Kernel-PCA data integration with enhanced interpretability

Background Nowadays, combining the different sources of information to improve the biological knowledge available is a challenge in bioinformatics. One of the most powerful methods for integrating heterogeneous data types are kernel-based methods. Kernel-based data integration approaches consist of two basic steps: firstly the right kernel is chosen for each data set; secondly the kernels from the different data sources are combined to give a complete representation of the available data for a given statistical task. Results We analyze the integration of data from several sources of information using kernel PCA, from the point of view of reducing dimensionality. Moreover, we improve the interpretability of kernel PCA by adding to the plot the representation of the input variables that belong to any dataset. In particular, for each input variable or linear combination of input variables, we can represent the direction of maximum growth locally, which allows us to identify those samples with higher/lower values of the variables analyzed. Conclusions The integration of different datasets and the simultaneous representation of samples and variables together give us a better understanding of biological knowledge.

Beurling-Landau densities of weighted Fekete sets and correlation kernel estimates

Let $Q$ be a suitable real function on $C$. An $n$-Fekete set corresponding to $Q$ is a subset ${Z_{n1}},\dotsb, Z_{nn}}$ of $C$ which maximizes the expression $\Pi^n_i_{

New kernel functions and learning methods for text and data mining

Recent advances in machine learning methods enable increasingly the automatic construction of various types of computer assisted methods that have been difficult or laborious to program by human experts. The tasks for which this kind of tools are needed arise in many areas, here especially in the fields of bioinformatics and natural language processing. The machine learning methods may not work satisfactorily if they are not appropriately tailored to the task in question. However, their learning performance can often be improved by taking advantage of deeper insight of the application domain or the learning problem at hand. This thesis considers developing kernel-based learning algorithms incorporating this kind of prior knowledge of the task in question in an advantageous way. Moreover, computationally efficient algorithms for training the learning machines for specific tasks are presented. In the context of kernel-based learning methods, the incorporation of prior knowledge is often done by designing appropriate kernel functions. Another well-known way is to develop cost functions that fit to the task under consideration. For disambiguation tasks in natural language, we develop kernel functions that take account of the positional information and the mutual similarities of words. It is shown that the use of this information significantly improves the disambiguation performance of the learning machine. Further, we design a new cost function that is better suitable for the task of information retrieval and for more general ranking problems than the cost functions designed for regression and classification. We also consider other applications of the kernel-based learning algorithms such as text categorization, and pattern recognition in differential display. We develop computationally efficient algorithms for training the considered learning machines with the proposed kernel functions. We also design a fast cross-validation algorithm for regularized least-squares type of learning algorithm. Further, an efficient version of the regularized least-squares algorithm that can be used together with the new cost function for preference learning and ranking tasks is proposed. In summary, we demonstrate that the incorporation of prior knowledge is possible and beneficial, and novel advanced kernels and cost functions can be used in algorithms efficiently.

Classification supervisée multi-étiquette en actes de dialogue: analyse discriminante et transformations de Schoenberg

Abstract This work studies the multi-label classification of turns in simple English Wikipedia talk pages into dialog acts. The treated dataset was created and multi-labeled by (Ferschke et al., 2012). The first part analyses dependences between labels, in order to examine the annotation coherence and to determine a classification method. Then, a multi-label classification is computed, after transforming the problem into binary relevance. Regarding features, whereas (Ferschke et al., 2012) use features such as uni-, bi-, and trigrams, time distance between turns or the indentation level of the turn, other features are considered here: lemmas, part-of-speech tags and the meaning of verbs (according to WordNet). The dataset authors applied approaches such as Naive Bayes or Support Vector Machines. The present paper proposes, as an alternative, to use Schoenberg transformations which, following the example of kernel methods, transform original Euclidean distances into other Euclidean distances, in a space of high dimensionality. Résumé Ce travail étudie la classification supervisée multi-étiquette en actes de dialogue des tours de parole des contributeurs aux pages de discussion de Simple English Wikipedia (Wikipédia en anglais simple). Le jeu de données considéré a été créé et multi-étiqueté par (Ferschke et al., 2012). Une première partie analyse les relations entre les étiquettes pour examiner la cohérence des annotations et pour déterminer une méthode de classification. Ensuite, une classification supervisée multi-étiquette est effectuée, après recodage binaire des étiquettes. Concernant les variables, alors que (Ferschke et al., 2012) utilisent des caractéristiques telles que les uni-, bi- et trigrammes, le temps entre les tours de parole ou l'indentation d'un tour de parole, d'autres descripteurs sont considérés ici : les lemmes, les catégories morphosyntaxiques et le sens des verbes (selon WordNet). Les auteurs du jeu de données ont employé des approches telles que le Naive Bayes ou les Séparateurs à Vastes Marges (SVM) pour la classification. Cet article propose, de façon alternative, d'utiliser et d'étendre l'analyse discriminante linéaire aux transformations de Schoenberg qui, à l'instar des méthodes à noyau, transforment les distances euclidiennes originales en d'autres distances euclidiennes, dans un espace de haute dimensionnalité.

Estimating extreme value cumulative distribution functions using bias-corrected kernel approaches

We propose a new kernel estimation of the cumulative distribution function based on transformation and on bias reducing techniques. We derive the optimal bandwidth that minimises the asymptotic integrated mean squared error. The simulation results show that our proposed kernel estimation improves alternative approaches when the variable has an extreme value distribution with heavy tail and the sample size is small.

Features extraction based on the Discrete Hartley Transform for closed contour

In this paper the authors propose a new closed contour descriptor that could be seen as a Feature Extractor of closed contours based on the Discrete Hartley Transform (DHT), its main characteristic is that uses only half of the coefficients required by Elliptical Fourier Descriptors (EFD) to obtain a contour approximation with similar error measure. The proposed closed contour descriptor provides an excellent capability of information compression useful for a great number of AI applications. Moreover it can provide scale, position and rotation invariance, and last but not least it has the advantage that both the parameterization and the reconstructed shape from the compressed set can be computed very efficiently by the fast Discrete Hartley Transform (DHT) algorithm. This Feature Extractor could be useful when the application claims for reversible features and when the user needs and easy measure of the quality for a given level of compression, scalable from low to very high quality.

Learning Preferences with Kernel-Based Methods

Learning of preference relations has recently received significant attention in machine learning community. It is closely related to the classification and regression analysis and can be reduced to these tasks. However, preference learning involves prediction of ordering of the data points rather than prediction of a single numerical value as in case of regression or a class label as in case of classification. Therefore, studying preference relations within a separate framework facilitates not only better theoretical understanding of the problem, but also motivates development of the efficient algorithms for the task. Preference learning has many applications in domains such as information retrieval, bioinformatics, natural language processing, etc. For example, algorithms that learn to rank are frequently used in search engines for ordering documents retrieved by the query. Preference learning methods have been also applied to collaborative filtering problems for predicting individual customer choices from the vast amount of user generated feedback. In this thesis we propose several algorithms for learning preference relations. These algorithms stem from well founded and robust class of regularized least-squares methods and have many attractive computational properties. In order to improve the performance of our methods, we introduce several non-linear kernel functions. Thus, contribution of this thesis is twofold: kernel functions for structured data that are used to take advantage of various non-vectorial data representations and the preference learning algorithms that are suitable for different tasks, namely efficient learning of preference relations, learning with large amount of training data, and semi-supervised preference learning. Proposed kernel-based algorithms and kernels are applied to the parse ranking task in natural language processing, document ranking in information retrieval, and remote homology detection in bioinformatics domain. Training of kernel-based ranking algorithms can be infeasible when the size of the training set is large. This problem is addressed by proposing a preference learning algorithm whose computation complexity scales linearly with the number of training data points. We also introduce sparse approximation of the algorithm that can be efficiently trained with large amount of data. For situations when small amount of labeled data but a large amount of unlabeled data is available, we propose a co-regularized preference learning algorithm. To conclude, the methods presented in this thesis address not only the problem of the efficient training of the algorithms but also fast regularization parameter selection, multiple output prediction, and cross-validation. Furthermore, proposed algorithms lead to notably better performance in many preference learning tasks considered.

New Distance Transforms for Gray Level Image Compression

This thesis deals with distance transforms which are a fundamental issue in image processing and computer vision. In this thesis, two new distance transforms for gray level images are presented. As a new application for distance transforms, they are applied to gray level image compression. The new distance transforms are both new extensions of the well known distance transform algorithm developed by Rosenfeld, Pfaltz and Lay. With some modification their algorithm which calculates a distance transform on binary images with a chosen kernel has been made to calculate a chessboard like distance transform with integer numbers (DTOCS) and a real value distance transform (EDTOCS) on gray level images. Both distance transforms, the DTOCS and EDTOCS, require only two passes over the graylevel image and are extremely simple to implement. Only two image buffers are needed: The original gray level image and the binary image which defines the region(s) of calculation. No other image buffers are needed even if more than one iteration round is performed. For large neighborhoods and complicated images the two pass distance algorithm has to be applied to the image more than once, typically 3 10 times. Different types of kernels can be adopted. It is important to notice that no other existing transform calculates the same kind of distance map as the DTOCS. All the other gray weighted distance function, GRAYMAT etc. algorithms find the minimum path joining two points by the smallest sum of gray levels or weighting the distance values directly by the gray levels in some manner. The DTOCS does not weight them that way. The DTOCS gives a weighted version of the chessboard distance map. The weights are not constant, but gray value differences of the original image. The difference between the DTOCS map and other distance transforms for gray level images is shown. The difference between the DTOCS and EDTOCS is that the EDTOCS calculates these gray level differences in a different way. It propagates local Euclidean distances inside a kernel. Analytical derivations of some results concerning the DTOCS and the EDTOCS are presented. Commonly distance transforms are used for feature extraction in pattern recognition and learning. Their use in image compression is very rare. This thesis introduces a new application area for distance transforms. Three new image compression algorithms based on the DTOCS and one based on the EDTOCS are presented. Control points, i.e. points that are considered fundamental for the reconstruction of the image, are selected from the gray level image using the DTOCS and the EDTOCS. The first group of methods select the maximas of the distance image to new control points and the second group of methods compare the DTOCS distance to binary image chessboard distance. The effect of applying threshold masks of different sizes along the threshold boundaries is studied. The time complexity of the compression algorithms is analyzed both analytically and experimentally. It is shown that the time complexity of the algorithms is independent of the number of control points, i.e. the compression ratio. Also a new morphological image decompression scheme is presented, the 8 kernels' method. Several decompressed images are presented. The best results are obtained using the Delaunay triangulation. The obtained image quality equals that of the DCT images with a 4 x 4

Combined application of continuous wavelet transform-zero crossing technique in the simultaneous spectrophotometric determination of perindopril and indapamid in tablets

Signal processing methods based on the combined use of the continuous wavelet transform (CWT) and zero-crossing technique were applied to the simultaneous spectrophotometric determination of perindopril (PER) and indapamide (IND) in tablets. These signal processing methods do not require any priory separation step. Initially, various wavelet families were tested to identify the optimum signal processing giving the best recovery results. From this procedure, the Haar and Biorthogonal1.5 continuous wavelet transform (HAAR-CWT and BIOR1.5-CWT, respectively) were found suitable for the analysis of the related compounds. After transformation of the absorbance vectors by using HAAR-CWT and BIOR1.5-CWT, the CWT-coefficients were drawn as a graph versus wavelength and then the HAAR-CWT and BIOR1.5-CWT spectra were obtained. Calibration graphs for PER and IND were obtained by measuring the CWT amplitudes at 231.1 and 291.0 nm in the HAAR-CWT spectra and at 228.5 and 246.8 nm in BIOR1.5-CWT spectra, respectively. In order to compare the performance of HAAR-CWT and BIOR1.5-CWT approaches, derivative spectrophotometric (DS) method and HPLC as comparison methods, were applied to the PER-IND samples. In this DS method, first derivative absorbance values at 221.6 for PER and 282.7 nm for IND were used to obtain the calibration graphs. The validation of the CWT and DS signal processing methods was carried out by using the recovery study and standard addition technique. In the following step, these methods were successfully applied to the commercial tablets containing PER and IND compounds and good accuracy and precision were reported for the experimental results obtained by all proposed signal processing methods.

Fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy and chemometric techniques for the determination of adulteration in petrodiesel/biodiesel blends

We propose an analytical method based on fourier transform infrared-attenuated total reflectance (FTIR-ATR) spectroscopy to detect the adulteration of petrodiesel and petrodiesel/palm biodiesel blends with African crude palm oil. The infrared spectral fingerprints from the sample analysis were used to perform principal components analysis (PCA) and to construct a prediction model using partial least squares (PLS) regression. The PCA results separated the samples into three groups, allowing identification of those subjected to adulteration with palm oil. The obtained model shows a good predictive capacity for determining the concentration of palm oil in petrodiesel/biodiesel blends. Advantages of the proposed method include cost-effectiveness and speed; it is also environmentally friendly.

Application of fourier transform infrared spectroscopy, chemical and chemometrics analyses to the characterization of agro-industrial waste

Agroindustrial waste in general presents significant levels of nutrients and organic matter and has therefore been frequently put to agricultural use. In this context, the objective of this study was to determine the chemical composition, nitrogen, phosphorus, potassium, calcium, magnesium and carbon content, as well as the qualitative characteristics through Fourier transform infrared spectroscopy of four samples of poultry litter and one sample of cattle manure, from the southwestern region of Paraná, Brazil. Results revealed that, in general, the poultry litter presented higher amount of nutrients and carbon than the cattle manure. The infrared spectra allowed identification of the functional groups present and the differences in degree of sample humification. The statistical treatment confirmed the quantitative and qualitative differences revealed.

Kernel-Based Ranking. Methods for Learning and Performance Estimation

Machine learning provides tools for automated construction of predictive models in data intensive areas of engineering and science. The family of regularized kernel methods have in the recent years become one of the mainstream approaches to machine learning, due to a number of advantages the methods share. The approach provides theoretically well-founded solutions to the problems of under- and overfitting, allows learning from structured data, and has been empirically demonstrated to yield high predictive performance on a wide range of application domains. Historically, the problems of classification and regression have gained the majority of attention in the field. In this thesis we focus on another type of learning problem, that of learning to rank. In learning to rank, the aim is from a set of past observations to learn a ranking function that can order new objects according to how well they match some underlying criterion of goodness. As an important special case of the setting, we can recover the bipartite ranking problem, corresponding to maximizing the area under the ROC curve (AUC) in binary classification. Ranking applications appear in a large variety of settings, examples encountered in this thesis include document retrieval in web search, recommender systems, information extraction and automated parsing of natural language. We consider the pairwise approach to learning to rank, where ranking models are learned by minimizing the expected probability of ranking any two randomly drawn test examples incorrectly. The development of computationally efficient kernel methods, based on this approach, has in the past proven to be challenging. Moreover, it is not clear what techniques for estimating the predictive performance of learned models are the most reliable in the ranking setting, and how the techniques can be implemented efficiently. The contributions of this thesis are as follows. First, we develop RankRLS, a computationally efficient kernel method for learning to rank, that is based on minimizing a regularized pairwise least-squares loss. In addition to training methods, we introduce a variety of algorithms for tasks such as model selection, multi-output learning, and cross-validation, based on computational shortcuts from matrix algebra. Second, we improve the fastest known training method for the linear version of the RankSVM algorithm, which is one of the most well established methods for learning to rank. Third, we study the combination of the empirical kernel map and reduced set approximation, which allows the large-scale training of kernel machines using linear solvers, and propose computationally efficient solutions to cross-validation when using the approach. Next, we explore the problem of reliable cross-validation when using AUC as a performance criterion, through an extensive simulation study. We demonstrate that the proposed leave-pair-out cross-validation approach leads to more reliable performance estimation than commonly used alternative approaches. Finally, we present a case study on applying machine learning to information extraction from biomedical literature, which combines several of the approaches considered in the thesis. The thesis is divided into two parts. Part I provides the background for the research work and summarizes the most central results, Part II consists of the five original research articles that are the main contribution of this thesis.