Epistemology, Theory, and Methodology in Knowledge Organization: Toward a Classification, Metatheory, and Research Framework

This paper proposes a preliminary classification of knowledge organization research, divided among epistemology, theory, and methodology plus three spheres of research: design, study, and critique. This work is situated in a metatheoretical framework, drawn from sociological thought. Example works are presented along with preliminary classification. The classification is then briefly described as a comparison tool which can be used to demonstrate overlap and divergence in cognate discourses of knowledge organization (such as ontology engineering).

Theory of mind and peer acceptance in preschool children

Two studies tested the hypothesis that preschool children's theory of mind ability is related to their levels of peer acceptance. In Study 1, 78 children between the ages of 4 and 6 provided peer nominations that allowed determination of social preference and social impact scores, and classification in one of five peer status groups (following Coie & Dodge, 1983). Children were also tested on five different theory of mind tasks. The results showed that theory of mind scores were significantly related to social preference scores in a subsample of children who were over 5 years old. Further, popular children were found to score higher on theory of mind tasks than children classified as rejected. Study 2 replicated and extended the first study with a new sample of 87 4- to 6-year-old children. Study 2 included measures of peer acceptance, theory of mind ability and verbal intelligence, as well as teacher ratings of prosocial and aggressive behaviours. The results of Study 2 showed that for the total group of children, prosocial behaviour was the best predictor of social preference scores. When the Study 2 sample was split into older and younger children, theory of mind ability was found to be the best predictor of social preference scores for the older children (over age 5), while aggressive and prosocial behaviours were the best predictors of peer acceptance in the younger children. Overall, the pattern of results suggests that the impact of theory of mind ability on peer acceptance is modest but increases with children's age.

Comparing the content of instruments assessing environmental factors using the International Classification of Functioning, Disability and Health

Purpose: To describe and compare the content of instruments that assess environmental factors using the International Classification of Functioning, Disability and Health (ICF). Methods: A systematic search of PubMed, CINAHL and PEDro databases was conducted using a pre-determined search strategy. The identified instruments were screened independently by two investigators, and meaningful concepts were linked to the most precise ICF category according to published linking rules. Results: Six instruments were included, containing 526 meaningful concepts. Instruments had between 20% and 98% of items linked to categories in Chapter 1. The highest percentage of items from one instrument linked to categories in Chapters 2–5 varied between 9% and 50%. The presence or absence of environmental factors in a specific context is assessed in 3 instruments, while the other 3 assess the intensity of the impact of environmental factors. Discussion: Instruments differ in their content, type of assessment, and have several items linked to the same ICF category. Most instruments primarily assess products and technology (Chapter 1), highlighting the need to deepen the discussion on the theory that supports the measurement of environmental factors. This discussion should be thorough and lead to the development of methodologies and new tools that capture the underlying concepts of the ICF.

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.

Coalition of distributed generation units to Virtual Power Players - a game theory approach

Smart Grids (SGs) have emerged as the new paradigm for power system operation and management, being designed to include large amounts of distributed energy resources. This new paradigm requires new Energy Resource Management (ERM) methodologies considering different operation strategies and the existence of new management players such as several types of aggregators. This paper proposes a methodology to facilitate the coalition between distributed generation units originating Virtual Power Players (VPP) considering a game theory approach. The proposed approach consists in the analysis of the classifications that were attributed by each VPP to the distributed generation units, as well as in the analysis of the previous established contracts by each player. The proposed classification model is based in fourteen parameters including technical, economical and behavioural ones. Depending of the VPP strategies, size and goals, each parameter has different importance. VPP can also manage other type of energy resources, like storage units, electric vehicles, demand response programs or even parts of the MV and LV distribution network. A case study with twelve VPPs with different characteristics and one hundred and fifty real distributed generation units is included in the paper.

Bayesian classification criterion for forensic multivariate data

This study presents a classification criteria for two-class Cannabis seedlings. As the cultivation of drug type cannabis is forbidden in Switzerland, law enforcement authorities regularly ask laboratories to determine cannabis plant's chemotype from seized material in order to ascertain that the plantation is legal or not. In this study, the classification analysis is based on data obtained from the relative proportion of three major leaf compounds measured by gas-chromatography interfaced with mass spectrometry (GC-MS). The aim is to discriminate between drug type (illegal) and fiber type (legal) cannabis at an early stage of the growth. A Bayesian procedure is proposed: a Bayes factor is computed and classification is performed on the basis of the decision maker specifications (i.e. prior probability distributions on cannabis type and consequences of classification measured by losses). Classification rates are computed with two statistical models and results are compared. Sensitivity analysis is then performed to analyze the robustness of classification criteria.

Automatic classification of MR scans in Alzheimer's disease.

To be diagnostically useful, structural MRI must reliably distinguish Alzheimer's disease (AD) from normal aging in individual scans. Recent advances in statistical learning theory have led to the application of support vector machines to MRI for detection of a variety of disease states. The aims of this study were to assess how successfully support vector machines assigned individual diagnoses and to determine whether data-sets combined from multiple scanners and different centres could be used to obtain effective classification of scans. We used linear support vector machines to classify the grey matter segment of T1-weighted MR scans from pathologically proven AD patients and cognitively normal elderly individuals obtained from two centres with different scanning equipment. Because the clinical diagnosis of mild AD is difficult we also tested the ability of support vector machines to differentiate control scans from patients without post-mortem confirmation. Finally we sought to use these methods to differentiate scans between patients suffering from AD from those with frontotemporal lobar degeneration. Up to 96% of pathologically verified AD patients were correctly classified using whole brain images. Data from different centres were successfully combined achieving comparable results from the separate analyses. Importantly, data from one centre could be used to train a support vector machine to accurately differentiate AD and normal ageing scans obtained from another centre with different subjects and different scanner equipment. Patients with mild, clinically probable AD and age/sex matched controls were correctly separated in 89% of cases which is compatible with published diagnosis rates in the best clinical centres. This method correctly assigned 89% of patients with post-mortem confirmed diagnosis of either AD or frontotemporal lobar degeneration to their respective group. Our study leads to three conclusions: Firstly, support vector machines successfully separate patients with AD from healthy aging subjects. Secondly, they perform well in the differential diagnosis of two different forms of dementia. Thirdly, the method is robust and can be generalized across different centres. This suggests an important role for computer based diagnostic image analysis for clinical practice.

A data-dependent skeleton estimate and a scale-sensitive dimension for classification

The classical binary classification problem is investigatedwhen it is known in advance that the posterior probability function(or regression function) belongs to some class of functions. We introduceand analyze a method which effectively exploits this knowledge. The methodis based on minimizing the empirical risk over a carefully selected``skeleton'' of the class of regression functions. The skeleton is acovering of the class based on a data--dependent metric, especiallyfitted for classification. A new scale--sensitive dimension isintroduced which is more useful for the studied classification problemthan other, previously defined, dimension measures. This fact isdemonstrated by performance bounds for the skeleton estimate in termsof the new dimension.

Natural classification of knots

The principal objective of the knot theory is to provide a simple way of classifying and ordering all the knot types. Here, we propose a natural classification of knots based on their intrinsic position in the knot space that is defined by the set of knots to which a given knot can be converted by individual intersegmental passages. In addition, we characterize various knots using a set of simple quantum numbers that can be determined upon inspection of minimal crossing diagram of a knot. These numbers include: crossing number; average three-dimensional writhe; number of topological domains; and the average relaxation value

Towards a theory of the credit-risk balance sheet

This article designs what it calls a Credit-Risk Balance Sheet (the risk being that of default by customers), a tool which, in principle, can contribute to revealing, controlling and managing the bad debt risk arising from a company¿s commercial credit, whose amount can represent a significant proportion of both its current and total assets.To construct it, we start from the duality observed in any credit transaction of this nature, whose basic identity can be summed up as Credit = Risk. ¿Credit¿ is granted by a company to its customer, and can be ranked by quality (we suggest the credit scoring system) and ¿risk¿ can either be assumed (interiorised) by the company itself or transferred to third parties (exteriorised).What provides the approach that leads to us being able to talk with confidence of a real Credit-Risk Balance Sheet with its methodological robustness is that the dual vision of the credit transaction is not, as we demonstrate, merely a classificatory duality (a double risk-credit classification of reality) but rather a true causal relationship, that is, a risk-credit causal duality.Once said Credit-Risk Balance Sheet (which bears a certain structural similarity with the classic net asset balance sheet) has been built, and its methodological coherence demonstrated, its properties ¿static and dynamic¿ are studied.Analysis of the temporal evolution of the Credit-Risk Balance Sheet and of its applications will be the object of subsequent works.

Towards a theory of the credit-risk balance sheet

This article designs what it calls a Credit-Risk Balance Sheet (the risk being that of default by customers), a tool which, in principle, can contribute to revealing, controlling and managing the bad debt risk arising from a company¿s commercial credit, whose amount can represent a significant proportion of both its current and total assets.To construct it, we start from the duality observed in any credit transaction of this nature, whose basic identity can be summed up as Credit = Risk. ¿Credit¿ is granted by a company to its customer, and can be ranked by quality (we suggest the credit scoring system) and ¿risk¿ can either be assumed (interiorised) by the company itself or transferred to third parties (exteriorised).What provides the approach that leads to us being able to talk with confidence of a real Credit-Risk Balance Sheet with its methodological robustness is that the dual vision of the credit transaction is not, as we demonstrate, merely a classificatory duality (a double risk-credit classification of reality) but rather a true causal relationship, that is, a risk-credit causal duality.Once said Credit-Risk Balance Sheet (which bears a certain structural similarity with the classic net asset balance sheet) has been built, and its methodological coherence demonstrated, its properties ¿static and dynamic¿ are studied.Analysis of the temporal evolution of the Credit-Risk Balance Sheet and of its applications will be the object of subsequent works.

Analysis, modelling and classification of geospatial data using machine learning

The research considers the problem of spatial data classification using machine learning algorithms: probabilistic neural networks (PNN) and support vector machines (SVM). As a benchmark model simple k-nearest neighbor algorithm is considered. PNN is a neural network reformulation of well known nonparametric principles of probability density modeling using kernel density estimator and Bayesian optimal or maximum a posteriori decision rules. PNN is well suited to problems where not only predictions but also quantification of accuracy and integration of prior information are necessary. An important property of PNN is that they can be easily used in decision support systems dealing with problems of automatic classification. Support vector machine is an implementation of the principles of statistical learning theory for the classification tasks. Recently they were successfully applied for different environmental topics: classification of soil types and hydro-geological units, optimization of monitoring networks, susceptibility mapping of natural hazards. In the present paper both simulated and real data case studies (low and high dimensional) are considered. The main attention is paid to the detection and learning of spatial patterns by the algorithms applied.

Generalized Schmidt decomposition and classification of three-quantum-bit states

We prove for any pure three-quantum-bit state the existence of local bases which allow one to build a set of five orthogonal product states in terms of which the state can be written in a unique form. This leads to a canonical form which generalizes the two-quantum-bit Schmidt decomposition. It is uniquely characterized by the five entanglement parameters. It leads to a complete classification of the three-quantum-bit states. It shows that the right outcome of an adequate local measurement always erases all entanglement between the other two parties.