相关论文: Celer: an Efficient Program for Genotype Eliminati…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…
Compared to a neutral model, purifying selection distorts the structure of genealogies and hence alters the patterns of sampled genetic variation. Although these distortions may be common in nature, our understanding of how we expect…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
Although the applications of Non-Homogeneous Poisson Processes to model and study the threshold overshoots of interest in different time series of measurements have proven to provide good results, they needed to be complemented with an…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
For families, kinship coefficients are quantifications of the amount of genetic sharing between a pair of individuals. These coefficients are critical for understanding the breeding habits and genetic diversity of diploid populations.…
Modern high-throughput sequencing assays efficiently capture not only gene expression and different levels of gene regulation but also a multitude of genome variants. Focused analysis of alternative alleles of variable sites at homologous…
Most available tools propose simulation frameworks to study models of biological systems, but simulation only explores a few of the most probable behaviours of the system. On the contrary, techniques such as model checking, coming from…
Feature selection is a problem of finding efficient features among all features in which the final feature set can improve accuracy and reduce complexity. In feature selection algorithms search strategies are key aspects. Since feature…
The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to…
Program synthesis aims to {\it automatically} find programs from an underlying programming language that satisfy a given specification. While this has the potential to revolutionize computing, how to search over the vast space of programs…
It is very challenging to select informative features from tens of thousands of measured features in high-throughput data analysis. Recently, several parametric/regression models have been developed utilizing the gene network information to…
Genetic Algorithms (GAs) are known for their efficiency in solving combinatorial optimization problems, thanks to their ability to explore diverse solution spaces, handle various representations, exploit parallelism, preserve good…
A deductive program synthesis tool takes a specification as input and derives a program that satisfies the specification. The drawback of this approach is that search spaces for such correct programs tend to be enormous, making it difficult…
Identifying promising compounds from a vast collection of feasible compounds is an important and yet challenging problem in the pharmaceutical industry. An efficient solution to this problem will help reduce the expenditure at the early…
Neural network models of real-world systems, such as industrial processes, made from sensor data must often rely on incomplete data. System states may not all be known, sensor data may be biased or noisy, and it is not often known which…
Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…
Automatically extracted metadata from scholarly documents in PDF formats is usually noisy and heterogeneous, often containing incomplete fields and erroneous values. One common way of cleaning metadata is to use a bibliographic reference…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…