A Study Of Vantage Point Neighbourhood Search In The Bees Algorithm For Combinatorial Optimization Problems

Tez (Yüksek Lisans) -- İstanbul Teknik Üniversitesi, Fen Bilimleri Enstitüsü, 2014Thesis (M.Sc. ) -- İstanbul Technical University, Institute of Science and Technology, 2014Bu tez çalışmasının temel amacı arıların kaynak arama davranışlarını modelleyen arı algoritmasının, kombinatoryal uzaylarda komşuluk arama fazına yeni bir yaklaşım geliştirilmesidir. Geliştirilen yaklaşım Gezgin Satıcı Problemine uygulanarak Gezgin Satıcı Problemi çözümünün en iyilenmesi amaçlanmıştır.This thesis focuses on nature-inspired optimisation algorithms, in particular, the Bees Algorithm that developed for combinatorial domains with new local search procedure and applied to Traveller Salesman Problem (TSP). An efficient and robust local neighborhood search algorithm is proposed for combinatorial domains to increase the efficiency of the Bees Algorithm.Yüksek LisansM.Sc

Mining a Small Medical Data Set by Integrating the Decision Tree and t-test

[[abstract]]Although several researchers have used statistical methods to prove that aspiration followed by the injection of 95% ethanol left in situ (retention) is an effective treatment for ovarian endometriomas, very few discuss the different conditions that could generate different recovery rates for the patients. Therefore, this study adopts the statistical method and decision tree techniques together to analyze the postoperative status of ovarian endometriosis patients under different conditions. Since our collected data set is small, containing only 212 records, we use all of these data as the training data. Therefore, instead of using a resultant tree to generate rules directly, we use the value of each node as a cut point to generate all possible rules from the tree first. Then, using t-test, we verify the rules to discover some useful description rules after all possible rules from the tree have been generated. Experimental results show that our approach can find some new interesting knowledge about recurrent ovarian endometriomas under different conditions.[[journaltype]]國外[[incitationindex]]EI[[booktype]]紙本[[countrycodes]]FI

Flood Forecasting Using Machine Learning Methods

This book is a printed edition of the Special Issue Flood Forecasting Using Machine Learning Methods that was published in Wate

Clustering analysis using Swarm Intelligence

This thesis is concerned with the application of the swarm intelligence methods in clustering analysis of datasets. The main objectives of the thesis are ∙ Take the advantage of a novel evolutionary algorithm, called artificial bee colony, to improve the capability of K-means in finding global optimum clusters in nonlinear partitional clustering problems. ∙ Consider partitional clustering as an optimization problem and an improved antbased algorithm, named Opposition-Based API (after the name of Pachycondyla APIcalis ants), to automatic grouping of large unlabeled datasets. ∙ Define partitional clustering as a multiobjective optimization problem. The aim is to obtain well-separated, connected, and compact clusters and for this purpose, two objective functions have been defined based on the concepts of data connectivity and cohesion. These functions are the core of an efficient multiobjective particle swarm optimization algorithm, which has been devised for and applied to automatic grouping of large unlabeled datasets. For that purpose, this thesis is divided is five main parts: ∙ The first part, including Chapter 1, aims at introducing state of the art of swarm intelligence based clustering methods. ∙ The second part, including Chapter 2, consists in clustering analysis with combination of artificial bee colony algorithm and K-means technique. ∙ The third part, including Chapter 3, consists in a presentation of clustering analysis using opposition-based API algorithm. ∙ The fourth part, including Chapter 4, consists in multiobjective clustering analysis using particle swarm optimization. ∙ Finally, the fifth part, including Chapter 5, concludes the thesis and addresses the future directions and the open issues of this research

Enhanced Pump Schedule Optimization For Large Water Distribution Networks To Maximize Environmental And Economic Benefits

For more than four decades researchers tried to develop optimization method and tools to reduce electricity consumption of pump stations of water distribution systems. Based on this ongoing research trend, about a decade ago, some commercial pump operation optimization software introduced to the market. Using metaheuristic and evolutionary techniques (e.g. Genetic Algorithm) make some commercial and research tools able to optimize the electricity cost of small water distribution systems (WDS). Still reducing the environmental footprint of these systems and dealing with large and complicated water distribution system is a challenge. In this study, we aimed to develop a multiobjective optimization tool (PEPSO) for reducing electricity cost and pollution emission (associated with energy consumption) of pump stations of WDSs. PEPSO designed to have a user-friendly graphical interface besides the state of art internal functions and procedures that lets users define and run customized optimization scenarios for even medium and large size WDSs. A customized version of non-dominated sorting genetic algorithm II is used as the core optimizer algorithm. EPANET toolkit is used as the hydraulic solver of PEPSO. In addition to the EPANET toolkit, a module is developed for training and using an artificial neural network instead of the high fidelity hydraulic model to speed up the optimization process. A unique measure that is called “Undesirability” is also introduced and used to help PEPSO in finding the promising path of optimization and making sure that the final results are desirable and practical. PEPSO is tested for optimizing the detailed hydraulic model of WDS of Monroe city, MI, USA and skeletonized hydraulic model of WDS of Richmond, UK. The various features of PEPSO are tested under 8 different scenarios, and its results are compared with results of Darwin Scheduler (a well-known commercial software in this field). The test results showed that in a reasonable amount of time, PEPSO is able to optimize and provide logical results for a medium size WDS model with 13 pumps and thousands of system components under different scenarios. It also is concluded that this tool in many aspects can provide better results in comparison with the famous commercial optimization tool in the market

Clustering analysis using Swarm Intelligence

This thesis is concerned with the application of the swarm intelligence methods in clustering analysis of datasets. The main objectives of the thesis are ∙ Take the advantage of a novel evolutionary algorithm, called artificial bee colony, to improve the capability of K-means in finding global optimum clusters in nonlinear partitional clustering problems. ∙ Consider partitional clustering as an optimization problem and an improved antbased algorithm, named Opposition-Based API (after the name of Pachycondyla APIcalis ants), to automatic grouping of large unlabeled datasets. ∙ Define partitional clustering as a multiobjective optimization problem. The aim is to obtain well-separated, connected, and compact clusters and for this purpose, two objective functions have been defined based on the concepts of data connectivity and cohesion. These functions are the core of an efficient multiobjective particle swarm optimization algorithm, which has been devised for and applied to automatic grouping of large unlabeled datasets. For that purpose, this thesis is divided is five main parts: ∙ The first part, including Chapter 1, aims at introducing state of the art of swarm intelligence based clustering methods. ∙ The second part, including Chapter 2, consists in clustering analysis with combination of artificial bee colony algorithm and K-means technique. ∙ The third part, including Chapter 3, consists in a presentation of clustering analysis using opposition-based API algorithm. ∙ The fourth part, including Chapter 4, consists in multiobjective clustering analysis using particle swarm optimization. ∙ Finally, the fifth part, including Chapter 5, concludes the thesis and addresses the future directions and the open issues of this research

From metaheuristics to learnheuristics: Applications to logistics, finance, and computing

Un gran nombre de processos de presa de decisions en sectors estratègics com el transport i la producció representen problemes NP-difícils. Sovint, aquests processos es caracteritzen per alts nivells d'incertesa i dinamisme. Les metaheurístiques són mètodes populars per a resoldre problemes d'optimització difícils en temps de càlcul raonables. No obstant això, sovint assumeixen que els inputs, les funcions objectiu, i les restriccions són deterministes i conegudes. Aquests constitueixen supòsits forts que obliguen a treballar amb problemes simplificats. Com a conseqüència, les solucions poden conduir a resultats pobres. Les simheurístiques integren la simulació a les metaheurístiques per resoldre problemes estocàstics d'una manera natural. Anàlogament, les learnheurístiques combinen l'estadística amb les metaheurístiques per fer front a problemes en entorns dinàmics, en què els inputs poden dependre de l'estructura de la solució. En aquest context, les principals contribucions d'aquesta tesi són: el disseny de les learnheurístiques, una classificació dels treballs que combinen l'estadística / l'aprenentatge automàtic i les metaheurístiques, i diverses aplicacions en transport, producció, finances i computació.Un gran número de procesos de toma de decisiones en sectores estratégicos como el transporte y la producción representan problemas NP-difíciles. Frecuentemente, estos problemas se caracterizan por altos niveles de incertidumbre y dinamismo. Las metaheurísticas son métodos populares para resolver problemas difíciles de optimización de manera rápida. Sin embargo, suelen asumir que los inputs, las funciones objetivo y las restricciones son deterministas y se conocen de antemano. Estas fuertes suposiciones conducen a trabajar con problemas simplificados. Como consecuencia, las soluciones obtenidas pueden tener un pobre rendimiento. Las simheurísticas integran simulación en metaheurísticas para resolver problemas estocásticos de una manera natural. De manera similar, las learnheurísticas combinan aprendizaje estadístico y metaheurísticas para abordar problemas en entornos dinámicos, donde los inputs pueden depender de la estructura de la solución. En este contexto, las principales aportaciones de esta tesis son: el diseño de las learnheurísticas, una clasificación de trabajos que combinan estadística / aprendizaje automático y metaheurísticas, y varias aplicaciones en transporte, producción, finanzas y computación.A large number of decision-making processes in strategic sectors such as transport and production involve NP-hard problems, which are frequently characterized by high levels of uncertainty and dynamism. Metaheuristics have become the predominant method for solving challenging optimization problems in reasonable computing times. However, they frequently assume that inputs, objective functions and constraints are deterministic and known in advance. These strong assumptions lead to work on oversimplified problems, and the solutions may demonstrate poor performance when implemented. Simheuristics, in turn, integrate simulation into metaheuristics as a way to naturally solve stochastic problems, and, in a similar fashion, learnheuristics combine statistical learning and metaheuristics to tackle problems in dynamic environments, where inputs may depend on the structure of the solution. The main contributions of this thesis include (i) a design for learnheuristics; (ii) a classification of works that hybridize statistical and machine learning and metaheuristics; and (iii) several applications for the fields of transport, production, finance and computing

Analysing functional genomics data using novel ensemble, consensus and data fusion techniques

Motivation: A rapid technological development in the biosciences and in computer science in the last decade has enabled the analysis of high-dimensional biological datasets on standard desktop computers. However, in spite of these technical advances, common properties of the new high-throughput experimental data, like small sample sizes in relation to the number of features, high noise levels and outliers, also pose novel challenges. Ensemble and consensus machine learning techniques and data integration methods can alleviate these issues, but often provide overly complex models which lack generalization capability and interpretability. The goal of this thesis was therefore to develop new approaches to combine algorithms and large-scale biological datasets, including novel approaches to integrate analysis types from different domains (e.g. statistics, topological network analysis, machine learning and text mining), to exploit their synergies in a manner that provides compact and interpretable models for inferring new biological knowledge. Main results: The main contributions of the doctoral project are new ensemble, consensus and cross-domain bioinformatics algorithms, and new analysis pipelines combining these techniques within a general framework. This framework is designed to enable the integrative analysis of both large- scale gene and protein expression data (including the tools ArrayMining, Top-scoring pathway pairs and RNAnalyze) and general gene and protein sets (including the tools TopoGSA , EnrichNet and PathExpand), by combining algorithms for different statistical learning tasks (feature selection, classification and clustering) in a modular fashion. Ensemble and consensus analysis techniques employed within the modules are redesigned such that the compactness and interpretability of the resulting models is optimized in addition to the predictive accuracy and robustness. The framework was applied to real-word biomedical problems, with a focus on cancer biology, providing the following main results: (1) The identification of a novel tumour marker gene in collaboration with the Nottingham Queens Medical Centre, facilitating the distinction between two clinically important breast cancer subtypes (framework tool: ArrayMining) (2) The prediction of novel candidate disease genes for Alzheimer’s disease and pancreatic cancer using an integrative analysis of cellular pathway definitions and protein interaction data (framework tool: PathExpand, collaboration with the Spanish National Cancer Centre) (3) The prioritization of associations between disease-related processes and other cellular pathways using a new rule-based classification method integrating gene expression data and pathway definitions (framework tool: Top-scoring pathway pairs) (4) The discovery of topological similarities between differentially expressed genes in cancers and cellular pathway definitions mapped to a molecular interaction network (framework tool: TopoGSA, collaboration with the Spanish National Cancer Centre) In summary, the framework combines the synergies of multiple cross-domain analysis techniques within a single easy-to-use software and has provided new biological insights in a wide variety of practical settings

Analysing functional genomics data using novel ensemble, consensus and data fusion techniques

Motivation: A rapid technological development in the biosciences and in computer science in the last decade has enabled the analysis of high-dimensional biological datasets on standard desktop computers. However, in spite of these technical advances, common properties of the new high-throughput experimental data, like small sample sizes in relation to the number of features, high noise levels and outliers, also pose novel challenges. Ensemble and consensus machine learning techniques and data integration methods can alleviate these issues, but often provide overly complex models which lack generalization capability and interpretability. The goal of this thesis was therefore to develop new approaches to combine algorithms and large-scale biological datasets, including novel approaches to integrate analysis types from different domains (e.g. statistics, topological network analysis, machine learning and text mining), to exploit their synergies in a manner that provides compact and interpretable models for inferring new biological knowledge. Main results: The main contributions of the doctoral project are new ensemble, consensus and cross-domain bioinformatics algorithms, and new analysis pipelines combining these techniques within a general framework. This framework is designed to enable the integrative analysis of both large- scale gene and protein expression data (including the tools ArrayMining, Top-scoring pathway pairs and RNAnalyze) and general gene and protein sets (including the tools TopoGSA , EnrichNet and PathExpand), by combining algorithms for different statistical learning tasks (feature selection, classification and clustering) in a modular fashion. Ensemble and consensus analysis techniques employed within the modules are redesigned such that the compactness and interpretability of the resulting models is optimized in addition to the predictive accuracy and robustness. The framework was applied to real-word biomedical problems, with a focus on cancer biology, providing the following main results: (1) The identification of a novel tumour marker gene in collaboration with the Nottingham Queens Medical Centre, facilitating the distinction between two clinically important breast cancer subtypes (framework tool: ArrayMining) (2) The prediction of novel candidate disease genes for Alzheimer’s disease and pancreatic cancer using an integrative analysis of cellular pathway definitions and protein interaction data (framework tool: PathExpand, collaboration with the Spanish National Cancer Centre) (3) The prioritization of associations between disease-related processes and other cellular pathways using a new rule-based classification method integrating gene expression data and pathway definitions (framework tool: Top-scoring pathway pairs) (4) The discovery of topological similarities between differentially expressed genes in cancers and cellular pathway definitions mapped to a molecular interaction network (framework tool: TopoGSA, collaboration with the Spanish National Cancer Centre) In summary, the framework combines the synergies of multiple cross-domain analysis techniques within a single easy-to-use software and has provided new biological insights in a wide variety of practical settings