The objective of this project was to apply machine learning methods to determine protein secondary structure content and protein fold class from ROA and Raman vibrational spectral data. Raman and ROA are sensitive to biomolecular structure with the bands of each spectra corresponding to structural elements in proteins and when combined give a fingerprint of the protein. However, there are many bands of which little is known. There is a need, therefore, to find ways of extrapolating information from spectral bands and investigate which regions of the spectra contain the most useful structural information. Support Vector Machines (SVM) classification and Random Forests (RF) trees classification were used to mine protein fold class information and Partial Least Squares (PLS) regression was used to determine secondary structure content of proteins. The classification methods were used to group proteins into α-helix, β-sheet, α/β and disordered fold classes. The PLS regression was used to determine percentage protein structural content from Raman and ROA spectral data. The analyses were performed on spectral bin widths of 10cm-1 and on the spectral amide regions I, II and III. The full spectra and different combinations of the amide regions were also analysed. The SVM analyses, classification and regression, generally did not perform well. SVM classification models for example, had low Matthew Correlation Coefficient (MCC) values below 0.5 but this is better than a negative value which would indicate a random chance prediction. The SVM regression analyses also showed very poor performances with average R2 values below 0.5. R2 is the Pearson's correlations coefficient and shows how well predicted and observed structural content values correlate. An R2 value 1 indicates a good correlation and therefore a good prediction model. The Partial Least Squares regression analyses yielded much improved results with very high accuracies. Analyses of full spectrum and the spectral amide regions produced high R2 values of 0.8-0.9 for both ROA and Raman spectral data. This high accuracy was also seen in the analysis of the 850-1100 cm-1 backbone region for both ROA and Raman spectra which indicates that this region could have an important contribution to protein structure analysis. 2nd derivative Raman spectra PLS regression analysis showed very improved performance with high accuracy R2 values of 0.81-0.97. The Random Forest algorithm used here for classification showed good performance. The 2-dimensional plots used to visualise the classification clusters showed clear clusters in some analyses, for example tighter clustering was observed for amide I, amide I & III and amide I & II & III spectral regions than for amide II, amide III and amide II&III spectra analysis. The Random Forest algorithm also determines variable importance which showed spectral bins were crucial in the classification decisions. The ROA Random Forest analyses performed generally better than Raman Random Forest analyses. ROA Random Forest analyses showed 75% as the highest percentage of correctly classified proteins while Raman analyses reported 50% as the highest percentage. The analyses presented in this thesis have shown that Raman and ROA vibrational spectral contains information about protein secondary structure and these data can be extracted using mathematical methods such as the machine learning techniques presented here. The machine learning methods applied in this project were used to mine information about protein secondary structure and the work presented here demonstrated that these techniques are useful and could be powerful tools in the determination protein structure from spectral data.

The aim of this master's thesis is to get familiar with problems of data mining and classification. This thesis also continues with application SUNAR, which is upgraded in practical part with SVM classification of persons passing between cameras. In the conclusion, we discuss ways to improve classification and person recognition in application SUNAR.

Heart rate variability (HRV) is the time variation between adjacent heartbeats. This variation is regulated by the autonomic nervous system (ANS) and its two branches, the sympathetic and parasympathetic nervous system. HRV is considered as an essential clinical tool to estimate the imbalance between the two branches, hence as an indicator of age and cardiac-related events.This thesis focuses on the ECG recordings during nocturnal rest to estimate the influence of HRV in predicting the age decade of healthy individuals. Time and frequency domains, as well as non-linear methods, are explored to extract the HRV features. Three feature-based methods (support vector machine (SVM), random forest, and extreme gradient boosting (XGBoost)) were employed, and the overall test accuracy achieved in capturing the actual class was relatively low (lower than 30%). SVM classifier had the lowest performance, while random forests and XGBoost performed slightly better. Although the difference is negligible, the random forest had the highest test accuracy, approximately 29%, using a subset of ten optimal HRV features. Furthermore, to validate the findings, the original dataset was shuffled and used as a test set and compared the performance to other related research outputs.

Substantial research has been done on the electroencephalogram (EEG) neural signals generated by feedback within a simple choice task, and there is much evidence for the existence of a reward prediction error signal generated in the anterior cingulate cortex of the brain when the outcome of this type of choice does not match expectations. However, less research has been done to date on the neural responses to intermediate outcomes in a multi-step choice task. Here, I investigated the neural signals generated by a complex, non-deterministic task that involved multiple choices before final win/loss feedback in order to see if the observed signals correspond to predictions made by reinforcement learning theory. In Experiment One, I conducted an EEG experiment to record neural signals while participants performed a computerized task designed to elicit the reward positivity, an event-related brain potential (ERP) component thought to be a biological reward prediction error signal. EEG results revealed a difference in amplitude of the reward positivity ERP component between experimental conditions comparing unexpected to expected feedback, as well as an interaction between valence and expectancy of the feedback. Additionally, results of an ERP analysis of the amplitude of the P300 component also showed an interaction between valence and expectancy. In Experiment Two, I used machine learning to classify epoched EEG data from Experiment One into experimental conditions to determine if individual states within the task could be differentiated based solely on the EEG data. My results showed that individual states could be differentiated with above-chance accuracy. I conclude by discussing how these results fit with the predictions made by reinforcement learning theory about the type of task investigated herein, and implications of those findings on our understanding of learning and decision-making in humans. / Graduate

Meadow vegetation in the Krkonoše Mountains National Park is classified in this master thesis using aerial hyperspectral data from sensor AISA and Support Vector Machines (SVM) and Neural Networks (NN) classification algorithms. The main goals of the master thesis are to determine the best settings of SVM parameters and to propose an ideal design for a training dataset for this classification algorithm and mapping of the meadows in the Krkonoše mountains. The criterion of the tests will be the result of classification accuracy (confusion matrices and kappa coefficient). The additional goal of the master thesis is to compare performances of both utilized classifiers, especially regarding the amount of training pixels necessary for successful classification of the mountainous meadow vegetation. Classification maps of the area of interest and Python scripts are the main outputs of the master thesis. These outputs will be handed over to the Administration of the Krkonoše Mountains National Park for further utilization in the monitoring and protecting these valuable meadow vegetation communities. Key words: hyperspectral data, AISA, Support Vector Machines, Neural Networks, training dataset, mountainous meadow vegetation

In this thesis, we present selected methods of regression and classification analysis in terms of robust optimization which aim to compensate for data imprecisions and measurement errors. In the first part, ordinary least squares method and its generalizations derived within the context of robust optimization - ridge regression and Lasso method are introduced. The connection between robust least squares and stated generalizations is also shown. Theoretical results are accompanied with simulation study investigating from a different perspective the robustness of stated methods. In the second part, we define a modern classification method - Support Vector Machines (SVM). Using the obtained knowledge, we formulate a robust SVM method, which can be applied in robust classification. The final part is devoted to the biometric identification of a style of typing and an individual based on keystroke dynamics using the formulated theory. Powered by TCPDF (www.tcpdf.org)

Text classification is a fundamental part of natural language processing. In this thesis, methods for text classification are used in an attempt to predict the political party affiliation of members of parliament (MPs). The objective is to evaluate the performance of Support Vector Machines (SVM), naive Bayes, and a fine-tuned Bidirectional Encoder Representations from Transformers (BERT) model in predicting MPs' political party affiliation based on speeches given in the Chamber of the Swedish Parliament. This study shows that BERT outperforms SVM and naive Bayes in correctly classifying MPs, and SVM makes better predictions than naive Bayes and performs reasonably well compared to BERT. The results show that all models correctly predict MPs representing the Sweden Democrats to the highest degree. Both BERT and SVM roughly classify every other speech correctly, which implies much better than making random predictions. These results indicate the potential use of methods for automatically classifying political speeches.

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Forecasting the weather remains a challenging task because of the atmosphere's complexity and unpredictable nature. A few of the factors that decide weather conditions, such as rain, clouds, clear skies, and sunshine, include temperature, pressure, humidity, wind speed, and direction. Currently, sophisticated, and physical models are used to forecast weather, but they have several limitations, particularly in terms of computational time. In the past few years, supervised machine learning algorithms have shown great promise for the precise forecasting of meteorological events. Using historical weather data, these strategies train a model to predict the weather in the future. This study employs supervised machine learning techniques, including k-nearest neighbors (KNNs), support vector machines (SVMs), random forests (RFs), and artificial neural networks (ANNs), for better weather forecast accuracy. To conduct this study, we employed historical weather data from the Weatherstack API. The data spans several years and contains information on several meteorological variables, including temperature, pressure, humidity, wind speed, and direction. The data is processed beforehand which includes normalizing it and dividing it into separate training and testing sets. Finally, the effectiveness of different models is examined to determine which is best for producing accurate weather forecasts. The results of this study provide information on the application of supervised machine learning methods for weather forecasting and support the creation of better weather prediction models. / Att förutsäga vädret är fortfarande en utmanande uppgift på grund av atmosfärens komplexitet och oförutsägbara natur. Några av faktorerna som påverkar väderförhållandena, som regn, moln, klart väder och solsken, inkluderar temperatur, tryck, luftfuktighet, vindhastighet och riktning. För närvarande används sofistikerade fysiska modeller för att förutsäga vädret, men de har flera begränsningar, särskilt när det gäller beräkningstid. Under de senaste åren har övervakade maskininlärningsalgoritmer visat stor potential för att noggrant förutsäga meteorologiska händelser. Genom att använda historiska väderdata tränar dessa strategier en modell för att förutsäga framtida väder. Denna studie använder övervakade maskininlärningstekniker, inklusive k-nearest neighbors (KNNs), support vector machines (SVMs), random forests (RFs) och artificial neural networks (ANNs), för att förbättra noggrannheten i väderprognoser. För att genomföra denna studie använde vi historiska väderdata från Weatherstack API. Data sträcker sig över flera år och innehåller information om flera meteorologiska variabler, inklusive temperatur, tryck, luftfuktighet, vindhastighet och riktning. Data bearbetas i förväg, vilket inkluderar normalisering och uppdelning i separata tränings- och testset. Slutligen undersöks effektiviteten hos olika modeller för att avgöra vilken som är bäst för att producera noggranna väderprognoser. Resultaten av denna studie ger information om tillämpningen av övervakade maskininlärningsmetoder för väderprognoser och stödjer skapandet av bättre väderprognosmodeller.

Quantum computing is an emerging field with potential applications in machine learning. This research project aimed to compare the performance of a quantum kernel to that of a classical kernel in machine learning binary classification tasks. Two Support Vector Machines, a popular classification model, was implemented for the respective Variational Quantum kernel and the classical Radial Basis Function kernel and tested on the same sets of artificial quantum-based testing data. The results show that the quantum kernel significantly outperformed the classical kernel for the specific type of data and parameters used in the study. The findings suggest that quantum kernels have the potential to improve machine learning performance for certain types of problems, such as search engines and self-driving vehicles. Further research is, however, needed to confirm their utility in general situations. / Kvantberäkning är ett växande forskningsområde med möjliga tillämpningar inom maskininlärning. I detta forskningsprojekt jämfördes prestandan hos en klassisk kärna med den hos en kvantkärna i binär klassificering för maskininlärninguppgifter, och implikationerna av resultaten diskuterades. Genom att implementera två stödvektormaskiner, en populär klassifikationsmodell, för respektive variabel kvantkärna och klassisk radiell basfunktionskärna kunde vi direkt testa båda kärnorna på samma uppsättning av artificiella kvant-baserad testdata. Resultaten visar på betydande prestandafördelar för kvantkärnan jämfört med den klassiska kärnan när det gäller denna specifika typ av data och de parametrar som användes i vår studie. Vi drar slutsatsen att kvantkärnor inom maskininlärning har potential att överträffa klassiska kärnor, men att mer forskning krävs för att fastställa om detta har någon nytta i allmänna situationer. Om det finns betydande prestandafördelar kan det finnas många tillämpningar, till exempel för sökmotorer och självkörande fordon.