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

Perceptual-based textures for scene labeling: a bottom-up and a top-down approach

Due to the semantic gap, the automatic interpretation of digital images is a very challenging task. Both the segmentation and classification are intricate because of the high variation of the data. Therefore, the application of appropriate features is of utter importance. This paper presents biologically inspired texture features for material classification and interpreting outdoor scenery images. Experiments show that the presented texture features obtain the best classification results for material recognition compared to other well-known texture features, with an average classification rate of 93.0%. For scene analysis, both a bottom-up and top-down strategy are employed to bridge the semantic gap. At first, images are segmented into regions based on the perceptual texture and next, a semantic label is calculated for these regions. Since this emerging interpretation is still error prone, domain knowledge is ingested to achieve a more accurate description of the depicted scene. By applying both strategies, 91.9% of the pixels from outdoor scenery images obtained a correct label

Classifying sequences by the optimized dissimilarity space embedding approach: a case study on the solubility analysis of the E. coli proteome

We evaluate a version of the recently-proposed classification system named Optimized Dissimilarity Space Embedding (ODSE) that operates in the input space of sequences of generic objects. The ODSE system has been originally presented as a classification system for patterns represented as labeled graphs. However, since ODSE is founded on the dissimilarity space representation of the input data, the classifier can be easily adapted to any input domain where it is possible to define a meaningful dissimilarity measure. Here we demonstrate the effectiveness of the ODSE classifier for sequences by considering an application dealing with the recognition of the solubility degree of the Escherichia coli proteome. Solubility, or analogously aggregation propensity, is an important property of protein molecules, which is intimately related to the mechanisms underlying the chemico-physical process of folding. Each protein of our dataset is initially associated with a solubility degree and it is represented as a sequence of symbols, denoting the 20 amino acid residues. The herein obtained computational results, which we stress that have been achieved with no context-dependent tuning of the ODSE system, confirm the validity and generality of the ODSE-based approach for structured data classification.Comment: 10 pages, 49 reference

Multi-View Face Recognition From Single RGBD Models of the Faces

This work takes important steps towards solving the following problem of current interest: Assuming that each individual in a population can be modeled by a single frontal RGBD face image, is it possible to carry out face recognition for such a population using multiple 2D images captured from arbitrary viewpoints? Although the general problem as stated above is extremely challenging, it encompasses subproblems that can be addressed today. The subproblems addressed in this work relate to: (1) Generating a large set of viewpoint dependent face images from a single RGBD frontal image for each individual; (2) using hierarchical approaches based on view-partitioned subspaces to represent the training data; and (3) based on these hierarchical approaches, using a weighted voting algorithm to integrate the evidence collected from multiple images of the same face as recorded from different viewpoints. We evaluate our methods on three datasets: a dataset of 10 people that we created and two publicly available datasets which include a total of 48 people. In addition to providing important insights into the nature of this problem, our results show that we are able to successfully recognize faces with accuracies of 95% or higher, outperforming existing state-of-the-art face recognition approaches based on deep convolutional neural networks

Designing labeled graph classifiers by exploiting the R\'enyi entropy of the dissimilarity representation

Representing patterns as labeled graphs is becoming increasingly common in the broad field of computational intelligence. Accordingly, a wide repertoire of pattern recognition tools, such as classifiers and knowledge discovery procedures, are nowadays available and tested for various datasets of labeled graphs. However, the design of effective learning procedures operating in the space of labeled graphs is still a challenging problem, especially from the computational complexity viewpoint. In this paper, we present a major improvement of a general-purpose classifier for graphs, which is conceived on an interplay between dissimilarity representation, clustering, information-theoretic techniques, and evolutionary optimization algorithms. The improvement focuses on a specific key subroutine devised to compress the input data. We prove different theorems which are fundamental to the setting of the parameters controlling such a compression operation. We demonstrate the effectiveness of the resulting classifier by benchmarking the developed variants on well-known datasets of labeled graphs, considering as distinct performance indicators the classification accuracy, computing time, and parsimony in terms of structural complexity of the synthesized classification models. The results show state-of-the-art standards in terms of test set accuracy and a considerable speed-up for what concerns the computing time.Comment: Revised versio

General fuzzy min-max neural network for clustering and classification

This paper describes a general fuzzy min-max (GFMM) neural network which is a generalization and extension of the fuzzy min-max clustering and classification algorithms of Simpson (1992, 1993). The GFMM method combines supervised and unsupervised learning in a single training algorithm. The fusion of clustering and classification resulted in an algorithm that can be used as pure clustering, pure classification, or hybrid clustering classification. It exhibits a property of finding decision boundaries between classes while clustering patterns that cannot be said to belong to any of existing classes. Similarly to the original algorithms, the hyperbox fuzzy sets are used as a representation of clusters and classes. Learning is usually completed in a few passes and consists of placing and adjusting the hyperboxes in the pattern space; this is an expansion-contraction process. The classification results can be crisp or fuzzy. New data can be included without the need for retraining. While retaining all the interesting features of the original algorithms, a number of modifications to their definition have been made in order to accommodate fuzzy input patterns in the form of lower and upper bounds, combine the supervised and unsupervised learning, and improve the effectiveness of operations. A detailed account of the GFMM neural network, its comparison with the Simpson's fuzzy min-max neural networks, a set of examples, and an application to the leakage detection and identification in water distribution systems are given