Hyperparameter Tuning for Machine and Deep Learning with R

This open access book provides a wealth of hands-on examples that illustrate how hyperparameter tuning can be applied in practice and gives deep insights into the working mechanisms of machine learning (ML) and deep learning (DL) methods. The aim of the book is to equip readers with the ability to achieve better results with significantly less time, costs, effort and resources using the methods described here. The case studies presented in this book can be run on a regular desktop or notebook computer. No high-performance computing facilities are required. The idea for the book originated in a study conducted by Bartz & Bartz GmbH for the Federal Statistical Office of Germany (Destatis). Building on that study, the book is addressed to practitioners in industry as well as researchers, teachers and students in academia. The content focuses on the hyperparameter tuning of ML and DL algorithms, and is divided into two main parts: theory (Part I) and application (Part II). Essential topics covered include: a survey of important model parameters; four parameter tuning studies and one extensive global parameter tuning study; statistical analysis of the performance of ML and DL methods based on severity; and a new, consensus-ranking-based way to aggregate and analyze results from multiple algorithms. The book presents analyses of more than 30 hyperparameters from six relevant ML and DL methods, and provides source code so that users can reproduce the results. Accordingly, it serves as a handbook and textbook alike

Hyperparameter Tuning for Machine and Deep Learning with R

This open access book provides a wealth of hands-on examples that illustrate how hyperparameter tuning can be applied in practice and gives deep insights into the working mechanisms of machine learning (ML) and deep learning (DL) methods. The aim of the book is to equip readers with the ability to achieve better results with significantly less time, costs, effort and resources using the methods described here. The case studies presented in this book can be run on a regular desktop or notebook computer. No high-performance computing facilities are required. The idea for the book originated in a study conducted by Bartz & Bartz GmbH for the Federal Statistical Office of Germany (Destatis). Building on that study, the book is addressed to practitioners in industry as well as researchers, teachers and students in academia. The content focuses on the hyperparameter tuning of ML and DL algorithms, and is divided into two main parts: theory (Part I) and application (Part II). Essential topics covered include: a survey of important model parameters; four parameter tuning studies and one extensive global parameter tuning study; statistical analysis of the performance of ML and DL methods based on severity; and a new, consensus-ranking-based way to aggregate and analyze results from multiple algorithms. The book presents analyses of more than 30 hyperparameters from six relevant ML and DL methods, and provides source code so that users can reproduce the results. Accordingly, it serves as a handbook and textbook alike

bflinks: Reliable Bugfix links via bidirectional references and tuned heuristics

Background: Data from software data repositories such as source code version archives and defect databases contains valuable information that can be used for insights (leading to subsequent improvements), in particular defect insertion circumstance analysis and defect prediction. The first step in such analyses is identifying defect-correcting changes in the version archive (bugfix commits) and linking them to corresponding entries in the defect database, thus establishing bugfix links, in order to enrich the content of the defect-correcting change with additional meta-data. Typically, identifying the bugfix commits in a version archive is done via heuristic string matching on the commit message. Research questions: Which filters could be used to obtain a set of bugfix links? How does one set the cutoff parameters of each? What effect (results loss and precision) does each filter then have? Which overall precision, results loss, and recall is achieved? Method: We analyze a comprehensive modular set of seven independent filters, including new ones that make use of reverse links. We describe and evaluate visual heuristics (based on simple diagnostic plots) for setting six filters' cutoff parameter. We apply these to a commercial repository from the Web CMS domain and validate the results with unprecendented precision by making use of a product expert to manually verify over 2500 links. Results: The parameter selection heuristics pick a very good parameter value in five of the six cases and a reasonably good one in the sixth. As a result, the combined filtering, called bflinks, proposes a set of bugfix links that has 93\% precision with only 7\% results loss. Conclusion: The modular filtering approach can provide high-quality results and can be adapted to repositories with different properties

Automatic generation of smell-free unit tests

Tese de mestrado, Engenharia Informática, 2022, Universidade de Lisboa, Faculdade de CiênciasAutomated test generation tools (such as EvoSuite) typically aim to maximize code coverage. However, they frequently disregard non-coverage aspects that can be relevant for testers, such as the quality of the generated tests. Therefore, automatically generated tests are often affected by a set of test-specific bad programming practices that may hinder the quality of both test and production code, i.e., test smells. Given that other researchers have successfully integrated non-coverage quality metrics into EvoSuite, we decided to extend the EvoSuite tool such that the generated test code is smell-free. To this aim, we compiled 54 test smells from several sources and selected 16 smells that are relevant to the context of this work. We then augmented the tool with the respective test smell metrics and investigated the diffusion of the selected smells and the distribution of the metrics. Finally, we implemented an approach to optimize the test smell metrics as secondary criteria. After establishing the optimal configuration to optimize as secondary criteria (which we used throughout the remainder of the study), we conducted an empirical study to assess whether the tests became significantly less smelly. Furthermore, we studied how the proposed metrics affect the fault detection effectiveness, coverage, and size of the generated tests. Our study revealed that the proposed approach reduces the overall smelliness of the generated tests; in particular, the diffusion of the “Indirect Testing” and “Unrelated Assertions” smells improved considerably. Moreover, our approach improved the smelliness of the tests generated by EvoSuite without compromising the code coverage or fault detection effectiveness. The size and length of the generated tests were also not affected by the new secondary criteria

Democratizing machine learning

Modelle des maschinellen Lernens sind zunehmend in der Gesellschaft verankert, oft in Form von automatisierten Entscheidungsprozessen. Ein wesentlicher Grund dafür ist die verbesserte Zugänglichkeit von Daten, aber auch von Toolkits für maschinelles Lernen, die den Zugang zu Methoden des maschinellen Lernens für Nicht-Experten ermöglichen. Diese Arbeit umfasst mehrere Beiträge zur Demokratisierung des Zugangs zum maschinellem Lernen, mit dem Ziel, einem breiterem Publikum Zugang zu diesen Technologien zu er- möglichen. Die Beiträge in diesem Manuskript stammen aus mehreren Bereichen innerhalb dieses weiten Gebiets. Ein großer Teil ist dem Bereich des automatisierten maschinellen Lernens (AutoML) und der Hyperparameter-Optimierung gewidmet, mit dem Ziel, die oft mühsame Aufgabe, ein optimales Vorhersagemodell für einen gegebenen Datensatz zu finden, zu vereinfachen. Dieser Prozess besteht meist darin ein für vom Benutzer vorgegebene Leistungsmetrik(en) optimales Modell zu finden. Oft kann dieser Prozess durch Lernen aus vorhergehenden Experimenten verbessert oder beschleunigt werden. In dieser Arbeit werden drei solcher Methoden vorgestellt, die entweder darauf abzielen, eine feste Menge möglicher Hyperparameterkonfigurationen zu erhalten, die wahrscheinlich gute Lösungen für jeden neuen Datensatz enthalten, oder Eigenschaften der Datensätze zu nutzen, um neue Konfigurationen vorzuschlagen. Darüber hinaus wird eine Sammlung solcher erforderlichen Metadaten zu den Experimenten vorgestellt, und es wird gezeigt, wie solche Metadaten für die Entwicklung und als Testumgebung für neue Hyperparameter- Optimierungsmethoden verwendet werden können. Die weite Verbreitung von ML-Modellen in vielen Bereichen der Gesellschaft erfordert gleichzeitig eine genauere Untersuchung der Art und Weise, wie aus Modellen abgeleitete automatisierte Entscheidungen die Gesellschaft formen, und ob sie möglicherweise Individuen oder einzelne Bevölkerungsgruppen benachteiligen. In dieser Arbeit wird daher ein AutoML-Tool vorgestellt, das es ermöglicht, solche Überlegungen in die Suche nach einem optimalen Modell miteinzubeziehen. Diese Forderung nach Fairness wirft gleichzeitig die Frage auf, ob die Fairness eines Modells zuverlässig geschätzt werden kann, was in einem weiteren Beitrag in dieser Arbeit untersucht wird. Da der Zugang zu Methoden des maschinellen Lernens auch stark vom Zugang zu Software und Toolboxen abhängt, sind mehrere Beiträge in Form von Software Teil dieser Arbeit. Das R-Paket mlr3pipelines ermöglicht die Einbettung von Modellen in sogenan- nte Machine Learning Pipelines, die Vor- und Nachverarbeitungsschritte enthalten, die im maschinellen Lernen und AutoML häufig benötigt werden. Das mlr3fairness R-Paket hingegen ermöglicht es dem Benutzer, Modelle auf potentielle Benachteiligung hin zu über- prüfen und diese durch verschiedene Techniken zu reduzieren. Eine dieser Techniken, multi-calibration wurde darüberhinaus als seperate Software veröffentlicht.Machine learning artifacts are increasingly embedded in society, often in the form of automated decision-making processes. One major reason for this, along with methodological improvements, is the increasing accessibility of data but also machine learning toolkits that enable access to machine learning methodology for non-experts. The core focus of this thesis is exactly this – democratizing access to machine learning in order to enable a wider audience to benefit from its potential. Contributions in this manuscript stem from several different areas within this broader area. A major section is dedicated to the field of automated machine learning (AutoML) with the goal to abstract away the tedious task of obtaining an optimal predictive model for a given dataset. This process mostly consists of finding said optimal model, often through hyperparameter optimization, while the user in turn only selects the appropriate performance metric(s) and validates the resulting models. This process can be improved or sped up by learning from previous experiments. Three such methods one with the goal to obtain a fixed set of possible hyperparameter configurations that likely contain good solutions for any new dataset and two using dataset characteristics to propose new configurations are presented in this thesis. It furthermore presents a collection of required experiment metadata and how such meta-data can be used for the development and as a test bed for new hyperparameter optimization methods. The pervasion of models derived from ML in many aspects of society simultaneously calls for increased scrutiny with respect to how such models shape society and the eventual biases they exhibit. Therefore, this thesis presents an AutoML tool that allows incorporating fairness considerations into the search for an optimal model. This requirement for fairness simultaneously poses the question of whether we can reliably estimate a model’s fairness, which is studied in a further contribution in this thesis. Since access to machine learning methods also heavily depends on access to software and toolboxes, several contributions in the form of software are part of this thesis. The mlr3pipelines R package allows for embedding models in so-called machine learning pipelines that include pre- and postprocessing steps often required in machine learning and AutoML. The mlr3fairness R package on the other hand enables users to audit models for potential biases as well as reduce those biases through different debiasing techniques. One such technique, multi-calibration is published as a separate software package, mcboost

Moving from phenomenological to predictive modelling: Progress and pitfalls of modelling brain stimulation in-silico

Brain stimulation is an increasingly popular neuromodulatory tool used in both clinical and research settings; however, the effects of brain stimulation, particularly those of non-invasive stimulation, are variable. This variability can be partially explained by an incomplete mechanistic understanding, coupled with a combinatorial explosion of possible stimulation parameters. Computational models constitute a useful tool to explore the vast sea of stimulation parameters and characterise their effects on brain activity. Yet the utility of modelling stimulation in-silico relies on its biophysical relevance, which needs to account for the dynamics of large and diverse neural populations and how underlying networks shape those collective dynamics. The large number of parameters to consider when constructing a model is no less than those needed to consider when planning empirical studies. This piece is centred on the application of phenomenological and biophysical models in non-invasive brain stimulation. We first introduce common forms of brain stimulation and computational models, and provide typical construction choices made when building phenomenological and biophysical models. Through the lens of four case studies, we provide an account of the questions these models can address, commonalities, and limitations across studies. We conclude by proposing future directions to fully realise the potential of computational models of brain stimulation for the design of personalized, efficient, and effective stimulation strategies

An Evolutionary Optimization Algorithm for Automated Classical Machine Learning

Machine learning is an evolving branch of computational algorithms that allow computers to learn from experiences, make predictions, and solve different problems without being explicitly programmed. However, building a useful machine learning model is a challenging process, requiring human expertise to perform various proper tasks and ensure that the machine learning\u27s primary objective --determining the best and most predictive model-- is achieved. These tasks include pre-processing, feature selection, and model selection. Many machine learning models developed by experts are designed manually and by trial and error. In other words, even experts need the time and resources to create good predictive machine learning models. The idea of automated machine learning (AutoML) is to automate a machine learning pipeline to release the burden of substantial development costs and manual processes. The algorithms leveraged in these systems have different hyper-parameters. On the other hand, different input datasets have various features. In both cases, the final performance of the model is closely related to the final selected configuration of features and hyper-parameters. That is why they are considered as crucial tasks in the AutoML. The challenges regarding the computationally expensive nature of tuning hyper-parameters and optimally selecting features create significant opportunities for filling the research gaps in the AutoML field. This dissertation explores how to select the features and tune the hyper-parameters of conventional machine learning algorithms efficiently and automatically. To address the challenges in the AutoML area, novel algorithms for hyper-parameter tuning and feature selection are proposed. The hyper-parameter tuning algorithm aims to provide the optimal set of hyper-parameters in three conventional machine learning models (Random Forest, XGBoost and Support Vector Machine) to obtain best scores regarding performance. On the other hand, the feature selection algorithm looks for the optimal subset of features to achieve the highest performance. Afterward, a hybrid framework is designed for both hyper-parameter tuning and feature selection. The proposed framework can discover close to the optimal configuration of features and hyper-parameters. The proposed framework includes the following components: (1) an automatic feature selection component based on artificial bee colony algorithms and machine learning training, and (2) an automatic hyper-parameter tuning component based on artificial bee colony algorithms and machine learning training for faster training and convergence of the learning models. The whole framework has been evaluated using four real-world datasets in different applications. This framework is an attempt to alleviate the challenges of hyper-parameter tuning and feature selection by using efficient algorithms. However, distributed processing, distributed learning, parallel computing, and other big data solutions are not taken into consideration in this framework

ACCEPT: Introduction of the Adverse Condition and Critical Event Prediction Toolbox

The prediction of anomalies or adverse events is a challenging task, and there are a variety of methods which can be used to address the problem. In this paper, we introduce a generic framework developed in MATLAB (sup registered mark) called ACCEPT (Adverse Condition and Critical Event Prediction Toolbox). ACCEPT is an architectural framework designed to compare and contrast the performance of a variety of machine learning and early warning algorithms, and tests the capability of these algorithms to robustly predict the onset of adverse events in any time-series data generating systems or processes