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Many companies use machine learning techniques to support decision-making and automate business processes by learning from the data that they have. In this thesis we investigate the theory behind the most widely used in practice machine learning algorithms for solving classification and regression problems.
In particular, the following algorithms were chosen for the classification problem: Logistic Regression, Decision Trees, Random Forest, Support Vector Machine (SVM), Learning Vector Quantization (LVQ). As for the regression problem, Decision Trees, Random Forest and Gradient Boosted Tree were used. We then apply those algorithms to real company data and compare their performances and results.
Prototype-based classification methods like Generalized Matrix Learning Vector Quantization (GMLVQ) are simple and easy to implement. An appropriate choice of the activation function plays an important role in the performance of (deep) multilayer perceptrons (MLP) that rely on a non-linearity for classification and regression learning. In this thesis, successful candidates of non-linear activation functions are investigated which are known for MLPs for application in GMLVQ to realize a non-linear mapping. The influence of the non-linear activation functions on the performance of the model with respect to accuracy, convergence rate are analyzed and experimental results are documented.
A relatively new research field of neurosciences, called Connectomics, aims to achieve a full understanding and mapping of neural circuits and fine neuronal structures of the nervous system in a variety of organisms. This detailed information will provide insight in how our brain is influenced by different genetic and psychiatric diseases, how memory traces are stored and ageing influences our brain structure. It is beyond question that new methods for data acquisition will produce large amounts of neuronal image data. This data will exceed the zetabyte range and is impossible to annotate manually for visualization and analysis. Nowadays, machine learning algorithms and specially deep convolutional neuronal networks are heavily used in medical imaging and computer vision, which brings the opportunity of designing fully automated pipelines for image analysis. This work presents a new automated workflow based on three major parts including image processing using consecutive deep convolutional networks, a pixel-grouping step called connected components and 3D visualization via neuroglancer to achieve a dense three dimensional reconstruction of neurons from EM image data.
Neural networks have become one of the most powerful algorithms when it comes to learning from big data sets and it is used extensively for classification. But the deeper the network models, the lesser is the interpretability of such models. Although many methods exist to explain
the output of such networks, the lack of interpretability makes them black boxes. On the other hand, prototype-based machine learning algorithms are known to be interpretable and robust.
Therefore, the aim of this thesis is to find a way to interpret the functioning of the neural networks by introducing a prototype layer to the neural network architecture. This prototype layer will train alongside the neural network and help us interpret the model. We present architectures of neural networks consisting of autoencoders and prototypes that perform activity recognition from heart rates extracted from ECG signals. These prototypes represent the different activity groups that the heart rates belong to and thereby aid in interpretability.
Genetic sequence variations at the level of gene promoters influence the binding of transcription factors. In plants, this often leads to differential gene expression across natural accessions and crop cultivars. Some of these differences are propagated through molecular networks and lead to macroscopic phenotypes. However, the link between promoter sequence variation and the variation of its activity is not yet well understood. In this project, we use the power of deep learning in 728 genotypes of Arabidopsis thaliana to shed light on some aspects of that link. Convolutional neural networks were successfully implemented to predict the likelihood of a gene being expressed from its promoter sequence. These networks were also capable of highlighting known and putative new sequence motifs causal for the expression of genes. We tested our algorithms in various scenarios, including single and multiple point mutations, as well as indels on synthetic and real promoter sequences and the respective performance characteristics of the algorithm have been estimated. Finally, we showed that the decision boundary to classify genes as expressed and non-expressed depends on the sensitivity of the transcriptome profiling assay and changing it has an impact on the algorithm’s performance.
Data streams change their statistical behaviour over the time. These changes can occur gradually or abruptly with unforeseen reasons, which may effect the expected outcome. Thus it is important to detect concept drift as soon as it occurs. In this thesis we chose distance based methodology to detect presence of concept drift in the data streams. We used generalized learning vector quantization(GLVQ) and generalized matrix learning vector quantization( GMLVQ) classifiers for distance calculation between prototypes and data points. Chi-square and Kolmogorov–Smirnov tests are used to compare the distance distributions of test and train data sets to indicate the drift presence.
Financial fraud for banks can be a reason for huge monetary losses. Studies have shown that, if not mitigated, financial fraud can lead to bankruptcy for big financial institutions and even insolvency for individuals. Credit card fraud is a type of financial fraud that is ever growing. In the future, these numbers are expected to increase exponentially and that’s why a lot of researchers are focusing on machine learning techniques for detecting frauds. This task, however, is not a simple task. There are mainly two reasons
• varying behaviour in committing fraud
• high level of imbalance in the dataset (the majority of normal or genuine cases largely outnumbers the number of fraudulent cases)
A predictive model usually tends to be biased towards the majority of samples, in an unbalanced dataset, when this dataset is provided as an input to a predictive model.
In this Thesis this problem is tackled by implementing a data-level approach where different resampling methods such as undersampling, oversampling, and hybrid strategies along with bagging and boosting algorithmic approaches have been applied to a highly skewed dataset with 492 idetified frauds out of 284,807 transactions.
Predictive modelling algorithms like Logistic Regression, Random Forest, and XGBoost have been implemented along with different resampling techniques to predict fraudulent transactions.
The performance of the predictive models was evaluated based on Receiver Operating CharacteristicArea under the curve (AUC-ROC), Precision Recall Area under the Curve (AUC-PR), Precision, Recall, F1 score metrics.
Drought is one of the most common and dangerous threats plants have to face, costing the global agricultural sector billions of dollars every year and leading to the loss of tons of harvest. Until people drastically reduce their consumption of animal products or cellular agriculture comes of age, more and more crops will need to be produced to sustain the ever growing human population. Even then, as more areas on earth are becoming prone to drought due to climate change, we may still have to find or breed plant varieties more suitable to grow and prosper in these changing environments.
Plants respond to drought stress with a complex interplay of hormones, transcription factors, and many other functional or regulatory proteins and mapping out this web of agents is no trivial task. In the last two to three decades or so, machine learning has become immensely popular and is increasingly used to find patterns in situations that are too complex for the human mind to overlook. Even though much of the hype is focused on the latest developments in deep learning, relatively simple methods often yield superior results, especially when data is limited and expensive to gather.
This Master Thesis, conducted at the IPK in Gatersleben, develops an approach for shedding light on the phenotypic and transcriptomic processes that occur when a plant is subjected to stress. It centers around a random forest feature selection algorithm and although it is used here to illuminate drought stress response in Arabidopsis thaliana, it can be applied to all kinds of stresses in all kinds of plants.
We present dimensionality reduction methods like autoencoders and t-SNE for visualization of high-dimensional data into a two-dimensional map. In this thesis, we initially implement basic and deep autoencoders using breast cancer and mushroom datasets. Next, we build another dimensionality reduction method t-SNE using the same datasets. The obtained visualization results of the datasets using the dimensionality reduction methods are documented in the experiments section of the thesis. The evaluation of classification and clustering for the dimensionality reduction techniques is also performed. The visualization and evaluation results of t-SNE are significantly better than the other dimensionality reduction techniques.
There are multiple ways to gain information about an individual and its health status, but an increasingly popular field in medicine has become the analysis of human breath, which carries a lot of information about metabolic processes within the individuals body. The information in exhaled breath consists of volatile (organic) compounds (VOCs). These VOCs are products of metabolic processes within the individuals body, thus might be an indicator for diseases disturbing those processes. The compounds are to be detected by mass-spectrometric (MS) or ion-mobility spectrometric (IMS) techniques, making the analysis of these compounds not only bounded to exhaled breath. The resulting data is spectral data, capturing concentrations of the VOCs indirectly through intensities. However, a number of about 3000 VOCs [1] could already be determined in human exhaled breath. The number of research paper about VOC-analysis and detection had risen nearly constantly over the last decade 1. Furthermore, the technique to identify VOCs could also be used to capture biomarker from alien species within the individuals body. Extracting VOCs from an individual can be done by non- or minimal invasive techniques. However, the manual identification of VOCs and biomarkers related to a certain disease or infection is not feasible due to the complexity of the sample and often unknown metabolic products, thus automized techniques are needed. [1–4] To establish breath analysis as a diagnosis tool, machine learning methodes could be used. Machine learning has become a popular and common technique when dealing with medical data, due to the rapid analysis. Taking this advantage, breath analysis using machine learning could become the model of choice for diagnosis, keeping in mind that conventional methodes are laboratory based and thus when trying detect bacterial infection need sometimes several days to identify the organism. [5]