On the role of metaheuristic optimization in bioinformatics

Metaheuristic algorithms are employed to solve complex and large-scale optimization problems in many different fields, from transportation and smart cities to finance. This paper discusses how metaheuristic algorithms are being applied to solve different optimization problems in the area of bioinformatics. While the text provides references to many optimization problems in the area, it focuses on those that have attracted more interest from the optimization community. Among the problems analyzed, the paper discusses in more detail the molecular docking problem, the protein structure prediction, phylogenetic inference, and different string problems. In addition, references to other relevant optimization problems are also given, including those related to medical imaging or gene selection for classification. From the previous analysis, the paper generates insights on research opportunities for the Operations Research and Computer Science communities in the field of bioinformatics

Elephant Search with Deep Learning for Microarray Data Analysis

Even though there is a plethora of research in Microarray gene expression data analysis, still, it poses challenges for researchers to effectively and efficiently analyze the large yet complex expression of genes. The feature (gene) selection method is of paramount importance for understanding the differences in biological and non-biological variation between samples. In order to address this problem, a novel elephant search (ES) based optimization is proposed to select best gene expressions from the large volume of microarray data. Further, a promising machine learning method is envisioned to leverage such high dimensional and complex microarray dataset for extracting hidden patterns inside to make a meaningful prediction and most accurate classification. In particular, stochastic gradient descent based Deep learning (DL) with softmax activation function is then used on the reduced features (genes) for better classification of different samples according to their gene expression levels. The experiments are carried out on nine most popular Cancer microarray gene selection datasets, obtained from UCI machine learning repository. The empirical results obtained by the proposed elephant search based deep learning (ESDL) approach are compared with most recent published article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl

Toplu taşıma sistemlerinin evrimsel algoritmalarla optimizasyonu

This study aims to examine, regulate, and update the land transportation of the Erzurum Metropolitan Municipality (EMM), Turkey using computerized calculation techniques. In line with these targets, some critical information has been obtained for study: the number of buses, the number of expeditions, the number of bus lines, and the number and maps of existing routes belonging to EMM. By using the information that has been obtained, this study aims at outlining specific outputs according to the input parameters, such as determining the optimal routes, the average travel, and the journey time. Once all of these situations were considered, various optimization algorithms were used to get the targeted outputs in response to the determined input parameters. In addition, the study found that the problem involved in modeling the land transport network of the EMM is in line with the so-called “traveling salesman problem,” which is a scenario about optimization often discussed in the literature. This study tried to solve this problem by using the genetic algorithm, the clonal selection algorithm, and the DNA computing algorithm. The location data for each bus stops on the bus lines selected for the study were obtained from the EMM, and the distances between these coordinates were obtained by using Google Maps via a Google API. These distances were stored in a distance matrix file and used as input parameters in the application and then were put through optimization algorithms developed initially on the MATLAB platform. The study’s results show that the algorithms developed for the proposed approaches work efficiently and that the distances for the selected bus lines can be shortened.Bu çalışma, Erzurum Büyükşehir Belediyesi'nin (EBB) Türkiye kara ulaşımını bilgisayarlı hesaplama teknikleri kullanarak incelemeyi, düzenlemeyi ve güncellemeyi amaçlamaktadır. Bu hedefler doğrultusunda, çalışma için bazı önemli bilgiler: otobüs sayısı, sefer sayısı, otobüs hattı sayısı ve EBB’ye ait mevcut güzergâh sayısı ve haritaları elde edilmiştir. Bu çalışma, elde edilen bilgileri kullanarak, optimal rotaların belirlenmesi, ortalama seyahat ve yolculuk süresi gibi girdi parametrelerine göre belirli çıktıların ana hatlarını çizmeyi amaçlamaktadır. Tüm bu durumlar göz önüne alındığında, belirlenen girdi parametrelerine karşılık hedeflenen çıktıları elde etmek için çeşitli optimizasyon algoritmaları kullanılmıştır. Çalışma, EBB’ nin ulaşım ağının modellenmesindeki problemin, literatürde sıklıkla tartışılan optimizasyonla ilgili bir senaryo olan “gezgin satıcı problemi” ile uyumlu olduğunu bulmuştur. Çalışmada genetik algoritma, klonal seçim algoritması ve DNA hesaplama algoritması kullanılarak bu problem çözülmeye çalışılmıştır. Çalışmada seçilen otobüs hatlarındaki her bir durak için konum bilgisi EBB'den alınmış ve bu koordinatlar arasındaki mesafeler bir Google API üzerinden Google Maps kullanılarak elde edilmiştir. Bu mesafeler bir mesafe matrisi dosyasında saklanmış ve uygulamada giriş parametreleri olarak kullanılmış daha sonra MATLAB platformunda geliştirilen optimizasyon algoritmalarına aktarılmıştır. Çalışmanın sonuçları, önerilen yaklaşımlar için geliştirilen algoritmaların verimli çalıştığını ve seçilen otobüs hatları için mesafelerin kısaltılabileceğini göstermektedir