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Learning a model over possible actions and using the learned model to maximize the obtained reward is an integral part of many applications. Trying to simultaneously learn the model by exploring state space and maximize the obtained reward using the learned model is an exploitation-exploitation tradeoff. Gaussian process upper confidence bound (GB-UCB) algorithm is an effective method for balancing between exploitation and exploration when exploring spatially dependent data in n-dimensional space. The balance between exploration and exploitation is required to limit the amount of user feedback required to achieve good prediction result in our context-based image retrieval system. The system starts with high amount of exploration and — as the confidence in the model increases — it starts exploiting the gathered information to direct the search towards better results. While the implementation of the GP-UCB is quite straightforward, it has time complexity of O(n^3) which limits its use in near real-time applications. In this thesis I present our reinforcement learning image retrieval system based on GP-UCB, with the focus on speed requirements for interactive applications. I also show simple methods to speed up the algorithm running time by doing some of the Gaussian process calculations on the GPU.

Alignment in genomics is the process of finding the positions where DNA strings fit best with one another, that is, where there are the least differences if they were placed side by side. This process, however, remains very computationally intensive, even with more recent algorithmic advancements in the field. Pseudoalignment is emerging as a new method over full alignment as an inexpensive alternative, both in terms of memory needed as well as in terms of power consumption. The process is to instead check for the existence of substrings within the target DNA, and this has been shown to produce good results for a lot of use cases. New methods for pseudoalignment are still evolving, and the goal of this thesis is to provide an implementation that massively parallelises the current state of the art, Themisto, by using all resources available. The most intensive parts of the pipeline are put on the GPU. Meanwhile, the components which run on the CPU are heavily parallelised. Reading and writing of the files is also done in parallel, so that parallel I/O can also be taken advantage of. Results on the Mahti supercomputer, using an NVIDIA A100, shows a 10 times end-to-end querying speedup over the best run of Themisto, using half the CPU cores as Themisto, on the dataset used in this thesis.

Due to the unique properties of foams, they can be found in many different applications in a wide variety of fields. The study of foams is also useful for the many properties they share with other phenomena, like impurities in cooling metals, where the impurities coarsen similarly to bubbles in foams. For these and other reasons foams have been studied extensively for over a hundred years and continue being an interesting area of study today due to new insights in both experimental and theoretical work and new applications waiting to be used and realized in different industries. The most impactful early work in the study of the properties of foams was done in the late 1800s by Plateau. His work was extended in the early to mid-1900s by Lifshitz, Slyozov, Wagner and von Neumann and by many more authors in recent years. The early work was mostly experimental or theoretical in the sense of performing mathematical calculations on paper, while the modern methods of study have kept the experimental part -- with more refined methods of measurement of course -- but shifted towards the implementation of the theory as simulations instead of solving problems on paper. In the early 90s Durian proposed a new method for simulating the mechanics of wet foams, based on repulsive spring-like forces between neighboring bubbles. This model was later extended to allow for the coarsening of the foam, and a slightly changed version of this model has been implemented in the code presented in this thesis. As foams consist of a very large number of bubbles, it is important to be able to simulate sufficiently large systems to realistically study the physics of foams. Very large systems have traditionally been too slow to simulate on the individual bubble level in the past, but thanks to the popularity of computer games and the continuous demand for better graphics in games, the graphics processing units have become very powerful and can nowadays be used to do highly parallel general computing. In this thesis, a modified version of Durian's wet foam model that runs on the GPU is presented. The code has been implemented in modern C++ using Nvidia's CUDA on the GPU. Using this program first a typical two-dimensional foam is simulated with 100000 bubbles. It is found that the simulation code replicates the expected behaviour for this kind of foam. After this, a more detailed analysis is done of a novel phenomenon of the separation of liquid and gas phases in low gas fraction foams that arises only with sufficiently large system sizes. It is found that the phase separation causes the foam to evolve as would a foam of higher gas fraction until the phases have mixed back together. It is hypothesized that the reason causing the phase separation is related to uneven energy distribution in the foam, which itself is related to jamming and uneven distribution of the sizes of the bubbles in the foam.

Grafeeni ja grafeenioksidi ovat kaksiulotteisia hiilimateriaaleja. Grafeeni koostuu pääosin sp2-hybridisoituneista hiiliatomeista. Grafeenioksidissa sp2-hybridisoituneiden hiiliatomien verkkoon on kiinnittynyt happea sisältäviä funktionaalisia ryhmiä ja osa hiiliatomeista on siten sp3-hybridisoituneita. Grafeenia voidaan erotella grafiitista erilaisin menetelmin tai valmistaa atomi kerrallaan. Grafeenioksidin valmistuksessa grafiitti hapetetaan esimerkiksi kloraateilla. Sekä grafeenia että grafeenioksidia voidaan muokata kovalenttisesti tai supramolekulaarisesti. Muokkauksella tavoitellaan usein materiaalin parempaa käsiteltävyyttä tai uudenlaisen toiminnallisuuden, kuten katalyyttisen aktiivisuuden tai sensoriominaisuuksien, saavuttamista. Katalyyttisissä prosesseissa muokkaamattoman grafeenin ja grafiitin sovelluksia ei ole monia. Sen sijaan grafeenioksidia on käytetty happokatalyytin tavoin sekä hapettimena monissa kemiallisissa prosesseissa, kuten alkyynien hydrauksissa, bentsyylialkoholien hapetuksessa aldehydiksi ja amiinien hapettavassa kytkennässä. Aktiivihiili on kolmiulotteinen huokoinen grafiitin kaltainen materiaali. Siitä on mahdollista valmistaa eri tavoin hapettuneita aktiivihiiliä typpihapon tai kuningasveden avulla. Hapetusolosuhteet vaikuttavat paljon syntyvän tuotteen funktionaalisten ryhmien jakaumaan. Eri tavoin valmistetuilla aktiivihiilillä on myös toisistaan poikkeava katalyyttinen aktiivisuus 2-aryyli-indolien homokytkentäreaktiossa.

Visualization is an indispensable method in the exploration of genomic data. However, the current state of the art in genome browsers – a class of interactive visualization tools – limit the exploration by coupling the visual representations with specific file formats. Because the tools do not support the exploration of the visualization design space, they are difficult to adapt to atypical data. Moreover, although the tools provide interactivity, the implementations are often rudimentary, encumbering the exploration of the data. This thesis introduces GenomeSpy, an interactive genome visualization tool that improves upon the current state of the art by providing better support for exploration. The tool uses a visualization grammar that allows for implementing novel visualization designs, which can display the underlying data more effectively. Moreover, the tool implements GPU-accelerated interactions that better support navigation in the genomic space. For instance, smoothly animated transitions between loci or sample sets improve the perception of causality and help the users stay in the flow of exploration. The expressivity of the visualization grammar and the benefit of fluid interactions are validated with two case studies. The case studies demonstrate visualization of high-grade serous ovarian cancer data at different analysis phases. First, GenomeSpy is being used to create a tool for scrutinizing raw copy-number variation data along with segmentation results. Second, the segmentations along with point mutations are used in a GenomeSpy-based multi-sample visualization that allows for exploring and comparing both multiple data dimensions and samples at the same time. Although the focus has been on cancer research, the tool could be applied to other domains as well.

Node classification is an important problem on networks in many different contexts. Optimizing the graph embedding has great potential to help improve the classification accuracy. The purpose of this thesis is to explore how graph embeddings can be exploited in the node classification task in the context of citation networks. More specifically, this thesis looks into the impact of different kinds of embeddings on the node classification, comparing their performance. Using three different similarity functions and different dimensions for the embedding vector ranging from 1 to 800, we examined the impact of graph embeddings on accuracy in node classification using three benchmark datasets: Cora, Citeseer, and PubMed. Our experimental results indicate that there are some common tendencies in the way dimensionality impacts the graph embedding quality regardless of the graph. We also established that some network-specific hyperparameter tuning clearly affects classification accuracy.

Introduction: The issue of climate change has emerged as a global challenge in response to the increasing consumption of natural resources. As the Information Technology (IT) sector has undergone significant growth in recent years, the implementation of environmentally sustainable practices which lower the environmental impact of software, such as electricity usage, has become imperative. The concept of green in software engineering seeks to address these challenges in the software engineering process. Methods: As the goal is to explore and evaluate different approaches to environmental sustainability in green in software engineering whilst also taking a look into the maturity and evidence level of research about the subject, this study adopts a systematic literature review approach. The search strings, search process and other relevant information are meticulously documented and explored in each step of the research process. Results: Green in software engineering has been identified as a promising field of research, but the absence of agreed-upon definitions and terminology often leads to research efforts replicating the previous studies without a clear reason as to why. The goal of increasing environmental sustainability is commonly agreed on in software engineering, but the concrete steps to achieve it are currently missing. Building a strong body of knowledge, common measurements and tooling to support them and increasing the knowledge about sustainability in the field of software engineering should all be taken into account in an effort to reach the environmental sustainability goals of tomorrow.

Two-electron integrals, which arise in the quantum mechanical description of electron-electron repulsion, are needed in electronic structure calculations. In this thesis, a fully numerical scheme for computing them has been developed and implemented. The accuracy and performance of the scheme is also demonstrated with proof-of-concept calculations. The work in this thesis is a part of the ongoing efforts aiming at a fully numerical electronic structure code for massively parallel computer architectures. The power of these emerging computational resources can be seized only if all computational tasks are divided to small and independent parts that are then processed concurrently. Such a divide and conquer approach is indeed the main characteristic of the present integration scheme. The scheme is a variant of the Fast Multipole Method (FMM) that is an algorithm originally designed for rapid evaluation of electrostatic and gravitational potential fields in point particle simulations. Since the two-electron integrals can be formulated as a problem in electrostatics involving electrostatic potentials and continuous charge densities, the FMM algorithm is also applicable for tackling them. The basic idea in the present scheme is to decompose the computational domain to sub-domains in which the electron densities and electrostatic potentials are further decomposed to finite element functions. The two-electron integrals are then computed as a sum of contributions from each sub-domain. As the current scheme performs all integrals on real-space grids, it has been titled as the Grid-based Fast Multipole Method (GB-FMM). Its computational cost scales linearly with respect to the number of sub-domains. The thesis consists of two parts – a literature review discussing the key features of electronic structure calculations at the Hartree-Fock level of theory and a documentation of the GB-FMM. The results of the proof-of-concept calculations are encouraging. The GB-FMM scheme can achieve parts per billion accuracy. In addition, an analysis of its performance in a single-core environment indicates that the computational cost of the GB-FMM scheme has a rather big prefactor but a favorable scaling with respect to system size. However, as the GB-FMM algorithm has been designed with parallel execution in mind, its full power is predicted to become evident only when massively parallel computers will become commonplace.

Sea level rise is among the most worrying consequences of climate change, and the biggest uncertainty of sea level predictions lies in the future behaviour of the ice sheets of Greenland and Antarctica. In this work, a literature review is made concerning the future of the Greenland ice sheet and the effect of its melting on Baltic Sea level. The relation between sea level and ice sheets is also considered more generally from a theoretical and historical point of view. Lately, surprisingly rapid changes in the amount of ice discharging into the sea have been observed along the coastal areas of the ice sheets, and the mass deficit of Greenland and West Antarctic ice sheets which are considered vulnerable to warming has been increasing from the 1990s. The changes are probably related to atmospheric or oceanic temperature variations which affect the flow speed of ice either via meltwater penetrating to the bottom of the ice sheet or via changes in the flow resistance generated by the floating parts of an ice stream. These phenomena are assumed to increase the mass deficit of the ice sheets in the warming climate; however, there is no comprehensive theory to explain and model them. Thus, it is not yet possible to make reliable predictions of the ice sheet contribution to sea level rise. On the grounds of the historical evidence it appears that sea level can rise rather rapidly, 1-2 metres per century, even during warm climate periods. Sea level rise projections of similar magnitude have been made with so-called semiempirical methods that are based on modelling the link between sea level and global mean temperature. Such a rapid rise would require considerable acceleration of the ice sheet flow. Stronger rise appears rather unlikely, among other things because the mountainous coastline restricts ice discharge from Greenland. The upper limit of sea level rise from Greenland alone has been estimated at half a metre by the end of this century. Due to changes in the Earth s gravity field, the sea level rise caused by melting ice is not spatially uniform. Near the melting ice sheet the sea level rise is considerably smaller than the global average, whereas farther away it is slightly greater than the average. Because of this phenomenon, the effect of the Greenland ice sheet on Baltic Sea level will probably be rather small during this century, 15 cm at most. Melting of the Antarctic ice sheet is clearly more dangerous for the Baltic Sea, but also very uncertain. It is likely that the sea level predictions will become more accurate in the near future as the ice sheet models develop.

Bedrock fracturing is considerably extensive and distinct in Finland, and the fractures that are open, conductive and interconnected usually control the groundwater flow paths in fractured bedrock. This highlights the importance of knowing the locations and hydraulic connections of water conducting fracture zones particularly in mining areas, because they can transport adverse substances outside the mining area. In this study, it is focused on examining possible hydraulic connections of bedrock groundwater by using the stable isotopes of oxygen (δ18O) and hydrogen (δ2H). The study was carried out in the Talvivaara mining area in Northeastern Finland alongside a project from the Geological Survey of Finland (GTK). After November 2012, when a leakage of acidic, metal-containing waste water occurred in the gypsum ponds, there was an urgent need to study the groundwater transport routes in the bedrock fractures. The aim was to find hydraulic connections between surface water and groundwater, and to study the flow of the groundwater in the fracture zones based on the different isotopic characteristics of waters from different sources and isotopic similarities. Most of the materials used in this study were obtained from the results of the project from the GTK. These materials included geophysical interpretations of the locations and water content of the main fracture zones and the results from the geochemical analyzes. Together with the interpretations of groundwater flow direction based on hydraulic heads these materials formed a frame for this study. The isotope composition of 39 water samples from bedrock wells, shallow wells and surface water was analyzed using cavity ring-down spectroscopy (CRDS) method. The surface waters were clearly distinguished based on their evident evaporation signal, but no significant such a signal was observed in the bedrock and shallow groundwaters. However, similarities between groundwater from different depths of same well were found, in addition to similarities between different wells along same fracture zones. Although the isotopes did not indicate surface water contamination, groundwater contamination with smaller amounts of water is possible, in which case the changes in isotope composition are not yet significant, while certain elements have elevated concentrations. A NE-SW oriented fracture zone passing in the center of the study area was concluded to have the most important role in collecting and transporting groundwater outside the mining area. More detailed interpretations would require regular sampling for a longer period of time to better distinguish naturally and artificially induced changes both in the isotopic but also geochemical compositions. Also the usage of packer tests possibly together with pumping tests would be useful in obtaining more comprehensive image of the groundwater flow in the fracture zones and their hydraulic connections.