SIBioX: A Matrix Based Bioinformatics Analysis Tool Based on Swarm Intelligence Algorithm.

Feature selection plays an important role in data mining and pattern recognition. However, most existing feature selection methods suffer from stagnation in local optimal and/or high computational cost. In general, the feature selection process can be considered as a global optimization problem. The swarm intelligence algorithm can effectively find the optimal feature subset due to its global search ability. But it usually consumes very long running time when dealing with large data sets. In this paper, feature selection is transformed into a global optimization problem, which provides a fast and efficient method based on swarm intelligence algorithm. First, we propose a global optimization framework for filter-based feature selection and its mathematical model. Furthermore, to solve the feature selection problem for acoustic defect detection, we combine the shuffled frog leaping algorithm (SFLA) with an improved minimum-redundancy maximum-relevancy (ImRMR), named SFLA-ImRMR. In the experiments, a back propagation neural network is employed to evaluate the classification performance of the selected feature subset on the test sets of acoustic defect detection. The results show that SFLA-ImRMR achieved similar performance to the other algorithms within the shortest time.

Biological data analysis is one of the most important and challenging tasks in today's world. Automated analysis of these data is necessary for quick and accurate diagnosis. Intelligent computing-based solutions are highly required to reduce the human intervention as well as time. Artificial intelligence-based methods are frequently used to analyze and mine information from biological data. There are several machine learning-based tools available, using which powerful and intelligent automated systems can be developed. In general, the amount and volume of this kind of data is quite huge and demands sophisticated tools that can efficiently handle this data and produce results within reasonable time by extracting useful information from big data. In this chapter, the authors have made a comprehensive study about different computer-aided automated methods and tools to analyze the different types of biological data. Moreover, this chapter gives an insight about various types of biological data and their real-life applications.

Finding effective and objective biomarkers to inform the diagnosis of schizophrenia is of great importance yet remains challenging. Relatively little work has been conducted on multi-biological data for the diagnosis of schizophrenia. In this cross-sectional study, we extracted multiple features from three types of biological data, including gut microbiota data, blood data, and electroencephalogram data. Then, an integrated framework of machine learning consisting of five classifiers, three feature selection algorithms, and four cross validation methods was used to discriminate patients with schizophrenia from healthy controls. Our results show that the support vector machine classifier without feature selection using the input features of multi-biological data achieved the best performance, with an accuracy of 91.7% and an AUC of 96.5% (p < 0.05). These results indicate that multi-biological data showed better discriminative capacity for patients with schizophrenia than single biological data. The top 5% discriminative features selected from the optimal model include the gut microbiota features (Lactobacillus, Haemophilus, and Prevotella), the blood features (superoxide dismutase level, monocyte-lymphocyte ratio, and neutrophil count), and the electroencephalogram features (nodal local efficiency, nodal efficiency, and nodal shortest path length in the temporal and frontal-parietal brain areas). The proposed integrated framework may be helpful for understanding the pathophysiology of schizophrenia and developing biomarkers for schizophrenia using multi-biological data.

Internet of Things (IoT) network is growing at a tremendous speed and is expected to occupy every field in the near future. Swarm Intelligence (SI) algorithms came into existence from the inspiration of nature, especially biological systems. SI algorithms gained importance among researchers due to their properties of decentralized control, self-organised structure, scalable framework, flexible nature, and getting solution for complex problems. This chapter examines some basic SI algorithms and explores the functioning of IoT network. It aims to bestow the exploitation of swarm intelligence for the betterment of IoT.

Chapter 14 - Review on hybrid feature selection and classification of microarray gene expression data

The application of swarm intelligence (SI) in the optimization field has been gaining much popularity, and various SI algorithms have been proposed in last decade. However, with the increased number of SI algorithms, most research focuses on the implementation of a specific choice of SI algorithms, and there has been rare research analyzing the common features among SI algorithms coherently. More importantly, no general principles for the implementation and improvement of SI algorithms exist for solving various optimization problems. In this research, aiming to cover such a research gap, a unified framework towards SI is proposed inspired by the in-depth analysis of SI algorithms. The unified framework consists of the most frequently used operations and strategies derived from typical examples of SI algorithms. Following the proposed unified framework, the intrinsic features of SI algorithms can be understood straightforwardly and the implementation and improvement of SI algorithms can be achieved effortlessly, which is of great importance in practice. The numerical experiments examine the effects of the possible strategies employed in the unified framework, and provide pilot attempts to validate the performance of different combinations of strategies, which can not only facilitate specific SI algorithm application, but also can motivate SI algorithm innovation.

Value function approximation, such as Q-learning, is widely used in the discrete control rather than the continuous one because the optimal action in the discrete setting is more easily selected. Optimizing the action is a non-convex optimization problem with respect to the complex value function. Some notable studies simplify the non-convex optimization problem by assuming the value function as quadratic in the actions or by discretizing the action space. However, the performance of the output policy will decline if these studies’ premises do not hold. In order to address the problem, we propose a framework that combines swarm intelligence algorithms with value-based Reinforcement Learning, where the swarm intelligence algorithms are employed to search for the optimal action with respect to the state and the value function. To ensure the correctness of this framework, we conditionally claim the convergence rate of swarm intelligence algorithms with high probability. We then implement it by searching the batch optimal actions to various states on the GPU platform for the batch training. Furthermore, we employ the population-based atomic actions for the compatibility with the existing related work about solving discrete control problems. Four classical control models and four robot simulation environments are utilized in the comparisons. According to empirical results, our framework outputs a policy comparable with that of the policy-based algorithms by 10% timesteps in the continuous control. <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Note to Practitioners</i> —This paper is motivated by the exploration-exploitation dilemma of Reinforcement Learning to solve continuous control tasks. To balance the exploration and exploitation, the stochastic exploration and the prioritized exploration are roughly two feasible ways, where the prioritized one is a better choice due to the higher data efficiency than the stochastic one, e.g. <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\varepsilon$</tex-math> </inline-formula> -greedy. Normally, the prioritized exploration works well in the value-based Reinforcement Learning algorithms rather than the policy-based ones; meanwhile, the policy-based algorithms are more suitable to continuous control tasks than the value-based ones. To tackle this conflict, we especially design a particle swarm optimization to maximize the Q-value of action in Q-learning. Our design can be hybridized by various swarm intelligence and value-based Reinforcement Learning algorithms. Also, it can be embedded in most intelligent control systems easily. The aim of this study is to solve the continuous control tasks by value-based algorithms as the first step of applying the prioritized exploration. The simulative results verify the effectiveness and efficiency of our design.

Symmetric uncertainty-incorporated probabilistic sequence-based ant colony optimization for feature selection in classification

Advances in data collection have resulted in an exponential growth of high-dimensional microarray datasets for binary classification in bioinformatics and medical diagnostics. These datasets generally possess many features but relatively few samples, resulting in challenges associated with the “curse of dimensionality”, such as feature redundancy and an elevated risk of overfitting. While traditional feature selection approaches, such as filter-based and wrapper-based approaches, can help to reduce dimensionality, they often struggle to capture feature interactions while adequately preserving model generalization. Therefore, this paper introduces the Adaptive Cluster-Guided Simple, Fast, and Efficient (ACG-SFE) feature selection, a hybrid approach designed to address the challenges of high-dimensional microarray data in binary classification. ACG-SFE enhances the Simple, Fast, and Efficient (SFE) evolutionary feature selection model by integrating hierarchical clustering to dynamically group correlated features based on the optimal number of clusters determined by the Silhouette index, Davies-Bouldin score, and the feature-to-observation ratio while adaptively selecting representative features within clusters using mutual information and adjusting the selection threshold through a progress factor. This hybrid filter-wrapper approach improves feature interactions, effectively minimizing redundancy and overfitting while enhancing classification performance. The proposed model is assessed against four state-of-the-art evolutionary feature selection models on 11 high-dimensional microarray datasets. Experimental results indicate that ACG-SFE effectively selects a small yet pertinent feature subset, minimizing redundancy while attaining enhanced classification accuracy and F-measure. Furthermore, its reduced RMSE between train and test accuracy substantiates its capability to reduce overfitting, outperforming comparative models. These findings establish ACG-SFE as an effective feature selection model for handling high-dimensional microarray data in binary classification, enhancing classification accuracy while selecting minimal relevant features to reduce unnecessary complexity and the risk of overfitting.

Nowadays, the high-dimensionality of data causes a variety of problems in machine learning. It is necessary to reduce the feature number by selecting only the most relevant of them. Different approaches called Feature Selection are used for this task. In this paper, we propose a Feature Selection method that uses Swarm Intelligence techniques. Swarm Intelligence algorithms perform optimization by searching for optimal points in the search space. We show the usability of these techniques for solving Feature Selection and compare the performance of five major swarm algorithms: Particle Swarm Optimization, Artificial Bee Colony, Invasive Weed Optimization, Bat Algorithm, and Grey Wolf Optimizer. The accuracy of a decision tree classifier was used to evaluate the algorithms. It turned out that the dimension of the data can be reduced about two times without a loss in accuracy. Moreover, the accuracy increased when abandoning redundant features. Based on our experiments GWO turned out to be the best. It has the highest ranking on different datasets, and its average iteration number to find the best solution is 30.8. ABC obtained the lowest ranking on high-dimensional datasets.

Multimodal feature extraction and fusion for audio-visual speech recognition

Reverse engineering of gene regulatory networks (GRNs) is one of the most challenging tasks in systems biology and bioinformatics. It aims at revealing network topologies and regulation relationships between components from biological data. Owing to the development of biotechnologies, various types of biological data are collected from experiments. With the availability of these data, many methods have been developed to infer GRNs. This paper firstly provides an introduction to the basic biological background and the general idea of GRN inferences. Then, different methods are surveyed from two aspects: models that those methods are based on and inference algorithms that those methods use. The advantages and disadvantages of these models and algorithms are discussed. © 2012 Wiley Periodicals, Inc.This article is categorized under: Algorithmic Development &gt; Biological Data Mining

PurposeIt is worth mentioning that in supply chain management (SCM), managerial decisions are often based on optimization of resources. Till the early 2000s, supply chain optimization problems were being addressed by conventional programming approaches such as Linear Programming, Mixed-Integer Linear Programming and Branch-and-Bound methods. However, the solution convergence in such approaches was slow. But with the advent of Swarm Intelligence (SI)-based algorithms like particle swarm optimization and ant colony optimization, a significant improvement in solution of these problems has been observed. The purpose of this paper is to present and analyze the application of SI algorithms in SCM. The analysis will eventually lead to development of a generalized SI implementation framework for optimization problems in SCM.Design/methodology/approachA structured state-of-the-art literature review is presented, which explores the applications of SI algorithms in SCM. It reviews 56 articles published in peer-reviewed journals since 1999 and uses several classification schemes which are critical in designing and solving a supply chain optimization problem using SI algorithms.FindingsThe paper revels growth of swarm-based algorithms and seems to be dominant among all nature-inspired algorithms. The SI algorithms have been used extensively in most of the realms of supply chain network design because of the flexibility in their design and rapid convergence. Large size problems, difficult to manage using exact algorithms could be efficiently handled using SI algorithms. A generalized framework for SI implementation in SCM is proposed which is beneficial to industry practitioners and researchers.Originality/valueThe paper proposes a generic formulation of optimization problems in distribution network design, vehicle routing, resource allocation, inventory management and supplier management areas of SCM which could be solved using SI algorithms. This review also provides a generic framework for SI implementation in supply chain network design and identifies promising emerging issues for further study in this area.

Machine learning methods are used to discover complex nonlinear relationships in biological and medical data. However, sophisticated learning models are computationally unfeasible for data with millions of features. Here we introduce the first feature selection method for nonlinear learning problems that can scale up to large, ultra-high dimensional biological data. More specifically, we scale up the novel Hilbert-Schmidt Independence Criterion Lasso (HSIC Lasso) to handle millions of features with tens of thousand samples. The proposed method is guaranteed to find an optimal subset of maximally predictive features with minimal redundancy, yielding higher predictive power and improved interpretability. Its effectiveness is demonstrated through applications to classify phenotypes based on module expression in human prostate cancer patients and to detect enzymes among protein structures. We achieve high accuracy with as few as 20 out of one million features --- a dimensionality reduction of 99.998%. Our algorithm can be implemented on commodity cloud computing platforms. The dramatic reduction of features may lead to the ubiquitous deployment of sophisticated prediction models in mobile health care applications.

BackgroundFunctional characterization of single nucleotide variants (SNVs) involves two steps, the first step is to convert DNA to protein and the second step is to visualize protein sequences with their structures. As massively parallel sequencing has emerged as a leading technology in genomics, resulting in a significant increase in data volume, direct visualization of SNVs together with associated protein sequences/structures in a new user interface (UI) would be a more effective way to assess their potential effects on protein function.ResultsWe have developed BioVR, an easy-to-use interactive, virtual reality (VR)-assisted platform for integrated visual analysis of DNA/RNA/protein sequences and protein structures using Unity3D and the C# programming language. It utilizes the cutting-edge Oculus Rift, and Leap Motion hand detection, resulting in intuitive navigation and exploration of various types of biological data. Using Gria2 and its associated gene product as an example, we present this proof-of-concept software to integrate protein and nucleic acid data. For any amino acid or nucleotide of interest in the Gria2 sequence, it can be quickly linked to its corresponding location on Gria2 protein structure and visualized within VR.ConclusionsUsing innovative 3D techniques, we provide a VR-based platform for visualization of DNA/RNA sequences and protein structures in aggregate, which can be extended to view omics data.