Genome sequence assembly algorithms and misassembly identification methods.

The sequence assembly algorithms have rapidly evolved with the vigorous growth of genome sequencing technology over the past two decades. Assembly mainly uses the iterative expansion of overlap relationships between sequences to construct the target genome. The assembly algorithms can be typically classified into several categories, such as the Greedy strategy, Overlap-Layout-Consensus (OLC) strategy, and de Bruijn graph (DBG) strategy. In particular, due to the rapid development of third-generation sequencing (TGS) technology, some prevalent assembly algorithms have been proposed to generate high-quality chromosome-level assemblies. However, due to the genome complexity, the length of short reads, and the high error rate of long reads, contigs produced by assembly may contain misassemblies adversely affecting downstream data analysis. Therefore, several read-based and reference-based methods for misassembly identification have been developed to improve assembly quality. This work primarily reviewed the development of DNA sequencing technologies and summarized sequencing data simulation methods, sequencing error correction methods, various mainstream sequence assembly algorithms, and misassembly identification methods. A large amount of computation makes the sequence assembly problem more challenging, and therefore, it is necessary to develop more efficient and accurate assembly algorithms and alternative algorithms.

An Ensemble Learning Method Based on an Evidential Reasoning Rule considering Combination Weighting.

As an extension of Dempster-Shafer (D-S) theory, the evidential reasoning (ER) rule can be used as a combination strategy in ensemble learning to deeply mine classifier information through decision-making reasoning. The weight of evidence is an important parameter in the ER rule, which has a significant effect on the result of ensemble learning. However, current research results on the weight of evidence are not ideal, leveraging expert knowledge to assign weights leads to the excessive subjectivity, and using sample statistical methods to assign weights relies too heavily on the samples, so the determined weights sometimes differ greatly from the actual importance of the attributes. Therefore, to solve the problem of excessive subjectivity and objectivity of the weights of evidence, and further improve the accuracy of ensemble learning based on the ER rule, we propose a novel combination weighting method to determine the weight of evidence. The combined weights are calculated by leveraging our proposed method to combine subjective and objective weights of evidence. The regularization of these weights is studied. Then, the evidential reasoning rule is used to integrate different classifiers. Five case studies of image classification datasets have been conducted to demonstrate the effectiveness of the combination weighting method.