Selection of relevant features in a fuzzy genetic learning algorithm

A novel ensemble fuzzy classification model in SARS-CoV-2 B-cell epitope identification for development of protein-based vaccine

B-cell epitope prediction research has received growing interest since the development of the first method. B-cell epitope identification with the aid of an accurate prediction method is one of the most important steps in epitope-based vaccine development, immunodiagnostic testing, antibody production, disease diagnosis, and treatment. Nevertheless, using experimental methods in epitope mapping is very time-consuming, costly, and labor-intensive. Therefore, although successful predictions with in silico methods are very important in epitope prediction, there are limited studies in this area. The aim of this study is to propose a new approach for successfully predicting B-cell epitopes for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, the SARS-CoV B-cell epitope prediction performances of different fuzzy learning classification models genetic cooperative competitive learning (GCCL), fuzzy genetics-based machine learning (GBML), Chi’s method (CHI), Ishibuchi’s method with weight factor (W), structural learning algorithm on vague environment (SLAVE) and the state-of-the-art ensemble fuzzy classification model were compared. The obtained results showed that the proposed ensemble approach has the lowest error in SARS-CoV B-cell epitope estimation compared to the base fuzzy learners (average error rates; ensemble fuzzy=8.33, GCCL=30.42, GBML=23.82, CHI=29.17, W=46.25, and SLAVE=20.42). SARS-CoV and SARS-CoV-2 have high genome similarities. Therefore, the most successful method determined for SARS-CoV B-cell epitope prediction was used in SARS-CoV-2 cell epitope prediction. Finally, the eventual B-cell epitope prediction results obtained for SARS-CoV-2 with the ensemble fuzzy classification model were compared with the epitope sequences predicted by the BepiPred server and immunoinformatics studies in the literature for the same protein sequences according to VaxiJen 2.0 scores. We hope that the developed epitope prediction method will help design effective vaccines and drugs against future outbreaks of the coronavirus family, especially SARS-CoV-2 and its possible mutations.

Max-plus and min-plus projection autoassociative morphological memories and their compositions for pattern classification

Autoassociative morphological memories (AMMs) are robust and computationally efficient memory models with unlimited storage capacity. In this paper, we present the max-plus and min-plus projection autoassociative morphological memories (PAMMs) as well as their compositions. Briefly, the max-plus PAMM yields the largest max-plus combination of the stored vectors which is less than or equal to the input. Dually, the vector recalled by the min-plus PAMM corresponds to the smallest min-plus combination which is larger than or equal to the input. Apart from unlimited absolute storage capacity and one step retrieval, PAMMs and their compositions exhibit an excellent noise tolerance. Furthermore, the new memories yielded quite promising results in classification problems with a large number of features and classes.

Application of artificial neural networks to investigate one-carbon metabolism in Alzheimer's disease and healthy matched individuals

Folate metabolism, also known as one-carbon metabolism, is required for several cellular processes including DNA synthesis, repair and methylation. Impairments of this pathway have been often linked to Alzheimer's disease (AD). In addition, increasing evidence from large scale case-control studies, genome-wide association studies, and meta-analyses of the literature suggest that polymorphisms of genes involved in one-carbon metabolism influence the levels of folate, homocysteine and vitamin B12, and might be among AD risk factors. We analyzed a dataset of 30 genetic and biochemical variables (folate, homocysteine, vitamin B12, and 27 genotypes generated by nine common biallelic polymorphisms of genes involved in folate metabolism) obtained from 40 late-onset AD patients and 40 matched controls to assess the predictive capacity of Artificial Neural Networks (ANNs) in distinguish consistently these two different conditions and to identify the variables expressing the maximal amount of relevant information to the condition of being affected by dementia of Alzheimer's type. Moreover, we constructed a semantic connectivity map to offer some insight regarding the complex biological connections among the studied variables and the two conditions (being AD or control). TWIST system, an evolutionary algorithm able to remove redundant and noisy information from complex data sets, selected 16 variables that allowed specialized ANNs to discriminate between AD and control subjects with over 90% accuracy. The semantic connectivity map provided important information on the complex biological connections among one-carbon metabolic variables highlighting those most closely linked to the AD condition.

HANDLING HIGHLY-DIMENSIONAL CLASSIFICATION TASKS WITH HIERARCHICAL GENETIC FUZZY RULE-BASED CLASSIFIERS

Many modern classification tasks are defined in highly-dimensional feature spaces. The derivation of high-performing genetic fuzzy rule-based classification systems (GFRBCSs) in such scenarios is a non-trivial task. This paper presents a framework for increasing the performance of GFRBCSs by creating a hierarchical fuzzy rule-based classifier. The proposed system is constructed through repeated invocations to a base GFRBCS procedure, considering at each step an input space fuzzy partition of a certain granularity. The best performing rules are inserted in the hierarchical rule base and the process is repeated again, considering a thicker granularity. The employed boosting scheme guides the algorithm in creating new rules to treat uncovered or misclassified patterns, thus monotonically increasing the performance of the classifier. Extensive experimental analysis in a number of real-world high-dimensional classification tasks proves the effectiveness of the proposed approach in increasing the performance of the base classifier, maintaining its interpretability to a considerable degree.

A FILTER PROPOSAL FOR INCLUDING FEATURE CONSTRUCTION IN A GENETIC LEARNING ALGORITHM

In system identification process often a predetermined set of features is used. However, in many cases it is difficult to know a priori whether the selected features were really the more appropriate ones. This is the reason why the feature construction techniques have been very interesting in many applications. Thus, the current proposal introduces the use of these techniques in order to improve the description of fuzzy rule-based systems. In particular, the idea is to include feature construction in a genetic learning algorithm. The construction of attributes in this study will be restricted to the inclusion of functions defined on the initial attributes of the system. Since the number of functions and the number of attributes can be very large, a filter model, based on the use of information measures, is introduced. In this way, the genetic algorithm only needs to explore the particular new features that may be of greater interest to the final identification of the system. In order to manage the knowledge provided by the new attributes based on the use of functions we propose a new model of rule by extending a basic learning fuzzy rule-based model. Finally, we show the experimental study associated with this work.

A Novel Generic Hebbian Ordering-Based Fuzzy Rule Base Reduction Approach to Mamdani Neuro-Fuzzy System

There are two important issues in neuro-fuzzy modeling: (1) interpretability—the ability to describe the behavior of the system in an interpretable way—and (2) accuracy—the ability to approximate the outcome of the system accurately. As these two objectives usually exert contradictory requirements on the neuro-fuzzy model, certain compromise has to be undertaken. This letter proposes a novel rule reduction algorithm, namely, Hebb rule reduction, and an iterative tuning process to balance interpretability and accuracy. The Hebb rule reduction algorithm uses Hebbian ordering, which represents the degree of coverage of the samples by the rule, as an importance measure of each rule to merge the membership functions and hence reduces the number of the rules. Similar membership functions (MFs) are merged by a specified similarity measure in an order of Hebbian importance, and the resultant equivalent rules are deleted from the rule base. The rule with a higher Hebbian importance will be retained among a set of rules. The MFs are tuned through the least mean square (LMS) algorithm to reduce the modeling error. The tuning of the MFs and the reduction of the rules proceed iteratively to achieve a balance between interpretability and accuracy. Three published data sets by Nakanishi (Nakanishi, Turksen, & Sugeno, 1993), the Pat synthetic data set (Pal, Mitra, & Mitra, 2003), and the traffic flow density prediction data set are used as benchmarks to demonstrate the effectiveness of the proposed method. Good interpretability, as well as high modeling accuracy, are derivable simultaneously and are suitably benchmarked against other well-established neuro-fuzzy models.

MODULAR FEATURE SELECTION USING RELATIVE IMPORTANCE FACTORS

Feature selection plays an important role in finding relevant or irrelevant features in classification. Genetic algorithms (GAs) have been used as conventional methods for classifiers to adaptively evolve solutions for classification problems. In this paper, we explore the use of feature selection in modular GA-based classification. We propose a new feature selection technique, Relative Importance Factor (RIF), to find irrelevant features in the feature space of each module. By removing these features, we aim to improve classification accuracy and reduce the dimensionality of classification problems. Benchmark classification data sets are used to evaluate the proposed approaches. The experiment results show that RIF can be used to determine irrelevant features and help achieve higher classification accuracy with the feature space dimension reduced. The complexity of the resulting rule sets is also reduced which means the modular classifiers with irrelevant features removed will be able to classify data with a higher throughput.

Genetically-designed Neural Networks for Error Reduction in an Optimized Biomechanical Model of the Human Elbow Joint Complex

A real time dynamic biomechanical model of the human elbow joint has been used as the first step in the process of calculating time varying joint position from the electromyograms (EMGs) of eight muscles crossing the joint. Since calculation of position has a high sensitivity to errors in the model torque calculation, a genetic algorithm (GA) neural network (NN) has been developed for automatic error reduction in the dynamic model. Genetic algorithms are used to design many neural network structures during a preliminary trial effort, and then each network's performance is ranked to choose a trained network that represents the most accurate result. Experimental results from three subjects have shown model error reduction in 84.2% of the data sets from a subject on which the model had been trained, and 52.6% of the data sets from the subjects on which the model had not been trained. Furthermore, the GA networks reduced the error standard deviation across all subjects, showing that progress in error reduction was made evenly across all data sets.

An Online GA-Based Output-Feedback Direct Adaptive Fuzzy-Neural Controller for Uncertain Nonlinear Systems

In this paper, we propose a novel design of a GA-based output-feedback direct adaptive fuzzy-neural controller (GODAF controller) for uncertain nonlinear dynamical systems. The weighting factors of the direct adaptive fuzzy-neural controller can successfully be tuned online via a GA approach. Because of the capability of genetic algorithms (GAs) in directed random search for global optimization, one is used to evolutionarily obtain the optimal weighting factors for the fuzzy-neural network. Specifically, we use a reduced-form genetic algorithm (RGA) to adjust the weightings of the fuzzy-neural network. In RGA, a sequential-search -based crossover point (SSCP) method determines a suitable crossover point before a single gene crossover actually takes place so that the speed of searching for an optimal weighting vector of the fuzzy-neural network can be improved. A new fitness function for online tuning the weighting vector of the fuzzy-neural controller is established by the Lyapunov design approach. A supervisory controller is incorporated into the GODAF controller to guarantee the stability of the closed-loop nonlinear system. Examples of nonlinear systems controlled by the GODAF controller are demonstrated to illustrate the effectiveness of the proposed method.