Improving the hierarchical classification of protein functions With swarm intelligence

This thesis investigates methods to improve the performance of hierarchical classification. In terms of this thesis hierarchical classification is a form of supervised learning, where the classes in a data set are arranged in a tree structure. As a base for our new methods we use the TDDC (top-down divide-and-conquer) approach for hierarchical classification, where each classifier is built only to discriminate between sibling classes. Firstly, we propose a swarm intelligence technique which varies the types of classifiers used at each divide within the TDDC tree. Our technique, PSO/ACO-CS (Particle Swarm Optimisation/Ant Colony Optimisation Classifier Selection), finds combinations of classifiers to be used in the TDDC tree using the global search ability of PSO/ACO. Secondly, we propose a technique that attempts to mitigate a major drawback of the TDDC approach. The drawback is that if at any point in the TDDC tree an example is misclassified it can never be correctly classified further down the TDDC tree. Our approach, PSO/ACO-RO (PSO/ACO-Recovery Optimisation) decides whether to redirect examples at a given classifier node using, again, the global search ability of PSO/ACO. Thirdly, we propose an ensemble based technique, HEHRS (Hierarchical Ensembles of Hierarchical Rule Sets), which attempts to boost the accuracy at each classifier node in the TDDC tree by using information from classifiers (rule sets) in the rest of that tree. We use Particle Swarm Optimisation to weight the individual rules within each ensemble. We evaluate these three new methods in hierarchical bioinformatics datasets that we have created for this research. These data sets represent the real world problem of protein function prediction. We find through extensive experimentation that the three proposed methods improve upon the baseline TDDC method to varying degrees. Overall the HEHRS and PSO/ACO- CS-RO approaches are most effective, although they are associated with a higher computational cost

Linear-PSO with binary search algorithm for DNA Motif Discovery / Hazaruddin Harun

Motif Discovery (MD) is the process of identifying meaningful patterns in DNA, RNA, or protein sequences. In the field of bioinformatics, a pattern is also known as a motif. Numerous algorithms had been developed for MD, but most of these were not designed to discover species specific motifs used in identifying a specifically selected species where the exact location of these motifs also needs to be identified. Evaluation of these algorithms showed that the results are unsatisfactory due to the lower validity and accuracy of these algorithms. At present, DNA sequencing analysis is the most utilised technique for species identification where patterns of DNA sequences are determined by comparing the sequence to comprehensive databases. However, several false and gap sequences had been identified to be present in these databases which lead to false identification. Therefore, this study addresses these problems by introducing a hybrid algorithm for MD. In this study, the MD is a process to discover all possible motifs that existed in DNA sequences whereas Motif Identification (MI) is a process to identify the correct motif that can represent a selected species. Particle Swarm Optimisation (PSO) was selected as the base algorithm that needs improvement and integration with other techniques. The Linear-PSO algorithm was the first version of improvement

A modified algorithm for species specific motif discovery

Motif discovery can be used to categorize unknown DNA sequences into their corresponding families. For this study, PSO was modified for discovering motif.The modified Linear-PSO is chosen even though it is a slower because linear search is not a choice but a necessary criteria for identifying motif of pig (Sus Scrofa).Pig motif identification is a critical for halal authentication.The modified Linear-PSO algorithm used linear number for population initializing and next position updating.For each cycle, only a particle called ‘target motif’ was selected and compared with other DNA sequences for fitness calculation. Motif discovered can be used as a standard motif for species identification. Experimental results show that the modified algorithm is able to identify motifs as expected. This study showed that a slower algorithm is still needed and has value based on how critical the problem is

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

Aco-based feature selection algorithm for classification

Dataset with a small number of records but big number of attributes represents a phenomenon called “curse of dimensionality”. The classification of this type of dataset requires Feature Selection (FS) methods for the extraction of useful information. The modified graph clustering ant colony optimisation (MGCACO) algorithm is an effective FS method that was developed based on grouping the highly correlated features. However, the MGCACO algorithm has three main drawbacks in producing a features subset because of its clustering method, parameter sensitivity, and the final subset determination. An enhanced graph clustering ant colony optimisation (EGCACO) algorithm is proposed to solve the three (3) MGCACO algorithm problems. The proposed improvement includes: (i) an ACO feature clustering method to obtain clusters of highly correlated features; (ii) an adaptive selection technique for subset construction from the clusters of features; and (iii) a genetic-based method for producing the final subset of features. The ACO feature clustering method utilises the ability of various mechanisms such as intensification and diversification for local and global optimisation to provide highly correlated features. The adaptive technique for ant selection enables the parameter to adaptively change based on the feedback of the search space. The genetic method determines the final subset, automatically, based on the crossover and subset quality calculation. The performance of the proposed algorithm was evaluated on 18 benchmark datasets from the University California Irvine (UCI) repository and nine (9) deoxyribonucleic acid (DNA) microarray datasets against 15 benchmark metaheuristic algorithms. The experimental results of the EGCACO algorithm on the UCI dataset are superior to other benchmark optimisation algorithms in terms of the number of selected features for 16 out of the 18 UCI datasets (88.89%) and the best in eight (8) (44.47%) of the datasets for classification accuracy. Further, experiments on the nine (9) DNA microarray datasets showed that the EGCACO algorithm is superior than the benchmark algorithms in terms of classification accuracy (first rank) for seven (7) datasets (77.78%) and demonstrates the lowest number of selected features in six (6) datasets (66.67%). The proposed EGCACO algorithm can be utilised for FS in DNA microarray classification tasks that involve large dataset size in various application domains