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In this work, we present an approach called Disease Informed Neural Networks (DINNs) that can be employed to effectively predict the spread of infectious diseases. This approach builds on a successful physics informed neural network…

Recent work on predicting patient outcomes in the Intensive Care Unit (ICU) has focused heavily on the physiological time series data, largely ignoring sparse data such as diagnoses and medications. When they are included, they are usually…

Accurate epidemic forecasting is crucial for effective disease control and prevention. Traditional compartmental models often struggle to estimate temporally and spatially varying epidemiological parameters, while deep learning models…

Graph neural networks (GNNs) excel at predictive tasks on graph-structured data but often lack the ability to incorporate symbolic domain knowledge and perform general reasoning. Relational Bayesian Networks (RBNs), in contrast, enable…

T-cell receptors (TCR) are key proteins of the adaptive immune system, generated randomly in each individual, whose diversity underlies our ability to recognize infections and malignancies. Modeling the distribution of TCR sequences is of…

The COVID-19 epidemic has become a major safety and health threat worldwide. Imaging diagnosis is one of the most effective ways to screen COVID-19. This project utilizes several open-source or public datasets to present an open-source…

The novel Coronavirus Disease 2019 (COVID-19) is a global pandemic disease spreading rapidly around the world. A robust and automatic early recognition of COVID-19, via auxiliary computer-aided diagnostic tools, is essential for disease…

Graph Convolutional Neural Networks (GCNs) are widely used for graph analysis. Specifically, in medical applications, GCNs can be used for disease prediction on a population graph, where graph nodes represent individuals and edges represent…

The ongoing COVID-19 pandemic has already taken millions of lives and damaged economies across the globe. Most COVID-19 deaths and economic losses are reported from densely crowded cities. It is comprehensible that the effective control and…

Background and Objective: The new type of coronavirus is also called COVID-19. It began to spread at the end of 2019 and has now spread across the world. Until October 2020, It has infected around 37 million people and claimed about 1…

Expanding the scope of graph-based, deep-learning models to noncovalent protein-ligand interactions has earned increasing attention in structure-based drug design. Modeling the protein-ligand interactions with graph neural networks (GNNs)…

Fast screening of drug molecules based on the ligand binding affinity is an important step in the drug discovery pipeline. Graph neural fingerprint is a promising method for developing molecular docking surrogates with high throughput and…

Graph Neural Networks (GNNs) have demonstrated significant application potential in various fields. However, GNNs are still vulnerable to adversarial attacks. Numerous adversarial defense methods on GNNs are proposed to address the problem…

Message-Passing Neural Networks (MPNNs) have become a cornerstone for processing and analyzing graph-structured data. However, their effectiveness is often hindered by phenomena such as over-squashing, where long-range dependencies or…

Graph Neural Networks (GNN) have recently gained popularity in the forecasting domain due to their ability to model complex spatial and temporal patterns in tasks such as traffic forecasting and region-based demand forecasting. Most of…

Representing a signal as a continuous function parameterized by neural network (a.k.a. Implicit Neural Representations, INRs) has attracted increasing attention in recent years. Neural Processes (NPs), which model the distributions over…

In multi-agent reinforcement learning (MARL), the integration of a communication mechanism, allowing agents to better learn to coordinate their actions and converge on their objectives by sharing information. Based on an interaction graph,…

The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…

In response to the COVID-19 pandemic, the integration of interpretable machine learning techniques has garnered significant attention, offering transparent and understandable insights crucial for informed clinical decision making. This…

Graph Neural Networks (GNNs) have been shown to be a powerful tool for generating predictions from biological data. Their application to neuroimaging data such as functional magnetic resonance imaging (fMRI) scans has been limited. However,…