Investigation of transmembrane proteins using a computational approach

Background: An important subfamily of membrane proteins are the transmembrane α-helical proteins, in which the membrane-spanning regions are made up of α-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmembrane segments. The difficulty of inferring the secondary or tertiary structure of transmembrane proteins using experimental techniques has led to a surge of interest in applying techniques from machine learning and bioinformatics to infer secondary structure from primary structure in these proteins. We are therefore interested in determining which physicochemical properties are most useful for discriminating transmembrane segments from non-transmembrane segments in transmembrane proteins, and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins, and in using the results of these investigations to develop classifiers to identify transmembrane segments in transmembrane proteins. Results: We determined that the most useful properties for discriminating transmembrane segments from non-transmembrane segments and for discriminating intrinsically unstructured segments from intrinsically structured segments in transmembrane proteins were hydropathy, polarity, and flexibility, and used the results of this analysis to construct classifiers to discriminate transmembrane segments from non-transmembrane segments using four classification techniques: two variants of the Self-Organizing Global Ranking algorithm, a decision tree algorithm, and a support vector machine algorithm. All four techniques exhibited good performance, with out-of-sample accuracies of approximately 75%. Conclusions: Several interesting observations emerged from our study: intrinsically unstructured segments and transmembrane segments tend to have opposite properties; transmembrane proteins appear to be much richer in intrinsically unstructured segments than other proteins; and, in approximately 70% of transmembrane proteins that contain intrinsically unstructured segments, the intrinsically unstructured segments are close to transmembrane segments

Combinational equivalence checking for threshold logic circuits

ABSTRACT Threshold logic is gaining prominence as an alternative to Boolean logic. The main reason for this trend is the availability of devices that implement these circuits efficiently (current mode, differential mode circuits), as well as the promise they hold for the future nano devices (RTDs, SETs, QCAs and other nano devices). This has generated renewed interest in the design automation community to design efficient CAD tools for threshold logic. Recently a lot of work has been done to synthesize threshold logic circuits. So far there has been no efficient method to verify the synthesized circuits. In this work we address the problem of combinational equivalence checking for threshold circuits. We propose a new algorithm, to obtain compact functional representation of threshold elements. We give the proof of correctness, and analyze its runtime complexity. We use this polynomial time algorithm to develop a new methodology to verify threshold circuits. We report the result of our experiments, comparing the proposed methodology to the naive approach. We get up to 189X improvement in the run time (23X on average), and could verify circuits that the naive approach could not

Whole Word Phonetic Displays for Speech Articulation Training

The main objective of this dissertation is to investigate and develop speech recognition technologies for speech training for people with hearing impairments. During the course of this work, a computer aided speech training system for articulation speech training was also designed and implemented. The speech training system places emphasis on displays to improve children\u27s pronunciation of isolated Consonant-Vowel-Consonant (CVC) words, with displays at both the phonetic level and whole word level. This dissertation presents two hybrid methods for combining Hidden Markov Models (HMMs) and Neural Networks (NNs) for speech recognition. The first method uses NN outputs as posterior probability estimators for HMMs. The second method uses NNs to transform the original speech features to normalized features with reduced correlation. Based on experimental testing, both of the hybrid methods give higher accuracy than standard HMM methods. The second method, using the NN to create normalized features, outperforms the first method in terms of accuracy. Several graphical displays were developed to provide real time visual feedback to users, to help them to improve and correct their pronunciations

Application de techniques parcimonieuses et hiérarchiques en reconnaissance de la parole

Les systèmes de reconnaissance de la parole sont fondamentalement dérivés des domaines du traitement et de la modélisation statistique des signaux. Depuis quelques années, d'importantes innovations de domaines connexes comme le traitement d'image et les neurosciences computationnelles tardent toutefois à améliorer la performance des systèmes actuels de reconnaissance de parole. La revue de la littérature a suggéré qu'un système de reconnaissance vocale intégrant les aspects de hiérarchie, parcimonie et grandes dimensions joindrait les avantages de chacun. L'objectif général est de comprendre comment l'intégration de tous ces aspects permettrait d'améliorer la robustesse aux bruits additifs d'un système de reconnaissance de la parole. La base de données TI46 (mots isolés, faible-vocabulaire) est utilisée pour effectuer l'apprentissage non-supervisé et les tests de classification. Les différents bruits additifs proviennent de la base de données NOISEX-92, et permettent d'évaluer la robustesse en conditions de bruit réalistes. L'extraction de caractéristiques dans le système proposé est effectuée par des projections linéaires successives sur des bases, permettant de couvrir de plus en plus de contexte temporel et spectral. Diverses méthodes de seuillage permettent de produire une représentation multi-échelle, binaire et parcimonieuse de la parole. Au niveau du dictionnaire de bases, l'apprentissage non-supervisé permet sous certaines conditions l'obtention de bases qui reflètent des caractéristiques phonétiques et syllabiques de la parole, donc visant une représentation par objets d'un signal. L'algorithme d'analyse en composantes indépendantes (ICA) s'est démontré mieux adapté à extraire de telles bases, principalement à cause du critère de réduction de redondance. Les analyses théoriques et expérimentales ont montré comment la parcimonie peut contourner les problèmes de discrimination des distances et d'estimation des densités de probabilité dans des espaces à grandes dimensions. Il est observé qu'un espace de caractéristiques parcimonieux à grandes dimensions peut définir un espace de paramètres (p.ex. modèle statistique) de mêmes propriétés. Ceci réduit la disparité entre les représentations de l'étage d'extraction des caractéristiques et celles de l'étage de classification. De plus, l'étage d'extraction des caractéristiques peut favoriser une réduction de la complexité de l'étage de classification. Un simple classificateur linéaire peut venir compléter un modèle de Markov caché (HMM), joignant une capacité de discrimination accrue à la polyvalence d'une segmentation en états d'un signal. Les résultats montrent que l'architecture développée offr de meilleurs taux de reconnaissance en conditions propres et bruités comparativement à une architecture conventionnelle utilisant les coefficients cepstraux (MFCC) et une machine à vecteurs de support (SVM) comme classificateur discriminant. Contrairement aux techniques de codage de la parole où la transformation doit être inversible, la reconstruction n'est pas importante en reconnaissance de la parole. Cet aspect a justifié la possibilité de réduire considérablement la complexité des espaces de caractéristiques et de paramètres, sans toutefois diminuer le pouvoir de discrimination et la robustesse

Evaluation of Tracking Confidence Indicators and Feature Extractors on a Visual Tracking Algorithm

For visual tracking, a radial basis function neural network algorithm will be used. Coupled with a feature extraction algorithm, the neural network has advantages for pattern recognition, including practical implementation in parallel hardware for real-time operation and low power requirements. Targets vary in terms of texture, contrast, sharpness of edge, relative speed, and size. Various feature extractors exhibit tradeoffs in terms of sensitivity and processing requirements as related to the characteristics of candidate target classes. An analysis of feature extractors based on the horizontal and vertical profile has been provided. A comparison of the distance traveled computed from vision to wheel encoders is presented to observe slipping. Feedback from the network can offer an indication of tracking confidence which will be useful in determining if the estimated position is correct. An attempt has been made to look at the various confidence factors to determine if the position estimated is correct.Computer Science Departmen

An evolutionary approach to optimising neural network predictors for passive sonar target tracking

Object tracking is important in autonomous robotics, military applications, financial time-series forecasting, and mobile systems. In order to correctly track through clutter, algorithms which predict the next value in a time series are essential. The competence of standard machine learning techniques to create bearing prediction estimates was examined. The results show that the classification based algorithms produce more accurate estimates than the state-of-the-art statistical models. Artificial Neural Networks (ANNs) and K-Nearest Neighbour were used, demonstrating that this technique is not specific to a single classifier. [Continues.