Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Fatty liver automatic diagnosis from ultrasound images

In this paper an automatic classification algorithm is proposed for the diagnosis of the liver steatosis, also known as, fatty liver, from ultrasound images. The features, automatically extracted from the ultrasound images used by the classifier, are basically the ones used by the physicians in the diagnosis of the disease based on visual inspection of the ultrasound images. The main novelty of the method is the utilization of the speckle noise that corrupts the ultrasound images to compute textural features of the liver parenchyma relevant for the diagnosis. The algorithm uses the Bayesian framework to compute a noiseless image, containing anatomic and echogenic information of the liver and a second image containing only the speckle noise used to compute the textural features. The classification results, with the Bayes classifier using manually classified data as ground truth show that the automatic classifier reaches an accuracy of 95% and a 100% of sensitivity.

Forest cover monitoring in the Bara district (Nepal) with remote sensing and geographic information systems

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Global localization with non-quantized local image features

In the field of appearance-based robot localization, the mainstream approach uses a quantized representation of local image features. An alternative strategy is the exploitation of raw feature descriptors, thus avoiding approximations due to quantization. In this work, the quantized and non-quantized representations are compared with respect to their discriminativity, in the context of the robot global localization problem. Having demonstrated the advantages of the non-quantized representation, the paper proposes mechanisms to reduce the computational burden this approach would carry, when applied in its simplest form. This reduction is achieved through a hierarchical strategy which gradually discards candidate locations and by exploring two simplifying assumptions about the training data. The potential of the non-quantized representation is exploited by resorting to the entropy-discriminativity relation. The idea behind this approach is that the non-quantized representation facilitates the assessment of the distinctiveness of features, through the entropy measure. Building on this finding, the robustness of the localization system is enhanced by modulating the importance of features according to the entropy measure. Experimental results support the effectiveness of this approach, as well as the validity of the proposed computation reduction methods.

Urban land use change analysis and modelling: a case study of Setubal-Sesimbra, Portugal

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Wetland Habitat Studies using various Classification Techniques on Multi-Spectral Landsat Imagery: Case study: Tram chim National Park, Dong Thap Vietnam

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Urban change monitoring using GIS and remote sensing tools in Kathmandu valley (Nepal)

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

The contribution of multitemporal information from multispectral satellite images for automatic land cover classification at the national scale

Thesis submitted to the Instituto Superior de Estatística e Gestão de Informação da Universidade Nova de Lisboa in partial fulfillment of the requirements for the Degree of Doctor of Philosophy in Information Management – Geographic Information Systems

Classification Performance of Multilayer Perceptrons with Different Risk Functionals

In the present paper we assess the performance of information-theoretic inspired risks functionals in multilayer perceptrons with reference to the two most popular ones, Mean Square Error and Cross-Entropy. The information-theoretic inspired risks, recently proposed, are: HS and HR2 are, respectively, the Shannon and quadratic Rényi entropies of the error; ZED is a risk reflecting the error density at zero errors; EXP is a generalized exponential risk, able to mimic a wide variety of risk functionals, including the information-thoeretic ones. The experiments were carried out with multilayer perceptrons on 35 public real-world datasets. All experiments were performed according to the same protocol. The statistical tests applied to the experimental results showed that the ubiquitous mean square error was the less interesting risk functional to be used by multilayer perceptrons. Namely, mean square error never achieved a significantly better classification performance than competing risks. Cross-entropy and EXP were the risks found by several tests to be significantly better than their competitors. Counts of significantly better and worse risks have also shown the usefulness of HS and HR2 for some datasets.

Exploiting the bin-class histograms for feature selection on discrete data

In machine learning and pattern recognition tasks, the use of feature discretization techniques may have several advantages. The discretized features may hold enough information for the learning task at hand, while ignoring minor fluctuations that are irrelevant or harmful for that task. The discretized features have more compact representations that may yield both better accuracy and lower training time, as compared to the use of the original features. However, in many cases, mainly with medium and high-dimensional data, the large number of features usually implies that there is some redundancy among them. Thus, we may further apply feature selection (FS) techniques on the discrete data, keeping the most relevant features, while discarding the irrelevant and redundant ones. In this paper, we propose relevance and redundancy criteria for supervised feature selection techniques on discrete data. These criteria are applied to the bin-class histograms of the discrete features. The experimental results, on public benchmark data, show that the proposed criteria can achieve better accuracy than widely used relevance and redundancy criteria, such as mutual information and the Fisher ratio.

Text classification using compression-based dissimilarity measures

Arguably, the most difficult task in text classification is to choose an appropriate set of features that allows machine learning algorithms to provide accurate classification. Most state-of-the-art techniques for this task involve careful feature engineering and a pre-processing stage, which may be too expensive in the emerging context of massive collections of electronic texts. In this paper, we propose efficient methods for text classification based on information-theoretic dissimilarity measures, which are used to define dissimilarity-based representations. These methods dispense with any feature design or engineering, by mapping texts into a feature space using universal dissimilarity measures; in this space, classical classifiers (e.g. nearest neighbor or support vector machines) can then be used. The reported experimental evaluation of the proposed methods, on sentiment polarity analysis and authorship attribution problems, reveals that it approximates, sometimes even outperforms previous state-of-the-art techniques, despite being much simpler, in the sense that they do not require any text pre-processing or feature engineering.

A toolbox for hyperspectral image analysis

This paper introduces a new toolbox for hyperspectral imagery, developed under the MATLAB environment. This toolbox provides easy access to different supervised and unsupervised classification methods. This new application is also versatile and fully dynamic since the user can embody their own methods, that can be reused and shared. This toolbox, while extends the potentiality of MATLAB environment, it also provides a user-friendly platform to assess the results of different methodologies. In this paper it is also presented, under the new application, a study of several different supervised and unsupervised classification methods on real hyperspectral data.

Spatial metrics and Landsat data for urban landuse change detection: case of Addis Ababa, Ethiopia.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Automated image tagging through tag propagation

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial Para obtenção do grau de Mestre em Engenharia Informática

Urban sprawl analysis and modeling in Asmara, Eritreia: Application of Geospatial Tools

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.