相关论文: Celer: an Efficient Program for Genotype Eliminati…

The research community continues to seek increasingly more advanced synthetic data generators to reliably evaluate the strengths and limitations of machine learning methods. This work aims to increase the availability of datasets…

A computational challenge to validate the candidate disease genes identified in a high-throughput genomic study is to elucidate the associations between the set of candidate genes and disease phenotypes. The conventional gene set enrichment…

Premature convergence is one of the important issues while using Genetic Programming for data modeling. It can be avoided by improving population diversity. Intelligent genetic operators can help to improve the population diversity.…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…

How does one verify that the output of a complicated program is correct? One can formally prove that the program is correct, but this may be beyond the power of existing methods. Alternatively one can check that the output produced for a…

In recent years, several machine learning approaches have been proposed to predict gene expression and epigenetic signals from the DNA sequence alone. These models are often used to deduce, and, to some extent, assess putative new…

When an evolving program is modified to address issues related to thread synchronization, there is a need to confirm the change is correct, i.e., it does not introduce unexpected behavior. However, manually comparing two programs to…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Some property graph databases do not have a fixed schema, which can result in data type inconsistencies for properties on nodes and relationships, especially when importing data into a running database. Here we present a tool which can…

This manuscript delves into the intersection of genomics and phenotypic prediction, focusing on the statistical innovation required to navigate the complexities introduced by noisy covariates and confounders. The primary emphasis is on the…

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…

The problem of mechanically formalizing and proving metatheoretic properties of programming language calculi, type systems, operational semantics, and related formal systems has received considerable attention recently. However, the dual…

Revealing relationships between genes and disease phenotypes is a critical problem in biomedical studies. This problem has been challenged by the heterogeneity of diseases. Patients of a perceived same disease may form multiple subgroups,…

Medical coding is essential for standardizing clinical data and communication but is often time-consuming and prone to errors. Traditional Natural Language Processing (NLP) methods struggle with automating coding due to the large label…

Background: With the fast development of next generation sequencing technologies, increasing numbers of genomes are being de novo sequenced and assembled. However, most are in fragmental and incomplete draft status, and thus it is often…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

We present new techniques for synthesizing programs through sequences of mutations. Among these are (1) a method of local scoring assigning a score to each expression in a program, allowing us to more precisely identify buggy code, (2)…

We consider the problem of detecting and estimating the strength of association between a trait of interest and alleles or haplotypes in a small genomic region (e.g. a gene or a gene complex), when no direct information on that region is…

Integrating heterogeneous datasets across different measurement platforms is a fundamental challenge in many scientific applications. A common example arises in deconvolution problems, such as cell type deconvolution, where one aims to…

In the past decade, the increased availability of genome-wide association studies summary data has popularized Mendelian Randomization (MR) for conducting causal inference. MR analyses, incorporating genetic variants as instrumental…