Segmentação do tecido tumoral cerebral em imagens de ressonância magnética

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

Pervasive business intelligence: a marketing intelligence framework proposal

Doctoral Thesis in Information Systems and Technologies Area of Information Systems and Technology

An R package for the integrated analysis of metabolomics and spectral data

Recently, there has been a growing interest in the field of metabolomics, materialized by a remarkable growth in experimental techniques, available data and related biological applications. Indeed, techniques as Nuclear Magnetic Resonance, Gas or Liquid Chromatography, Mass Spectrometry, Infrared and UV-visible spectroscopies have provided extensive datasets that can help in tasks as biological and biomedical discovery, biotechnology and drug development. However, as it happens with other omics data, the analysis of metabolomics datasets provides multiple challenges, both in terms of methodologies and in the development of appropriate computational tools. Indeed, from the available software tools, none addresses the multiplicity of existing techniques and data analysis tasks. In this work, we make available a novel R package, named specmine, which provides a set of methods for metabolomics data analysis, including data loading in different formats, pre-processing, metabolite identification, univariate and multivariate data analysis, machine learning, and feature selection. Importantly, the implemented methods provide adequate support for the analysis of data from diverse experimental techniques, integrating a large set of functions from several R packages in a powerful, yet simple to use environment. The package, already available in CRAN, is accompanied by a web site where users can deposit datasets, scripts and analysis reports to be shared with the community, promoting the efficient sharing of metabolomics data analysis pipelines.

Using free data mining software and clustering algorithms to find predictors from student qualifications

In this project a research both in finding predictors via clustering techniques and in reviewing the Data Mining free software is achieved. The research is based in a case of study, from where additionally to the KDD free software used by the scientific community; a new free tool for pre-processing the data is presented. The predictors are intended for the e-learning domain as the data from where these predictors have to be inferred are student qualifications from different e-learning environments. Through our case of study not only clustering algorithms are tested but also additional goals are proposed.

A Monte Carlo method for accelerating the computation of animated radiosity sequences

Realistic rendering animation is known to be an expensive processing task when physically-based global illumination methods are used in order to improve illumination details. This paper presents an acceleration technique to compute animations in radiosity environments. The technique is based on an interpolated approach that exploits temporal coherence in radiosity. A fast global Monte Carlo pre-processing step is introduced to the whole computation of the animated sequence to select important frames. These are fully computed and used as a base for the interpolation of all the sequence. The approach is completely view-independent. Once the illumination is computed, it can be visualized by any animated camera. Results present significant high speed-ups showing that the technique could be an interesting alternative to deterministic methods for computing non-interactive radiosity animations for moderately complex scenarios

Parametric imaging for characterizing focal liver lesions in contrast-enhanced ultrasound.

The differentiation between benign and malignant focal liver lesions plays an important role in diagnosis of liver disease and therapeutic planning of local or general disease. This differentiation, based on characterization, relies on the observation of the dynamic vascular patterns (DVP) of lesions with respect to adjacent parenchyma, and may be assessed during contrast-enhanced ultrasound imaging after a bolus injection. For instance, hemangiomas (i.e., benign lesions) exhibit hyper-enhanced signatures over time, whereas metastases (i.e., malignant lesions) frequently present hyperenhanced foci during the arterial phase and always become hypo-enhanced afterwards. The objective of this work was to develop a new parametric imaging technique, aimed at mapping the DVP signatures into a single image called a DVP parametric image, conceived as a diagnostic aid tool for characterizing lesion types. The methodology consisted in processing a time sequence of images (DICOM video data) using four consecutive steps: (1) pre-processing combining image motion correction and linearization to derive an echo-power signal, in each pixel, proportional to local contrast agent concentration over time; (2) signal modeling, by means of a curve-fitting optimization, to compute a difference signal in each pixel, as the subtraction of adjacent parenchyma kinetic from the echopower signal; (3) classification of difference signals; and (4) parametric image rendering to represent classified pixels as a support for diagnosis. DVP parametric imaging was the object of a clinical assessment on a total of 146 lesions, imaged using different medical ultrasound systems. The resulting sensitivity and specificity were 97% and 91%, respectively, which compare favorably with scores of 81 to 95% and 80 to 95% reported in medical literature for sensitivity and specificity, respectively.

A pipeline approach with spatial information for segmenting multiple sclerosis lesions on brain magnetic resonance imaging

Background: Conventional magnetic resonance imaging (MRI) techniques are highly sensitive to detect multiple sclerosis (MS) plaques, enabling a quantitative assessment of inflammatory activity and lesion load. In quantitative analyses of focal lesions, manual or semi-automated segmentations have been widely used to compute the total number of lesions and the total lesion volume. These techniques, however, are both challenging and time-consuming, being also prone to intra-observer and inter-observer variability.Aim: To develop an automated approach to segment brain tissues and MS lesions from brain MRI images. The goal is to reduce the user interaction and to provide an objective tool that eliminates the inter- and intra-observer variability.Methods: Based on the recent methods developed by Souplet et al. and de Boer et al., we propose a novel pipeline which includes the following steps: bias correction, skull stripping, atlas registration, tissue classification, and lesion segmentation. After the initial pre-processing steps, a MRI scan is automatically segmented into 4 classes: white matter (WM), grey matter (GM), cerebrospinal fluid (CSF) and partial volume. An expectation maximisation method which fits a multivariate Gaussian mixture model to T1-w, T2-w and PD-w images is used for this purpose. Based on the obtained tissue masks and using the estimated GM mean and variance, we apply an intensity threshold to the FLAIR image, which provides the lesion segmentation. With the aim of improving this initial result, spatial information coming from the neighbouring tissue labels is used to refine the final lesion segmentation.Results:The experimental evaluation was performed using real data sets of 1.5T and the corresponding ground truth annotations provided by expert radiologists. The following values were obtained: 64% of true positive (TP) fraction, 80% of false positive (FP) fraction, and an average surface distance of 7.89 mm. The results of our approach were quantitatively compared to our implementations of the works of Souplet et al. and de Boer et al., obtaining higher TP and lower FP values.Conclusion: Promising MS lesion segmentation results have been obtained in terms of TP. However, the high number of FP which is still a well-known problem of all the automated MS lesion segmentation approaches has to be improved in order to use them for the standard clinical practice. Our future work will focus on tackling this issue.

Modelling ecological niches with support vector machines

1. The ecological niche is a fundamental biological concept. Modelling species' niches is central to numerous ecological applications, including predicting species invasions, identifying reservoirs for disease, nature reserve design and forecasting the effects of anthropogenic and natural climate change on species' ranges. 2. A computational analogue of Hutchinson's ecological niche concept (the multidimensional hyperspace of species' environmental requirements) is the support of the distribution of environments in which the species persist. Recently developed machine-learning algorithms can estimate the support of such high-dimensional distributions. We show how support vector machines can be used to map ecological niches using only observations of species presence to train distribution models for 106 species of woody plants and trees in a montane environment using up to nine environmental covariates. 3. We compared the accuracy of three methods that differ in their approaches to reducing model complexity. We tested models with independent observations of both species presence and species absence. We found that the simplest procedure, which uses all available variables and no pre-processing to reduce correlation, was best overall. Ecological niche models based on support vector machines are theoretically superior to models that rely on simulating pseudo-absence data and are comparable in empirical tests. 4. Synthesis and applications. Accurate species distribution models are crucial for effective environmental planning, management and conservation, and for unravelling the role of the environment in human health and welfare. Models based on distribution estimation rather than classification overcome theoretical and practical obstacles that pervade species distribution modelling. In particular, ecological niche models based on machine-learning algorithms for estimating the support of a statistical distribution provide a promising new approach to identifying species' potential distributions and to project changes in these distributions as a result of climate change, land use and landscape alteration.

Forecasting tourism demand to Catalonia: neural networks vs. time series models

The increasing interest aroused by more advanced forecasting techniques, together with the requirement for more accurate forecasts of tourismdemand at the destination level due to the constant growth of world tourism, has lead us to evaluate the forecasting performance of neural modelling relative to that of time seriesmethods at a regional level. Seasonality and volatility are important features of tourism data, which makes it a particularly favourable context in which to compare the forecasting performance of linear models to that of nonlinear alternative approaches. Pre-processed official statistical data of overnight stays and tourist arrivals fromall the different countries of origin to Catalonia from 2001 to 2009 is used in the study. When comparing the forecasting accuracy of the different techniques for different time horizons, autoregressive integrated moving average models outperform self-exciting threshold autoregressions and artificial neural network models, especially for shorter horizons. These results suggest that the there is a trade-off between the degree of pre-processing and the accuracy of the forecasts obtained with neural networks, which are more suitable in the presence of nonlinearity in the data. In spite of the significant differences between countries, which can be explained by different patterns of consumer behaviour,we also find that forecasts of tourist arrivals aremore accurate than forecasts of overnight stays.

Sulautetun moniprosessorijärjestelmän suunnittelu sähkömoottorien ohjaus- ja valvontatarpeisiin

Universal Converter (UNICON) –projektin osana suunniteltiin sähkömoottorikäyttöjen ohjaukseen ja mittaukseen soveltuva digitaaliseen signaaliprosessoriin (DSP) pohjautuva sulautettu järjestelmä. Riittävän laskentatehon varmistamiseksi päädyttiin käyttämään moniprosessorijärjestelmää. Prosessorijärjestelmässä käytettävää DSP-piiriä valittaessa valintaperusteina olivat piirien tarjoama prosessointiteho ja moniprosessorituki. Analog Devices:n SHARC-sarjan DSP-piirit täyttivät parhaiten asetetut vaatimukset: Ne tarjoavat tehokkaan käskykannan lisäksi suuren sisäisen muistin ja sisäänrakennetun moniprosessorituen. Järjestelmän mittalaiteluonteisuudesta johtuen keskeinen suunnitteluparametri oli luoda nopeat tiedonsiirtoyhteydet mittausantureilta DSP-järjestelmään. Tämä toteutettiin käyttäen ohjelmointavia FPGA-logiikkapiirejä digitaalimuotoisen mittausdatan vastaanotossa ja esikäsittelyssä. Tiedonsiirtoyhteys PC-tietokoneelle toteutettiin käyttäen erityistä liityntäkorttia DSP-järjestelmän ja PC-tietokoneen välillä. Liityntäkortin päätehtävänä on puskuroida siirrettävä data. Järjestelyllä estetään PC-tietokoneen vaikutus DSP-järjestelmän toimintaan, jotta kyetään takaamaan järjestelmän reaaliaikainen toiminta kaikissa olosuhteissa.

Feature-based matching of underwater images

This work investigates performance of recent feature-based matching techniques when applied to registration of underwater images. Matching methods are tested versus different contrast enhancing pre-processing of images. As a result of the performed experiments for various dominating in images underwater artifacts and present deformation, the outperforming preprocessing, detection and description methods are proposed

Akustisen emission anturin signaalin esikäsittelypiirin selvittäminen ja prototyypin toteuttaminen

Tämän työn tavoitteena oli selvittää ja toteuttaa esikäsittelypiirin prototyyppi akustisen emission anturin signaalille. Toteutettu esikäsittelypiiri toimii yksipuoleisella käyttöjännitteellä. Työssä käydään läpi esikäsittelypiirin suunnitteluun liittyvät vaiheet laskelmien ja simulaatioiden muodossa. Lisäksi työssä esitetään mittaustulokset esikäsittelypiirin toiminnasta.

Teurasjätteiden jalostaminen liikennepolttoaineiksi

Työssä määritettiin luokan 2 eläinperäisistä sivutuotteista liikennekäyttöön tuotettujen biodieselin ja biometaanin elinkaaren aikaiset kasvihuonekaasupäästöt ja tuotantoprosessien energiankulutukset perustuen kirjallisuuslähteistä saatuihin lähtötietoihin. Tätä kautta tutkittiin yhdistelmäprosessia, jossa tuotetaan molempia polttoaineita ja selvitettiin onko tällaisella tuotantotavalla mahdollista vähentää päästöjä ja parantaa polttoaineiden tuotannon energiatehokkuutta. Kasvihuone-kaasupäästöjen laskentamenetelmä pohjautuu direktiivissä 2009/28/EY annettuun ohjeistukseen ja eri kasvihuonekaasupäästöjen karakterisointi IPCC:n sadan vuoden tarkastelumalliin. Käytännön laskenta suoritettiin standardien SFS-EN ISO 14040 ja 14044 määrittelemän elinkaariarviointiselvityksen muodossa. Työssä käytetyn laskentamenetelmän ja tarkasteluun valittujen tuotanto-teknologioiden perusteella lasketut tulokset osoittavat, että yhdistelmäprosessilla ei saavuteta suurempia päästövähenemiä eikä parempaa energiatehokkuutta kuin nykyisin käytössä olevilla tuotantotavoilla. Tulokset ovat kuitenkin hyvin herkkiä laskennassa tehtyjen oletusten ja käytettyjen lähtötietojen vaihtelulle sekä valittujen laskentamenetelmien muutoksille. Suurin päästöjä ja energiankulutusta aiheuttava yksittäinen tekijä on kaikissa tuotejärjestelmissä luokan 2 sivutuotteiden esikäsittelyssä vaadittavaan steri-lointiin tarvittavan lämmön tuotanto. Tutkituissa tuotejärjestelmissä lämpö tuotetaan kokonaan tai osittain fossiilisilla polttoaineilla. Kasvihuone-kaasupäästöjä olisi mahdollista alentaa merkittävästi siirtymällä lämmön tuotannossa kokonaan uusiutuviin polttoaineisiin. Sterilointi on lain edellyttämä käsittelytapa ja siksi energiankulutusta on vallitsevissa olosuhteissa hyvin vaikea pienentää merkittävästi.

Detection of Illicit Drugs and Drug Precursors with Cantilever-Enhanced Photoacoustic Spectroscopy

In this study, cantilever-enhanced photoacoustic spectroscopy (CEPAS) was applied in different drug detection schemes. The study was divided into two different applications: trace detection of vaporized drugs and drug precursors in the gas-phase, and detection of cocaine abuse in hair. The main focus, however, was the study of hair samples. In the gas-phase, methyl benzoate, a hydrolysis product of cocaine hydrochloride, and benzyl methyl ketone (BMK), a precursor of amphetamine and methamphetamine were investigated. In the solid-phase, hair samples from cocaine overdose patients were measured and compared to a drug-free reference group. As hair consists mostly of long fibrous proteins generally called keratin, proteins from fingernails and saliva were also studied for comparison. Different measurement setups were applied in this study. Gas measurements were carried out using quantum cascade lasers (QLC) as a source in the photoacoustic detection. Also, an external cavity (EC) design was used for a broader tuning range. Detection limits of 3.4 particles per billion (ppb) for methyl benzoate and 26 ppb for BMK in 0.9 s were achieved with the EC-QCL PAS setup. The achieved detection limits are sufficient for realistic drug detection applications. The measurements from drug overdose patients were carried out using Fourier transform infrared (FTIR) PAS. The drug-containing hair samples and drug-free samples were both measured with the FTIR-PAS setup, and the measured spectra were analyzed statistically with principal component analysis (PCA). The two groups were separated by their spectra with PCA and proper spectral pre-processing. To improve the method, ECQCL measurements of the hair samples, and studies using photoacoustic microsampling techniques, were performed. High quality, high-resolution spectra with a broad tuning range were recorded from a single hair fiber. This broad tuning range of an EC-QCL has not previously been used in the photoacoustic spectroscopy of solids. However, no drug detection studies were performed with the EC-QCL solid-phase setup.

Towards sustainable Iron- and steelmaking with economic optimization

The iron and steelmaking industry is among the major contributors to the anthropogenic emissions of carbon dioxide in the world. The rising levels of CO2 in the atmosphere and the global concern about the greenhouse effect and climate change have brought about considerable investigations on how to reduce the energy intensity and CO2 emissions of this industrial sector. In this thesis the problem is tackled by mathematical modeling and optimization using three different approaches. The possibility to use biomass in the integrated steel plant, particularly as an auxiliary reductant in the blast furnace, is investigated. By pre-processing the biomass its heating value and carbon content can be increased at the same time as the oxygen content is decreased. As the compression strength of the preprocessed biomass is lower than that of coke, it is not suitable for replacing a major part of the coke in the blast furnace burden. Therefore the biomass is assumed to be injected at the tuyere level of the blast furnace. Carbon capture and storage is, nowadays, mostly associated with power plants but it can also be used to reduce the CO2 emissions of an integrated steel plant. In the case of a blast furnace, the effect of CCS can be further increased by recycling the carbon dioxide stripped top gas back into the process. However, this affects the economy of the integrated steel plant, as the amount of top gases available, e.g., for power and heat production is decreased. High quality raw materials are a prerequisite for smooth blast furnace operation. High quality coal is especially needed to produce coke with sufficient properties to ensure proper gas permeability and smooth burden descent. Lower quality coals as well as natural gas, which some countries have in great volumes, can be utilized with various direct and smelting reduction processes. The DRI produced with a direct reduction process can be utilized as a feed material for blast furnace, basic oxygen furnace or electric arc furnace. The liquid hot metal from a smelting reduction process can in turn be used in basic oxygen furnace or electric arc furnace. The unit sizes and investment costs of an alternative ironmaking process are also lower than those of a blast furnace. In this study, the economy of an integrated steel plant is investigated by simulation and optimization. The studied system consists of linearly described unit processes from coke plant to steel making units, with a more detailed thermodynamical model of the blast furnace. The results from the blast furnace operation with biomass injection revealed the importance of proper pre-processing of the raw biomass as the composition of the biomass as well as the heating value and the yield are all affected by the pyrolysis temperature. As for recycling of CO2 stripped blast furnace top gas, substantial reductions in the emission rates are achieved if the stripped CO2 can be stored. However, the optimal recycling degree together with other operation conditions is heavily dependent on the cost structure of CO2 emissions and stripping/storage. The economical feasibility related to the use of DRI in the blast furnace depends on the price ratio between the DRI pellets and the BF pellets. The high amount of energy needed in the rotary hearth furnace to reduce the iron ore leads to increased CO2 emissions.