Philosophiae Doctor - PhD / Antimicrobial peptides (AMPs) play a key role in the innate immune response. They can be ubiquitously found in a wide range of eukaryotes including mammals, amphibians, insects, plants, and protozoa. In lower organisms, AMPs function merely as antibiotics by permeabilizing cell membranes and lysing invading microbes. Prediction of antimicrobial peptides is important because experimental methods used in characterizing AMPs are costly, time consuming and resource intensive and identification of AMPs in insects can serve as a template for the design of novel antibiotic. In order to fulfil this, firstly, data on antimicrobial peptides is extracted from UniProt, manually curated and stored into a centralized database called dragon antimicrobial peptide database (DAMPD). Secondly, based on the curated data, models to predict antimicrobial peptides are created using support vector machine with optimized hyperparameters. In particular, global optimization methods such as grid search, pattern search and derivative-free methods are utilised to optimize the SVM hyperparameters. These models are useful in characterizing unknown antimicrobial peptides. Finally, a webserver is created that will be used to predict antimicrobial peptides in haemotophagous insects such as Glossina morsitan and Anopheles gambiae. / South Africa

>Magister Scientiae - MSc / This research proposes an approach to recognizing facial expressions in the presence of rotations and partial occlusions of the face. The research is in the context of automatic machine translation of South African Sign Language (SASL) to English. The proposed method is able to accurately recognize frontal facial images at an average accuracy of 75%. It also achieves a high recognition accuracy of 70% for faces rotated to 60◦. It was also shown that the method is able to continue to recognize facial expressions even in the presence of full occlusions of the eyes, mouth and left/right sides of the face. The accuracy was as high as 70% for occlusion of some areas. An additional finding was that both the left and the right sides of the face are required for recognition. As an addition, the foundation was laid for a fully automatic facial expression recognition system that can accurately segment frontal or rotated faces in a video sequence.

We investigate the factors that determine the performance of text-based language identification, with a particular focus on the 11 official languages of South Africa. Our study uses n-gram statistics as features for classification. In particular, we compare support vector machines, Naïve Bayesian and difference-in-frequency classifiers on different amounts of input text and various values of n, for different amounts of training data. For a fixed value of n the support vector machines generally outperforms the other classifiers, but the simpler classifiers are able to handle larger values of n. The additional computational complexity of training the support vector machine classifier may not be justified in light of importance of using a large value of n, except possibly for small sizes of the input window when limited training data is available. We find that it is more difficult to discriminate languages within language families then those across families. The accuracy on small input strings is low due to this reason, but for input strings of 100 characters or more there is only a slight confusion within families and accuracies as high as 99.4% are achieved. For the smallest input strings studied here, which consist of 15 characters, the best accuracy achieved is only 83%, but when the languages in different families are grouped together, this corresponds to a usable 95.1% accuracy. The relationship between the amount of training data and the accuracy achieved is found to depend on the window size – for the largest window (300 characters) about 400 000 characters are sufficient to achieve close-to-optimal accuracy, whereas improvements in accuracy are found even beyond 1.6 million characters of training data. Finally, we show that the confusions between the different languages in our set can be used to derive informative graphical representations of the relationships between the languages. / Dissertation (MEng)--University of Pretoria, 2008. / Electrical, Electronic and Computer Engineering / unrestricted

This thesis focuses on bare hand gesture recognition by proposing a new architecture to solve the problem of real-time vision-based hand detection, tracking, and gesture recognition for interaction with an application via hand gestures. The first stage of our system allows detecting and tracking a bare hand in a cluttered background using face subtraction, skin detection and contour comparison. The second stage allows recognizing hand gestures using bag-of-features and multi-class Support Vector Machine (SVM) algorithms. Finally, a grammar has been developed to generate gesture commands for application control. Our hand gesture recognition system consists of two steps: offline training and online testing. In the training stage, after extracting the keypoints for every training image using the Scale Invariance Feature Transform (SIFT), a vector quantization technique will map keypoints from every training image into a unified dimensional histogram vector (bag-of-words) after K-means clustering. This histogram is treated as an input vector for a multi-class SVM to build the classifier. In the testing stage, for every frame captured from a webcam, the hand is detected using my algorithm. Then, the keypoints are extracted for every small image that contains the detected hand posture and fed into the cluster model to map them into a bag-of-words vector, which is fed into the multi-class SVM classifier to recognize the hand gesture. Another hand gesture recognition system was proposed using Principle Components Analysis (PCA). The most eigenvectors and weights of training images are determined. In the testing stage, the hand posture is detected for every frame using my algorithm. Then, the small image that contains the detected hand is projected onto the most eigenvectors of training images to form its test weights. Finally, the minimum Euclidean distance is determined among the test weights and the training weights of each training image to recognize the hand gesture. Two application of gesture-based interaction with a 3D gaming virtual environment were implemented. The exertion videogame makes use of a stationary bicycle as one of the main inputs for game playing. The user can control and direct left-right movement and shooting actions in the game by a set of hand gesture commands, while in the second game, the user can control and direct a helicopter over the city by a set of hand gesture commands.

Many protein structure prediction programs exist and they can efficiently generate a number of protein models of a varying quality. One of the problems is that it is difficult to know which model is the best one for a given target sequence. Selecting the best model is one of the major tasks of Model Quality Assessment Programs (MQAPs). These programs are able to predict model accuracy before the native structure is determined. The accuracy estimation can be divided into two parts: global (the whole model accuracy) and local (the accuracy of each residue). ProQ2 is one of the most successful MQAPs for prediction of both local and global model accuracy and is based on a Machine Learning approach. In this thesis, I present my own contribution to Model Quality Assessment (MQA) and the newest developments of ProQ program series. Firstly, I describe a new ProQ2 implementation in the protein modelling software package Rosetta. This new implementation allows use of ProQ2 as a scoring function for conformational sampling inside Rosetta, which was not possible before. Moreover, I present two new methods, ProQ3 and ProQ3D that both outperform their predecessor. ProQ3 introduces new training features that are calculated from Rosetta energy functions and ProQ3D introduces a new machine learning approach based on deep learning. ProQ3 program participated in the 12th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP12) and was one of the best methods in the MQA category. Finally, an important issue in model quality assessment is how to select a target function that the predictor is trying to learn. In the fourth manuscript, I show that MQA results can be improved by selecting a contact-based target function instead of more conventional superposition based functions. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.</p>

Orientador: Ronei Jesus Popi / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-18T17:27:36Z (GMT). No. of bitstreams: 1 Maretto_DaniloAlthmann_D.pdf: 2617064 bytes, checksum: 1ebea2b6ab73ef552155cd9b79b6fd1b (MD5) Previous issue date: 2011 / Resumo: O objetivo desta tese de doutorado foi de utilizar o algoritmo Máquinas de Vetores de Suporte (SVM) em problemas de classificação e calibração, onde algoritmos mais tradicionais (SIMCA e PLS, respectivamente) encontram problemas. Foram realizadas quatro aplicações utilizando dados de espectroscopia no infravermelho. Na primeira o SVM se mostrou ser uma ferramenta mais indicada para a determinação de Carbono e Nitrogênio em solo por NIR, quando estes elementos estão em solos sem que se saiba se há ou não a presença do mineral gipsita, obtendo concentrações desses elementos com erros consideravelmente menores do que a previsão feita pelo PLS. Na determinação da concentração de um mineral em polímero por NIR, que foi a segunda aplicação, o PLS conseguiu previsões com erros aceitáveis, entretanto, através da análise do teste F e o gráfico de erros absolutos das previsões, foi possível concluir que o modelo SVM conseguiu chegar a um modelo mais ajustado. Na terceira aplicação, que consistiu na classificação de bactérias quanto às condições de crescimento (temperaturas 30 ou 40°C e na presença ou ausência de fosfato) por MIR, o SIMCA não foi capaz de classificar corretamente a grande maioria das amostras enquanto o SVM produziu apenas uma previsão errada. E por fim, na última aplicação, que foi a diferenciação de nódulos cirróticos e de hepatocarcinoma por microespectroscopia MIR, a taxa das previsões corretas para os conjuntos de validação do SVM foram maiores do que do SIMCA. Nas quatro aplicações o SVM produziu resultados melhores do que o SIMCA e o PLS, mostrando que pode ser uma alternativa aos métodos mais tradicionais de classificação e calibração multivariada / Abstract: The objective of this thesis was to use the algorithm Support Vector Machines (SVM) in problems of classification and calibration, where more traditional algorithms (SIMCA and PLS, respectively) present problems. Four applications were developed using data for infrared spectra. In the first one, the SVM proved to be a most suitable tool for determination of carbon and nitrogen in soil by NIR, when these elements are in soils without knowledge whether or not the presence of the gypsum mineral, obtaining concentrations of these elements with errors considerably smaller than the estimated by the PLS. In the determination of the concentration of a mineral in a polymer by NIR, which was the second application, the PLS presented predictions with acceptable errors, however, by examining the F test and observing absolute errors of predictions, it was concluded that the SVM was able to reach a more adjusted model. In the third application, classification of bacteria on the different growth conditions (temperatures 30 or 40 ° C and in the presence or absence of phosphate) by MIR, the SIMCA was not able to correctly classify the majority of the samples while the SVM produced only one false prediction. Finally, in the last application, which was the differentiation of cirrhotic nodules and Hepatocellular carcinoma by infrared microspectroscopy, the rate of correct predictions for the validation of sets of SVM was higher than the SIMCA. In the four applications SVM produced better results than SIMCA and PLS, showing that it can be an alternative to the traditional algorithms for classification and multivariate calibration / Doutorado / Quimica Analitica / Doutor em Ciências

The diploma thesis is focused on predictions of mean monthly flows for a purpose of control of storage functions when thinking differently positions of fictive reservoirs in the catchment area. One of the reservoir is situated in the upper part of the catchment area and the second is situated in the middle part of catchment area. Predictions are made by Support vector machine method in RStudio and with the use of R language. Predicted values of flows was evaluated by the correlation coefficient, coefficient of determination, Root mean square error and than was made the simulation of operation of storage function, which was evaluated by Total sum of squares modificated for problems of water management. In the end was made a comparison of both of the reservoirs for assessment of the suitability of the method.

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Object recognition is one of many tasks in which the computer is still behind the human. Therefore, development in this area takes inspiration from nature and especially from the function of the human brain. This work focuses on object recognition based on extracting relevant information from images, features. Features are obtained in a similar way as the human brain processes visual stimuli. Subsequently, these features are used to train classifiers for object recognition (e.g. SVM, k-NN, ANN). This work examines the feature extraction stage. Its aim is to improve the feature extraction and thereby increase performance of object recognition by computer.

The document is discussing the issue of the computer vision with ability to character recignition in the image. Wavelet transform is used for preprocessing the image. Pixel energy feature is firstly used for searchich candidate text pixels. Density region growing method is then used to collect candidate pixels to the separate regions, which will be candidate text regions. Several of the features are calculated over the regions and the SVM classifier is used to derive, if the region is really a text region or not.