相关论文: Detecting epistasis via Markov bases
High-dimensional biomarkers such as genomics are increasingly being measured in randomized clinical trials. Consequently, there is a growing interest in developing methods that improve the power to detect biomarker-treatment interactions.…
The analysis of the interaction matrix between two distinct sets is essential across diverse fields, from pharmacovigilance to transcriptomics. Not all interactions are equally informative: a marker gene associated with a few specific…
Epilepsy is one of the most common neurological disorders that can be diagnosed through electroencephalogram (EEG), in which the following epileptic events can be observed: pre-ictal, ictal, post-ictal, and interictal. In this paper, we…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model.…
Motivated by an increasing demand for models that can effectively describe features of complex multivariate time series, e.g. from sensor data in biomechanics, motion analysis, and sports science, we introduce a novel state-space modeling…
In any Markov chain Monte Carlo analysis, rapid convergence of the chain to its target probability distribution is of practical and theoretical importance. A chain that converges at a geometric rate is geometrically ergodic. In this paper,…
Darwinian evolution can be illustrated as an uphill walk in a landscape, where the surface consists of genotypes, the height coordinates represent fitness, and each step corresponds to a point mutation. Epistasis, roughly defined as the…
Epilepsy significantly impacts global health, affecting about 65 million people worldwide, along with various animal species. The diagnostic processes of epilepsy are often hindered by the transient and unpredictable nature of seizures.…
Biochemical and regulatory interactions central to biological networks are expected to cause extensive genetic interactions or epistasis affecting the heritability of complex traits and the distribution of genotypes in populations. However,…
The genotype-fitness map plays a fundamental role in shaping the dynamics of evolution. However, it is difficult to directly measure a fitness landscape in practice, because the number of possible genotypes is astronomical. One approach is…
Epilepsy is a common neurological disorder characterized by recurrent seizures accompanied by excessive synchronous brain activity. The process of structural and functional brain alterations leading to increased seizure susceptibility and…
In early-phase clinical trials, a predictive biomarker may identify subgroups that benefit from an experimental therapy, even when the overall average treatment effect is negligible. Recently proposed nonparametric interaction tests such as…
To evaluate a fitting of a statistical model to given data, calculating a conditional $p$ value by a Markov chain Monte Carlo method is one of the effective approaches. For this purpose, a Markov basis plays an important role because it…
Technological advances in genotyping have given rise to hypothesis-based association studies of increasing scope. As a result, the scientific hypotheses addressed by these studies have become more complex and more difficult to address using…
Phylogenetic inference is an intractable statistical problem on a complex space. Markov chain Monte Carlo methods are the primary tool for Bayesian phylogenetic inference but it is challenging to construct efficient schemes to explore the…
This paper presents a novel and effective technique for extracting multiple ellipses from an image. The approach employs an evolutionary algorithm to mimic the way animals behave collectively assuming the overall detection process as a…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands…
We study the detection problem for a finite set of Markov decision processes (MDPs) where the MDPs have the same state and action spaces but possibly different probabilistic transition functions. Any one of these MDPs could be the model for…