Compositional class refinement in object-Z

Object-Z allows coupling constraints between classes which, on the one hand, facilitate specification at a high level of abstraction, but, on the other hand, make class refinement non-compositional. The consequence of this is that refinement is not practical for large Systems. This paper overcomes this limitation by introducing a methodology for compositional class refinement in Object-Z. The key step is an equivalence transformation of an arbitrary Object-Z specification to one in which introduced constraints prohibit non-compositional refinements. The methodology also allows the constraints which couple classes to be refined yielding an unrestricted approach to compositional class refinement.

Precision-recall operating characteristic (P-ROC) curves in imprecise environments

Traditionally, machine learning algorithms have been evaluated in applications where assumptions can be reliably made about class priors and/or misclassification costs. In this paper, we consider the case of imprecise environments, where little may be known about these factors and they may well vary significantly when the system is applied. Specifically, the use of precision-recall analysis is investigated and compared to the more well known performance measures such as error-rate and the receiver operating characteristic (ROC). We argue that while ROC analysis is invariant to variations in class priors, this invariance in fact hides an important factor of the evaluation in imprecise environments. Therefore, we develop a generalised precision-recall analysis methodology in which variation due to prior class probabilities is incorporated into a multi-way analysis of variance (ANOVA). The increased sensitivity and reliability of this approach is demonstrated in a remote sensing application.

Training with noise is equivalent to Tikhonov regularization

It is well known that the addition of noise to the input data of a neural network during training can, in some circumstances, lead to significant improvements in generalization performance. Previous work has shown that such training with noise is equivalent to a form of regularization in which an extra term is added to the error function. However, the regularization term, which involves second derivatives of the error function, is not bounded below, and so can lead to difficulties if used directly in a learning algorithm based on error minimization. In this paper we show that, for the purposes of network training, the regularization term can be reduced to a positive definite form which involves only first derivatives of the network mapping. For a sum-of-squares error function, the regularization term belongs to the class of generalized Tikhonov regularizers. Direct minimization of the regularized error function provides a practical alternative to training with noise.

Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies

Modelling class B G-protein-coupled receptors (GPCRs) using class A GPCR structural templates is difficult due to lack of homology. The plant GPCR, GCR1, has homology to both class A and class B GPCRs. We have used this to generate a class A-class B alignment, and by incorporating maximum lagged correlation of entropy and hydrophobicity into a consensus score, we have been able to align receptor transmembrane regions. We have applied this analysis to generate active and inactive homology models of the class B calcitonin gene-related peptide (CGRP) receptor, and have supported it with site-directed mutagenesis data using 122 CGRP receptor residues and 144 published mutagenesis results on other class B GPCRs. The variation of sequence variability with structure, the analysis of polarity violations, the alignment of group-conserved residues and the mutagenesis results at 27 key positions were particularly informative in distinguishing between the proposed and plausible alternative alignments. Furthermore, we have been able to associate the key molecular features of the class B GPCR signalling machinery with their class A counterparts for the first time. These include the [K/R]KLH motif in intracellular loop 1, [I/L]xxxL and KxxK at the intracellular end of TM5 and TM6, the NPXXY/VAVLY motif on TM7 and small group-conserved residues in TM1, TM2, TM3 and TM7. The equivalent of the class A DRY motif is proposed to involve Arg(2.39), His(2.43) and Glu(3.46), which makes a polar lock with T(6.37). These alignments and models provide useful tools for understanding class B GPCR function.

The multiple pheromone ant clustering algorithm and its application to real world domains

The Multiple Pheromone Ant Clustering Algorithm (MPACA) models the collective behaviour of ants to find clusters in data and to assign objects to the most appropriate class. It is an ant colony optimisation approach that uses pheromones to mark paths linking objects that are similar and potentially members of the same cluster or class. Its novelty is in the way it uses separate pheromones for each descriptive attribute of the object rather than a single pheromone representing the whole object. Ants that encounter other ants frequently enough can combine the attribute values they are detecting, which enables the MPACA to learn influential variable interactions. This paper applies the model to real-world data from two domains. One is logistics, focusing on resource allocation rather than the more traditional vehicle-routing problem. The other is mental-health risk assessment. The task for the MPACA in each domain was to predict class membership where the classes for the logistics domain were the levels of demand on haulage company resources and the mental-health classes were levels of suicide risk. Results on these noisy real-world data were promising, demonstrating the ability of the MPACA to find patterns in the data with accuracy comparable to more traditional linear regression models. © 2013 Polish Information Processing Society.

Psychological cue use and implications for a clinical decision support system

Effective clinical decision making depends upon identifying possible outcomes for a patient, selecting relevant cues, and processing the cues to arrive at accurate judgements of each outcome's probability of occurrence. These activities can be considered as classification tasks. This paper describes a new model of psychological classification that explains how people use cues to determine class or outcome likelihoods. It proposes that clinicians respond to conditional probabilities of outcomes given cues and that these probabilities compete with each other for influence on classification. The model explains why people appear to respond to base rates inappropriately, thereby overestimating the occurrence of rare categories, and a clinical example is provided for predicting suicide risk. The model makes an effective representation for expert clinical judgements and its psychological validity enables it to generate explanations in a form that is comprehensible to clinicians. It is a strong candidate for incorporation within a decision support system for mental-health risk assessment, where it can link with statistical and pattern recognition tools applied to a database of patients. The symbiotic combination of empirical evidence and clinical expertise can provide an important web-based resource for risk assessment, including multi-disciplinary education and training. © 2002 Informa UK Ltd All rights reserved.

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Background - MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. Results - A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. Conclusion - The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.

Toward prediction of class II mouse major histocompatibility complex peptide binding affinity:in silico bioinformatic evaluation using partial least squares, a robust multivariate statistical technique

The accurate identification of T-cell epitopes remains a principal goal of bioinformatics within immunology. As the immunogenicity of peptide epitopes is dependent on their binding to major histocompatibility complex (MHC) molecules, the prediction of binding affinity is a prerequisite to the reliable prediction of epitopes. The iterative self-consistent (ISC) partial-least-squares (PLS)-based additive method is a recently developed bioinformatic approach for predicting class II peptide−MHC binding affinity. The ISC−PLS method overcomes many of the conceptual difficulties inherent in the prediction of class II peptide−MHC affinity, such as the binding of a mixed population of peptide lengths due to the open-ended class II binding site. The method has applications in both the accurate prediction of class II epitopes and the manipulation of affinity for heteroclitic and competitor peptides. The method is applied here to six class II mouse alleles (I-Ab, I-Ad, I-Ak, I-As, I-Ed, and I-Ek) and included peptides up to 25 amino acids in length. A series of regression equations highlighting the quantitative contributions of individual amino acids at each peptide position was established. The initial model for each allele exhibited only moderate predictivity. Once the set of selected peptide subsequences had converged, the final models exhibited a satisfactory predictive power. Convergence was reached between the 4th and 17th iterations, and the leave-one-out cross-validation statistical terms - q2, SEP, and NC - ranged between 0.732 and 0.925, 0.418 and 0.816, and 1 and 6, respectively. The non-cross-validated statistical terms r2 and SEE ranged between 0.98 and 0.995 and 0.089 and 0.180, respectively. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made freely available online (http://www.jenner.ac.uk/MHCPred).

A Cognitive Science Reasoning in Recognition of Emotions in Audio-Visual Speech

In this report we summarize the state-of-the-art of speech emotion recognition from the signal processing point of view. On the bases of multi-corporal experiments with machine-learning classifiers, the observation is made that existing approaches for supervised machine learning lead to database dependent classifiers which can not be applied for multi-language speech emotion recognition without additional training because they discriminate the emotion classes following the used training language. As there are experimental results showing that Humans can perform language independent categorisation, we made a parallel between machine recognition and the cognitive process and tried to discover the sources of these divergent results. The analysis suggests that the main difference is that the speech perception allows extraction of language independent features although language dependent features are incorporated in all levels of the speech signal and play as a strong discriminative function in human perception. Based on several results in related domains, we have suggested that in addition, the cognitive process of emotion-recognition is based on categorisation, assisted by some hierarchical structure of the emotional categories, existing in the cognitive space of all humans. We propose a strategy for developing language independent machine emotion recognition, related to the identification of language independent speech features and the use of additional information from visual (expression) features.

A Sensitive Metric of Class Cohesion

Metrics estimate the quality of different aspects of software. In particular, cohesion indicates how well the parts of a system hold together. A metric to evaluate class cohesion is important in object-oriented programming because it gives an indication of a good design of classes. There are several proposals of metrics for class cohesion but they have several problems (for instance, low discrimination). In this paper, a new metric to evaluate class cohesion is proposed, called SCOM, which has several relevant features. It has an intuitive and analytical formulation, what is necessary to apply it to large-size software systems. It is normalized to produce values in the range [0..1], thus yielding meaningful values. It is also more sensitive than those previously reported in the literature. The attributes and methods used to evaluate SCOM are unambiguously stated. SCOM has an analytical threshold, which is a very useful but rare feature in software metrics. We assess the metric with several sample cases, showing that it gives more sensitive values than other well know cohesion metrics.

Application of Subordination Principle to Log-Harmonic alpha-spirallike Mappings

MSC 2010: 30C45, 30C55

Hybrid multi-objective optimization and hybridized self-organizing response surface method

Numerical optimization is a technique where a computer is used to explore design parameter combinations to find extremes in performance factors. In multi-objective optimization several performance factors can be optimized simultaneously. The solution to multi-objective optimization problems is not a single design, but a family of optimized designs referred to as the Pareto frontier. The Pareto frontier is a trade-off curve in the objective function space composed of solutions where performance in one objective function is traded for performance in others. A Multi-Objective Hybridized Optimizer (MOHO) was created for the purpose of solving multi-objective optimization problems by utilizing a set of constituent optimization algorithms. MOHO tracks the progress of the Pareto frontier approximation development and automatically switches amongst those constituent evolutionary optimization algorithms to speed the formation of an accurate Pareto frontier approximation. Aerodynamic shape optimization is one of the oldest applications of numerical optimization. MOHO was used to perform shape optimization on a 0.5-inch ballistic penetrator traveling at Mach number 2.5. Two objectives were simultaneously optimized: minimize aerodynamic drag and maximize penetrator volume. This problem was solved twice. The first time the problem was solved by using Modified Newton Impact Theory (MNIT) to determine the pressure drag on the penetrator. In the second solution, a Parabolized Navier-Stokes (PNS) solver that includes viscosity was used to evaluate the drag on the penetrator. The studies show the difference in the optimized penetrator shapes when viscosity is absent and present in the optimization. In modern optimization problems, objective function evaluations may require many hours on a computer cluster to perform these types of analysis. One solution is to create a response surface that models the behavior of the objective function. Once enough data about the behavior of the objective function has been collected, a response surface can be used to represent the actual objective function in the optimization process. The Hybrid Self-Organizing Response Surface Method (HYBSORSM) algorithm was developed and used to make response surfaces of objective functions. HYBSORSM was evaluated using a suite of 295 non-linear functions. These functions involve from 2 to 100 variables demonstrating robustness and accuracy of HYBSORSM.

Business process quantitative analysis and optimization for service industries

The total time a customer spends in the business process system, called the customer cycle-time, is a major contributor to overall customer satisfaction. Business process analysts and designers are frequently asked to design process solutions with optimal performance. Simulation models have been very popular to quantitatively evaluate the business processes; however, simulation is time-consuming and it also requires extensive modeling experiences to develop simulation models. Moreover, simulation models neither provide recommendations nor yield optimal solutions for business process design. A queueing network model is a good analytical approach toward business process analysis and design, and can provide a useful abstraction of a business process. However, the existing queueing network models were developed based on telephone systems or applied to manufacturing processes in which machine servers dominate the system. In a business process, the servers are usually people. The characteristics of human servers should be taken into account by the queueing model, i.e. specialization and coordination. ^ The research described in this dissertation develops an open queueing network model to do a quick analysis of business processes. Additionally, optimization models are developed to provide optimal business process designs. The queueing network model extends and improves upon existing multi-class open-queueing network models (MOQN) so that the customer flow in the human-server oriented processes can be modeled. The optimization models help business process designers to find the optimal design of a business process with consideration of specialization and coordination. ^ The main findings of the research are, first, parallelization can reduce the cycle-time for those customer classes that require more than one parallel activity; however, the coordination time due to the parallelization overwhelms the savings from parallelization under the high utilization servers since the waiting time significantly increases, thus the cycle-time increases. Third, the level of industrial technology employed by a company and coordination time to mange the tasks have strongest impact on the business process design; as the level of industrial technology employed by the company is high; more division is required to improve the cycle-time; as the coordination time required is high; consolidation is required to improve the cycle-time. ^

Three essays on dual-class stock structure

Dual-class stock structure is characterized by the separation of voting rights and cash flow rights. The departure from a common "one share-one vote" configuration creates ideal conditions for conflicts of interest and agency problems between controlling insiders (the holders of voting rights) and remaining shareholders. The owners of voting rights have the opportunity to extract private benefits and act in their personal interest; as a result, dual-class firms are often perceived to have low transparency and high information asymmetry. This dissertation investigates the quality of information and the information environment of firms with two classes of stock. The first essay examines the quality of information by studying accruals in dual-class firms in comparison to firms with only one class of stock. The results suggest that the quality of accruals is better in dual-class firms than in single-class firms. In addition, the difference in the quality of accruals between firms that abolish their dual-class share structure by unification and singe-class firms disappears in the post-unification period. The second essay investigates the earnings informativeness of dual-class firms by examining the explanatory power of earnings for returns. The results indicate that the earnings informativeness is lower for dual-class firms as compared to single-class firms. Earnings informativeness improves in firms that unify their shares. The third essay compares the level of information asymmetry between dual-class firms and single-class firms. It is documented that the information environment for dual-class firms is worse than for single-class firms. Also, the finding suggests that the difference in information environment between dual-class firms and single-class firms disappears after dual-class stock unification.

Real-time scheduling of embedded applications on multi-core platforms

For the past several decades, we have experienced the tremendous growth, in both scale and scope, of real-time embedded systems, thanks largely to the advances in IC technology. However, the traditional approach to get performance boost by increasing CPU frequency has been a way of past. Researchers from both industry and academia are turning their focus to multi-core architectures for continuous improvement of computing performance. In our research, we seek to develop efficient scheduling algorithms and analysis methods in the design of real-time embedded systems on multi-core platforms. Real-time systems are the ones with the response time as critical as the logical correctness of computational results. In addition, a variety of stringent constraints such as power/energy consumption, peak temperature and reliability are also imposed to these systems. Therefore, real-time scheduling plays a critical role in design of such computing systems at the system level. We started our research by addressing timing constraints for real-time applications on multi-core platforms, and developed both partitioned and semi-partitioned scheduling algorithms to schedule fixed priority, periodic, and hard real-time tasks on multi-core platforms. Then we extended our research by taking temperature constraints into consideration. We developed a closed-form solution to capture temperature dynamics for a given periodic voltage schedule on multi-core platforms, and also developed three methods to check the feasibility of a periodic real-time schedule under peak temperature constraint. We further extended our research by incorporating the power/energy constraint with thermal awareness into our research problem. We investigated the energy estimation problem on multi-core platforms, and developed a computation efficient method to calculate the energy consumption for a given voltage schedule on a multi-core platform. In this dissertation, we present our research in details and demonstrate the effectiveness and efficiency of our approaches with extensive experimental results.