A novel fuzzy and multi-objective evolutionary algorithm based gene assignment for clustering short time series expression data

Conventional clustering algorithms based on Euclidean distance or Pearson correlation coefficient are not able to include order information in the distance metric and also unable to distinguish between random and real biological patterns. We present template based clustering algorithm for time series gene expression data. Template profiles are defined based on up-down regulation of genes between consecutive time points. Assignment of genes to templates is based on fuzzy membership function. Multi-objective evolutionary algorithm is used to determine compact clusters with varying number of templates. Statistical significance of each template is determined using permutation based non-parametric test. Statistically significant profiles are further tested for their biological relevance using gene ontology analysis. The algorithm was able to distinguish between real and noisy pattern when tested on artificial and real biological data. The proposed algorithm has shown better or similar performance compared to STEM and better than k-means on a real biological data

A Comprehensive Survey on Particle Swarm Optimization Algorithm and Its Applications

Particle swarm optimization (PSO) is a heuristic global optimization method, proposed originally by Kennedy and Eberhart in 1995. It is now one of the most commonly used optimization techniques. This survey presented a comprehensive investigation of PSO. On one hand, we provided advances with PSO, including its modifications (including quantum-behaved PSO, bare-bones PSO, chaotic PSO, and fuzzy PSO), population topology (as fully connected, von Neumann, ring, star, random, etc.), hybridization (with genetic algorithm, simulated annealing, Tabu search, artificial immune system, ant colony algorithm, artificial bee colony, differential evolution, harmonic search, and biogeography-based optimization), extensions (to multiobjective, constrained, discrete, and binary optimization), theoretical analysis (parameter selection and tuning, and convergence analysis), and parallel implementation (in multicore, multiprocessor, GPU, and cloud computing forms). On the other hand, we offered a survey on applications of PSO to the following eight fields: electrical and electronic engineering, automation control systems, communication theory, operations research, mechanical engineering, fuel and energy, medicine, chemistry, and biology. It is hoped that this survey would be beneficial for the researchers studying PSO algorithms

A Survey on Soft Subspace Clustering

Subspace clustering (SC) is a promising clustering technology to identify clusters based on their associations with subspaces in high dimensional spaces. SC can be classified into hard subspace clustering (HSC) and soft subspace clustering (SSC). While HSC algorithms have been extensively studied and well accepted by the scientific community, SSC algorithms are relatively new but gaining more attention in recent years due to better adaptability. In the paper, a comprehensive survey on existing SSC algorithms and the recent development are presented. The SSC algorithms are classified systematically into three main categories, namely, conventional SSC (CSSC), independent SSC (ISSC) and extended SSC (XSSC). The characteristics of these algorithms are highlighted and the potential future development of SSC is also discussed.Comment: This paper has been published in Information Sciences Journal in 201

Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

Monte Carlo Method with Heuristic Adjustment for Irregularly Shaped Food Product Volume Measurement

Volume measurement plays an important role in the production and processing of food products. Various methods have been proposed to measure the volume of food products with irregular shapes based on 3D reconstruction. However, 3D reconstruction comes with a high-priced computational cost. Furthermore, some of the volume measurement methods based on 3D reconstruction have a low accuracy. Another method for measuring volume of objects uses Monte Carlo method. Monte Carlo method performs volume measurements using random points. Monte Carlo method only requires information regarding whether random points fall inside or outside an object and does not require a 3D reconstruction. This paper proposes volume measurement using a computer vision system for irregularly shaped food products without 3D reconstruction based on Monte Carlo method with heuristic adjustment. Five images of food product were captured using five cameras and processed to produce binary images. Monte Carlo integration with heuristic adjustment was performed to measure the volume based on the information extracted from binary images. The experimental results show that the proposed method provided high accuracy and precision compared to the water displacement method. In addition, the proposed method is more accurate and faster than the space carving method

Metaheuristic design of feedforward neural networks: a review of two decades of research

Over the past two decades, the feedforward neural network (FNN) optimization has been a key interest among the researchers and practitioners of multiple disciplines. The FNN optimization is often viewed from the various perspectives: the optimization of weights, network architecture, activation nodes, learning parameters, learning environment, etc. Researchers adopted such different viewpoints mainly to improve the FNN's generalization ability. The gradient-descent algorithm such as backpropagation has been widely applied to optimize the FNNs. Its success is evident from the FNN's application to numerous real-world problems. However, due to the limitations of the gradient-based optimization methods, the metaheuristic algorithms including the evolutionary algorithms, swarm intelligence, etc., are still being widely explored by the researchers aiming to obtain generalized FNN for a given problem. This article attempts to summarize a broad spectrum of FNN optimization methodologies including conventional and metaheuristic approaches. This article also tries to connect various research directions emerged out of the FNN optimization practices, such as evolving neural network (NN), cooperative coevolution NN, complex-valued NN, deep learning, extreme learning machine, quantum NN, etc. Additionally, it provides interesting research challenges for future research to cope-up with the present information processing era

Advances in Evolutionary Algorithms

With the recent trends towards massive data sets and significant computational power, combined with evolutionary algorithmic advances evolutionary computation is becoming much more relevant to practice. Aim of the book is to present recent improvements, innovative ideas and concepts in a part of a huge EA field

Temporal Information in Data Science: An Integrated Framework and its Applications

Data science is a well-known buzzword, that is in fact composed of two distinct keywords, i.e., data and science. Data itself is of great importance: each analysis task begins from a set of examples. Based on such a consideration, the present work starts with the analysis of a real case scenario, by considering the development of a data warehouse-based decision support system for an Italian contact center company. Then, relying on the information collected in the developed system, a set of machine learning-based analysis tasks have been developed to answer specific business questions, such as employee work anomaly detection and automatic call classification. Although such initial applications rely on already available algorithms, as we shall see, some clever analysis workflows had also to be developed. Afterwards, continuously driven by real data and real world applications, we turned ourselves to the question of how to handle temporal information within classical decision tree models. Our research brought us the development of J48SS, a decision tree induction algorithm based on Quinlan's C4.5 learner, which is capable of dealing with temporal (e.g., sequential and time series) as well as atemporal (such as numerical and categorical) data during the same execution cycle. The decision tree has been applied into some real world analysis tasks, proving its worthiness. A key characteristic of J48SS is its interpretability, an aspect that we specifically addressed through the study of an evolutionary-based decision tree pruning technique. Next, since a lot of work concerning the management of temporal information has already been done in automated reasoning and formal verification fields, a natural direction in which to proceed was that of investigating how such solutions may be combined with machine learning, following two main tracks. First, we show, through the development of an enriched decision tree capable of encoding temporal information by means of interval temporal logic formulas, how a machine learning algorithm can successfully exploit temporal logic to perform data analysis. Then, we focus on the opposite direction, i.e., that of employing machine learning techniques to generate temporal logic formulas, considering a natural language processing scenario. Finally, as a conclusive development, the architecture of a system is proposed, in which formal methods and machine learning techniques are seamlessly combined to perform anomaly detection and predictive maintenance tasks. Such an integration represents an original, thrilling research direction that may open up new ways of dealing with complex, real-world problems.Data science is a well-known buzzword, that is in fact composed of two distinct keywords, i.e., data and science. Data itself is of great importance: each analysis task begins from a set of examples. Based on such a consideration, the present work starts with the analysis of a real case scenario, by considering the development of a data warehouse-based decision support system for an Italian contact center company. Then, relying on the information collected in the developed system, a set of machine learning-based analysis tasks have been developed to answer specific business questions, such as employee work anomaly detection and automatic call classification. Although such initial applications rely on already available algorithms, as we shall see, some clever analysis workflows had also to be developed. Afterwards, continuously driven by real data and real world applications, we turned ourselves to the question of how to handle temporal information within classical decision tree models. Our research brought us the development of J48SS, a decision tree induction algorithm based on Quinlan's C4.5 learner, which is capable of dealing with temporal (e.g., sequential and time series) as well as atemporal (such as numerical and categorical) data during the same execution cycle. The decision tree has been applied into some real world analysis tasks, proving its worthiness. A key characteristic of J48SS is its interpretability, an aspect that we specifically addressed through the study of an evolutionary-based decision tree pruning technique. Next, since a lot of work concerning the management of temporal information has already been done in automated reasoning and formal verification fields, a natural direction in which to proceed was that of investigating how such solutions may be combined with machine learning, following two main tracks. First, we show, through the development of an enriched decision tree capable of encoding temporal information by means of interval temporal logic formulas, how a machine learning algorithm can successfully exploit temporal logic to perform data analysis. Then, we focus on the opposite direction, i.e., that of employing machine learning techniques to generate temporal logic formulas, considering a natural language processing scenario. Finally, as a conclusive development, the architecture of a system is proposed, in which formal methods and machine learning techniques are seamlessly combined to perform anomaly detection and predictive maintenance tasks. Such an integration represents an original, thrilling research direction that may open up new ways of dealing with complex, real-world problems