Algorithm for the Parkinson’s disease behavioural models characterization using a biosensor

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Análise comparada da classificação “pixel a pixel” e orientada por objecto de uma imagem WorldView 2 de Maputo, Moçambique

O desenvolvimento das tecnologias associadas à Detecção Remota e aos Sistemas de Informação Geográfica encontram-se cada vez mais na ordem do dia. E, graças a este desenvolvimento de métodos para acelerar a produção de informação geográfica, assiste-se a um crescente aumento da resolução geométrica, espectral e radiométrica das imagens, e simultaneamente, ao aparecimento de novas aplicações com o intuito de facilitar o processamento e a análise de imagens através da melhoria de algoritmos para extracção de informação. Resultado disso são as imagens de alta resolução, provenientes do satélite WorldView 2 e o mais recente software Envi 5.0, utilizados neste estudo. O presente trabalho tem como principal objectivo desenvolver um projecto de cartografia de uso do solo para a cidade de Maputo, com recurso ao tratamento e à exploração de uma imagem de alta resolução, comparando as potencialidades e limitações dos resultados extraídos através da classificação “pixel a pixel”, através do algoritmo Máxima Verossimilhança, face às potencialidades e eventuais limitações da classificação orientada por objecto, através dos algoritmos K Nearest Neighbor (KNN) e Support Vector Machine (SVM), na extracção do mesmo número e tipo de classes de ocupação/uso do solo. Na classificação “pixel a pixel”, com a aplicação do algoritmo classificação Máxima Verosimilhança, foram ensaiados dois tipos de amostra: uma primeira constituída por 20 classes de ocupação/uso do solo, e uma segunda por 18 classes. Após a fase de experimentação, os resultados obtidos com a primeira amostra ficaram aquém das espectativas, pois observavam-se muitos erros de classificação. A segunda amostra formulada com base nestes erros de classificação e com o objectivo de os minimizar, permitiu obter um resultado próximo das espectativas idealizadas inicialmente, onde as classes de interesse coincidem com a realidade geográfica da cidade de Maputo. Na classificação orientada por objecto foram 4 as etapas metodológicas utilizadas: a atribuição do valor 5 para a segmentação e 90 para a fusão de segmentos; a selecção de 15 exemplos sobre os segmentos gerados para cada classe de interesse; bandas diferentemente distribuídas para o cálculo dos atributos espectrais e de textura; os atributos de forma Elongation e Form Factor e a aplicação dos algoritmos KNN e SVM. Confrontando as imagens resultantes das duas abordagens aplicadas, verificou-se que a qualidade do mapa produzido pela classificação “pixel a pixel” apresenta um nível de detalhe superior aos mapas resultantes da classificação orientada por objecto. Esta diferença de nível de detalhe é justificada pela unidade mínima do processamento de cada classificador: enquanto que na primeira abordagem a unidade mínima é o pixel, traduzinho uma maior detalhe, a segunda abordagem utiliza um conjunto de pixels, objecto, como unidade mínima despoletando situações de generalização. De um modo geral, a extracção da forma dos elementos e a distribuição das classes de interesse correspondem à realidade geográfica em si e, os resultados são bons face ao que é frequente em processamento semiautomático.

Land cover mapping analysis and urban growth modeling using remote sensing techniques

The rapid growth of big cities has been noticed since 1950s when the majority of world population turned to live in urban areas rather than villages, seeking better job opportunities and higher quality of services and lifestyle circumstances. This demographic transition from rural to urban is expected to have a continuous increase. Governments, especially in less developed countries, are going to face more challenges in different sectors, raising the essence of understanding the spatial pattern of the growth for an effective urban planning. The study aimed to detect, analyse and model the urban growth in Greater Cairo Region (GCR) as one of the fast growing mega cities in the world using remote sensing data. Knowing the current and estimated urbanization situation in GCR will help decision makers in Egypt to adjust their plans and develop new ones. These plans should focus on resources reallocation to overcome the problems arising in the future and to achieve a sustainable development of urban areas, especially after the high percentage of illegal settlements which took place in the last decades. The study focused on a period of 30 years; from 1984 to 2014, and the major transitions to urban were modelled to predict the future scenarios in 2025. Three satellite images of different time stamps (1984, 2003 and 2014) were classified using Support Vector Machines (SVM) classifier, then the land cover changes were detected by applying a high level mapping technique. Later the results were analyzed for higher accurate estimations of the urban growth in the future in 2025 using Land Change Modeler (LCM) embedded in IDRISI software. Moreover, the spatial and temporal urban growth patterns were analyzed using statistical metrics developed in FRAGSTATS software. The study resulted in an overall classification accuracy of 96%, 97.3% and 96.3% for 1984, 2003 and 2014’s map, respectively. Between 1984 and 2003, 19 179 hectares of vegetation and 21 417 hectares of desert changed to urban, while from 2003 to 2014, the transitions to urban from both land cover classes were found to be 16 486 and 31 045 hectares, respectively. The model results indicated that 14% of the vegetation and 4% of the desert in 2014 will turn into urban in 2025, representing 16 512 and 24 687 hectares, respectively.

Assistive locomotion strategies for active lower limb devices

Dissertação de mestrado integrado em Engenharia Biomédica (área de especialização em Eletrónica Médica)

Reconstructing historical forest cover change in the Lower Amazon floodplains using the LandTrendr algorithm

ABSTRACTThe Amazon várzeas are an important component of the Amazon biome, but anthropic and climatic impacts have been leading to forest loss and interruption of essential ecosystem functions and services. The objectives of this study were to evaluate the capability of the Landsat-based Detection of Trends in Disturbance and Recovery (LandTrendr) algorithm to characterize changes in várzeaforest cover in the Lower Amazon, and to analyze the potential of spectral and temporal attributes to classify forest loss as either natural or anthropogenic. We used a time series of 37 Landsat TM and ETM+ images acquired between 1984 and 2009. We used the LandTrendr algorithm to detect forest cover change and the attributes of "start year", "magnitude", and "duration" of the changes, as well as "NDVI at the end of series". Detection was restricted to areas identified as having forest cover at the start and/or end of the time series. We used the Support Vector Machine (SVM) algorithm to classify the extracted attributes, differentiating between anthropogenic and natural forest loss. Detection reliability was consistently high for change events along the Amazon River channel, but variable for changes within the floodplain. Spectral-temporal trajectories faithfully represented the nature of changes in floodplain forest cover, corroborating field observations. We estimated anthropogenic forest losses to be larger (1.071 ha) than natural losses (884 ha), with a global classification accuracy of 94%. We conclude that the LandTrendr algorithm is a reliable tool for studies of forest dynamics throughout the floodplain.

Estimativa dos parâmetros de compactação de solos usando técnicas de data mining

Dissertação de mestrado integrado em Engenharia Civil

Urban image classification with semisupervised multiscale cluster kernels

This paper presents a semisupervised support vector machine (SVM) that integrates the information of both labeled and unlabeled pixels efficiently. Method's performance is illustrated in the relevant problem of very high resolution image classification of urban areas. The SVM is trained with the linear combination of two kernels: a base kernel working only with labeled examples is deformed by a likelihood kernel encoding similarities between labeled and unlabeled examples. Results obtained on very high resolution (VHR) multispectral and hyperspectral images show the relevance of the method in the context of urban image classification. Also, its simplicity and the few parameters involved make the method versatile and workable by unexperienced users.

Automatic Mallampati Classification Using Active Appearance Models

Difficult tracheal intubation assessment is an important research topic in anesthesia as failed intubations are important causes of mortality in anesthetic practice. The modified Mallampati score is widely used, alone or in conjunction with other criteria, to predict the difficulty of intubation. This work presents an automatic method to assess the modified Mallampati score from an image of a patient with the mouth wide open. For this purpose we propose an active appearance models (AAM) based method and use linear support vector machines (SVM) to select a subset of relevant features obtained using the AAM. This feature selection step proves to be essential as it improves drastically the performance of classification, which is obtained using SVM with RBF kernel and majority voting. We test our method on images of 100 patients undergoing elective surgery and achieve 97.9% accuracy in the leave-one-out crossvalidation test and provide a key element to an automatic difficult intubation assessment system.

A control flow prototype for a dose recommending device for chronic myeloid leukemia patients

In this paper we present a prototype of a control flow for an a posteriori drug dose adaptation for Chronic Myelogenous Leukemia (CML) patients. The control flow is modeled using Timed Automata extended with Tasks (TAT) model. The feedback loop of the control flow includes the decision-making process for drug dose adaptation. This is based on the outputs of the body response model represented by the Support Vector Machine (SVM) algorithm for drug concentration prediction. The decision is further checked for conformity with the dose level rules of a medical guideline. We also have developed an automatic code synthesizer for the icycom platform as an extension of the TIMES tool.

A drug administration decision support system

Drug delivery is one of the most common clinical routines in hospitals, and is critical to patients' health and recovery. It includes a decision making process in which a medical doctor decides the amount (dose) and frequency (dose interval) on the basis of a set of available patients' feature data and the doctor's clinical experience (a priori adaptation). This process can be computerized in order to make the prescription procedure in a fast, objective, inexpensive, non-invasive and accurate way. This paper proposes a Drug Administration Decision Support System (DADSS) to help clinicians/patients with the initial dose computing. The system is based on a Support Vector Machine (SVM) algorithm for estimation of the potential drug concentration in the blood of a patient, from which a best combination of dose and dose interval is selected at the level of a DSS. The addition of the RANdom SAmple Consensus (RANSAC) technique enhances the prediction accuracy by selecting inliers for SVM modeling. Experiments are performed for the drug imatinib case study which shows more than 40% improvement in the prediction accuracy compared with previous works. An important extension to the patient features' data is also proposed in this paper.

Cluster kernels for semisupervised classification of VHR urban images

In this paper, we present and apply a semisupervised support vector machine based on cluster kernels for the problem of very high resolution image classification. In the proposed setting, a base kernel working with labeled samples only is deformed by a likelihood kernel encoding similarities between unlabeled examples. The resulting kernel is used to train a standard support vector machine (SVM) classifier. Experiments carried out on very high resolution (VHR) multispectral and hyperspectral images using very few labeled examples show the relevancy of the method in the context of urban image classification. Its simplicity and the small number of parameters involved make it versatile and workable by unexperimented users.

Learning spatial filters for multispectral image segmentation

We present a novel filtering method for multispectral satellite image classification. The proposed method learns a set of spatial filters that maximize class separability of binary support vector machine (SVM) through a gradient descent approach. Regularization issues are discussed in detail and a Frobenius-norm regularization is proposed to efficiently exclude uninformative filters coefficients. Experiments carried out on multiclass one-against-all classification and target detection show the capabilities of the learned spatial filters.

Mapping of Environmental Data Using Kernel-Based Methods

Recently, kernel-based Machine Learning methods have gained great popularity in many data analysis and data mining fields: pattern recognition, biocomputing, speech and vision, engineering, remote sensing etc. The paper describes the use of kernel methods to approach the processing of large datasets from environmental monitoring networks. Several typical problems of the environmental sciences and their solutions provided by kernel-based methods are considered: classification of categorical data (soil type classification), mapping of environmental and pollution continuous information (pollution of soil by radionuclides), mapping with auxiliary information (climatic data from Aral Sea region). The promising developments, such as automatic emergency hot spot detection and monitoring network optimization are discussed as well.

Aplicació de predicció del risc d'una cartera

L'objectiu principal del projecte és la creació d'una aplicació per a telèfons intel·ligents que intenti predir la volatilitat no atribuïble al mercat per tal de permetre a l'usuari crear portfolios òptims utilitzant tècniques d'intel·ligència artificial com són les Support Vector Machines (SVM). Una vegada s'hagi predit aquesta volatilitat es crearà un portfolio òptim amb el pes adequat de cada un dels valors, per tal d'obtenir una inversió amb el mínim risc possible.

Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation.

BACKGROUND: With the large amount of biological data that is currently publicly available, many investigators combine multiple data sets to increase the sample size and potentially also the power of their analyses. However, technical differences ("batch effects") as well as differences in sample composition between the data sets may significantly affect the ability to draw generalizable conclusions from such studies. FOCUS: The current study focuses on the construction of classifiers, and the use of cross-validation to estimate their performance. In particular, we investigate the impact of batch effects and differences in sample composition between batches on the accuracy of the classification performance estimate obtained via cross-validation. The focus on estimation bias is a main difference compared to previous studies, which have mostly focused on the predictive performance and how it relates to the presence of batch effects. DATA: We work on simulated data sets. To have realistic intensity distributions, we use real gene expression data as the basis for our simulation. Random samples from this expression matrix are selected and assigned to group 1 (e.g., 'control') or group 2 (e.g., 'treated'). We introduce batch effects and select some features to be differentially expressed between the two groups. We consider several scenarios for our study, most importantly different levels of confounding between groups and batch effects. METHODS: We focus on well-known classifiers: logistic regression, Support Vector Machines (SVM), k-nearest neighbors (kNN) and Random Forests (RF). Feature selection is performed with the Wilcoxon test or the lasso. Parameter tuning and feature selection, as well as the estimation of the prediction performance of each classifier, is performed within a nested cross-validation scheme. The estimated classification performance is then compared to what is obtained when applying the classifier to independent data.