Search results for: Curse of dimensionality

Authors: Elif Derya UBEYLI, Inan GULER

Abstract:

A new approach based on the consideration that electroencephalogram (EEG) signals are chaotic signals was presented for automated diagnosis of electroencephalographic changes. This consideration was tested successfully using the nonlinear dynamics tools, like the computation of Lyapunov exponents. This paper presented the usage of statistics over the set of the Lyapunov exponents in order to reduce the dimensionality of the extracted feature vectors. Since classification is more accurate when the pattern is simplified through representation by important features, feature extraction and selection play an important role in classifying systems such as neural networks. Multilayer perceptron neural network (MLPNN) architectures were formulated and used as basis for detection of electroencephalographic changes. Three types of EEG signals (EEG signals recorded from healthy volunteers with eyes open, epilepsy patients in the epileptogenic zone during a seizure-free interval, and epilepsy patients during epileptic seizures) were classified. The selected Lyapunov exponents of the EEG signals were used as inputs of the MLPNN trained with Levenberg- Marquardt algorithm. The classification results confirmed that the proposed MLPNN has potential in detecting the electroencephalographic changes.

Keywords: Chaotic signal, Electroencephalogram (EEG) signals, Feature extraction/selection, Lyapunov exponents

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Authors: Malay K. Pakhira, Rajat K. De

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In this paper, a pipelined version of genetic algorithm, called PLGA, and a corresponding hardware platform are described. The basic operations of conventional GA (CGA) are made pipelined using an appropriate selection scheme. The selection operator, used here, is stochastic in nature and is called SA-selection. This helps maintaining the basic generational nature of the proposed pipelined GA (PLGA). A number of benchmark problems are used to compare the performances of conventional roulette-wheel selection and the SA-selection. These include unimodal and multimodal functions with dimensionality varying from very small to very large. It is seen that the SA-selection scheme is giving comparable performances with respect to the classical roulette-wheel selection scheme, for all the instances, when quality of solutions and rate of convergence are considered. The speedups obtained by PLGA for different benchmarks are found to be significant. It is shown that a complete hardware pipeline can be developed using the proposed scheme, if parallel evaluation of the fitness expression is possible. In this connection a low-cost but very fast hardware evaluation unit is described. Results of simulation experiments show that in a pipelined hardware environment, PLGA will be much faster than CGA. In terms of efficiency, PLGA is found to outperform parallel GA (PGA) also.

Keywords: Hardware evaluation, Hardware pipeline, Optimization, Pipelined genetic algorithm, SA-selection.

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Authors: Lavanya Srinivasan

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Biometric identification is to identify unique features in a person like fingerprints, iris, ear, and voice recognition that need the subject's permission and physical contact. Gait biometric is used to identify the unique gait of the person by extracting moving features. The main advantage of gait biometric to identify the gait of a person at a distance, without any physical contact. In this work, the gait biometric is used for person re-identification. The person walking naturally compared with the same person walking with bag, coat and case recorded using long wave infrared, short wave infrared, medium wave infrared and visible cameras. The videos are recorded in rural and in urban environments. The pre-processing technique includes human identified using You Only Look Once, background subtraction, silhouettes extraction and synthesis Gait Entropy Image by averaging the silhouettes. The moving features are extracted from the Gait Entropy Energy Image. The extracted features are dimensionality reduced by the Principal Component Analysis and recognized using different classifiers. The comparative results with the different classifier show that Linear Discriminant Analysis outperform other classifiers with 95.8% for visible in the rural dataset and 94.8% for longwave infrared in the urban dataset.

Keywords: biometric, gait, silhouettes, You Only Look Once

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Authors: Kasthurirangan Gopalakrishnan, Siddhartha Khaitan, Anshu Manik

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Cluster analysis is the name given to a diverse collection of techniques that can be used to classify objects (e.g. individuals, quadrats, species etc). While Kohonen's Self-Organizing Feature Map (SOFM) or Self-Organizing Map (SOM) networks have been successfully applied as a classification tool to various problem domains, including speech recognition, image data compression, image or character recognition, robot control and medical diagnosis, its potential as a robust substitute for clustering analysis remains relatively unresearched. SOM networks combine competitive learning with dimensionality reduction by smoothing the clusters with respect to an a priori grid and provide a powerful tool for data visualization. In this paper, SOM is used for creating a toroidal mapping of two-dimensional lattice to perform cluster analysis on results of a chemical analysis of wines produced in the same region in Italy but derived from three different cultivators, referred to as the “wine recognition data" located in the University of California-Irvine database. The results are encouraging and it is believed that SOM would make an appealing and powerful decision-support system tool for clustering tasks and for data visualization.

Keywords: Artificial neural networks, cluster analysis, Kohonen maps, wine recognition.

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Authors: N. Patten, T. M. Young, P. Griffin

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Preliminary results for a new flat plate test facility are presented here in the form of Computational Fluid Dynamics (CFD), flow visualisation, pressure measurements and thermal anemometry. The results from the CFD and flow visualisation show the effectiveness of the plate design, with the trailing edge flap anchoring the stagnation point on the working surface and reducing the extent of the leading edge separation. The flow visualization technique demonstrates the two-dimensionality of the flow in the location where the thermal anemometry measurements are obtained. Measurements of the boundary layer mean velocity profiles compare favourably with the Blasius solution, thereby allowing for comparison of future measurements with the wealth of data available on zero pressure gradient Blasius flows. Results for the skin friction, boundary layer thickness, frictional velocity and wall shear stress are shown to agree well with the Blasius theory, with a maximum experimental deviation from theory of 5%. Two turbulence generating grids have been designed and characterized and it is shown that the turbulence decay downstream of both grids agrees with established correlations. It is also demonstrated that there is little dependence of turbulence on the freestream velocity.

Keywords: CFD, Flow Visualisation, Thermal Anemometry, Turbulence Grids.

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Authors: Dyah E. Herwindiati

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A clustering is process to identify a homogeneous groups of object called as cluster. Clustering is one interesting topic on data mining. A group or class behaves similarly characteristics. This paper discusses a robust clustering process for data images with two reduction dimension approaches; i.e. the two dimensional principal component analysis (2DPCA) and principal component analysis (PCA). A standard approach to overcome this problem is dimension reduction, which transforms a high-dimensional data into a lower-dimensional space with limited loss of information. One of the most common forms of dimensionality reduction is the principal components analysis (PCA). The 2DPCA is often called a variant of principal component (PCA), the image matrices were directly treated as 2D matrices; they do not need to be transformed into a vector so that the covariance matrix of image can be constructed directly using the original image matrices. The decomposed classical covariance matrix is very sensitive to outlying observations. The objective of paper is to compare the performance of robust minimizing vector variance (MVV) in the two dimensional projection PCA (2DPCA) and the PCA for clustering on an arbitrary data image when outliers are hiden in the data set. The simulation aspects of robustness and the illustration of clustering images are discussed in the end of paper

Keywords: Breakdown point, Consistency, 2DPCA, PCA, Outlier, Vector Variance

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Authors: Dima Stopel, Zvi Boger, Robert Moskovitch, Yuval Shahar, Yuval Elovici

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Computer worm detection is commonly performed by antivirus software tools that rely on prior explicit knowledge of the worm-s code (detection based on code signatures). We present an approach for detection of the presence of computer worms based on Artificial Neural Networks (ANN) using the computer's behavioral measures. Identification of significant features, which describe the activity of a worm within a host, is commonly acquired from security experts. We suggest acquiring these features by applying feature selection methods. We compare three different feature selection techniques for the dimensionality reduction and identification of the most prominent features to capture efficiently the computer behavior in the context of worm activity. Additionally, we explore three different temporal representation techniques for the most prominent features. In order to evaluate the different techniques, several computers were infected with five different worms and 323 different features of the infected computers were measured. We evaluated each technique by preprocessing the dataset according to each one and training the ANN model with the preprocessed data. We then evaluated the ability of the model to detect the presence of a new computer worm, in particular, during heavy user activity on the infected computers.

Keywords: Artificial Neural Networks, Feature Selection, Temporal Analysis, Worm Detection.

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Authors: Fouad Salha , X. Guillaud

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Directional over current relays (DOCR) are commonly used in power system protection as a primary protection in distribution and sub-transmission electrical systems and as a secondary protection in transmission systems. Coordination of protective relays is necessary to obtain selective tripping. In this paper, an approach for efficiency reduction of DOCRs nonlinear optimum coordination (OC) is proposed. This was achieved by modifying the objective function and relaxing several constraints depending on the four constraints classification, non-valid, redundant, pre-obtained and valid constraints. According to this classification, the far end fault effect on the objective function and constraints, and in consequently on relay operating time, was studied. The study was carried out, firstly by taking into account the near-end and far-end faults in DOCRs coordination problem formulation; and then faults very close to the primary relays (nearend faults). The optimal coordination (OC) was achieved by simultaneously optimizing all variables (TDS and Ip) in nonlinear environment by using of Genetic algorithm nonlinear programming techniques. The results application of the above two approaches on 6-bus and 26-bus system verify that the far-end faults consideration on OC problem formulation don-t lose the optimality.

Keywords: Backup/Primary relay, Coordination time interval (CTI), directional over current relays, Genetic algorithm, time dial setting (TDS), pickup current setting (Ip), nonlinear programming.

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Authors: C. Villegas-Quezada, J. Climent

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Several works regarding facial recognition have dealt with methods which identify isolated characteristics of the face or with templates which encompass several regions of it. In this paper a new technique which approaches the problem holistically dispensing with the need to identify geometrical characteristics or regions of the face is introduced. The characterization of a face is achieved by randomly sampling selected attributes of the pixels of its image. From this information we construct a set of data, which correspond to the values of low frequencies, gradient, entropy and another several characteristics of pixel of the image. Generating a set of “p" variables. The multivariate data set with different polynomials minimizing the data fitness error in the minimax sense (L∞ - Norm) is approximated. With the use of a Genetic Algorithm (GA) it is able to circumvent the problem of dimensionality inherent to higher degree polynomial approximations. The GA yields the degree and values of a set of coefficients of the polynomials approximating of the image of a face. By finding a family of characteristic polynomials from several variables (pixel characteristics) for each face (say Fi ) in the data base through a resampling process the system in use, is trained. A face (say F ) is recognized by finding its characteristic polynomials and using an AdaBoost Classifier from F -s polynomials to each of the Fi -s polynomials. The winner is the polynomial family closer to F -s corresponding to target face in data base.

Keywords: AdaBoost Classifier, Holistic Face Recognition, Minimax Multivariate Approximation, Genetic Algorithm.

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Authors: Rabab M. Ramadan, Elaraby A. Elgallad

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With extensive application, the performance of unimodal biometrics systems has to face a diversity of problems such as signal and background noise, distortion, and environment differences. Therefore, multimodal biometric systems are proposed to solve the above stated problems. This paper introduces a bimodal biometric recognition system based on the extracted features of the human palm print and iris. Palm print biometric is fairly a new evolving technology that is used to identify people by their palm features. The iris is a strong competitor together with face and fingerprints for presence in multimodal recognition systems. In this research, we introduced an algorithm to the combination of the palm and iris-extracted features using a texture-based descriptor, the Scale Invariant Feature Transform (SIFT). Since the feature sets are non-homogeneous as features of different biometric modalities are used, these features will be concatenated to form a single feature vector. Particle swarm optimization (PSO) is used as a feature selection technique to reduce the dimensionality of the feature. The proposed algorithm will be applied to the Institute of Technology of Delhi (IITD) database and its performance will be compared with various iris recognition algorithms found in the literature.

Keywords: Iris recognition, particle swarm optimization, feature extraction, feature selection, palm print, scale invariant feature transform.

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Authors: Gaetano Zazzaro, Angelo Martone, Roberto V. Montaquila, Luigi Pavone

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Seizure is the main factor that affects the quality of life of epileptic patients. The diagnosis of epilepsy, and hence the identification of epileptogenic zone, is commonly made by using continuous Electroencephalogram (EEG) signal monitoring. Seizure identification on EEG signals is made manually by epileptologists and this process is usually very long and error prone. The aim of this paper is to describe an automated method able to detect seizures in EEG signals, using knowledge discovery in database process and data mining methods and algorithms, which can support physicians during the seizure detection process. Our detection method is based on Artificial Neural Network classifier, trained by applying the multilayer perceptron algorithm, and by using a software application, called Training Builder that has been developed for the massive extraction of features from EEG signals. This tool is able to cover all the data preparation steps ranging from signal processing to data analysis techniques, including the sliding window paradigm, the dimensionality reduction algorithms, information theory, and feature selection measures. The final model shows excellent performances, reaching an accuracy of over 99% during tests on data of a single patient retrieved from a publicly available EEG dataset.

Keywords: Artificial Neural Network, Data Mining, Electroencephalogram, Epilepsy, Feature Extraction, Seizure Detection, Signal Processing.

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Authors: M. Analoui, M. Fadavi Amiri

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The design of a pattern classifier includes an attempt to select, among a set of possible features, a minimum subset of weakly correlated features that better discriminate the pattern classes. This is usually a difficult task in practice, normally requiring the application of heuristic knowledge about the specific problem domain. The selection and quality of the features representing each pattern have a considerable bearing on the success of subsequent pattern classification. Feature extraction is the process of deriving new features from the original features in order to reduce the cost of feature measurement, increase classifier efficiency, and allow higher classification accuracy. Many current feature extraction techniques involve linear transformations of the original pattern vectors to new vectors of lower dimensionality. While this is useful for data visualization and increasing classification efficiency, it does not necessarily reduce the number of features that must be measured since each new feature may be a linear combination of all of the features in the original pattern vector. In this paper a new approach is presented to feature extraction in which feature selection, feature extraction, and classifier training are performed simultaneously using a genetic algorithm. In this approach each feature value is first normalized by a linear equation, then scaled by the associated weight prior to training, testing, and classification. A knn classifier is used to evaluate each set of feature weights. The genetic algorithm optimizes a vector of feature weights, which are used to scale the individual features in the original pattern vectors in either a linear or a nonlinear fashion. By this approach, the number of features used in classifying can be finely reduced.

Keywords: Feature reduction, genetic algorithm, pattern classification, nearest neighbor rule classifiers (k-NNR).

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Authors: Hiram I. Beltrán, Arturo Rojo-Domínguez, Máximo Eduardo Sánchez Gutiérrez, Pedro Pablo González Pérez

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A computational platform is presented in this contribution. It has been designed as a virtual laboratory to be used for exploring optimization algorithms in biological problems. This platform is built on a blackboard-based agent architecture. As a test case, the version of the platform presented here is devoted to the study of protein folding, initially with a bead-like description of the chain and with the widely used model of hydrophobic and polar residues (HP model). Some details of the platform design are presented along with its capabilities and also are revised some explorations of the protein folding problems with different types of discrete space. It is also shown the capability of the platform to incorporate specific tools for the structural analysis of the runs in order to understand and improve the optimization process. Accordingly, the results obtained demonstrate that the ensemble of computational tools into a single platform is worthwhile by itself, since experiments developed on it can be designed to fulfill different levels of information in a self-consistent fashion. By now, it is being explored how an experiment design can be useful to create a computational agent to be included within the platform. These inclusions of designed agents –or software pieces– are useful for the better accomplishment of the tasks to be developed by the platform. Clearly, while the number of agents increases the new version of the virtual laboratory thus enhances in robustness and functionality.

Keywords: genetic algorithms, multi-agent systems, bioinformatics, optimization, protein folding, structural biology.

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Authors: Akinola Ikudayisi, Josiah Adeyemo

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The correct estimation of reference evapotranspiration (ETₒ) is required for effective irrigation water resources planning and management. However, there are some variables that must be considered while estimating and modeling ETₒ. This study therefore determines the multivariate analysis of correlated variables involved in the estimation and modeling of ETₒ at Vaalharts irrigation scheme (VIS) in South Africa using Principal Component Analysis (PCA) technique. Weather and meteorological data between 1994 and 2014 were obtained both from South African Weather Service (SAWS) and Agricultural Research Council (ARC) in South Africa for this study. Average monthly data of minimum and maximum temperature (°C), rainfall (mm), relative humidity (%), and wind speed (m/s) were the inputs to the PCA-based model, while ETₒ is the output. PCA technique was adopted to extract the most important information from the dataset and also to analyze the relationship between the five variables and ETₒ. This is to determine the most significant variables affecting ETₒ estimation at VIS. From the model performances, two principal components with a variance of 82.7% were retained after the eigenvector extraction. The results of the two principal components were compared and the model output shows that minimum temperature, maximum temperature and windspeed are the most important variables in ETₒ estimation and modeling at VIS. In order words, ETₒ increases with temperature and windspeed. Other variables such as rainfall and relative humidity are less important and cannot be used to provide enough information about ETₒ estimation at VIS. The outcome of this study has helped to reduce input variable dimensionality from five to the three most significant variables in ETₒ modelling at VIS, South Africa.

Keywords: Irrigation, principal component analysis, reference evapotranspiration, Vaalharts.

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Authors: Abeer Aljohani

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The COVID-19 virus spread has been one of the extreme pandemics across the globe. It is also referred as corona virus which is a contagious disease that continuously mutates into numerous variants. Currently, the B.1.1.529 variant labeled as Omicron is detected in South Africa. The huge spread of COVID-19 disease has affected several lives and has surged exceptional pressure on the healthcare systems worldwide. Also, everyday life and the global economy have been at stake. Numerous COVID-19 cases have produced a huge burden on hospitals as well as health workers. To reduce this burden, this paper predicts COVID-19 disease based on the symptoms and medical history of the patient. As machine learning is a widely accepted area and gives promising results for healthcare, this research presents an architecture for COVID-19 detection using ML techniques integrated with feature dimensionality reduction. This paper uses a standard University of California Irvine (UCI) dataset for predicting COVID-19 disease. This dataset comprises symptoms of 5434 patients. This paper also compares several supervised ML techniques on the presented architecture. The architecture has also utilized 10-fold cross validation process for generalization and Principal Component Analysis (PCA) technique for feature reduction. Standard parameters are used to evaluate the proposed architecture including F1-Score, precision, accuracy, recall, Receiver Operating Characteristic (ROC) and Area under Curve (AUC). The results depict that Decision tree, Random Forest and neural networks outperform all other state-of-the-art ML techniques. This result can be used to effectively identify COVID-19 infection cases.

Keywords: Supervised machine learning, COVID-19 prediction, healthcare analytics, Random Forest, Neural Network.

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Authors: Daniel Schwarz, Jan Fivaz, Alessia Neuroni

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Although digitization is a buzzword in almost every election campaign, the political parties leave voters largely in the dark about their specific positions on digital issues. In the run-up to the 2019 elections in Switzerland, the ‘Digitization Monitor’ project (DMP) was launched in order to change this situation. Within the framework of the DMP, all 4,736 candidates were surveyed about their digital policy positions and values. The DMP is designed as a digital policy supplement to the existing ‘smartvote’ voting advice application. This enabled a direct comparison of the digital policy attitudes according to the DMP with the topics of the ‘smartvote’ questionnaire which are comprehensive in content but mainly related to conventional policy areas. This paper’s main research goal is to analyze and visualize possible differences between conventional and digital policy areas in terms of response patterns between and within political parties. The analysis is based on dimensionality reduction methods (multidimensional scaling and principal component analysis) for the visualization of inter-party differences, and on standard deviation as a measure of variation for the evaluation of intra-party unity. The results reveal that digital issues show a lower degree of inter-party polarization compared to conventional policy areas. Thus, the parties have more common ground in issues on digitization than in conventional policy areas. In contrast, the study reveals a mixed picture regarding intra-party unity. Homogeneous parties show a lower degree of unity in digitization issues whereas parties with heterogeneous positions in conventional areas have more united positions in digital areas. All things considered, the findings are encouraging as less polarized conditions apply to the debate on digital development compared to conventional politics. For the future, it would be desirable if in further countries similar projects to the DMP could emerge to broaden the basis for conclusions.

Keywords: Comparison of political issue dimensions, digital awareness of candidates, digital policy space, party positions on digital issues.

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Authors: M.K. Bhuyan, Aragala Jagan.

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Current image-based individual human recognition methods, such as fingerprints, face, or iris biometric modalities generally require a cooperative subject, views from certain aspects, and physical contact or close proximity. These methods cannot reliably recognize non-cooperating individuals at a distance in the real world under changing environmental conditions. Gait, which concerns recognizing individuals by the way they walk, is a relatively new biometric without these disadvantages. The inherent gait characteristic of an individual makes it irreplaceable and useful in visual surveillance. In this paper, an efficient gait recognition system for human identification by extracting two features namely width vector of the binary silhouette and the MPEG-7-based region-based shape descriptors is proposed. In the proposed method, foreground objects i.e., human and other moving objects are extracted by estimating background information by a Gaussian Mixture Model (GMM) and subsequently, median filtering operation is performed for removing noises in the background subtracted image. A moving target classification algorithm is used to separate human being (i.e., pedestrian) from other foreground objects (viz., vehicles). Shape and boundary information is used in the moving target classification algorithm. Subsequently, width vector of the outer contour of binary silhouette and the MPEG-7 Angular Radial Transform coefficients are taken as the feature vector. Next, the Principal Component Analysis (PCA) is applied to the selected feature vector to reduce its dimensionality. These extracted feature vectors are used to train an Hidden Markov Model (HMM) for identification of some individuals. The proposed system is evaluated using some gait sequences and the experimental results show the efficacy of the proposed algorithm.

Keywords: Gait Recognition, Gaussian Mixture Model, PrincipalComponent Analysis, MPEG-7 Angular Radial Transform.

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Authors: Kottaridi Klimentia, Demopoulos Vasilis, Sidiropoulos Anastasios, Ihara Diego, Nikolaidis Vasileios, Antonopoulos Dimitrios

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Aflatoxins are highly poisonous and carcinogenic compounds produced by species of the genus Aspergillus spp. that can infect a variety of agricultural foods, including dried figs. Biological and environmental factors, such as population, pathogenicity and aflatoxinogenic capacity of the strains, topography, soil and climate parameters of the fig orchards are believed to have a strong effect on aflatoxin levels. Existing methods for aflatoxin detection and measurement, such as high-performance liquid chromatography (HPLC), and enzyme-linked immunosorbent assay (ELISA), can provide accurate results, but the procedures are usually time-consuming, sample-destructive and expensive. Predicting aflatoxin levels prior to crop harvest is useful for minimizing the health and financial impact of a contaminated crop. Consequently, there is interest in developing a tool that predicts aflatoxin levels based on topography and soil analysis data of fig orchards. This paper describes the development of a risk assessment tool for the contamination of aflatoxin on dried figs, based on the location and altitude of the fig orchards, the population of the fungus Aspergillus spp. in the soil, and soil parameters such as pH, saturation percentage (SP), electrical conductivity (EC), organic matter, particle size analysis (sand, silt, clay), concentration of the exchangeable cations (Ca, Mg, K, Na), extractable P and trace of elements (B, Fe, Mn, Zn and Cu), by employing machine learning methods. In particular, our proposed method integrates three machine learning techniques i.e., dimensionality reduction on the original dataset (Principal Component Analysis), metric learning (Mahalanobis Metric for Clustering) and K-nearest Neighbors learning algorithm (KNN), into an enhanced model, with mean performance equal to 85% by terms of the Pearson Correlation Coefficient (PCC) between observed and predicted values.

Keywords: aflatoxins, Aspergillus spp., dried figs, k-nearest neighbors, machine learning, prediction

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Authors: D. S. A. Nanayakkara, K. J. P. G. Perera

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E-commerce platforms have revolutionized the shopping experience, offering convenient ways for consumers to make purchases. To improve interactions with customers and optimize marketing strategies, it is essential for businesses to understand user behavior, preferences, and needs on these platforms. This paper focuses on recommending businesses to customize interactions with users based on their behavioral patterns, leveraging data-driven analysis and machine learning techniques. Businesses can improve engagement and boost the adoption of e-commerce platforms by aligning behavioral patterns with user goals of usability and satisfaction. We propose TheAnalyzer, a clustering-based system designed to enhance business productivity by analyzing user-profiles and improving human-computer interaction. TheAnalyzer seamlessly integrates with business applications, collecting relevant data points based on users' natural interactions without additional burdens such as questionnaires or surveys. It defines five key user analytics as features for its dataset, which are easily captured through users' interactions with e-commerce platforms. This research presents a study demonstrating the successful distinction of users into specific groups based on the five key analytics considered by TheAnalyzer. With the assistance of domain experts, customized business rules can be attached to each group, enabling TheAnalyzer to influence business applications and provide an enhanced personalized user experience. The outcomes are evaluated quantitatively and qualitatively, demonstrating that utilizing TheAnalyzer’s capabilities can optimize business outcomes, enhance customer satisfaction, and drive sustainable growth. The findings of this research contribute to the advancement of personalized interactions in e-commerce platforms. By leveraging user behavioral patterns and analyzing both new and existing users, businesses can effectively tailor their interactions to improve customer satisfaction, loyalty and ultimately drive sales.

Keywords: Data clustering, data standardization, dimensionality reduction, human-computer interaction, user profiling.

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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

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Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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