Related papers: Using GWAS Data to Identify Copy Number Variants C…

Graph Neural Networks (GNNs) have emerged as powerful representation learning tools for capturing complex dependencies within diverse graph-structured data. Despite their success in a wide range of graph mining tasks, GNNs have raised…

This study explores the effectiveness of graph neural networks (GNNs) for vulnerability detection in software code, utilizing a real-world dataset of Java vulnerability-fixing commits. The dataset's structure, based on the number of…

Advancement in sequencing technology enables the study of association between complex disorders and rare variants with low minor allele frequencies. One of the major challenges in rare variant testing is lack of statistical power of…

Identifying disease-associated genes enables the development of precision medicine and the understanding of biological processes. Genome-wide association studies (GWAS), gene expression data, biological pathway analysis, and protein network…

Although genome-wide association studies (GWAS) on complex traits have achieved great successes, the current leading GWAS approaches simply perform to test each genotype-phenotype association separately for each genetic variant. Curiously,…

Accurate variant descriptions are of paramount importance in the field of genomics. The domain is confronted with increasingly complex variants, e.g., combinations of multiple indels, making it challenging to generate proper variant…

Neural processes are a family of models which use neural networks to directly parametrise a map from data sets to predictions. Directly parametrising this map enables the use of expressive neural networks in small-data problems where neural…

This study proposed a hybrid model of a convolutional neural network (CNN) and a Transformer to predict and diagnose heart disease. Based on CNN's strength in detecting local features and the Transformer's high capacity in sensing global…

We provide a view on high-dimensional statistical inference for genome-wide association studies (GWAS). It is in part a review but covers also new developments for meta analysis with multiple studies and novel software in terms of an…

To understand how genetic variants in human genomes manifest in phenotypes -- traits like height or diseases like asthma -- geneticists have sequenced and measured hundreds of thousands of individuals. Geneticists use this data to build…

As network data applications continue to expand, causal inference within networks has garnered increasing attention. However, hidden confounders complicate the estimation of causal effects. Most methods rely on the strong ignorability…

Graph Convolutional Network (GCN) is an emerging technique for information retrieval (IR) applications. While GCN assumes the homophily property of a graph, real-world graphs are never perfect: the local structure of a node may contain…

Approaches for testing sets of variants, such as a set of rare or common variants within a gene or pathway, for association with complex traits are important. In particular, set tests allow for aggregation of weak signal within a set, can…

Early-warning signals of delicate design are always used to predict critical transitions in complex systems, which makes it possible to render the systems far away from the catastrophic state by introducing timely interventions. Traditional…

Genomic surveillance of infectious diseases allows monitoring circulating and emerging variants and quantifying their epidemic potential. However, due to the high costs associated with genomic sequencing, only a limited number of samples…

Graph Convolutional Networks (GCNs) have become a standard approach for semi-supervised node classification, yet practitioners lack clear guidance on when GCNs provide meaningful improvements over simpler baselines. We present a diagnostic…

In many applications such as copy number variant (CNV) detection, the goal is to identify short segments on which the observations have different means or medians from the background. Those segments are usually short and hidden in a long…

The multifactorial etiology of autism spectrum disorder (ASD) suggests that its study would benefit greatly from multimodal approaches that combine data from widely varying platforms, e.g., neuroimaging, genetics, and clinical…

During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…

Principal Component analysis (PCA) is a useful statistical technique that is commonly used for multivariate analysis of correlated variables. It is usually applied as a dimension reduction method: the top principal components (PCs)…