An Efficient High-Dimensional Gene Selection Approach based on Binary Horse Herd Optimization Algorithm for Biological Data Classification

The Horse Herd Optimization Algorithm (HOA) is a new meta-heuristic algorithm based on the behaviors of horses at different ages. The HOA was introduced recently to solve complex and high-dimensional problems. This paper proposes a binary version of the Horse Herd Optimization Algorithm (BHOA) in order to solve discrete problems and select prominent feature subsets. Moreover, this study provides a novel hybrid feature selection framework based on the BHOA and a minimum Redundancy Maximum Relevance (MRMR) filter method. This hybrid feature selection, which is more computationally efficient, produces a beneficial subset of relevant and informative features. Since feature selection is a binary problem, we have applied a new Transfer Function (TF), called X-shape TF, which transforms continuous problems into binary search spaces. Furthermore, the Support Vector Machine (SVM) is utilized to examine the efficiency of the proposed method on ten microarray datasets, namely Lymphoma, Prostate, Brain-1, DLBCL, SRBCT, Leukemia, Ovarian, Colon, Lung, and MLL. In comparison to other state-of-the-art, such as the Gray Wolf (GW), Particle Swarm Optimization (PSO), and Genetic Algorithm (GA), the proposed hybrid method (MRMR-BHOA) demonstrates superior performance in terms of accuracy and minimum selected features. Also, experimental results prove that the X-Shaped BHOA approach outperforms others methods

A particle swarm based hybrid system for imbalanced medical data sampling

BackgroundMedical and biological data are commonly with small sample size, missing values, and most importantly, imbalanced class distribution. In this study we propose a particle swarm based hybrid system for remedying the class imbalance problem in medical and biological data mining. This hybrid system combines the particle swarm optimization (PSO) algorithm with multiple classifiers and evaluation metrics for evaluation fusion. Samples from the majority class are ranked using multiple objectives according to their merit in compensating the class imbalance, and then combined with the minority class to form a balanced dataset.ResultsOne important finding of this study is that different classifiers and metrics often provide different evaluation results. Nevertheless, the proposed hybrid system demonstrates consistent improvements over several alternative methods with three different metrics. The sampling results also demonstrate good generalization on different types of classification algorithms, indicating the advantage of information fusion applied in the hybrid system.ConclusionThe experimental results demonstrate that unlike many currently available methods which often perform unevenly with different datasets the proposed hybrid system has a better generalization property which alleviates the method-data dependency problem. From the biological perspective, the system provides indication for further investigation of the highly ranked samples, which may result in the discovery of new conditions or disease subtypes.<br /

Memetic micro-genetic algorithms for cancer data classification

Fast and precise medical diagnosis of human cancer is crucial for treatment decisions. Gene selection consists of identifying a set of informative genes from microarray data to allow high predictive accuracy in human cancer classification. This task is a combinatorial search problem, and optimisation methods can be applied for its resolution. In this paper, two memetic micro-genetic algorithms (MμV1 and MμV2) with different hybridisation approaches are proposed for feature selection of cancer microarray data. Seven gene expression datasets are used for experimentation. The comparison with stochastic state-of-the-art optimisation techniques concludes that problem-dependent local search methods combined with micro-genetic algorithms improve feature selection of cancer microarray data.Fil: Rojas, Matias Gabriel. Universidad Nacional de Lujan. Centro de Investigacion Docencia y Extension En Tecnologias de la Informacion y Las Comunicaciones.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Olivera, Ana Carolina. Universidad Nacional de Cuyo. Facultad de Ingeniería; Argentina. Universidad Nacional de Lujan. Centro de Investigacion Docencia y Extension En Tecnologias de la Informacion y Las Comunicaciones.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; ArgentinaFil: Carballido, Jessica Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca. Instituto de Ciencias e Ingeniería de la Computación; ArgentinaFil: Vidal, Pablo Javier. Universidad Nacional de Cuyo. Facultad de Ingeniería; Argentina. Universidad Nacional del Sur. Departamento de Ciencias e Ingeniería de la Computación; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza; Argentin

Supervised Methods for Biomarker Detection from Microarray Experiments

Biomarkers are valuable indicators of the state of a biological system. Microarray technology has been extensively used to identify biomarkers and build computational predictive models for disease prognosis, drug sensitivity and toxicity evaluations. Activation biomarkers can be used to understand the underlying signaling cascades, mechanisms of action and biological cross talk. Biomarker detection from microarray data requires several considerations both from the biological and computational points of view. In this chapter, we describe the main methodology used in biomarkers discovery and predictive modeling and we address some of the related challenges. Moreover, we discuss biomarker validation and give some insights into multiomics strategies for biomarker detection.Non peer reviewe

Filter-Wrapper Methods For Gene Selection In Cancer Classification

In microarray gene expression studies, finding the smallest subset of informative genes from microarray datasets for clinical diagnosis and accurate cancer classification is one of the most difficult challenges in machine learning task. Many researchers have devoted their efforts to address this problem by using a filter method, a wrapper method or a combination of both approaches. A hybrid method is a hybridisation approach between filter and wrapper methods. It benefits from the speed of the filter approach and the accuracy of the wrapper approach. Several hybrid filter-wrapper methods have been proposed to select informative genes. However, hybrid methods encounter a number of limitations, which are associated with filter and wrapper approaches. The gene subset that is produced by filter approaches lacks predictiveness and robustness. The wrapper approach encounters problems of complex interactions among genes and stagnation in local optima. To address these drawbacks, this study investigates filter and wrapper methods to develop effective hybrid methods for gene selection. This study proposes new hybrid filter-wrapper methods based on Maximum Relevancy Minimum Redundancy (MRMR) as a filter approach and adapted bat-inspired algorithm (BA) as a wrapper approach. First, MRMR hybridisation and BA adaptation are investigated to resolve the gene selection problem. The proposed method is called MRMR-BA

DepthTools: an R package for a robust analysis of gene expression data

The use of DNA microarrays and oligonucleotide chips of high density in modern biomedical research provides complex, high dimensional data which have been proven to convey crucial information about gene expression levels and to play an important role in disease diagnosis. Therefore, there is a need for developing new, robust statistical techniques to analyze these data. Results: depthTools is an R package for a robust statistical analysis of gene expression data, based on an efficient implementation of a feasible notion of depth, the Modified Band Depth. This software includes several visualization and inference tools successfully applied to high dimensional gene expression data. A user-friendly interface is also provided via an R-commander plugin. Conclusion: We illustrate the utility of the depthTools package, that could be used, for instance, to achieve a better understanding of genome-level variation between tumors and to facilitate the development of personalized treatments

Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm

BACKGROUND: Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear. METHODS: This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups). RESULTS: The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance. CONCLUSIONS: This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion

Contributions `a la r´esolution de probl`emes d’optimisation combinatoires NP-difficiles

Cette th�ese porte sur des algorithmes e�caces pour la r�esolution de probl�emes d'optimisation combinatoires NP-di�ciles, avec deux contributions. La premi�ere contribution consiste en la proposition d'un nouvel algorithme multiob- jectif hybride combinant un algorithme g�en�etique avec un op�erateur de recherche bas�e sur l'optimisation par essaims de particules. L'objectif de cette hybridation est de surmonter les situations de convergence lente des algorithmes g�en�etiques multiobjectifs lors de la r�e- solution de probl�emes di�ciles �a plus de deux objectifs. Dans le sch�ema hybride propos�e, un algorithme g�en�etique multiobjectif Pareto applique p�eriodiquement un algorithme d'op- timisation par essaim de particules pour optimiser une fonction d'adaptation scalaire sur une population archive. Deux variantes de cet algorithme hybride sont propos�ees et adap- t�ees pour la r�esolution du probl�eme du sac �a dos multiobjectif. Les r�esultats exp�erimentaux prouvent que les algorithmes hybrides sont plus performants que les algorithmes standards. La seconde contribution concerne l'am�elioration d'un algorithme heuristique de recherche locale dit PALS (pour l'anglais Problem Aware Local Search) sp�eci�que au probl�eme d'as- semblage de fragments d'ADN, un probl�eme d'optimisation combinatoire NP-di�cile en bio-informatique des s�equences. Deux modi�cations �a PALS sont propos�ees. La premi�ere modi�cation permet d'�eviter les ph�enom�enes de convergence pr�ematur�ee vers des optima lo- caux. La seconde modi�cation conduit �a une r�eduction signi�cative des temps de calcul tout en conservant la pr�ecision des r�esultats. Apr�es des exp�erimentations r�ealis�ees sur les jeux de donn�ees disponibles dans la litt�erature, nos nouvelles variantes de PALS se r�ev�elent tr�es comp�etitives par rapport aux variantes existantes et �a d'autres algorithmes d'assemblage

Document analysis by means of data mining techniques

The huge amount of textual data produced everyday by scientists, journalists and Web users, allows investigating many different aspects of information stored in the published documents. Data mining and information retrieval techniques are exploited to manage and extract information from huge amount of unstructured textual data. Text mining also known as text data mining is the processing of extracting high quality information (focusing relevance, novelty and interestingness) from text by identifying patterns etc. Text mining typically involves the process of structuring input text by means of parsing and other linguistic features or sometimes by removing extra data and then finding patterns from structured data. Patterns are then evaluated at last and interpretation of output is performed to accomplish the desired task. Recently, text mining has got attention in several fields such as in security (involves analysis of Internet news), for commercial (for search and indexing purposes) and in academic departments (such as answering query). Beyond searching the documents consisting the words given in a user query, text mining may provide direct answer to user by semantic web for content based (content meaning and its context). It can also act as intelligence analyst and can also be used in some email spam filters for filtering out unwanted material. Text mining usually includes tasks such as clustering, categorization, sentiment analysis, entity recognition, entity relation modeling and document summarization. In particular, summarization approaches are suitable for identifying relevant sentences that describe the main concepts presented in a document dataset. Furthermore, the knowledge existed in the most informative sentences can be employed to improve the understanding of user and/or community interests. Different approaches have been proposed to extract summaries from unstructured text documents. Some of them are based on the statistical analysis of linguistic features by means of supervised machine learning or data mining methods, such as Hidden Markov models, neural networks and Naive Bayes methods. An appealing research field is the extraction of summaries tailored to the major user interests. In this context, the problem of extracting useful information according to domain knowledge related to the user interests is a challenging task. The main topics have been to study and design of novel data representations and data mining algorithms useful for managing and extracting knowledge from unstructured documents. This thesis describes an effort to investigate the application of data mining approaches, firmly established in the subject of transactional data (e.g., frequent itemset mining), to textual documents. Frequent itemset mining is a widely exploratory technique to discover hidden correlations that frequently occur in the source data. Although its application to transactional data is well-established, the usage of frequent itemsets in textual document summarization has never been investigated so far. A work is carried on exploiting frequent itemsets for the purpose of multi-document summarization so a novel multi-document summarizer, namely ItemSum (Itemset-based Summarizer) is presented, that is based on an itemset-based model, i.e., a framework comprise of frequent itemsets, taken out from the document collection. Highly representative and not redundant sentences are selected for generating summary by considering both sentence coverage, with respect to a sentence relevance score, based on tf-idf statistics, and a concise and highly informative itemset-based model. To evaluate the ItemSum performance a suite of experiments on a collection of news articles has been performed. Obtained results show that ItemSum significantly outperforms mostly used previous summarizers in terms of precision, recall, and F-measure. We also validated our approach against a large number of approaches on the DUC’04 document collection. Performance comparisons, in terms of precision, recall, and F-measure, have been performed by means of the ROUGE toolkit. In most cases, ItemSum significantly outperforms the considered competitors. Furthermore, the impact of both the main algorithm parameters and the adopted model coverage strategy on the summarization performance are investigated as well. In some cases, the soundness and readability of the generated summaries are unsatisfactory, because the summaries do not cover in an effective way all the semantically relevant data facets. A step beyond towards the generation of more accurate summaries has been made by semantics-based summarizers. Such approaches combine the use of general-purpose summarization strategies with ad-hoc linguistic analysis. The key idea is to also consider the semantics behind the document content to overcome the limitations of general-purpose strategies in differentiating between sentences based on their actual meaning and context. Most of the previously proposed approaches perform the semantics-based analysis as a preprocessing step that precedes the main summarization process. Therefore, the generated summaries could not entirely reflect the actual meaning and context of the key document sentences. In contrast, we aim at tightly integrating the ontology-based document analysis into the summarization process in order to take the semantic meaning of the document content into account during the sentence evaluation and selection processes. With this in mind, we propose a new multi-document summarizer, namely Yago-based Summarizer, that integrates an established ontology-based entity recognition and disambiguation step. Named Entity Recognition from Yago ontology is being used for the task of text summarization. The Named Entity Recognition (NER) task is concerned with marking occurrences of a specific object being mentioned. These mentions are then classified into a set of predefined categories. Standard categories include “person”, “location”, “geo-political organization”, “facility”, “organization”, and “time”. The use of NER in text summarization improved the summarization process by increasing the rank of informative sentences. To demonstrate the effectiveness of the proposed approach, we compared its performance on the DUC’04 benchmark document collections with that of a large number of state-of-the-art summarizers. Furthermore, we also performed a qualitative evaluation of the soundness and readability of the generated summaries and a comparison with the results that were produced by the most effective summarizers. A parallel effort has been devoted to integrating semantics-based models and the knowledge acquired from social networks into a document summarization model named as SociONewSum. The effort addresses the sentence-based generic multi-document summarization problem, which can be formulated as follows: given a collection of news articles ranging over the same topic, the goal is to extract a concise yet informative summary, which consists of most salient document sentences. An established ontological model has been used to improve summarization performance by integrating a textual entity recognition and disambiguation step. Furthermore, the analysis of the user-generated content coming from Twitter has been exploited to discover current social trends and improve the appealing of the generated summaries. An experimental evaluation of the SociONewSum performance was conducted on real English-written news article collections and Twitter posts. The achieved results demonstrate the effectiveness of the proposed summarizer, in terms of different ROUGE scores, compared to state-of-the-art open source summarizers as well as to a baseline version of the SociONewSum summarizer that does not perform any UGC analysis. Furthermore, the readability of the generated summaries has also been analyzed