Cost-sensitive Bayesian network learning using sampling

A significant advance in recent years has been the development of cost-sensitive decision tree learners, recognising that real world classification problems need to take account of costs of misclassification and not just focus on accuracy. The literature contains well over 50 cost-sensitive decision tree induction algorithms, each with varying performance profiles. Obtaining good Bayesian networks can be challenging and hence several algorithms have been proposed for learning their structure and parameters from data. However, most of these algorithms focus on learning Bayesian networks that aim to maximise the accuracy of classifications. Hence an obvious question that arises is whether it is possible to develop cost-sensitive Bayesian networks and whether they would perform better than cost-sensitive decision trees for minimising classification cost? This paper explores this question by developing a new Bayesian network learning algorithm based on changing the data distribution to reflect the costs of misclassification. The proposed method is explored by conducting experiments on over 20 data sets. The results show that this approach produces good results in comparison to more complex cost-sensitive decision tree algorithms

Learning cost-sensitive Bayesian networks via direct and indirect methods

Cost-Sensitive learning has become an increasingly important area that recognizes that real world classification problems need to take the costs of misclassification and accuracy into account. Much work has been done on cost-sensitive decision tree learning, but very little has been done on cost-sensitive Bayesian networks. Although there has been significant research on Bayesian networks there has been relatively little research on learning cost-sensitive Bayesian networks. Hence, this paper explores whether it is possible to develop algorithms that learn cost-sensitive Bayesian networks by taking (i) an indirect approach that changes the data distribution to reflect the costs of misclassification; and (ii) a direct approach that amends an existing accuracy based algorithm for learning Bayesian networks. An empirical comparison of the new approaches is carried out with cost-sensitive decision tree learning algorithms on 33 data sets, and the results show that the new algorithms perform better in terms of misclassification cost and maintaining accuracy

MEMPREDIKSI PENINGKATAN H-INDEKS UNTUK JURNAL PENELITIAN DENGAN MENGGUNAKAN ALGORITMA COST-SENSITIVE SELECTIVE NAIVE BAYES CLASSIFIERS

Machine learning community is not only interested in maximizing classification accuracy, but also in minimizing the distances between the actual and the predicted class. Some ideas, like the cost-sensitive learning approach, are proposed to face this problem. In this paper, we propose two greedy wrapper forward cost-sensitive selective naive Bayes approaches. Both approaches readjust the probability thresholds of each class to select the class with the minimum-expected cost. The first algorithm (CSSNB-Accuracy) considers adding each variable to the model and measures the performance of the resulting model on the training data. The variable that most improves the accuracy, that is, the percentage of well classified instances between the readjusted class and actual class, is permanently added to the model. In contrast, the second algorithm (CS-SNB-Cost) considers adding variables that reduce the misclassification cost, that is, the distance between the readjusted class and actual class. We have tested our algorithms on the bibliometric indices prediction area. Considering the popularity of the well-known h-index, we have researched and built several prediction models to forecast the annual increase of the h-index for Neurosciences journals in a four-year time horizon. Results show that our approaches, particularly CS-SNB-Accuracy, achieved higher accuracy values than the analyzed cost sensitive classifiers and Bayesian classifiers. Furthermore, we also noted that the CS-SNB-Cost always achieved a lower average cost than all analyzed cost-sensitive and cost-insensitive classifiers. These cost sensitive selective naive Bayes approaches outperform the selective naive Bayes in terms of accuracy and average cost, so the cost-sensitive learning approach could be also applied in different probabilistic classification approaches

Recent Trends in Computational Intelligence

Traditional models struggle to cope with complexity, noise, and the existence of a changing environment, while Computational Intelligence (CI) offers solutions to complicated problems as well as reverse problems. The main feature of CI is adaptability, spanning the fields of machine learning and computational neuroscience. CI also comprises biologically-inspired technologies such as the intellect of swarm as part of evolutionary computation and encompassing wider areas such as image processing, data collection, and natural language processing. This book aims to discuss the usage of CI for optimal solving of various applications proving its wide reach and relevance. Bounding of optimization methods and data mining strategies make a strong and reliable prediction tool for handling real-life applications

Development and application of distributed computing tools for virtual screening of large compound libraries

Im derzeitigen Drug Discovery Prozess ist die Identifikation eines neuen Targetproteins und dessen potenziellen Liganden langwierig, teuer und zeitintensiv. Die Verwendung von in silico Methoden gewinnt hier zunehmend an Bedeutung und hat sich als wertvolle Strategie zur Erkennung komplexer Zusammenhänge sowohl im Bereich der Struktur von Proteinen wie auch bei Bioaktivitäten erwiesen. Die zunehmende Nachfrage nach Rechenleistung im wissenschaftlichen Bereich sowie eine detaillierte Analyse der generierten Datenmengen benötigen innovative Strategien für die effiziente Verwendung von verteilten Computerressourcen, wie z.B. Computergrids. Diese Grids ergänzen bestehende Technologien um einen neuen Aspekt, indem sie heterogene Ressourcen zur Verfügung stellen und koordinieren. Diese Ressourcen beinhalten verschiedene Organisationen, Personen, Datenverarbeitung, Speicherungs- und Netzwerkeinrichtungen, sowie Daten, Wissen, Software und Arbeitsabläufe. Das Ziel dieser Arbeit war die Entwicklung einer universitätsweit anwendbaren Grid-Infrastruktur - UVieCo (University of Vienna Condor pool) -, welche für die Implementierung von akademisch frei verfügbaren struktur- und ligandenbasierten Drug Discovery Anwendungen verwendet werden kann. Firewall- und Sicherheitsprobleme wurden mittels eines virtuellen privaten Netzwerkes gelöst, wohingegen die Virtualisierung der Computerhardware über das CoLinux Konzept ermöglicht wurde. Dieses ermöglicht, dass unter Linux auszuführende Aufträge auf Windows Maschinen laufen können. Die Effektivität des Grids wurde durch Leistungsmessungen anhand sequenzieller und paralleler Aufgaben ermittelt. Als Anwendungsbeispiel wurde die Assoziation der Expression bzw. der Sensitivitätsprofile von ABC-Transportern mit den Aktivitätsprofilen von Antikrebswirkstoffen durch Data-Mining des NCI (National Cancer Institute) Datensatzes analysiert. Die dabei generierten Datensätze wurden für liganden-basierte Computermethoden wie Shape-Similarity und Klassifikationsalgorithmen mit dem Ziel verwendet, P-glycoprotein (P-gp) Substrate zu identifizieren und sie von Nichtsubstraten zu trennen. Beim Erstellen vorhersagekräftiger Klassifikationsmodelle konnte das Problem der extrem unausgeglichenen Klassenverteilung durch Verwendung der „Cost-Sensitive Bagging“ Methode gelöst werden. Applicability Domain Studien ergaben, dass unser Modell nicht nur die NCI Substanzen gut vorhersagen kann, sondern auch für wirkstoffähnliche Moleküle verwendet werden kann. Die entwickelten Modelle waren relativ einfach, aber doch präzise genug um für virtuelles Screening einer großen chemischen Bibliothek verwendet werden zu können. Dadurch könnten P-gp Substrate schon frühzeitig erkannt werden, was möglicherweise nützlich sein kann zur Entfernung von Substanzen mit schlechten ADMET-Eigenschaften bereits in einer frühen Phase der Arzneistoffentwicklung. Zusätzlich wurden Shape-Similarity und Self-organizing Map Techniken verwendet um neue Substanzen in einer hauseigenen sowie einer großen kommerziellen Datenbank zu identifizieren, die ähnlich zu selektiven Serotonin-Reuptake-Inhibitoren (SSRI) sind und Apoptose induzieren können. Die erhaltenen Treffer besitzen neue chemische Grundkörper und können als Startpunkte für Leitstruktur-Optimierung in Betracht gezogen werden. Die in dieser Arbeit beschriebenen Studien werden nützlich sein um eine verteilte Computerumgebung zu kreieren die vorhandene Ressourcen in einer Organisation nutzt, und die für verschiedene Anwendungen geeignet ist, wie etwa die effiziente Handhabung der Klassifizierung von unausgeglichenen Datensätzen, oder mehrstufiges virtuelles Screening.In the current drug discovery process, the identification of new target proteins and potential ligands is very tedious, expensive and time-consuming. Thus, use of in silico techniques is of utmost importance and proved to be a valuable strategy in detecting complex structural and bioactivity relationships. Increased demands of computational power for tremendous calculations in scientific fields and timely analysis of generated piles of data require innovative strategies for efficient utilization of distributed computing resources in the form of computational grids. Such grids add a new aspect to the emerging information technology paradigm by providing and coordinating the heterogeneous resources such as various organizations, people, computing, storage and networking facilities as well as data, knowledge, software and workflows. The aim of this study was to develop a university-wide applicable grid infrastructure, UVieCo (University of Vienna Condor pool) which can be used for implementation of standard structure- and ligand-based drug discovery applications using freely available academic software. Firewall and security issues were resolved with a virtual private network setup whereas virtualization of computer hardware was done using the CoLinux concept in a way to run Linux-executable jobs inside Windows machines. The effectiveness of the grid was assessed by performance measurement experiments using sequential and parallel tasks. Subsequently, the association of expression/sensitivity profiles of ABC transporters with activity profiles of anticancer compounds was analyzed by mining the data from NCI (National Cancer Institute). The datasets generated in this analysis were utilized with ligand-based computational methods such as shape similarity and classification algorithms to identify and separate P-gp substrates from non-substrates. While developing predictive classification models, the problem of imbalanced class distribution was proficiently addressed using the cost-sensitive bagging approach. Applicability domain experiment revealed that our model not only predicts NCI compounds well, but it can also be applied to drug-like molecules. The developed models were relatively simple but precise enough to be applicable for virtual screening of large chemical libraries for the early identification of P-gp substrates which can potentially be useful to remove compounds of poor ADMET properties in an early phase of drug discovery. Additionally, shape-similarity and self-organizing maps techniques were used to screen in-house as well as a large vendor database for identification of novel selective serotonin reuptake inhibitor (SSRI) like compounds to induce apoptosis. The retrieved hits possess novel chemical scaffolds and can be considered as a starting point for lead optimization studies. The work described in this thesis will be useful to create distributed computing environment using available resources within an organization and can be applied to various applications such as efficient handling of imbalanced data classification problems or multistep virtual screening approach