In recent years, many researches focused on the supervised machine learning classification methods using Lidar and remotely sensed image to provide buildings, trees, roads, and grass categories for urban ground feature classification. First, this research performed urban ground feature classification based on true color aerial imagey and Lidar Intensity. Second, Lidar derived normalized DSM (nDSM) was added to the classification. Finally, the concept of height level rules was applied. This research utilized two-level height rule-based classification exteneded from three-level height rule-based classification (Huang, 2007). It is obvious to observ the overlap for the roads and houses, and grass and trees in the feature space plot where result in the classification confusion. These confusions can be resolved by fusion the height information. After comparing classification accuracy, the two-level height is better than three-level height classification scheme. This research proposed hybrid classification method based on Maximum likelihood classification (MLC) and two-level height rules. This method reveals the role of height information in urban ground feature classification. The height level rules were also applied to other supervised classification method such as Back-Propagation Network (BPN) and Support Vector Machine (SVM). The classification results show that the accuracy of hybrid method is better than the orgional classification method. However, the time required to look for the classification parameters for BPN and SVM is greater than MLC but only can derived considerable results. Therefore, the hybrid classification method based on MLC is better than other two methods.

Bottomland hardwood forests are highly productive ecosystems which perform many important ecological services. Unfortunately, many bottomland hardwood forests have been degraded or lost. Accurate land cover mapping is crucial for management decisions affecting these disappearing systems. SPOT-5 imagery from 2005 was combined with Light Detection and Ranging (LiDAR) data from 2006 and several ancillary datasets to map a portion of the bottomland hardwood system found in the Sulphur River Basin of Northeast Texas. Pixel-based classification techniques, rulebased classification techniques, and object-based classification techniques were used to distinguish nine land cover types in the area. The rule-based classification (84.41% overall accuracy) outperformed the other classification methods because it more effectively incorporated the LiDAR and ancillary datasets when needed. This output was compared to previous classifications from 1974, 1984, 1991, and 1997 to determine abundance trends in the area’s bottomland hardwood forests. The classifications from 1974-1991 were conducted using identical class definitions and input imagery (Landsat MSS 60m), and the direct comparison demonstrates an overall declining trend in bottomland hardwood abundance. The trend levels off in 1997 when medium resolution imagery was first utilized (Landsat TM 30m) and the 2005 classification also shows an increase in bottomland hardwood from 1997 to 2005, when SPOT-5 10m imagery was used. However, when the classifications are re-sampled to the same resolution (60m), the percent area of bottomland hardwood consistently decreases from 1974-2005. Additional investigation of object-oriented classification proved useful. A major shortcoming of object-based classification is limited justification regarding the selection of segmentation parameters. Often, segmentation parameters are arbitrarily defined using general guidelines or are determined through a large number of parameter combinations. This research justifies the selection of segmentation parameters through a process that utilizes landscape metrics and statistical techniques to determine ideal segmentation parameters. The classification resulting from these parameters outperforms the classification resulting from arbitrary parameters by approximately three to six percent in terms of overall accuracy, demonstrating that landscape metrics can be successfully linked to segmentation parameters in order to create image objects that more closely resemble real-world objects and result in a more accurate final classification.

As we gain increased understanding of genetic disorders and gene regulation more focus has turned towards complex interactions. Combinations of genes or gene and environmental factors have been suggested to explain the missing heritability behind complex diseases. Furthermore, gene activation and splicing seem to be governed by a complex machinery of histone modification (HM), transcription factor (TF), and DNA sequence signals. This thesis aimed to apply and develop multivariate machine learning methods for use on such biological problems. Monte Carlo feature selection was combined with rule-based classification to identify interactions between HMs and to study the interplay of factors with importance for asthma and allergy. Firstly, publicly available ChIP-seq data (Paper I) for 38 HMs was studied. We trained a classifier for predicting exon inclusion levels based on the HMs signals. We identified HMs important for splicing and illustrated that splicing could be predicted from the HM patterns. Next, we applied a similar methodology on data from two large birth cohorts describing asthma and allergy in children (Paper II). We identified genetic and environmental factors with importance for allergic diseases which confirmed earlier results and found candidate gene-gene and gene-environment interactions. In order to interpret and present the classifiers we developed Ciruvis, a web-based tool for network visualization of classification rules (Paper III). We applied Ciruvis on classifiers trained on both simulated and real data and compared our tool to another methodology for interaction detection using classification. Finally, we continued the earlier study on epigenetics by analyzing HM and TF signals in genes with or without evidence of bidirectional transcription (Paper IV). We identified several HMs and TFs with different signals between unidirectional and bidirectional genes. Among these, the CTCF TF was shown to have a well-positioned peak 60-80 bp upstream of the transcription start site in unidirectional genes.

Urban land cover mapping represents one of the most important remote sensing applications in the context of rapid global urbanization. In recent years, high resolution spaceborne Polarimetric Synthetic Aperture Radar (PolSAR) has been increasingly used for urban land cover/land-use mapping, since more information could be obtained in multiple polarizations and the collection of such data is less influenced by solar illumination and weather conditions.  The overall objective of this research is to develop effective methods to extract accurate and detailed urban land cover information from spaceborne PolSAR data. Six RADARSAT-2 fine-beam polarimetric SAR and three RADARSAT-2 ultra-fine beam SAR images were used. These data were acquired from June to September 2008 over the north urban-rural fringe of the Greater Toronto Area, Canada. The major landuse/land-cover classes in this area include high-density residential areas, low-density residential areas, industrial and commercial areas, construction sites, roads, streets, parks, golf courses, forests, pasture, water and two types of agricultural crops. In this research, various polarimetric SAR parameters were evaluated for urban land cover mapping. They include the parameters from Pauli, Freeman and Cloude-Pottier decompositions, coherency matrix, intensities of each polarization and their logarithms.  Both object-based and pixel-based classification approaches were investigated. Through an object-based Support Vector Machine (SVM) and a rule-based approach, efficiencies of various PolSAR features and the multitemporal data combinations were evaluated. For the pixel-based approach, a contextual Stochastic Expectation-Maximization (SEM) algorithm was proposed. With an adaptive Markov Random Field (MRF) and a modified Multiscale Pappas Adaptive Clustering (MPAC), contextual information was explored to improve the mapping results. To take full advantages of alternative PolSAR distribution models, a rule-based model selection approach was put forward in comparison with a dictionary-based approach.  Moreover, the capability of multitemporal fine-beam PolSAR data was compared with multitemporal ultra-fine beam C-HH SAR data. Texture analysis and a rule-based approach which explores the object features and the spatial relationships were applied for further improvement. Using the proposed approaches, detailed urban land-cover classes and finer urban structures could be mapped with high accuracy in contrast to most of the previous studies which have only focused on the extraction of urban extent or the mapping of very few urban classes. It is also one of the first comparisons of various PolSAR parameters for detailed urban mapping using an object-based approach. Unlike other multitemporal studies, the significance of complementary information from both ascending and descending SAR data and the temporal relationships in the data were the focus in the multitemporal analysis. Further, the proposed novel contextual analyses could effectively improve the pixel-based classification accuracy and present homogenous results with preserved shape details avoiding over-averaging. The proposed contextual SEM algorithm, which is one of the first to combine the adaptive MRF and the modified MPAC, was able to mitigate the degenerative problem in the traditional EM algorithms with fast convergence speed when dealing with many classes. This contextual SEM outperformed the contextual SVM in certain situations with regard to both accuracy and computation time. By using such a contextual algorithm, the common PolSAR data distribution models namely Wishart, G0p, Kp and KummerU were compared for detailed urban mapping in terms of both mapping accuracy and time efficiency. In the comparisons, G0p, Kp and KummerU demonstrated better performances with higher overall accuracies than Wishart. Nevertheless, the advantages of Wishart and the other models could also be effectively integrated by the proposed rule-based adaptive model selection, while limited improvement could be observed by the dictionary-based selection, which has been applied in previous studies. The use of polarimetric SAR data for identifying various urban classes was then compared with the ultra-fine-beam C-HH SAR data. The grey level co-occurrence matrix textures generated from the ultra-fine-beam C-HH SAR data were found to be more efficient than the corresponding PolSAR textures for identifying urban areas from rural areas. An object-based and pixel-based fusion approach that uses ultra-fine-beam C-HH SAR texture data with PolSAR data was developed. In contrast to many other fusion approaches that have explored pixel-based classification results to improve object-based classifications, the proposed rule-based fusion approach using the object features and contextual information was able to extract several low backscatter classes such as roads, streets and parks with reasonable accuracy. / <p>QC 20121112</p>

An expert system is useful when conventional programming techniques fall short of capturing human expert knowledge and making decisions using this information. In this study, we describe a framework for capturing expert knowledge under a decision tree form and this framework can be used for making decisions based on captured knowledge. The framework proposed in this study is generic and can be used to create domain specific expert systems for different problems. Features are created or processed by the nodes of decision tree and a final conclusion is reached for each feature. Framework supplies 3 types of nodes to construct a decision tree. First type is the decision node, which guides the search path with its answers. Second type is the operator node, which creates new features using the inputs. Last type of node is the end node, which corresponds to a conclusion about a feature. Once the nodes of the tree are developed, then user can interactively create the decision tree and run the supplied inference engine to collect the result on a specific problem. The framework proposed is experimented with two case studies / &quot / Airport Runway Detection in High Resolution Satellite Images&quot / and &quot / Urban Area Detection in High Resolution Satellite Images&quot / . In these studies linear features are used for structural decisions and Scale Invariant Feature Transform (SIFT) features are used for testing existence of man made structures.

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Dans de nombreux problèmes de classification, les données sont intrinsèquement incertaines. Les données d’apprentissage disponibles peuvent être imprécises, incomplètes, ou même peu fiables. En outre, des connaissances spécialisées partielles qui caractérisent le problème de classification peuvent également être disponibles. Ces différents types d’incertitude posent de grands défis pour la conception de classifieurs. La théorie des fonctions de croyance fournit un cadre rigoureux et élégant pour la représentation et la combinaison d’une grande variété d’informations incertaines. Dans cette thèse, nous utilisons cette théorie pour résoudre les problèmes de classification des données incertaines sur la base de deux approches courantes, à savoir, la méthode des k plus proches voisins (kNN) et la méthode à base de règles.Pour la méthode kNN, une préoccupation est que les données d’apprentissage imprécises dans les régions où les classes de chevauchent peuvent affecter ses performances de manière importante. Une méthode d’édition a été développée dans le cadre de la théorie des fonctions de croyance pour modéliser l’information imprécise apportée par les échantillons dans les régions qui se chevauchent. Une autre considération est que, parfois, seul un ensemble de données d’apprentissage incomplet est disponible, auquel cas les performances de la méthode kNN se dégradent considérablement. Motivé par ce problème, nous avons développé une méthode de fusion efficace pour combiner un ensemble de classifieurs kNN couplés utilisant des métriques couplées apprises localement. Pour la méthode à base de règles, afin d’améliorer sa performance dans les applications complexes, nous étendons la méthode traditionnelle dans le cadre des fonctions de croyance. Nous développons un système de classification fondé sur des règles de croyance pour traiter des informations incertains dans les problèmes de classification complexes. En outre, dans certaines applications, en plus de données d’apprentissage, des connaissances expertes peuvent également être disponibles. Nous avons donc développé un système de classification hybride fondé sur des règles de croyance permettant d’utiliser ces deux types d’information pour la classification. / In many classification problems, data are inherently uncertain. The available training data might be imprecise, incomplete, even unreliable. Besides, partial expert knowledge characterizing the classification problem may also be available. These different types of uncertainty bring great challenges to classifier design. The theory of belief functions provides a well-founded and elegant framework to represent and combine a large variety of uncertain information. In this thesis, we use this theory to address the uncertain data classification problems based on two popular approaches, i.e., the k-nearest neighbor rule (kNN) andrule-based classification systems. For the kNN rule, one concern is that the imprecise training data in class over lapping regions may greatly affect its performance. An evidential editing version of the kNNrule was developed based on the theory of belief functions in order to well model the imprecise information for those samples in over lapping regions. Another consideration is that, sometimes, only an incomplete training data set is available, in which case the ideal behaviors of the kNN rule degrade dramatically. Motivated by this problem, we designedan evidential fusion scheme for combining a group of pairwise kNN classifiers developed based on locally learned pairwise distance metrics.For rule-based classification systems, in order to improving their performance in complex applications, we extended the traditional fuzzy rule-based classification system in the framework of belief functions and develop a belief rule-based classification system to address uncertain information in complex classification problems. Further, considering that in some applications, apart from training data collected by sensors, partial expert knowledge can also be available, a hybrid belief rule-based classification system was developed to make use of these two types of information jointly for classification.

La découverte de motifs est une tâche importante en fouille de données. Cemémoire traite de l’extraction des motifs émergents minimaux. Nous proposons une nouvelleméthode efficace qui permet d’extraire les motifs émergents minimaux sans ou avec contraintede support ; contrairement aux méthodes existantes qui extraient généralement les motifs émergentsminimaux les plus supportés, au risque de passer à côté de motifs très intéressants maispeu supportés par les données. De plus, notre méthode prend en compte l’absence d’attributqui apporte une nouvelle connaissance intéressante.En considérant les règles associées aux motifs émergents avec un support élevé comme desrègles prototypes, on a montré expérimentalement que cet ensemble de règles possède unebonne confiance sur les objets couverts mais malheureusement ne couvre pas une bonne partiedes objets ; ce qui constitue un frein pour leur usage en classification. Nous proposons uneméthode de sélection à base de prototypes qui améliore la couverture de l’ensemble des règlesprototypes sans pour autant dégrader leur confiance. Au vu des résultats encourageants obtenus,nous appliquons cette méthode de sélection sur un jeu de données chimique ayant rapport àl’environnement aquatique : Aquatox. Cela permet ainsi aux chimistes, dans un contexte declassification, de mieux expliquer la classification des molécules, qui sans cette méthode desélection serait prédites par l’usage d’une règle par défaut. / Pattern discovery is an important field of Knowledge Discovery in Databases.This work deals with the extraction of minimal emerging patterns. We propose a new efficientmethod which allows to extract the minimal emerging patterns with or without constraint ofsupport ; unlike existing methods that typically extract the most supported minimal emergentpatterns, at the risk of missing interesting but less supported patterns. Moreover, our methodtakes into account the absence of attribute that brings a new interesting knowledge.Considering the rules associated with emerging patterns highly supported as prototype rules,we have experimentally shown that this set of rules has good confidence on the covered objectsbut unfortunately does not cover a significant part of the objects ; which is a disavadntagefor their use in classification. We propose a prototype-based selection method that improvesthe coverage of the set of the prototype rules without a significative loss on their confidence.We apply our prototype-based selection method to a chemical data relating to the aquaticenvironment : Aquatox. In a classification context, it allows chemists to better explain theclassification of molecules, which, without this method of selection, would be predicted by theuse of a default rule.