Search results for: DNA sequences classification

Authors: Saed Khawaldeh, Mohamed Elsharnouby, Alaa Eddin Alchalabi, Usama Pervaiz, Tajwar Aleef, Vu Hoang Minh

Abstract:

Taxonomic classification has a wide-range of applications such as finding out more about the evolutionary history of organisms that can be done by making a comparison between species living now and species that lived in the past. This comparison can be made using different kinds of extracted species’ data which include DNA sequences. Compared to the estimated number of the organisms that nature harbours, humanity does not have a thorough comprehension of which specific species they all belong to, in spite of the significant development of science and scientific knowledge over many years. One of the methods that can be applied to extract information out of the study of organisms in this regard is to use the DNA sequence of a living organism as a marker, thus making it available to classify it into a taxonomy. The classification of living organisms can be done in many machine learning techniques including Neural Networks (NNs). In this study, DNA sequences classification is performed using Convolutional Neural Networks (CNNs) which is a special type of NNs.

Keywords: deep networks, convolutional neural networks, taxonomic classification, DNA sequences classification

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Authors: Yaw-Ling Lin

Abstract:

A de Bruijn graph of order k is a graph whose vertices representing all length-k sequences with edges joining pairs of vertices whose sequences have maximum possible overlap (length k−1). Every Hamiltonian cycle of this graph defines a distinct, minimum length de Bruijn sequence containing all k-mers exactly once. A Kautz sequence is the minimal generating sequence so as the sequence of minimal length that produces all possible length-k sequences with the restriction that every two consecutive alphabets in the sequences must be different. A collection of de Bruijn/Kautz sequences are orthogonal if any two sequences are of maximally differ in sequence composition; that is, the maximum length of their common substring is k. In this paper, we discuss how such a collection of (maximal) orthogonal de Bruijn/Kautz sequences can be made and use the algorithm to build up a web application service for the synthesized DNA and other related biomolecular sequences.

Keywords: biomolecular sequence synthesis, de Bruijn sequences, Eulerian cycle, Hamiltonian cycle, Kautz sequences, orthogonal sequences

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Authors: Abdesselem Dakhli, Wajdi Bellil, Chokri Ben Amar

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DNA Barcode, a short mitochondrial DNA fragment, made up of three subunits; a phosphate group, sugar and nucleic bases (A, T, C, and G). They provide good sources of information needed to classify living species. Such intuition has been confirmed by many experimental results. Species classification with DNA Barcode sequences has been studied by several researchers. The classification problem assigns unknown species to known ones by analyzing their Barcode. This task has to be supported with reliable methods and algorithms. To analyze species regions or entire genomes, it becomes necessary to use similarity sequence methods. A large set of sequences can be simultaneously compared using Multiple Sequence Alignment which is known to be NP-complete. To make this type of analysis feasible, heuristics, like progressive alignment, have been developed. Another tool for similarity search against a database of sequences is BLAST, which outputs shorter regions of high similarity between a query sequence and matched sequences in the database. However, all these methods are still computationally very expensive and require significant computational infrastructure. Our goal is to build predictive models that are highly accurate and interpretable. This method permits to avoid the complex problem of form and structure in different classes of organisms. On empirical data and their classification performances are compared with other methods. Our system consists of three phases. The first is called transformation, which is composed of three steps; Electron-Ion Interaction Pseudopotential (EIIP) for the codification of DNA Barcodes, Fourier Transform and Power Spectrum Signal Processing. The second is called approximation, which is empowered by the use of Multi Llibrary Wavelet Neural Networks (MLWNN).The third is called the classification of DNA Barcodes, which is realized by applying the algorithm of hierarchical classification.

Keywords: DNA barcode, electron-ion interaction pseudopotential, Multi Library Wavelet Neural Networks (MLWNN)

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Authors: Henni Sid Ahmed, Belbachir Mohamed Faouzi, Jean Caelen

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Behavior recognition has been studied for realizing drivers assisting system and automated navigation and is an important studied field in the intelligent Building. In this paper, a recognition method of behavior recognition separated from a real image was studied. Images were divided into several categories according to the actual weather, distance and angle of view etc. SIFT was firstly used to detect key points and describe them because the SIFT (Scale Invariant Feature Transform) features were invariant to image scale and rotation and were robust to changes in the viewpoint and illumination. My goal is to develop a robust and reliable system which is composed of two fixed cameras in every room of intelligent building which are connected to a computer for acquisition of video sequences, with a program using these video sequences as inputs, we use SIFT represented different images of video sequences, and SVM (support vector machine) Lights as a programming tool for classification of images in order to classify people’s behaviors in the intelligent building in order to give maximum comfort with optimized energy consumption.

Keywords: video analysis, people behavior, intelligent building, classification

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Authors: Lauren M. McKinnon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge

Abstract:

Background: Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Methods: Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences were analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene. Results: Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance. Discussion: Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

Keywords: codon usage bias, phylogenetics, phylogenomics, ramp sequence

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Authors: Guofan Shao, Lina Tang, Hao Zhang

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The values of image classification accuracy are affected by class size distributions and classification schemes, making it difficult to compare the performance of classification algorithms across different remote sensing data sources and classification systems. Based on the term efficacy from medicine and pharmacology, we have developed the metrics of image classification efficacy at the map and class levels. The novelty of this approach is that a baseline classification is involved in computing image classification efficacies so that the effects of class statistics are reduced. Furthermore, the image classification efficacies are interpretable and comparable, and thus, strengthen the assessment of image data classification methods. We use real-world and hypothetical examples to explain the use of image classification efficacies. The metrics of image classification efficacy meet the critical need to rectify the strategy for the assessment of image classification performance as image classification methods are becoming more diversified.

Keywords: accuracy assessment, efficacy, image classification, machine learning, uncertainty

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Authors: Ouafae Baida, Najma Hamzaoui, Maha Akbib, Abdelfettah Sedqui, Abdelouahid Lyhyaoui

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Numerous scientific works present various methods to analyze the data for several domains, specially the comparison of classifications. In our recent work, we presented a new approach to help the user choose the best classification method from the results obtained by every method, by basing itself on the distances between the trees of classification. The result of our approach was in the form of a dendrogram contains methods as a succession of connections. This approach is much needed in phylogeny analysis. This discipline is intended to analyze the sequences of biological macro molecules for information on the evolutionary history of living beings, including their relationship. The product of phylogeny analysis is a phylogenetic tree. In this paper, we recommend the use of a new method of construction the phylogenetic tree based on comparison of different classifications obtained by different molecular genes.

Keywords: hierarchical classification, classification methods, structure of tree, genes, phylogenetic analysis

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Authors: Bin Liu

Abstract:

Prokaryotic promoter, consisted of two short DNA sequences located at in -35 and -10 positions, is responsible for controlling the initiation and expression of gene expression. Different types of promoters have different functions, and their consensus sequences are similar. In addition, their consensus sequences may be different for the same type of promoter, which poses difficulties for promoter identification. Unfortunately, all existing computational methods treat promoter identification as a binary classification task and can only identify whether a query sequence belongs to a specific promoter type. It is desired to develop computational methods for effectively identifying promoters and their types. Here, a two-layer predictor is proposed to try to deal with the problem. The first layer is designed to predict whether a given sequence is a promoter and the second layer predicts the type of promoter that is judged as a promoter. Meanwhile, we also analyze the importance of feature and sequence conversation in two aspects: promoter identification and promoter type identification. To the best knowledge of ours, it is the first computational predictor to detect promoters and their types.

Keywords: promoter, promoter type, random forest, sequence information

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Authors: Paula Verdugo-Hernandez, Patricio Cumsille

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We analyze a first-class on the convergence of real number sequences, named hereafter sequences, to foster exploration and discovery of concepts through graphical representations before engaging students in proving. The main goal was to differentiate between sequences and continuous functions-of-a-real-variable and better understand concepts at an initial stage. We applied the analytic frame of mathematical working spaces, which we expect to contribute to extending to sequences since, as far as we know, it has only developed for other objects, and which is relevant to analyze how mathematical work is built systematically by connecting the epistemological and cognitive perspectives, and involving the semiotic, instrumental, and discursive dimensions.

Keywords: convergence, graphical representations, mathematical working spaces, paradigms of real analysis, real number sequences

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Authors: Yuan-Hsiang Chang, Pin-Chi Lin, Li-Der Jeng

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Advance in techniques of image and video processing has enabled the development of intelligent video surveillance systems. This study was aimed to automatically detect moving human objects and to analyze events of dual human interaction in a surveillance scene. Our system was developed in four major steps: image preprocessing, human object detection, human object tracking, and motion trajectory analysis. The adaptive background subtraction and image processing techniques were used to detect and track moving human objects. To solve the occlusion problem during the interaction, the Kalman filter was used to retain a complete trajectory for each human object. Finally, the motion trajectory analysis was developed to distinguish between the interaction and non-interaction events based on derivatives of trajectories related to the speed of the moving objects. Using a database of 60 video sequences, our system could achieve the classification accuracy of 80% in interaction events and 95% in non-interaction events, respectively. In summary, we have explored the idea to investigate a system for the automatic classification of events for interaction and non-interaction events using surveillance cameras. Ultimately, this system could be incorporated in an intelligent surveillance system for the detection and/or classification of abnormal or criminal events (e.g., theft, snatch, fighting, etc.).

Keywords: motion detection, motion tracking, trajectory analysis, video surveillance

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Authors: Lamyaa Gamal El-Deen Taha, Ashraf Sharawi

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China launched satellite GF-2 in 2014. This study deals with comparing nearest neighbor object-based classification and neural network classification methods for classification of the fused GF-2 image. Firstly, rectification of GF-2 image was performed. Secondly, a comparison between nearest neighbor object-based classification and neural network classification for classification of fused GF-2 was performed. Thirdly, the overall accuracy of classification and kappa index were calculated. Results indicate that nearest neighbor object-based classification is better than neural network classification for urban mapping.

Keywords: GF-2 images, feature extraction-rectification, nearest neighbour object based classification, segmentation algorithms, neural network classification, multilayer perceptron

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Authors: Rami Ayadi, Mohsen Maraoui, Mounir Zrigui

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In this paper, we have presented a brief current state of the art for Arabic text representation and classification methods. We decomposed Arabic Task Classification into four categories. First we describe some algorithms applied to classification on Arabic text. Secondly, we cite all major works when comparing classification algorithms applied on Arabic text, after this, we mention some authors who proposing new classification methods and finally we investigate the impact of preprocessing on Arabic TC.

Keywords: text classification, Arabic, impact of preprocessing, classification algorithms

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Authors: Priya Arora, Ashutosh Mishra

Abstract:

Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Mpho Mokoatle, Darlington Mapiye, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

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Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on $k$-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0%, 80.5%, 80.5%, 63.6%, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms.

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Darlington Mapiye, Mpho Mokoatle, James Mashiyane, Stephanie Muller, Gciniwe Dlamini

Abstract:

Great advances in high-throughput sequencing technologies have resulted in availability of huge amounts of sequencing data in public and private repositories, enabling a holistic understanding of complex biological phenomena. Sequence data are used for a wide range of applications such as gene annotations, expression studies, personalized treatment and precision medicine. However, this rapid growth in sequence data poses a great challenge which calls for novel data processing and analytic methods, as well as huge computing resources. In this work, a machine and statistical learning approach for DNA sequence classification based on k-mer representation of sequence data is proposed. The approach is tested using whole genome sequences of Mycobacterium tuberculosis (MTB) isolates to (i) reduce the size of genomic sequence data, (ii) identify an optimum size of k-mers and utilize it to build classification models, (iii) predict the phenotype from whole genome sequence data of a given bacterial isolate, and (iv) demonstrate computing challenges associated with the analysis of whole genome sequence data in producing interpretable and explainable insights. The classification models were trained on 104 whole genome sequences of MTB isoloates. Cluster analysis showed that k-mers maybe used to discriminate phenotypes and the discrimination becomes more concise as the size of k-mers increase. The best performing classification model had a k-mer size of 10 (longest k-mer) an accuracy, recall, precision, specificity, and Matthews Correlation coeffient of 72.0 %, 80.5 %, 80.5 %, 63.6 %, and 0.4 respectively. This study provides a comprehensive approach for resampling whole genome sequencing data, objectively selecting a k-mer size, and performing classification for phenotype prediction. The analysis also highlights the importance of increasing the k-mer size to produce more biological explainable results, which brings to the fore the interplay that exists amongst accuracy, computing resources and explainability of classification results. However, the analysis provides a new way to elucidate genetic information from genomic data, and identify phenotype relationships which are important especially in explaining complex biological mechanisms

Keywords: AWD-LSTM, bootstrapping, k-mers, next generation sequencing

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Authors: Makram Ben Jeddou

Abstract:

The ABC classification is widely used by managers for inventory control. The classical ABC classification is based on the Pareto principle and according to the criterion of the annual use value only. Single criterion classification is often insufficient for a closely inventory control. Multi-criteria inventory classification models have been proposed by researchers in order to take into account other important criteria. From these models, we will consider the ZF model in order to make a sensitive analysis on the composite score calculated for each item. In fact, this score based on a normalized average between a good and a bad optimized index can affect the ABC items classification. We will then focus on the weights assigned to each index and propose a classification compromise.

Keywords: ABC classification, multi criteria inventory classification models, ZF-model

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: Kunal Shah, Swati Patel

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Many real world problems involve data which can be considered as multi-label data streams. Efficient methods exist for multi-label classification in non streaming scenarios. However, learning in evolving streaming scenarios is more challenging, as the learners must be able to adapt to change using limited time and memory. Classification is used to predict class of unseen instance as accurate as possible. Multi label classification is a variant of single label classification where set of labels associated with single instance. Multi label classification is used by modern applications, such as text classification, functional genomics, image classification, music categorization etc. This paper introduces the task of multi-label classification, methods for multi-label classification and evolution measure for multi-label classification. Also, comparative analysis of multi label classification methods on the basis of theoretical study, and then on the basis of simulation was done on various data sets.

Keywords: binary relevance, concept drift, data stream mining, MLSC, multiple window with buffer

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Authors: Rosa Figueroa, Christopher Flores

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Text categorization is the problem of assigning a new document to a set of predetermined categories, on the basis of a training set of free-text data that contains documents whose category membership is known. To train a classification model, it is necessary to extract characteristics in the form of tokens that facilitate the learning and classification process. In text categorization, the feature extraction process involves the use of word sequences also known as N-grams. In general, it is expected that documents belonging to the same category share similar features. The Smith-Waterman (SW) algorithm is a dynamic programming algorithm that performs a local sequence alignment in order to determine similar regions between two strings or protein sequences. This work explores the use of SW algorithm as an alternative to feature extraction in text categorization. The dataset used for this purpose, contains 2,610 annotated documents with the classes Obese/Non-Obese. This dataset was represented in a matrix form using the Bag of Word approach. The score selected to represent the occurrence of the tokens in each document was the term frequency-inverse document frequency (TF-IDF). In order to extract features for classification, four experiments were conducted: the first experiment used SW to extract features, the second one used unigrams (single word), the third one used bigrams (two word sequence) and the last experiment used a combination of unigrams and bigrams to extract features for classification. To test the effectiveness of the extracted feature set for the four experiments, a Support Vector Machine (SVM) classifier was tuned using 20% of the dataset. The remaining 80% of the dataset together with 5-Fold Cross Validation were used to evaluate and compare the performance of the four experiments of feature extraction. Results from the tuning process suggest that SW performs better than the N-gram based feature extraction. These results were confirmed by using the remaining 80% of the dataset, where SW performed the best (accuracy = 97.10%, weighted average F-measure = 97.07%). The second best was obtained by the combination of unigrams-bigrams (accuracy = 96.04, weighted average F-measure = 95.97) closely followed by the bigrams (accuracy = 94.56%, weighted average F-measure = 94.46%) and finally unigrams (accuracy = 92.96%, weighted average F-measure = 92.90%).

Keywords: comorbidities, machine learning, obesity, Smith-Waterman algorithm

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Authors: Karim Abouelmehdi, Loubna Dali, Elmoutaoukkil Abdelmajid, Hoda Elsayed, Eladnani Fatiha, Benihssane Abderahim

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The security of cloud services is the concern of cloud service providers. In this paper, we will mention different classifications of cloud attacks referred by specialized organizations. Each agency has its classification of well-defined properties. The purpose is to present a high-level classification of current research in cloud computing security. This classification is organized around attack strategies and corresponding defenses.

Keywords: cloud computing, classification, risk, security

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Authors: Suzan Wedyan

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Data mining is one of the main phases in the Knowledge Discovery Database (KDD) which is responsible of finding hidden and useful knowledge from databases. There are many different tasks for data mining including regression, pattern recognition, clustering, classification, and association rule. In recent years a promising data mining approach called associative classification (AC) has been proposed, AC integrates classification and association rule discovery to build classification models (classifiers). This paper surveys and critically compares several AC algorithms with reference of the different procedures are used in each algorithm, such as rule learning, rule sorting, rule pruning, classifier building, and class allocation for test cases.

Keywords: associative classification, classification, data mining, learning, rule ranking, rule pruning, prediction

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Authors: Fabio Fabris, Alex A. Freitas

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Hierarchical classification is a special type of classification task where the class labels are organised into a hierarchy, with more generic class labels being ancestors of more specific ones. Meta-learning for classification-algorithm recommendation consists of recommending to the user a classification algorithm, from a pool of candidate algorithms, for a dataset, based on the past performance of the candidate algorithms in other datasets. Meta-learning is normally used in conventional, non-hierarchical classification. By contrast, this paper proposes a meta-learning approach for more challenging task of hierarchical classification, and evaluates it in a large number of bioinformatics datasets. Hierarchical classification is especially relevant for bioinformatics problems, as protein and gene functions tend to be organised into a hierarchy of class labels. This work proposes meta-learning approach for recommending the best hierarchical classification algorithm to a hierarchical classification dataset. This work’s contributions are: 1) proposing an algorithm for splitting hierarchical datasets into new datasets to increase the number of meta-instances, 2) proposing meta-features for hierarchical classification, and 3) interpreting decision-tree meta-models for hierarchical classification algorithm recommendation.

Keywords: algorithm recommendation, meta-learning, bioinformatics, hierarchical classification

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Authors: Sujata S. Kulkarni

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Effective and efficient texture feature extraction and classification is an important problem in image understanding and recognition. This paper gives a review on effective texture classification method. The objective of the problem of texture representation is to reduce the amount of raw data presented by the image, while preserving the information needed for the task. Texture analysis is important in many applications of computer image analysis for classification include industrial and biomedical surface inspection, for example for defects and disease, ground classification of satellite or aerial imagery and content-based access to image databases.

Keywords: compressed sensing, feature extraction, image classification, texture analysis

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Authors: Tao Youjun, Zhao Younan

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The separation effect of fine coal can be improved by the process of pre-desliming. It was significantly enhanced when the fine coal was processed using Falcon concentrator with the removal of -45um coal slime. Ultrafine classification tests using Krebs classification cyclone with annular rinse water showed that increasing feeding pressure can effectively avoid the phenomena of heavy particles passing into overflow and light particles slipping into underflow. The increase of rinse water pressure could reduce the content of fine-grained particles while increasing the classification size. The increase in feeding concentration had a negative effect on the efficiency of classification, meanwhile increased the classification size due to the enhanced hindered settling caused by high underflow concentration. As a result of optimization experiments with response indicator of classification efficiency which based on orthogonal design using Design-Expert software indicated that the optimal classification efficiency reached 91.32% with the feeding pressure of 0.03MPa, the rinse water pressure of 0.02MPa and the feeding concentration of 12.5%. Meanwhile, the classification size was 49.99 μm which had a good agreement with the predicted value.

Keywords: hydrocyclone, ultrafine classification, slime, classification efficiency, classification size

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Authors: Yuhei Kunihiro, Sorin V. Sabau, Kazuhiro Shibuya

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We study the molecular evolution of insulin from the metric geometry point of view. In mathematics, and particularly in geometry, distances and metrics between objects are of fundamental importance. Using a weaker notion than the classical distance, namely the weighted quasi-metrics, one can study the geometry of biological sequences (DNA, mRNA, or proteins) space. We analyze from the geometrical point of view a family of 60 insulin homologous sequences ranging on a large variety of living organisms from human to the nematode C. elegans. We show that the distances between sequences provide important information about the evolution and function of insulin.

Keywords: metric geometry, evolution, insulin, C. elegans

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Authors: Kolade Olawande Owoeye, George R. S. Weir

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The widespread of terrorism and extremism activities on the internet has become a major threat to the government and national securities due to their potential dangers which have necessitated the need for intelligence gathering via web and real-time monitoring of potential websites for extremist activities. However, the manual classification for such contents is practically difficult or time-consuming. In response to this challenge, an automated classification system called composite technique was developed. This is a computational framework that explores the combination of both semantics and syntactic features of textual contents of a web. We implemented the framework on a set of extremist webpages dataset that has been subjected to the manual classification process. Therein, we developed a classification model on the data using J48 decision algorithm, this is to generate a measure of how well each page can be classified into their appropriate classes. The classification result obtained from our method when compared with other states of arts, indicated a 96% success rate in classifying overall webpages when matched against the manual classification.

Keywords: extremist, web pages, classification, semantics, posit

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Authors: Tamas Madl

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Sudden cardiac death (SCD) constitutes a large proportion of cardiovascular mortalities, provides little advance warning, and the risk is difficult to recognize based on ubiquitous, low cost medical equipment such as the standard, 12-lead, ten second ECG. Autonomic abnormalities have been shown to be strongly predictive of SCD risk; yet current methods are not trivially applicable to the brevity and low temporal and electrical resolution of standard ECGs. Here, we build horizontal visibility graph representations of very short inter-beat interval time series, and perform unsuper- vised representation learning in order to convert these variable size objects into fixed-length vectors preserving similarity rela- tions. We show that such representations facilitate classification into healthy vs. at-risk patients on two different datasets, the Mul- tiparameter Intelligent Monitoring in Intensive Care II and the PhysioNet Sudden Cardiac Death Holter Database. Our results suggest that graph representation learning of heartbeat interval time series facilitates robust classification even in sequences as short as ten seconds.

Keywords: sudden cardiac death, heart rate variability, ECG analysis, time series classification

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Authors: Shreya Pare, Parvin Akhter

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Remotely sensing image classification becomes a very challenging task owing to the high dimensionality of hyperspectral images. The pixel-wise classification methods fail to take the spatial structure information of an image. Therefore, to improve the performance of classification, spatial information can be integrated into the classification process. In this paper, the multilevel thresholding algorithm based on a modified fuzzy entropy function is used to perform the segmentation of hyperspectral images. The fuzzy parameters of the MFE function have been optimized by using a new meta-heuristic algorithm based on the Tree-Search algorithm. The segmented image is classified by a large distribution machine (LDM) classifier. Experimental results are shown on a hyperspectral image dataset. The experimental outputs indicate that the proposed technique (MFE-TSA-LDM) achieves much higher classification accuracy for hyperspectral images when compared to state-of-art classification techniques. The proposed algorithm provides accurate segmentation and classification maps, thus becoming more suitable for image classification with large spatial structures.

Keywords: classification, hyperspectral images, large distribution margin, modified fuzzy entropy function, multilevel thresholding, tree search algorithm, hyperspectral image classification using tree search algorithm

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Authors: Bingquan Shen

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Convolutional Neural Networks (CNN) have demonstrated their effectiveness in synthesizing 3D views of object instances at various viewpoints. Given the problem where one have limited viewpoints of a particular object for classification, we present a pose normalization architecture to transform the object to existing viewpoints in the training dataset before classification to yield better classification performance. We have demonstrated that this Pose Normalization Network (PNN) can capture the style of the target object and is able to re-render it to a desired viewpoint. Moreover, we have shown that the PNN improves the classification result for the 3D chairs dataset and ShapeNet airplanes dataset when given only images at limited viewpoint, as compared to a CNN baseline.

Keywords: convolutional neural networks, object classification, pose normalization, viewpoint invariant

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Authors: Y. Tiamaz, N. Souissi

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The purpose of this paper is to present a classification of Lean models which aims to capture all the concepts related to this approach and thus facilitate its implementation. This classification allows the identification of the most relevant models according to several dimensions. From this perspective, we present a review and an analysis of Lean models literature and we propose dimensions for the classification of the current proposals while respecting among others the axes of the Lean approach, the maturity of the models as well as their application domains. This classification allowed us to conclude that researchers essentially consider the Lean approach as a toolbox also they design their models to solve problems related to a specific environment. Since Lean approach is no longer intended only for the automotive sector where it was invented, but to all fields (IT, Hospital, ...), we consider that this approach requires a generic model that is capable of being implemented in all areas.

Keywords: lean approach, lean models, classification, dimensions, holistic view

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