Application of the transferable belief model to pattern recognition

We present in this paper a new approach to Pattern Recognition based on the Transferable Belief Model, a non probabilistic interpretation of Dempster and Shafer's theory of belief functions . This method uses the formalism of belief functions to represent the information provided by the training set concerning the class of a new pattern. Various decision strategies generalizing Bayes decision theory are presented and demonstrated using a real example.Nous présentons dans cet article une nouvelle approche de la Reconnaissance de Formes basée sur le Modèle des Croyances Transférables, une interprétation non probabiliste de la théorie des fonctions de croyance de Dempster et Shafer. Le principe de cette méthode consiste à caractériser sous la forme d'une fonction de croyance l'information apportée par un ensemble d'apprentissage, relativement à la classe d'un nouveau vecteur. Différentes stratégies de décision avec coûts arbitraires, généralisant l'approche bayésienne, sont présentées et illustrées à l'aide d'un exemple

Approximated Computation of Belief Functions for Robust Design Optimization

This paper presents some ideas to reduce the computational cost of evidence-based robust design optimization. Evidence Theory crystallizes both the aleatory and epistemic uncertainties in the design parameters, providing two quantitative measures, Belief and Plausibility, of the credibility of the computed value of the design budgets. The paper proposes some techniques to compute an approximation of Belief and Plausibility at a cost that is a fraction of the one required for an accurate calculation of the two values. Some simple test cases will show how the proposed techniques scale with the dimension of the problem. Finally a simple example of spacecraft system design is presented.Comment: AIAA-2012-1932 14th AIAA Non-Deterministic Approaches Conference. 23-26 April 2012 Sheraton Waikiki, Honolulu, Hawai

Comparative performance of some popular ANN algorithms on benchmark and function approximation problems

We report an inter-comparison of some popular algorithms within the artificial neural network domain (viz., Local search algorithms, global search algorithms, higher order algorithms and the hybrid algorithms) by applying them to the standard benchmarking problems like the IRIS data, XOR/N-Bit parity and Two Spiral. Apart from giving a brief description of these algorithms, the results obtained for the above benchmark problems are presented in the paper. The results suggest that while Levenberg-Marquardt algorithm yields the lowest RMS error for the N-bit Parity and the Two Spiral problems, Higher Order Neurons algorithm gives the best results for the IRIS data problem. The best results for the XOR problem are obtained with the Neuro Fuzzy algorithm. The above algorithms were also applied for solving several regression problems such as cos(x) and a few special functions like the Gamma function, the complimentary Error function and the upper tail cumulative $\chi^2$-distribution function. The results of these regression problems indicate that, among all the ANN algorithms used in the present study, Levenberg-Marquardt algorithm yields the best results. Keeping in view the highly non-linear behaviour and the wide dynamic range of these functions, it is suggested that these functions can be also considered as standard benchmark problems for function approximation using artificial neural networks.Comment: 18 pages 5 figures. Accepted in Pramana- Journal of Physic

Evidential Bagging: Combining Heterogeneous Classifiers in the Belief Functions Framework

International audienceIn machine learning, Ensemble Learning methodologies are known to improve predictive accuracy and robustness. They consist in the learning of many classifiers that produce outputs which are finally combined according to different techniques. Bagging, or Bootstrap Aggre-gating, is one of the most famous Ensemble methodologies and is usually applied to the same classification base algorithm, i.e. the same type of classifier is learnt multiple times on bootstrapped versions of the initial learning dataset. In this paper, we propose a bagging methodology that involves different types of classifier. Classifiers' probabilist outputs are used to build mass functions which are further combined within the belief functions framework. Three different ways of building mass functions are proposed; preliminary experiments on benchmark datasets showing the relevancy of the approach are presented

MemBrain: Improving the Accuracy of Predicting Transmembrane Helices

Prediction of transmembrane helices (TMH) in α helical membrane proteins provides valuable information about the protein topology when the high resolution structures are not available. Many predictors have been developed based on either amino acid hydrophobicity scale or pure statistical approaches. While these predictors perform reasonably well in identifying the number of TMHs in a protein, they are generally inaccurate in predicting the ends of TMHs, or TMHs of unusual length. To improve the accuracy of TMH detection, we developed a machine-learning based predictor, MemBrain, which integrates a number of modern bioinformatics approaches including sequence representation by multiple sequence alignment matrix, the optimized evidence-theoretic K-nearest neighbor prediction algorithm, fusion of multiple prediction window sizes, and classification by dynamic threshold. MemBrain demonstrates an overall improvement of about 20% in prediction accuracy, particularly, in predicting the ends of TMHs and TMHs that are shorter than 15 residues. It also has the capability to detect N-terminal signal peptides. The MemBrain predictor is a useful sequence-based analysis tool for functional and structural characterization of helical membrane proteins; it is freely available at http://chou.med.harvard.edu/bioinf/MemBrain/

Generalised max entropy classifiers

In this paper we propose a generalised maximum-entropy classification framework, in which the empirical expectation of the feature functions is bounded by the lower and upper expectations associated with the lower and upper probabilities associated with a belief measure. This generalised setting permits a more cautious appreciation of the information content of a training set. We analytically derive the KarushKuhn-Tucker conditions for the generalised max-entropy classifier in the case in which a Shannon-like entropy is adopted

TS-Models from Evidential Clustering

We study how to derive a fuzzy rule-based classification model using the theoretical framework of belief functions. For this purpose we use the recently proposed Evidential c-means (ECM) to derive Takagi-Sugeno (TS) models solely from data. ECM allocates, for each object, a mass of belief to any subsets of possible clusters, which allows to gain a deeper insight in the data while being robust with respect to outliers. Some classification examples are discussed, which show the advantages and disadvantages of the proposed algorithm

Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network

One of the most important and challenging problems in biomedicine and genomics is how to identify the disease genes. In this study, we developed a computational method to identify colorectal cancer-related genes based on (i) the gene expression profiles, and (ii) the shortest path analysis of functional protein association networks. The former has been used to select differentially expressed genes as disease genes for quite a long time, while the latter has been widely used to study the mechanism of diseases. With the existing protein-protein interaction data from STRING (Search Tool for the Retrieval of Interacting Genes), a weighted functional protein association network was constructed. By means of the mRMR (Maximum Relevance Minimum Redundancy) approach, six genes were identified that can distinguish the colorectal tumors and normal adjacent colonic tissues from their gene expression profiles. Meanwhile, according to the shortest path approach, we further found an additional 35 genes, of which some have been reported to be relevant to colorectal cancer and some are very likely to be relevant to it. Interestingly, the genes we identified from both the gene expression profiles and the functional protein association network have more cancer genes than the genes identified from the gene expression profiles alone. Besides, these genes also had greater functional similarity with the reported colorectal cancer genes than the genes identified from the gene expression profiles alone. All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying colorectal cancer genes. It has not escaped our notice that the method can be applied to identify the genes of other diseases as well

Classification and Analysis of Regulatory Pathways Using Graph Property, Biochemical and Physicochemical Property, and Functional Property

Given a regulatory pathway system consisting of a set of proteins, can we predict which pathway class it belongs to? Such a problem is closely related to the biological function of the pathway in cells and hence is quite fundamental and essential in systems biology and proteomics. This is also an extremely difficult and challenging problem due to its complexity. To address this problem, a novel approach was developed that can be used to predict query pathways among the following six functional categories: (i) “Metabolism”, (ii) “Genetic Information Processing”, (iii) “Environmental Information Processing”, (iv) “Cellular Processes”, (v) “Organismal Systems”, and (vi) “Human Diseases”. The prediction method was established trough the following procedures: (i) according to the general form of pseudo amino acid composition (PseAAC), each of the pathways concerned is formulated as a 5570-D (dimensional) vector; (ii) each of components in the 5570-D vector was derived by a series of feature extractions from the pathway system according to its graphic property, biochemical and physicochemical property, as well as functional property; (iii) the minimum redundancy maximum relevance (mRMR) method was adopted to operate the prediction. A cross-validation by the jackknife test on a benchmark dataset consisting of 146 regulatory pathways indicated that an overall success rate of 78.8% was achieved by our method in identifying query pathways among the above six classes, indicating the outcome is quite promising and encouraging. To the best of our knowledge, the current study represents the first effort in attempting to identity the type of a pathway system or its biological function. It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area