A hybrid method based on artificial immune system and k-NN algorithm for better prediction of protein cellular localization sites

The use of machine learning tools in biological data analysis is increasing gradually. This is mainly because the effectiveness of classification and recognition systems has improved in a great deal to help medical experts in diagnosing. In this paper, we investigate the performance of an artificial immune system based k-nearest neighbors algorithm with and without cross-validation in a class of imbalanced problems from bioinformatics field. Furthermore, we used an unsupervised artificial immune system algorithm for reduction training data dimension and k-nearest neighbors algorithm for classification purpose. The conducted experiments showed the effectiveness of the proposed schema. By selecting the E. coli database, we could compare our classification accuracy with other methods which were presented in the literature. The proposed hybrid system produced much more accurate results than the Horton and Nakai's proposal [P. Horton, K. Nakai, A probabilistic classification system for predicting the cellular localization sites of proteins, in: Proceedings of the 4th International Conference on Intelligent Systems for Molecular Biology, AAAI Press, St. Louis, 1996, pp. 109–115; P. Horton, K. Nakai, Better prediction of protein cellular localization sites with the k-nearest neighbors classifier, in: Proceedings of Intelligent Systems in Molecular Biology, Halkidiki, Greece, 1997, pp. 368–383]. Besides the accuracy improvement, one of the important aspects of the proposed methodology is the complexity. As the artificial immune system provided data reduction, the training complexity of the proposed system is considerably low against the k-nearest neighbors classifier.     

Modified nearest neighbour classifier for hyperspectral data classification

A modified k-nearest neighbour (k-NN) classifier is proposed for supervised remote sensing classification of hyperspectral data. To compare its performance in terms of classification accuracy and computational cost, k-NN and a back-propagation neural network classifier were used. A classification accuracy of 91.2% was achieved by the proposed classifier with the data set used. Results from this study suggest that the accuracy achieved with this classifier is significantly better than the k-NN and comparable to a back-propagation neural network. Comparison in terms of computational cost also suggests the effectiveness of modified k-NN classifier for hyperspectral data classification. A fuzzy entropy-based filter approach was used for feature selection to compare the performance of modified and k-NN classifiers with a reduced data set. The results suggest a significant increase in classification accuracy by the modified k-NN classifier in comparison with k-NN classifier with selected features.     

Classification of Parkinson's disease using feature weighting method on the basis of fuzzy C-means clustering

This study presents the application of fuzzy c-means (FCM) clustering-based feature weighting (FCMFW) for the detection of Parkinson's disease (PD). In the classification of PD dataset taken from University of California – Irvine machine learning database, practical values of the existing traditional and non-standard measures for distinguishing healthy people from people with PD by detecting dysphonia were applied to the input of FCMFW. The main aims of FCM clustering algorithm are both to transform from a linearly non-separable dataset to a linearly separable one and to increase the distinguishing performance between classes. The weighted PD dataset is presented to k-nearest neighbour (k-NN) classifier system. In the classification of PD, the various k-values in k-NN classifier were used and compared with each other. Also, the effects of k-values in k-NN classifier on the classification of Parkinson disease datasets have been investigated and the best k-value found. The experimental results have demonstrated that the combination of the proposed weighting method called FCMFW and k-NN classifier has obtained very promising results on the classification of PD.     

Hybrid intelligent techniques for MRI brain images classification

This paper presents a hybrid technique for the classification of the magnetic resonance images (MRI). The proposed hybrid technique consists of three stages, namely, feature extraction, dimensionality reduction, and classification. In the first stage, we have obtained the features related to MRI images using discrete wavelet transformation (DWT). In the second stage, the features of magnetic resonance images have been reduced, using principal component analysis (PCA), to the more essential features. In the classification stage, two classifiers have been developed. The first classifier based on feed forward back-propagation artificial neural network (FP-ANN) and the second classifier is based on k-nearest neighbor (k-NN). The classifiers have been used to classify subjects as normal or abnormal MRI human images. A classification with a success of 97% and 98% has been obtained by FP-ANN and k-NN, respectively. This result shows that the proposed technique is robust and effective compared with other recent work.     

The effect to diagnostic accuracy of decision tree classifier of fuzzy and k-NN based weighted pre-processing methods to diagnosis of erythemato-squamous diseases

This paper presents a novel method for differential diagnosis of erythemato-squamous disease. The proposed method is based on fuzzy weighted pre-processing, k-NN (nearest neighbor) based weighted pre-processing, and decision tree classifier. The proposed method consists of three parts. In the first part, we have used decision tree classifier to diagnosis erythemato-squamous disease. In the second part, first of all, fuzzy weighted pre-processing, which can improved by ours, is a new method and applied to inputs erythemato-squamous disease dataset. Then, the obtained weighted inputs were classified using decision tree classifier. In the third part, k-NN based weighted pre-processing, which can improved by ours, is a new method and applied to inputs erythemato-squamous disease dataset. Then, the obtained weighted inputs were classified via decision tree classifier. The employed decision tree classifier, fuzzy weighted pre-processing decision tree classifier, and k-NN based weighted pre-processing decision tree classifier have reached to 86.18, 97.57, and 99.00% classification accuracies using 20-fold cross validation, respectively.     

A multiple-point spatially weighted k-NN classifier for remote sensing

A novel classification method based on multiple-point statistics (MPS) is proposed in this article. The method is a modified version of the spatially weighted k-nearest neighbour (k-NN) classifier, which accounts for spatial correlation through weights applied to neighbouring pixels. The MPS characterizes the spatial correlation between multiple points of land-cover classes by learning local patterns in a training image. This rich spatial information is then converted to multiple-point probabilities and incorporated into the k-NN classifier. Experiments were conducted in two study areas, in which the proposed method for classification was tested on a WorldView-2 sub-scene of the Sichuan mountainous area and an IKONOS image of the Beijing urban area. The multiple-point weighted k-NN method (MPk-NN) was compared to several alternatives; including the traditional k-NN and two previously published spatially weighted k-NN schemes; the inverse distance weighted k-NN, and the geostatistically weighted k-NN. The classifiers using the Bayesian and Support Vector Machine (SVM) methods, and these classifiers weighted with spatial context using the Markov random field (MRF) model, were also introduced to provide a benchmark comparison with the MPk-NN method. The proposed approach increased classification accuracy significantly relative to the alternatives, and it is, thus, recommended for the identification of land-cover types with complex and diverse spatial distributions.     

Boosting k-nearest neighbor classifier by means of input space projection

The k-nearest neighbors classifier is one of the most widely used methods of classification due to several interesting features, such as good generalization and easy implementation. Although simple, it is usually able to match, and even beat, more sophisticated and complex methods. However, no successful method has been reported so far to apply boosting to k-NN. As boosting methods have proved very effective in improving the generalization capabilities of many classification algorithms, proposing an appropriate application of boosting to k-nearest neighbors is of great interest.Ensemble methods rely on the instability of the classifiers to improve their performance, as k-NN is fairly stable with respect to resampling, these methods fail in their attempt to improve the performance of k-NN classifier. On the other hand, k-NN is very sensitive to input selection. In this way, ensembles based on subspace methods are able to improve the performance of single k-NN classifiers. In this paper we make use of the sensitivity of k-NN to input space for developing two methods for boosting k-NN. The two approaches modify the view of the data that each classifier receives so that the accurate classification of difficult instances is favored.The two approaches are compared with the classifier alone and bagging and random subspace methods with a marked and significant improvement of the generalization error. The comparison is performed using a large test set of 45 problems from the UCI Machine Learning Repository. A further study on noise tolerance shows that the proposed methods are less affected by class label noise than the standard methods.     

A direct boosting algorithm for the k-nearest neighbor classifier via local warping of the distance metric

Though the k-nearest neighbor (k-NN) pattern classifier is an effective learning algorithm, it can result in large model sizes. To compensate, a number of variant algorithms have been developed that condense the model size of the k-NN classifier at the expense of accuracy. To increase the accuracy of these condensed models, we present a direct boosting algorithm for the k-NN classifier that creates an ensemble of models with locally modified distance weighting. An empirical study conducted on 10 standard databases from the UCI repository shows that this new Boosted k-NN algorithm has increased generalization accuracy in the majority of the datasets and never performs worse than standard k-NN.     

Best basis-based wavelet packet entropy feature extraction and hierarchical EEG classification for epileptic detection

In this study, a hierarchical electroencephalogram (EEG) classification system for epileptic seizure detection is proposed. The system includes the following three stages: (i) original EEG signals representation by wavelet packet coefficients and feature extraction using the best basis-based wavelet packet entropy method, (ii) cross-validation (CV) method together with k-Nearest Neighbor (k-NN) classifier used in the training stage to hierarchical knowledge base (HKB) construction, and (iii) in the testing stage, computing classification accuracy and rejection rate using the top-ranked discriminative rules from the HKB. The data set is taken from a publicly available EEG database which aims to differentiate healthy subjects and subjects suffering from epilepsy diseases. Experimental results show the efficiency of our proposed system. The best classification accuracy is about 100% via 2-, 5-, and 10-fold cross-validation, which indicates the proposed method has potential in designing a new intelligent EEG-based assistance diagnosis system for early detection of the electroencephalographic changes.     

Image mining by spectral features: A case study of scenery image classification

Spectral features of images, such as Gabor filters and wavelet transform can be used for texture image classification. That is, a classifier is trained based on some labeled texture features as the training set to classify unlabeled texture features of images into some pre-defined classes. The aim of this paper is twofold. First, it investigates the classification performance of using Gabor filters, wavelet transform, and their combination respectively, as the texture feature representation of scenery images (such as mountain, castle, etc.). A k-nearest neighbor (k-NN) classifier and support vector machine (SVM) are also compared. Second, three k-NN classifiers and three SVMs are combined respectively, in which each of the combined three classifiers uses one of the above three texture feature representations respectively, to see whether combining multiple classifiers can outperform the single classifier in terms of scenery image classification. The result shows that a single SVM using Gabor filters provides the highest classification accuracy than the other two spectral features and the combined three k-NN classifiers and three SVMs.     

Locally adaptive <Emphasis Type="Italic">k</Emphasis> parameter selection for nearest neighbor classifier: one nearest cluster

The k nearest neighbors (k-NN) classification technique has a worldly wide fame due to its simplicity, effectiveness, and robustness. As a lazy learner, k-NN is a versatile algorithm and is used in many fields. In this classifier, the k parameter is generally chosen by the user, and the optimal k value is found by experiments. The chosen constant k value is used during the whole classification phase. The same k value used for each test sample can decrease the overall prediction performance. The optimal k value for each test sample should vary from others in order to have more accurate predictions. In this study, a dynamic k value selection method for each instance is proposed. This improved classification method employs a simple clustering procedure. In the experiments, more accurate results are found. The reasons of success have also been understood and presented.     

Hierarchical distance learning by stacking nearest neighbor classifiers

We propose a two-layer decision fusion technique, called Fuzzy Stacked Generalization (FSG) which establishes a hierarchical distance learning architecture. At the base-layer of an FSG, fuzzy k-NN classifiers receive different feature sets each of which is extracted from the same dataset to gain multiple views of the dataset. At the meta-layer, first, a fusion space is constructed by aggregating decision spaces of all the base-layer classifiers. Then, a fuzzy k-NN classifier is trained in the fusion space by minimizing the difference between the large sample and N-sample classification error. In order to measure the degree of collaboration among the base-layer classifiers and the diversity of the feature spaces, a new measure called, shareability, is introduced. Shearability is defined as the number of samples that are correctly classified by at least one of the base-layer classifiers in FSG. In the experiments, we observe that FSG performs better than the popular distance learning and ensemble learning algorithms when the shareability measure is large enough such that most of the samples are correctly classified by at least one of the base-layer classifiers. The relationship between the proposed and state-of-the-art diversity measures is experimentally analyzed. The tests performed on a variety of artificial and real-world benchmark datasets show that the classification performance of FSG increases compared to that of state-of-the art ensemble learning and distance learning methods as the number of classes increases.     

SVOIS: Support Vector Oriented Instance Selection for text classification

Automatic text classification is usually based on models constructed through learning from training examples. However, as the size of text document repositories grows rapidly, the storage requirements and computational cost of model learning is becoming ever higher. Instance selection is one solution to overcoming this limitation. The aim is to reduce the amount of data by filtering out noisy data from a given training dataset. A number of instance selection algorithms have been proposed in the literature, such as ENN, IB3, ICF, and DROP3. However, all of these methods have been developed for the k-nearest neighbor (k-NN) classifier. In addition, their performance has not been examined over the text classification domain where the dimensionality of the dataset is usually very high. The support vector machines (SVM) are core text classification techniques. In this study, a novel instance selection method, called Support Vector Oriented Instance Selection (SVOIS), is proposed. First of all, a regression plane in the original feature space is identified by utilizing a threshold distance between the given training instances and their class centers. Then, another threshold distance, between the identified data (forming the regression plane) and the regression plane, is used to decide on the support vectors for the selected instances. The experimental results based on the TechTC-100 dataset show the superior performance of SVOIS over other state-of-the-art algorithms. In particular, using SVOIS to select text documents allows the k-NN and SVM classifiers perform better than without instance selection.     

Adaptive soft k-nearest-neighbour classifiers

A novel classifier is introduced to overcome the limitations of the k-NN classification systems. It estimates the posterior class probabilities using a local Parzen window estimation with the k-nearest-neighbour prototypes (in the Euclidean sense) to the pattern to classify. A learning algorithm is also presented to reduce the number of data points to store. Experimental results in two hand-written classification problems demonstrate the potential of the proposed classification system.     

Evolutionary-modified fuzzy nearest-neighbor rule for pattern classification

This paper presents an improved version of the well-established k nearest neighbor (k-NN) and fuzzy NN (FNN), termed the multi-objective genetic-algorithm-modified FNN (MOGA-MFNN). The MFNN design problem is converted into a multi-modal objective maximization problem constrained by four objective functions. Thereafter, the associated parameter set of the MFNN and the feature attributes can be determined optimally and automatically via the non-dominated sorting genetic algorithm II. We introduce two new objective functions termed the Margin-I and Margin-II, which are used to improve the generalization capability of the MFNN for the unknown data, along with two existing performance functions: the geometric mean and the area under the receiver-operated characteristic curve for the training accuracy. Moreover, we proposed a novel data-dependent weight-assignment technique for local class membership functions of the MFNN. The technique enables the MFNN to determine its local neighbors adaptively through the MOGA algorithm. To expedite the classification, the MOGA-MFNN is implemented on a graphical processing unit (GPU), which significantly increases the computation speed. Furthermore, the local class-membership function of the MFNN can be computed in advance, rather than delaying it to the classification stage. This again can improve the classification speed. The MOGA-MFNN is evaluated on 20 datasets obtained from the repository of the University of California, Irvine (UCI). The experiments with rigorous statistical significance tests demonstrate that the proposed method performs competitively with the existing methods.     

Improved k-nearest neighbor classification

k-nearest neighbor (k-NN) classification is a well-known decision rule that is widely used in pattern classification. However, the traditional implementation of this method is computationally expensive. In this paper we develop two effective techniques, namely, template condensing and preprocessing, to significantly speed up k-NN classification while maintaining the level of accuracy. Our template condensing technique aims at “sparsifying” dense homogeneous clusters of prototypes of any single class. This is implemented by iteratively eliminating patterns which exhibit high attractive capacities. Our preprocessing technique filters a large portion of prototypes which are unlikely to match against the unknown pattern. This again accelerates the classification procedure considerably, especially in cases where the dimensionality of the feature space is high. One of our case studies shows that the incorporation of these two techniques to k-NN rule achieves a seven-fold speed-up without sacrificing accuracy.     

DESIGN OF A FUZZY MIN-MAX HYPERBOX CLASSIFIER USING A SUPERVISED LEARNING METHOD

ABSTRACT

This investigation proposes a fuzzy min-max hyperbox classifier to solve M-class classification problems. In the proposed fuzzy min-max hyperbox classifier, a supervised learning method is implemented to generate min-max hyperboxes for the training patterns in each class so that the generated fuzzy min-max hyperbox classifier has a perfect classification rate in the training set. However, the 100% correct classification of the training set generally leads to overfitting. In order to improve this drawback, a procedure is employed to decrease the complexity of the input decision boundaries so that the generated fuzzy hyperbox classifier has a good generalization performance. Finally, two benchmark data sets are considered to demonstrate the good performance of the proposed approach for solving this classification problem.