupervised graph representation learning aims to learn low-dimensional node embeddings without supervision while preserving graph topological structures and node attributive features. Previous graph neural networks (GNN) require a large…

Graph embedding algorithms are used to efficiently represent (encode) a graph in a low-dimensional continuous vector space that preserves the most important properties of the graph. One aspect that is often overlooked is whether the graph…

Graph neural networks are increasingly becoming the framework of choice for graph-based machine learning. In this paper, we propose a new graph neural network architecture that substitutes classical message passing with an analysis of the…

Self-supervised learning with masked autoencoders has recently gained popularity for its ability to produce effective image or textual representations, which can be applied to various downstream tasks without retraining. However, we observe…

Gene interaction graphs aim to capture various relationships between genes and can represent decades of biology research. When trying to make predictions from genomic data, those graphs could be used to overcome the curse of dimensionality…

Understanding how small molecules perturb gene expression is essential for uncovering drug mechanisms, predicting off-target effects, and identifying repurposing opportunities. While prior deep learning frameworks have integrated multimodal…

Can neural networks learn to compare graphs without feature engineering? In this paper, we show that it is possible to learn representations for graph similarity with neither domain knowledge nor supervision (i.e.\ feature engineering or…

Timely detected anomalies in the chemical technological processes, as well as the earliest detection of the cause of the fault, significantly reduce the production cost in the industrial factories. Data on the state of the technological…

Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder…

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet…

Machine learning techniques have recently been adopted in various applications in medicine, biology, chemistry, and material engineering. An important task is to predict the properties of molecules, which serves as the main subroutine in…

The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…

Finding the biomarkers associated with ASD is helpful for understanding the underlying roots of the disorder and can lead to earlier diagnosis and more targeted treatment. A promising approach to identify biomarkers is using Graph Neural…

Learning node representations that incorporate information from graph structure benefits wide range of tasks on graph. The majority of existing graph neural networks (GNNs) have limited power in capturing position information for a given…

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly…

We present the Topology Transformation Equivariant Representation learning, a general paradigm of self-supervised learning for node representations of graph data to enable the wide applicability of Graph Convolutional Neural Networks…

Generative models for graph data are an important research topic in machine learning. Graph data comprise two levels that are typically analyzed separately: node-level properties such as the existence of a link between a pair of nodes, and…

Graph neural networks (GNNs) have shown prominent performance on attributed network embedding. However, existing efforts mainly focus on exploiting network structures, while the exploitation of node attributes is rather limited as they only…

Although a number of studies have explored deep learning in neuroscience, the application of these algorithms to neural systems on a microscopic scale, i.e. parameters relevant to lower scales of organization, remains relatively novel.…

Recent interest in graph embedding methods has focused on learning a single representation for each node in the graph. But can nodes really be best described by a single vector representation? In this work, we propose a method for learning…