Search results for: clustering analysis
27471 An Infinite Mixture Model for Modelling Stutter Ratio in Forensic Data Analysis
Authors: M. A. C. S. Sampath Fernando, James M. Curran, Renate Meyer
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Forensic DNA analysis has received much attention over the last three decades, due to its incredible usefulness in human identification. The statistical interpretation of DNA evidence is recognised as one of the most mature fields in forensic science. Peak heights in an Electropherogram (EPG) are approximately proportional to the amount of template DNA in the original sample being tested. A stutter is a minor peak in an EPG, which is not masking as an allele of a potential contributor, and considered as an artefact that is presumed to be arisen due to miscopying or slippage during the PCR. Stutter peaks are mostly analysed in terms of stutter ratio that is calculated relative to the corresponding parent allele height. Analysis of mixture profiles has always been problematic in evidence interpretation, especially with the presence of PCR artefacts like stutters. Unlike binary and semi-continuous models; continuous models assign a probability (as a continuous weight) for each possible genotype combination, and significantly enhances the use of continuous peak height information resulting in more efficient reliable interpretations. Therefore, the presence of a sound methodology to distinguish between stutters and real alleles is essential for the accuracy of the interpretation. Sensibly, any such method has to be able to focus on modelling stutter peaks. Bayesian nonparametric methods provide increased flexibility in applied statistical modelling. Mixture models are frequently employed as fundamental data analysis tools in clustering and classification of data and assume unidentified heterogeneous sources for data. In model-based clustering, each unknown source is reflected by a cluster, and the clusters are modelled using parametric models. Specifying the number of components in finite mixture models, however, is practically difficult even though the calculations are relatively simple. Infinite mixture models, in contrast, do not require the user to specify the number of components. Instead, a Dirichlet process, which is an infinite-dimensional generalization of the Dirichlet distribution, is used to deal with the problem of a number of components. Chinese restaurant process (CRP), Stick-breaking process and Pólya urn scheme are frequently used as Dirichlet priors in Bayesian mixture models. In this study, we illustrate an infinite mixture of simple linear regression models for modelling stutter ratio and introduce some modifications to overcome weaknesses associated with CRP.Keywords: Chinese restaurant process, Dirichlet prior, infinite mixture model, PCR stutter
Procedia PDF Downloads 32227470 Clustering Using Cooperative Multihop Mini-Groups in Wireless Sensor Network: A Novel Approach
Authors: Virender Ranga, Mayank Dave, Anil Kumar Verma
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Recently wireless sensor networks (WSNs) are used in many real life applications like environmental monitoring, habitat monitoring, health monitoring etc. Due to power constraint cheaper devices used in these applications, the energy consumption of each device should be kept as low as possible such that network operates for longer period of time. One of the techniques to prolong the network lifetime is an intelligent grouping of sensor nodes such that they can perform their operation in cooperative and energy efficient manner. With this motivation, we propose a novel approach by organize the sensor nodes in cooperative multihop mini-groups so that the total global energy consumption of the network can be reduced and network lifetime can be improved. Our proposed approach also reduces the number of transmitted messages inside the WSNs, which further minimizes the energy consumption of the whole network. The experimental simulations show that our proposed approach outperforms over the state-of-the-art approach in terms of stability period and aggregated data.Keywords: clustering, cluster-head, mini-group, stability period
Procedia PDF Downloads 35027469 Clustering-Based Threshold Model for Condition Rating of Concrete Bridge Decks
Authors: M. Alsharqawi, T. Zayed, S. Abu Dabous
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To ensure safety and serviceability of bridge infrastructure, accurate condition assessment and rating methods are needed to provide basis for bridge Maintenance, Repair and Replacement (MRR) decisions. In North America, the common practices to assess condition of bridges are through visual inspection. These practices are limited to detect surface defects and external flaws. Further, the thresholds that define the severity of bridge deterioration are selected arbitrarily. The current research discusses the main deteriorations and defects identified during visual inspection and Non-Destructive Evaluation (NDE). NDE techniques are becoming popular in augmenting the visual examination during inspection to detect subsurface defects. Quality inspection data and accurate condition assessment and rating are the basis for determining appropriate MRR decisions. Thus, in this paper, a novel method for bridge condition assessment using the Quality Function Deployment (QFD) theory is utilized. The QFD model is designed to provide an integrated condition by evaluating both the surface and subsurface defects for concrete bridges. Moreover, an integrated condition rating index with four thresholds is developed based on the QFD condition assessment model and using K-means clustering technique. Twenty case studies are analyzed by applying the QFD model and implementing the developed rating index. The results from the analyzed case studies show that the proposed threshold model produces robust MRR recommendations consistent with decisions and recommendations made by bridge managers on these projects. The proposed method is expected to advance the state of the art of bridges condition assessment and rating.Keywords: concrete bridge decks, condition assessment and rating, quality function deployment, k-means clustering technique
Procedia PDF Downloads 21827468 Fault-Detection and Self-Stabilization Protocol for Wireless Sensor Networks
Authors: Ather Saeed, Arif Khan, Jeffrey Gosper
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Sensor devices are prone to errors and sudden node failures, which are difficult to detect in a timely manner when deployed in real-time, hazardous, large-scale harsh environments and in medical emergencies. Therefore, the loss of data can be life-threatening when the sensed phenomenon is not disseminated due to sudden node failure, battery depletion or temporary malfunctioning. We introduce a set of partial differential equations for localizing faults, similar to Green’s and Maxwell’s equations used in Electrostatics and Electromagnetism. We introduce a node organization and clustering scheme for self-stabilizing sensor networks. Green’s theorem is applied to regions where the curve is closed and continuously differentiable to ensure network connectivity. Experimental results show that the proposed GTFD (Green’s Theorem fault-detection and Self-stabilization) protocol not only detects faulty nodes but also accurately generates network stability graphs where urgent intervention is required for dynamically self-stabilizing the network.Keywords: Green’s Theorem, self-stabilization, fault-localization, RSSI, WSN, clustering
Procedia PDF Downloads 6927467 Design of Agricultural Machinery Factory Facility Layout
Authors: Nilda Tri Putri, Muhammad Taufik
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Tools and agricultural machinery (Alsintan) is a tool used in agribusiness activities. Alsintan used to change the traditional farming systems generally use manual equipment into modern agriculture with mechanization. CV Nugraha Chakti Consultant make an action plan for industrial development Alsintan West Sumatra in 2012 to develop medium industries of Alsintan become a major industry of Alsintan, one of efforts made is increase the production capacity of the industry Alsintan. Production capacity for superior products as hydrotiller and threshers set each for 2.000 units per year. CV Citra Dragon as one of the medium industry alsintan in West Sumatra has a plan to relocate the existing plant to meet growing consumer demand each year. Increased production capacity and plant relocation plan has led to a change in the layout; therefore need to design the layout of the plant facility CV Citra Dragon. First step the to design of plant layout is design the layout of the production floor. The design of the production floor layout is done by applying group technology layout. The initial step is to do a machine grouping and part family using the Average Linkage Clustering (ALC) and Rank Order Clustering (ROC). Furthermore done independent work station design and layout design using the Modified Spanning Tree (MST). Alternative selection layout is done to select the best production floor layout between ALC and ROC cell grouping. Furthermore, to design the layout of warehouses, offices and other production support facilities. Activity Relationship Chart methods used to organize the placement of factory facilities has been designed. After structuring plan facilities, calculated cost manufacturing facility plant establishment. Type of layout is used on the production floor layout technology group. The production floor is composed of four cell machinery, assembly area and painting area. The total distance of the displacement of material in a single production amounted to 1120.16 m which means need 18,7minutes of transportation time for one time production. Alsintan Factory has designed a circular flow pattern with 11 facilities. The facilities were designed consisting of 10 rooms and 1 parking space. The measure of factory building is 84 m x 52 m.Keywords: Average Linkage Clustering (ALC), Rank Order Clustering (ROC), Modified Spanning Tree (MST), Activity Relationship Chart (ARC)
Procedia PDF Downloads 48927466 Production Optimization under Geological Uncertainty Using Distance-Based Clustering
Authors: Byeongcheol Kang, Junyi Kim, Hyungsik Jung, Hyungjun Yang, Jaewoo An, Jonggeun Choe
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It is important to figure out reservoir properties for better production management. Due to the limited information, there are geological uncertainties on very heterogeneous or channel reservoir. One of the solutions is to generate multiple equi-probable realizations using geostatistical methods. However, some models have wrong properties, which need to be excluded for simulation efficiency and reliability. We propose a novel method of model selection scheme, based on distance-based clustering for reliable application of production optimization algorithm. Distance is defined as a degree of dissimilarity between the data. We calculate Hausdorff distance to classify the models based on their similarity. Hausdorff distance is useful for shape matching of the reservoir models. We use multi-dimensional scaling (MDS) to describe the models on two dimensional space and group them by K-means clustering. Rather than simulating all models, we choose one representative model from each cluster and find out the best model, which has the similar production rates with the true values. From the process, we can select good reservoir models near the best model with high confidence. We make 100 channel reservoir models using single normal equation simulation (SNESIM). Since oil and gas prefer to flow through the sand facies, it is critical to characterize pattern and connectivity of the channels in the reservoir. After calculating Hausdorff distances and projecting the models by MDS, we can see that the models assemble depending on their channel patterns. These channel distributions affect operation controls of each production well so that the model selection scheme improves management optimization process. We use one of useful global search algorithms, particle swarm optimization (PSO), for our production optimization. PSO is good to find global optimum of objective function, but it takes too much time due to its usage of many particles and iterations. In addition, if we use multiple reservoir models, the simulation time for PSO will be soared. By using the proposed method, we can select good and reliable models that already matches production data. Considering geological uncertainty of the reservoir, we can get well-optimized production controls for maximum net present value. The proposed method shows one of novel solutions to select good cases among the various probabilities. The model selection schemes can be applied to not only production optimization but also history matching or other ensemble-based methods for efficient simulations.Keywords: distance-based clustering, geological uncertainty, particle swarm optimization (PSO), production optimization
Procedia PDF Downloads 14127465 Unseen Classes: The Paradigm Shift in Machine Learning
Authors: Vani Singhal, Jitendra Parmar, Satyendra Singh Chouhan
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Unseen class discovery has now become an important part of a machine-learning algorithm to judge new classes. Unseen classes are the classes on which the machine learning model is not trained on. With the advancement in technology and AI replacing humans, the amount of data has increased to the next level. So while implementing a model on real-world examples, we come across unseen new classes. Our aim is to find the number of unseen classes by using a hierarchical-based active learning algorithm. The algorithm is based on hierarchical clustering as well as active sampling. The number of clusters that we will get in the end will give the number of unseen classes. The total clusters will also contain some clusters that have unseen classes. Instead of first discovering unseen classes and then finding their number, we directly calculated the number by applying the algorithm. The dataset used is for intent classification. The target data is the intent of the corresponding query. We conclude that when the machine learning model will encounter real-world data, it will automatically find the number of unseen classes. In the future, our next work would be to label these unseen classes correctly.Keywords: active sampling, hierarchical clustering, open world learning, unseen class discovery
Procedia PDF Downloads 16727464 Study for an Optimal Cable Connection within an Inner Grid of an Offshore Wind Farm
Authors: Je-Seok Shin, Wook-Won Kim, Jin-O Kim
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The offshore wind farm needs to be designed carefully considering economics and reliability aspects. There are many decision-making problems for designing entire offshore wind farm, this paper focuses on an inner grid layout which means the connection between wind turbines as well as between wind turbines and an offshore substation. A methodology proposed in this paper determines the connections and the cable type for each connection section using K-clustering, minimum spanning tree and cable selection algorithms. And then, a cost evaluation is performed in terms of investment, power loss and reliability. Through the cost evaluation, an optimal layout of inner grid is determined so as to have the lowest total cost. In order to demonstrate the validity of the methodology, the case study is conducted on 240MW offshore wind farm, and the results show that it is helpful to design optimally offshore wind farm.Keywords: offshore wind farm, optimal layout, k-clustering algorithm, minimum spanning algorithm, cable type selection, power loss cost, reliability cost
Procedia PDF Downloads 38327463 Optimal Maintenance Clustering for Rail Track Components Subject to Possession Capacity Constraints
Authors: Cuong D. Dao, Rob J.I. Basten, Andreas Hartmann
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This paper studies the optimal maintenance planning of preventive maintenance and renewal activities for components in a single railway track when the available time for maintenance is limited. The rail-track system consists of several types of components, such as rail, ballast, and switches with different preventive maintenance and renewal intervals. To perform maintenance or renewal on the track, a train free period for maintenance, called a possession, is required. Since a major possession directly affects the regular train schedule, maintenance and renewal activities are clustered as much as possible. In a highly dense and utilized railway network, the possession time on the track is critical since the demand for train operations is very high and a long possession has a severe impact on the regular train schedule. We present an optimization model and investigate the maintenance schedules with and without the possession capacity constraint. In addition, we also integrate the social-economic cost related to the effects of the maintenance time to the variable possession cost into the optimization model. A numerical example is provided to illustrate the model.Keywords: rail-track components, maintenance, optimal clustering, possession capacity
Procedia PDF Downloads 25427462 Spatial Pattern and Predictors of Malaria in Ethiopia: Application of Auto Logistics Spatial Regression
Authors: Melkamu A. Zeru, Yamral M. Warkaw, Aweke A. Mitku, Muluwerk Ayele
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Introduction: Malaria is a severe health threat in the World, mainly in Africa. It is the major cause of health problems in which the risk of morbidity and mortality associated with malaria cases are characterized by spatial variations across the county. This study aimed to investigate the spatial patterns and predictors of malaria distribution in Ethiopia. Methods: A weighted sample of 15,239 individuals with rapid diagnosis tests was obtained from the Central Statistical Agency and Ethiopia malaria indicator survey of 2015. Global Moran's I and Moran scatter plots were used in determining the distribution of malaria cases, whereas the local Moran's I statistic was used in identifying exposed areas. In data manipulation, machine learning was used for variable reduction and statistical software R, Stata, and Python were used for data management and analysis. The auto logistics spatial binary regression model was used to investigate the predictors of malaria. Results: The final auto logistics regression model reported that male clients had a positive significant effect on malaria cases as compared to female clients [AOR=2.401, 95 % CI: (2.125 - 2.713)]. The distribution of malaria across the regions was different. The highest incidence of malaria was found in Gambela [AOR=52.55, 95%CI: (40.54-68.12)] followed by Beneshangul [AOR=34.95, 95%CI: (27.159 - 44.963)]. Similarly, individuals in Amhara [AOR=0.243, 95% CI:(0.1950.303],Oromiya[AOR=0.197,95%CI:(0.1580.244)],DireDawa[AOR=0.064,95%CI(0.049-0.082)],AddisAbaba[AOR=0.057,95%CI:(0.044-0.075)], Somali[AOR=0.077,95%CI:(0.059-0.097)], SNNPR[OR=0.329, 95%CI: (0.261- 0.413)] and Harari [AOR=0.256, 95%CI:(0.201 - 0.325)] were less likely to had low incidence of malaria as compared with Tigray. Furthermore, for a one-meter increase in altitude, the odds of a positive rapid diagnostic test (RDT) decrease by 1.6% [AOR = 0.984, 95% CI :( 0.984 - 0.984)]. The use of a shared toilet facility was found as a protective factor for malaria in Ethiopia [AOR=1.671, 95% CI: (1.504 - 1.854)]. The spatial autocorrelation variable changes the constant from AOR = 0.471 for logistic regression to AOR = 0.164 for auto logistics regression. Conclusions: This study found that the incidence of malaria in Ethiopia had a spatial pattern that is associated with socio-economic, demographic, and geographic risk factors. Spatial clustering of malaria cases had occurred in all regions, and the risk of clustering was different across the regions. The risk of malaria was found to be higher for those who live in soil floor-type houses as compared to those who live in cement or ceramics floor type. Similarly, households with thatched, metal and thin, and other roof-type houses have a higher risk of malaria than ceramic tiles roof houses. Moreover, using a protected anti-mosquito net reduced the risk of malaria incidence.Keywords: malaria, Ethiopia, auto logistics, spatial model, spatial clustering
Procedia PDF Downloads 2427461 Optical Flow Based System for Cross Traffic Alert
Authors: Giuseppe Spampinato, Salvatore Curti, Ivana Guarneri, Arcangelo Bruna
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This document describes an advanced system and methodology for Cross Traffic Alert (CTA), able to detect vehicles that move into the vehicle driving path from the left or right side. The camera is supposed to be not only on a vehicle still, e.g. at a traffic light or at an intersection, but also moving slowly, e.g. in a car park. In all of the aforementioned conditions, a driver’s short loss of concentration or distraction can easily lead to a serious accident. A valid support to avoid these kinds of car crashes is represented by the proposed system. It is an extension of our previous work, related to a clustering system, which only works on fixed cameras. Just a vanish point calculation and simple optical flow filtering, to eliminate motion vectors due to the car relative movement, is performed to let the system achieve high performances with different scenarios, cameras and resolutions. The proposed system just uses as input the optical flow, which is hardware implemented in the proposed platform and since the elaboration of the whole system is really speed and power consumption, it is inserted directly in the camera framework, allowing to execute all the processing in real-time.Keywords: clustering, cross traffic alert, optical flow, real time, vanishing point
Procedia PDF Downloads 19327460 Building User Behavioral Models by Processing Web Logs and Clustering Mechanisms
Authors: Madhuka G. P. D. Udantha, Gihan V. Dias, Surangika Ranathunga
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Today Websites contain very interesting applications. But there are only few methodologies to analyze User navigations through the Websites and formulating if the Website is put to correct use. The web logs are only used if some major attack or malfunctioning occurs. Web Logs contain lot interesting dealings on users in the system. Analyzing web logs has become a challenge due to the huge log volume. Finding interesting patterns is not as easy as it is due to size, distribution and importance of minor details of each log. Web logs contain very important data of user and site which are not been put to good use. Retrieving interesting information from logs gives an idea of what the users need, group users according to their various needs and improve site to build an effective and efficient site. The model we built is able to detect attacks or malfunctioning of the system and anomaly detection. Logs will be more complex as volume of traffic and the size and complexity of web site grows. Unsupervised techniques are used in this solution which is fully automated. Expert knowledge is only used in validation. In our approach first clean and purify the logs to bring them to a common platform with a standard format and structure. After cleaning module web session builder is executed. It outputs two files, Web Sessions file and Indexed URLs file. The Indexed URLs file contains the list of URLs accessed and their indices. Web Sessions file lists down the indices of each web session. Then DBSCAN and EM Algorithms are used iteratively and recursively to get the best clustering results of the web sessions. Using homogeneity, completeness, V-measure, intra and inter cluster distance and silhouette coefficient as parameters these algorithms self-evaluate themselves to input better parametric values to run the algorithms. If a cluster is found to be too large then micro-clustering is used. Using Cluster Signature Module the clusters are annotated with a unique signature called finger-print. In this module each cluster is fed to Associative Rule Learning Module. If it outputs confidence and support as value 1 for an access sequence it would be a potential signature for the cluster. Then the access sequence occurrences are checked in other clusters. If it is found to be unique for the cluster considered then the cluster is annotated with the signature. These signatures are used in anomaly detection, prevent cyber attacks, real-time dashboards that visualize users, accessing web pages, predict actions of users and various other applications in Finance, University Websites, News and Media Websites etc.Keywords: anomaly detection, clustering, pattern recognition, web sessions
Procedia PDF Downloads 28027459 A Literature Review on the Role of Local Potential for Creative Industries
Authors: Maya Irjayanti
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Local creativity utilization has been a strategic investment to be expanded as a creative industry due to its significant contribution to the national gross domestic product. Many developed and developing countries look toward creative industries as an agenda for the economic growth. This study aims to identify the role of local potential for creative industries from various empirical studies. The method performed in this study will involve a peer-reviewed journal articles and conference papers review addressing local potential and creative industries. The literature review analysis will include several steps: material collection, descriptive analysis, category selection, and material evaluation. Finally, the outcome expected provides a creative industries clustering based on the local potential of various nations. In addition, the finding of this study will be used as future research reference to explore a particular area with well-known aspects of local potential for creative industry products.Keywords: business, creativity, local potential, local wisdom
Procedia PDF Downloads 37527458 Analytical Study of Data Mining Techniques for Software Quality Assurance
Authors: Mariam Bibi, Rubab Mehboob, Mehreen Sirshar
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Satisfying the customer requirements is the ultimate goal of producing or developing any product. The quality of the product is decided on the bases of the level of customer satisfaction. There are different techniques which have been reported during the survey which enhance the quality of the product through software defect prediction and by locating the missing software requirements. Some mining techniques were proposed to assess the individual performance indicators in collaborative environment to reduce errors at individual level. The basic intention is to produce a product with zero or few defects thereby producing a best product quality wise. In the analysis of survey the techniques like Genetic algorithm, artificial neural network, classification and clustering techniques and decision tree are studied. After analysis it has been discovered that these techniques contributed much to the improvement and enhancement of the quality of the product.Keywords: data mining, defect prediction, missing requirements, software quality
Procedia PDF Downloads 46027457 Cluster Analysis and Benchmarking for Performance Optimization of a Pyrochlore Processing Unit
Authors: Ana C. R. P. Ferreira, Adriano H. P. Pereira
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Given the frequent variation of mineral properties throughout the Araxá pyrochlore deposit, even if a good homogenization work has been carried out before feeding the processing plants, an operation with quality and performance’s high variety standard is expected. These results could be improved and standardized if the blend composition parameters that most influence the processing route are determined, and then the types of raw materials are grouped by them, finally presenting a great reference with operational settings for each group. Associating the physical and chemical parameters of a unit operation through benchmarking or even an optimal reference of metallurgical recovery and product quality reflects in the reduction of the production costs, optimization of the mineral resource, and guarantee of greater stability in the subsequent processes of the production chain that uses the mineral of interest. Conducting a comprehensive exploratory data analysis to identify which characteristics of the ore are most relevant to the process route, associated with the use of Machine Learning algorithms for grouping the raw material (ore) and associating these with reference variables in the process’ benchmark is a reasonable alternative for the standardization and improvement of mineral processing units. Clustering methods through Decision Tree and K-Means were employed, associated with algorithms based on the theory of benchmarking, with criteria defined by the process team in order to reference the best adjustments for processing the ore piles of each cluster. A clean user interface was created to obtain the outputs of the created algorithm. The results were measured through the average time of adjustment and stabilization of the process after a new pile of homogenized ore enters the plant, as well as the average time needed to achieve the best processing result. Direct gains from the metallurgical recovery of the process were also measured. The results were promising, with a reduction in the adjustment time and stabilization when starting the processing of a new ore pile, as well as reaching the benchmark. Also noteworthy are the gains in metallurgical recovery, which reflect a significant saving in ore consumption and a consequent reduction in production costs, hence a more rational use of the tailings dams and life optimization of the mineral deposit.Keywords: mineral clustering, machine learning, process optimization, pyrochlore processing
Procedia PDF Downloads 14027456 Microbial Biogeography of Greek Olive Varieties Assessed by Amplicon-Based Metagenomics Analysis
Authors: Lena Payati, Maria Kazou, Effie Tsakalidou
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Table olives are one of the most popular fermented vegetables worldwide, which along with olive oil, have a crucial role in the world economy. They are highly appreciated by the consumers for their characteristic taste and pleasant aromas, while several health and nutritional benefits have been reported as well. Until recently, microbial biogeography, i.e., the study of microbial diversity over time and space, has been mainly associated with wine. However, nowadays, the term 'terroir' has been extended to other crops and food products so as to link the geographical origin and environmental conditions to quality aspects of fermented foods. Taking the above into consideration, the present study focuses on the microbial fingerprinting of the most important olive varieties of Greece with the state-of-the-art amplicon-based metagenomics analysis. Towards this, in 2019, 61 samples from 38 different olive varieties were collected at the final stage of ripening from 13 well spread geographical regions in Greece. For the metagenomics analysis, total DNA was extracted from the olive samples, and the 16S rRNA gene and ITS DNA region were sequenced and analyzed using bioinformatics tools for the identification of bacterial and yeasts/fungal diversity, respectively. Furthermore, principal component analysis (PCA) was also performed for data clustering based on the average microbial composition of all samples from each region of origin. According to the composition, results obtained, when samples were analyzed separately, the majority of both bacteria (such as Pantoea, Enterobacter, Roserbergiella, and Pseudomonas) and yeasts/fungi (such as Aureobasidium, Debaromyces, Candida, and Cladosporium) genera identified were found in all 61 samples. Even though interesting differences were observed at the relative abundance level of the identified genera, the bacterial genus Pantoea and the yeast/fungi genus Aureobasidium were the dominant ones in 35 and 40 samples, respectively. Of note, olive samples collected from the same region had similar fingerprint (genera identified and relative abundance level) regardless of the variety, indicating a potential association between the relative abundance of certain taxa and the geographical region. When samples were grouped by region of origin, distinct bacterial profiles per region were observed, which was also evident from the PCA analysis. This was not the case for the yeast/fungi profiles since 10 out of the 13 regions were grouped together mainly due to the dominance of the genus Aureobasidium. A second cluster was formed for the islands Crete and Rhodes, both of which are located in the Southeast Aegean Sea. These two regions clustered together mainly due to the identification of the genus Toxicocladosporium in relatively high abundances. Finally, the Agrinio region was separated from the others as it showed a completely different microbial fingerprinting. However, due to the limited number of olive samples from some regions, a subsequent PCA analysis with more samples from these regions is expected to yield in a more clear clustering. The present study is part of a bigger project, the first of its kind in Greece, with the ultimate goal to analyze a larger set of olive samples of different varieties and from different regions in Greece in order to have a reliable olives’ microbial biogeography.Keywords: amplicon-based metagenomics analysis, bacteria, microbial biogeography, olive microbiota, yeasts/fungi
Procedia PDF Downloads 11027455 Decision Support System in Air Pollution Using Data Mining
Authors: E. Fathallahi Aghdam, V. Hosseini
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Environmental pollution is not limited to a specific region or country; that is why sustainable development, as a necessary process for improvement, pays attention to issues such as destruction of natural resources, degradation of biological system, global pollution, and climate change in the world, especially in the developing countries. According to the World Health Organization, as a developing city, Tehran (capital of Iran) is one of the most polluted cities in the world in terms of air pollution. In this study, three pollutants including particulate matter less than 10 microns, nitrogen oxides, and sulfur dioxide were evaluated in Tehran using data mining techniques and through Crisp approach. The data from 21 air pollution measuring stations in different areas of Tehran were collected from 1999 to 2013. Commercial softwares Clementine was selected for this study. Tehran was divided into distinct clusters in terms of the mentioned pollutants using the software. As a data mining technique, clustering is usually used as a prologue for other analyses, therefore, the similarity of clusters was evaluated in this study through analyzing local conditions, traffic behavior, and industrial activities. In fact, the results of this research can support decision-making system, help managers improve the performance and decision making, and assist in urban studies.Keywords: data mining, clustering, air pollution, crisp approach
Procedia PDF Downloads 42427454 Identification of Disease Causing DNA Motifs in Human DNA Using Clustering Approach
Authors: G. Tamilpavai, C. Vishnuppriya
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Studying DNA (deoxyribonucleic acid) sequence is useful in biological processes and it is applied in the fields such as diagnostic and forensic research. DNA is the hereditary information in human and almost all other organisms. It is passed to their generations. Earlier stage detection of defective DNA sequence may lead to many developments in the field of Bioinformatics. Nowadays various tedious techniques are used to identify defective DNA. The proposed work is to analyze and identify the cancer-causing DNA motif in a given sequence. Initially the human DNA sequence is separated as k-mers using k-mer separation rule. The separated k-mers are clustered using Self Organizing Map (SOM). Using Levenshtein distance measure, cancer associated DNA motif is identified from the k-mer clusters. Experimental results of this work indicate the presence or absence of cancer causing DNA motif. If the cancer associated DNA motif is found in DNA, it is declared as the cancer disease causing DNA sequence. Otherwise the input human DNA is declared as normal sequence. Finally, elapsed time is calculated for finding the presence of cancer causing DNA motif using clustering formation. It is compared with normal process of finding cancer causing DNA motif. Locating cancer associated motif is easier in cluster formation process than the other one. The proposed work will be an initiative aid for finding genetic disease related research.Keywords: bioinformatics, cancer motif, DNA, k-mers, Levenshtein distance, SOM
Procedia PDF Downloads 18327453 Spatio-Temporal Analysis of Rabies Incidence in Herbivores of Economic Interest in Brazil
Authors: Francisco Miroslav Ulloa-Stanojlovic, Gina Polo, Ricardo Augusto Dias
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In Brazil, there is a high incidence of rabies in herbivores of economic interest (HEI) transmitted by the common vampire bat Desmodus rotundus, the presence of human rabies cases and the huge economic losses in the world's largest cattle industry, it is important to assist the National Program for Control of Rabies in herbivores in Brazil, that aims to reduce the incidence of rabies in HEI populations, mainly through epidemiological surveillance, vaccination of herbivores and control of vampire-bat roosts. Material and Methods: A spatiotemporal retrospective Kulldorff's spatial scan statistic based on a Poisson model and Monte Carlo simulation and an Anselin's Local Moran's I statistic were used to uncover spatial clustering of HEI rabies from 2000 – 2014. Results: Were identify three important clusters with significant year-to-year variation (Figure 1). In 2000, was identified one area of clustering in the North region, specifically in the State of Tocantins. Between the year 2000 and 2004, a cluster centered in the Midwest and Southeast region including the States of Goiás, Minas Gerais, Rio de Janeiro, Espirito Santo and São Paulo was prominent. And finally between 2000 and 2005 was found an important cluster in the North, Midwest and South region. Conclusions: The HEI rabies is endemic in the country, in addition, appears to be significant differences among the States according to their surveillance services, that may be difficulting the control of the disease, also other factors could be influencing in the maintenance of this problem like the lack of information of vampire-bat roosts identification, and limited human resources for realization of field monitoring. A review of the program control by the authorities it’s necessary.Keywords: Brazil, Desmodus rotundus, herbivores, rabies
Procedia PDF Downloads 41327452 Combined Analysis of m⁶A and m⁵C Modulators on the Prognosis of Hepatocellular Carcinoma
Authors: Hongmeng Su, Luyu Zhao, Yanyan Qian, Hong Fan
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Aim: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors that endanger human health seriously. RNA methylation, especially N6-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C), a crucial epigenetic transcriptional regulatory mechanism, plays an important role in tumorigenesis, progression and prognosis. This research aims to systematically evaluate the prognostic value of m⁶A and m⁵C modulators in HCC patients. Methods: Twenty-four modulators of m⁶A and m⁵C were candidates to analyze their expression level and their contribution to predict the prognosis of HCC. Consensus clustering analysis was applied to classify HCC patients. Cox and LASSO regression were used to construct the risk model. According to the risk score, HCC patients were divided into high-risk and low/medium-risk groups. The clinical pathology factors of HCC patients were analyzed by univariate and multivariate Cox regression analysis. Results: The HCC patients were classified into 2 clusters with significant differences in overall survival and clinical characteristics. Nine-gene risk model was constructed including METTL3, VIRMA, YTHDF1, YTHDF2, NOP2, NSUN4, NSUN5, DNMT3A and ALYREF. It was indicated that the risk score could serve as an independent prognostic factor for patients with HCC. Conclusion: This study constructed a Nine-gene risk model by modulators of m⁶A and m⁵C and investigated its effect on the clinical prognosis of HCC. This model may provide important consideration for the therapeutic strategy and prognosis evaluation analysis of patients with HCC.Keywords: hepatocellular carcinoma, m⁶A, m⁵C, prognosis, RNA methylation
Procedia PDF Downloads 6227451 Molecular Survey and Genetic Diversity of Bartonella henselae Strains Infecting Stray Cats from Algeria
Authors: Naouelle Azzag, Nadia Haddad, Benoit Durand, Elisabeth Petit, Ali Ammouche, Bruno Chomel, Henri J. Boulouis
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Bartonella henselae is a small, gram negative, arthropod-borne bacterium that has been shown to cause multiple clinical manifestations in humans including cat scratch disease, bacillary angiomatosis, endocarditis, and bacteremia. In this research, we report the results of a cross sectional study of Bartonella henselae bacteremia in stray cats from Algiers. Whole blood of 227 stray cats from Algiers was tested for the presence of Bartonella species by culture and for the evaluation of the genetic diversity of B. henselae strains by multi-locus variable number of tandem repeats assay (MLVA). Bacteremia prevalence was 17% and only B. henselae was identified. Type I was the predominant type (64%). MLVA typing of 259 strains from 30 bacteremic cats revealed 52 different profiles. 51 of these profiles were specific to Algerian cats/identified for the first time. 20/30 cats (67%) harbored 2 to 7 MLVA profiles simultaneously. The similarity of MLVA profiles obtained from the same cat, neighbor-joining clustering and structure-neighbor clustering showed that such a diversity likely results from two different mechanisms occurring either independently or simultaneously independent infections and genetic drift from a primary strain.Keywords: Bartonella, cat, MLVA, genetic
Procedia PDF Downloads 14227450 Unsupervised Detection of Burned Area from Remote Sensing Images Using Spatial Correlation and Fuzzy Clustering
Authors: Tauqir A. Moughal, Fusheng Yu, Abeer Mazher
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Land-cover and land-use change information are important because of their practical uses in various applications, including deforestation, damage assessment, disasters monitoring, urban expansion, planning, and land management. Therefore, developing change detection methods for remote sensing images is an important ongoing research agenda. However, detection of change through optical remote sensing images is not a trivial task due to many factors including the vagueness between the boundaries of changed and unchanged regions and spatial dependence of the pixels to its neighborhood. In this paper, we propose a binary change detection technique for bi-temporal optical remote sensing images. As in most of the optical remote sensing images, the transition between the two clusters (change and no change) is overlapping and the existing methods are incapable of providing the accurate cluster boundaries. In this regard, a methodology has been proposed which uses the fuzzy c-means clustering to tackle the problem of vagueness in the changed and unchanged class by formulating the soft boundaries between them. Furthermore, in order to exploit the neighborhood information of the pixels, the input patterns are generated corresponding to each pixel from bi-temporal images using 3×3, 5×5 and 7×7 window. The between images and within image spatial dependence of the pixels to its neighborhood is quantified by using Pearson product moment correlation and Moran’s I statistics, respectively. The proposed technique consists of two phases. At first, between images and within image spatial correlation is calculated to utilize the information that the pixels at different locations may not be independent. Second, fuzzy c-means technique is used to produce two clusters from input feature by not only taking care of vagueness between the changed and unchanged class but also by exploiting the spatial correlation of the pixels. To show the effectiveness of the proposed technique, experiments are conducted on multispectral and bi-temporal remote sensing images. A subset (2100×1212 pixels) of a pan-sharpened, bi-temporal Landsat 5 thematic mapper optical image of Los Angeles, California, is used in this study which shows a long period of the forest fire continued from July until October 2009. Early forest fire and later forest fire optical remote sensing images were acquired on July 5, 2009 and October 25, 2009, respectively. The proposed technique is used to detect the fire (which causes change on earth’s surface) and compared with the existing K-means clustering technique. Experimental results showed that proposed technique performs better than the already existing technique. The proposed technique can be easily extendable for optical hyperspectral images and is suitable for many practical applications.Keywords: burned area, change detection, correlation, fuzzy clustering, optical remote sensing
Procedia PDF Downloads 16527449 Image Segmentation Techniques: Review
Authors: Lindani Mbatha, Suvendi Rimer, Mpho Gololo
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Image segmentation is the process of dividing an image into several sections, such as the object's background and the foreground. It is a critical technique in both image-processing tasks and computer vision. Most of the image segmentation algorithms have been developed for gray-scale images and little research and algorithms have been developed for the color images. Most image segmentation algorithms or techniques vary based on the input data and the application. Nearly all of the techniques are not suitable for noisy environments. Most of the work that has been done uses the Markov Random Field (MRF), which involves the computations and is said to be robust to noise. In the past recent years' image segmentation has been brought to tackle problems such as easy processing of an image, interpretation of the contents of an image, and easy analysing of an image. This article reviews and summarizes some of the image segmentation techniques and algorithms that have been developed in the past years. The techniques include neural networks (CNN), edge-based techniques, region growing, clustering, and thresholding techniques and so on. The advantages and disadvantages of medical ultrasound image segmentation techniques are also discussed. The article also addresses the applications and potential future developments that can be done around image segmentation. This review article concludes with the fact that no technique is perfectly suitable for the segmentation of all different types of images, but the use of hybrid techniques yields more accurate and efficient results.Keywords: clustering-based, convolution-network, edge-based, region-growing
Procedia PDF Downloads 8527448 Sentiment Classification of Documents
Authors: Swarnadip Ghosh
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Sentiment Analysis is the process of detecting the contextual polarity of text. In other words, it determines whether a piece of writing is positive, negative or neutral.Sentiment analysis of documents holds great importance in today's world, when numerous information is stored in databases and in the world wide web. An efficient algorithm to illicit such information, would be beneficial for social, economic as well as medical purposes. In this project, we have developed an algorithm to classify a document into positive or negative. Using our algorithm, we obtained a feature set from the data, and classified the documents based on this feature set. It is important to note that, in the classification, we have not used the independence assumption, which is considered by many procedures like the Naive Bayes. This makes the algorithm more general in scope. Moreover, because of the sparsity and high dimensionality of such data, we did not use empirical distribution for estimation, but developed a method by finding degree of close clustering of the data points. We have applied our algorithm on a movie review data set obtained from IMDb and obtained satisfactory results.Keywords: sentiment, Run's Test, cross validation, higher dimensional pmf estimation
Procedia PDF Downloads 39227447 Development of a Robust Protein Classifier to Predict EMT Status of Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (CESC) Tumors
Authors: ZhenlinJu, Christopher P. Vellano, RehanAkbani, Yiling Lu, Gordon B. Mills
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The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells acquire mesenchymal characteristics, such as profound disruption of cell-cell junctions, loss of apical-basolateral polarity, and extensive reorganization of the actin cytoskeleton to induce cell motility and invasion. A hallmark of EMT is its capacity to promote metastasis, which is due in part to activation of several transcription factors and subsequent downregulation of E-cadherin. Unfortunately, current approaches have yet to uncover robust protein marker sets that can classify tumors as possessing strong EMT signatures. In this study, we utilize reverse phase protein array (RPPA) data and consensus clustering methods to successfully classify a subset of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumors into an EMT protein signaling group (EMT group). The overall survival (OS) of patients in the EMT group is significantly worse than those in the other Hormone and PI3K/AKT signaling groups. In addition to a shrinkage and selection method for linear regression (LASSO), we applied training/test set and Monte Carlo resampling approaches to identify a set of protein markers that predicts the EMT status of CESC tumors. We fit a logistic model to these protein markers and developed a classifier, which was fixed in the training set and validated in the testing set. The classifier robustly predicted the EMT status of the testing set with an area under the curve (AUC) of 0.975 by Receiver Operating Characteristic (ROC) analysis. This method not only identifies a core set of proteins underlying an EMT signature in cervical cancer patients, but also provides a tool to examine protein predictors that drive molecular subtypes in other diseases.Keywords: consensus clustering, TCGA CESC, Silhouette, Monte Carlo LASSO
Procedia PDF Downloads 46027446 Microsatellite-Based Genetic Variations and Relationships among Some Farmed Nile Tilapia Populations in Ghana: Implications for Nile Tilapia Culture
Authors: Acheampong Addo, Emmanuel Odartei Armah, Seth Koranteng Agyakwah, Ruby Asmah, Emmanuel Tetteh-Doku Mensah, Rhoda Lims Diyie, Sena Amewu, Catherine Ragasa, Edward Kofi Abban, Mike Yaw Osei-Atweneboana
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The study investigated genetic variation and relationships among populations of Nile tilapia cultured in small-scale fish farms in selected regions of Ghana. A total of 700 samples were collected. All samples were screened with five microsatellite markers and results were analyzed using (Genetic Analysis in Excel), (Molecular and Evolutionary Genetic Analysis software, and Genpop on the web for Heterozygosity and Shannon diversity, (Analysis of Molecular Variance), and (Principal Coordinate Analysis). Fish from the 16 populations (made up of 14 farms and 2 selectively bred populations) clustered into three groups: 7 populations clustered with the GIFT-derived strain, 4 populations clustered with the Akosombo strain, and three populations were in a separate cluster. The clustering pattern indicated groups of different strains of Nile tilapia cultured. Mantel correlation test also showed low genetic variations among the 16 populations hence the need to boost seed quality in order to accelerate aquaculture production in Ghana.Keywords: microsatellites, small- scale, Nile tilapia, akosombo strain, GIFT strain
Procedia PDF Downloads 15427445 Performance Evaluation of Various Segmentation Techniques on MRI of Brain Tissue
Authors: U.V. Suryawanshi, S.S. Chowhan, U.V Kulkarni
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Accuracy of segmentation methods is of great importance in brain image analysis. Tissue classification in Magnetic Resonance brain images (MRI) is an important issue in the analysis of several brain dementias. This paper portraits performance of segmentation techniques that are used on Brain MRI. A large variety of algorithms for segmentation of Brain MRI has been developed. The objective of this paper is to perform a segmentation process on MR images of the human brain, using Fuzzy c-means (FCM), Kernel based Fuzzy c-means clustering (KFCM), Spatial Fuzzy c-means (SFCM) and Improved Fuzzy c-means (IFCM). The review covers imaging modalities, MRI and methods for noise reduction and segmentation approaches. All methods are applied on MRI brain images which are degraded by salt-pepper noise demonstrate that the IFCM algorithm performs more robust to noise than the standard FCM algorithm. We conclude with a discussion on the trend of future research in brain segmentation and changing norms in IFCM for better results.Keywords: image segmentation, preprocessing, MRI, FCM, KFCM, SFCM, IFCM
Procedia PDF Downloads 32427444 The Data Quality Model for the IoT based Real-time Water Quality Monitoring Sensors
Authors: Rabbia Idrees, Ananda Maiti, Saurabh Garg, Muhammad Bilal Amin
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IoT devices are the basic building blocks of IoT network that generate enormous volume of real-time and high-speed data to help organizations and companies to take intelligent decisions. To integrate this enormous data from multisource and transfer it to the appropriate client is the fundamental of IoT development. The handling of this huge quantity of devices along with the huge volume of data is very challenging. The IoT devices are battery-powered and resource-constrained and to provide energy efficient communication, these IoT devices go sleep or online/wakeup periodically and a-periodically depending on the traffic loads to reduce energy consumption. Sometime these devices get disconnected due to device battery depletion. If the node is not available in the network, then the IoT network provides incomplete, missing, and inaccurate data. Moreover, many IoT applications, like vehicle tracking and patient tracking require the IoT devices to be mobile. Due to this mobility, If the distance of the device from the sink node become greater than required, the connection is lost. Due to this disconnection other devices join the network for replacing the broken-down and left devices. This make IoT devices dynamic in nature which brings uncertainty and unreliability in the IoT network and hence produce bad quality of data. Due to this dynamic nature of IoT devices we do not know the actual reason of abnormal data. If data are of poor-quality decisions are likely to be unsound. It is highly important to process data and estimate data quality before bringing it to use in IoT applications. In the past many researchers tried to estimate data quality and provided several Machine Learning (ML), stochastic and statistical methods to perform analysis on stored data in the data processing layer, without focusing the challenges and issues arises from the dynamic nature of IoT devices and how it is impacting data quality. A comprehensive review on determining the impact of dynamic nature of IoT devices on data quality is done in this research and presented a data quality model that can deal with this challenge and produce good quality of data. This research presents the data quality model for the sensors monitoring water quality. DBSCAN clustering and weather sensors are used in this research to make data quality model for the sensors monitoring water quality. An extensive study has been done in this research on finding the relationship between the data of weather sensors and sensors monitoring water quality of the lakes and beaches. The detailed theoretical analysis has been presented in this research mentioning correlation between independent data streams of the two sets of sensors. With the help of the analysis and DBSCAN, a data quality model is prepared. This model encompasses five dimensions of data quality: outliers’ detection and removal, completeness, patterns of missing values and checks the accuracy of the data with the help of cluster’s position. At the end, the statistical analysis has been done on the clusters formed as the result of DBSCAN, and consistency is evaluated through Coefficient of Variation (CoV).Keywords: clustering, data quality, DBSCAN, and Internet of things (IoT)
Procedia PDF Downloads 12927443 Occurrence of Porcine circovirus Type 2 in Pigs of Eastern Cape Province South Africa
Authors: Kayode O. Afolabi, Benson C. Iweriebor, Anthony I. Okoh, Larry C. Obi
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Porcine circovirus type 2 (PCV2) is the major etiological viral agent of porcine multisystemic wasting syndrome (PWMS) and other porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. In an effort to determine the status of swine herds in the Province as regarding the ‘small but powerful’ viral pathogen; a total of 375 blood, faecal and nasal swab samples were obtained from seven pig farms (commercial and communal) in Amathole, O.R. Tambo and Chris-Hani District Municipalities of Eastern Cape Province between the year 2015 and 2016. Three hundred and thirty nine (339) samples out of the total sample were subjected to molecular screening using PCV2 specific primers by conventional polymerase chain reaction (PCR). Selected sequences were further analyzed and confirmed through genome sequencing and phylogenetic analyses. The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6% to 60% in the studied farms. The Majority, precisely 15 out of 17 (88%) analyzed sequences were found clustering with other PCV2b reference strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to curb its spread effectively.Keywords: pigs, polymerase chain reaction, porcine circovirus type 2, South Africa
Procedia PDF Downloads 20227442 Remote Assessment and Change Detection of GreenLAI of Cotton Crop Using Different Vegetation Indices
Authors: Ganesh B. Shinde, Vijaya B. Musande
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Cotton crop identification based on the timely information has significant advantage to the different implications of food, economic and environment. Due to the significant advantages, the accurate detection of cotton crop regions using supervised learning procedure is challenging problem in remote sensing. Here, classifiers on the direct image are played a major role but the results are not much satisfactorily. In order to further improve the effectiveness, variety of vegetation indices are proposed in the literature. But, recently, the major challenge is to find the better vegetation indices for the cotton crop identification through the proposed methodology. Accordingly, fuzzy c-means clustering is combined with neural network algorithm, trained by Levenberg-Marquardt for cotton crop classification. To experiment the proposed method, five LISS-III satellite images was taken and the experimentation was done with six vegetation indices such as Simple Ratio, Normalized Difference Vegetation Index, Enhanced Vegetation Index, Green Atmospherically Resistant Vegetation Index, Wide-Dynamic Range Vegetation Index, Green Chlorophyll Index. Along with these indices, Green Leaf Area Index is also considered for investigation. From the research outcome, Green Atmospherically Resistant Vegetation Index outperformed with all other indices by reaching the average accuracy value of 95.21%.Keywords: Fuzzy C-Means clustering (FCM), neural network, Levenberg-Marquardt (LM) algorithm, vegetation indices
Procedia PDF Downloads 310