Related papers: Variable-length haplotype construction for gene-ge…
A biological pathway represents a set of genes that serves a particular cellular or a physiological function. The genes within the same pathway are expected to function together and hence may interact with each other. It is also known that…
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the…
Given genetic variations and various phenotypical traits, such as Magnetic Resonance Imaging (MRI) features, we consider two important and related tasks in biomedical research: i)to select genetic and phenotypical markers for disease…
In high throughput settings we inspect a great many candidate variables (e.g., genes) searching for associations with a primary variable (e.g., a phenotype). High throughput hypothesis testing can be made difficult by the presence of…
Heritability is a central parameter in quantitative genetics, both from an evolutionary and a breeding perspective. For plant traits heritability is traditionally estimated by comparing within and between genotype variability. This approach…
Due to its direct relevance to post-disaster operations, meter reading and civil refuse collection, the Uncertain Capacitated Arc Routing Problem (UCARP) is an important optimisation problem. Stochastic models are critical to study as they…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Hypergraphs (i.e., sets of hyperedges) naturally represent group relations (e.g., researchers co-authoring a paper and ingredients used together in a recipe), each of which corresponds to a hyperedge (i.e., a subset of nodes). Predicting…
The rapid growth in feature dimension may introduce implicit associations between features and labels in multi-label datasets, making the relationships between features and labels increasingly complex. Moreover, existing methods often adopt…
Hyperparameter optimization (HPO) is a crucial step in achieving strong predictive performance. Yet, the impact of individual hyperparameters on model generalization is highly context-dependent, prohibiting a one-size-fits-all solution and…
High-dimensional phenotypes hold promise for richer findings in association studies, but testing of several phenotype traits aggravates the grand challenge of association studies, that of multiple testing. Several methods have recently been…
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…
It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…
Predicting genetic perturbations enables the identification of potentially crucial genes prior to wet-lab experiments, significantly improving overall experimental efficiency. Since genes are the foundation of cellular life, building gene…
Background: The learning of genotype-phenotype associations and history of human disease by doing detailed and precise analysis of phenotypic abnormalities can be defined as deep phenotyping. To understand and detect this interaction…
This study presents the approach to analyzing the evolution of an arbitrary complex system whose behavior is characterized by a set of different time-dependent factors. The key requirement for these factors is only that they must contain an…
Sample overlap is a common issue in evidence synthesis in the field of medical research, particularly when integrating findings from observational studies utilizing existing databases such as registries. Due to the general inaccessibility…
Fashion attribute classification is of great importance to many high-level tasks such as fashion item search, fashion trend analysis, fashion recommendation, etc. The task is challenging due to the extremely imbalanced data distribution,…
The association of a given human phenotype to a genetic variant remains a critical challenge for biology. We present a novel system called PhenoLinker capable of associating a score to a phenotype-gene relationship by using heterogeneous…
Gene-gene interactions play a crucial role in the manifestation of complex human diseases. Uncovering significant gene-gene interactions is a challenging task. Here, we present an innovative approach utilizing data-driven computational…