Visual Feature Learning

Categorization is a fundamental problem of many computer vision applications, e.g., image classification, pedestrian detection and face recognition. The robustness of a categorization system heavily relies on the quality of features, by which data are represented. The prior arts of feature extraction can be concluded in different levels, which, in a bottom up order, are low level features (e.g., pixels and gradients) and middle/high-level features (e.g., the BoW model and sparse coding). Low level features can be directly extracted from images or videos, while middle/high-level features are constructed upon low-level features, and are designed to enhance the capability of categorization systems based on different considerations (e.g., guaranteeing the domain-invariance and improving the discriminative power). This thesis focuses on the study of visual feature learning. Challenges that remain in designing visual features lie in intra-class variation, occlusions, illumination and view-point changes and insufficient prior knowledge. To address these challenges, I present several visual feature learning methods, where these methods cover the following sub-topics: (i) I start by introducing a segmentation-based object recognition system. (ii) When training data are insufficient, I seek data from other resources, which include images or videos in a different domain, actions captured from a different viewpoint and information in a different media form. In order to appropriately transfer such resources into the target categorization system, four transfer learning-based feature learning methods are presented in this section, where both cross-view, cross-domain and cross-modality scenarios are addressed accordingly. (iii) Finally, I present a random-forest based feature fusion method for multi-view action recognition

Neural Network Potential Simulations of Copper Supported on Zinc Oxide Surfaces

Heterogeneous catalysis is an area of active research, because many industrially relevant reactions involve gaseous reactants and are accelerated by solid phase catalysts. In recent years, activity in the field has become more intense due to the development of surface science and simulation techniques that allow for acquiring deeper insight into these catalysts, with the goal of producing more active, cheaper and less toxic catalytic materials. One particularly crucial case study for heterogeneous catalysis is the synthesis of methanol from synthesis gas, composed of H2, CO and CO2. The reaction is catalyzed by a mixture of Cu and ZnO nanoparticles with Al2O3 as a support material. This process is important not only due to methanol’s many uses as a solvent, raw material for organic synthesis, and possible energy and carbon capture material, but also as an example for many other metal/metal oxide catalysts. A plethora of experimental studies are available for this catalyst, as well as for simpler model systems of Cu clusters supported on ZnO surfaces. Unfortunately, there is still a lack of theoretical studies that can support these experi- mental results by providing an atom-by-atom representation of the system. This scarcity of atomic level simulations is due to the absence of fast but ab-initio level accurate potentials that would allow for reaching larger systems and longer simulated time scales. A promising possibility to bridge this gap in potentials is the rise of machine learning potentials, which utilize the tools of machine learning to reproduce the potential energy surface of a system under study, as sampled by an expensive electronic structure reference method of choice. One early and fruitful example of such machine learning force fields are neural network potentials, as initially developed by Behler and Parrinello. In this thesis, a neural network potential of the Behler-Parrinello type has been constructed for ternary Cu/Zn/O systems, focusing on supported Cu clusters on the ZnO(10-10) surface, as a model for the industrial catalyst. This potential was subsequently utilized to perform a number of simulations. Small supported Cu clusters between 4 and 10 atoms were optimized with a genetic algorithm, and a number of structural trends observed. These clusters revealed the first hints of the structure of the Cu/ZnO interface, where Cu prefers to interact with the support through configurations in the continuum between Cu(110) and Cu(111). Simulated annealing runs for Cu clusters between 200 and 500 atoms reinforced this observation, with these larger clusters also adopting this sort of interface with the support. Additionally, in these simulations the effect of strain induced by the support can be observed, with deviations from ideal lattice constants reaching the top of all of the clusters. To further investigate the influence of strain in this system, large coincident surfaces of Cu were deposited on ZnO supports. Due to the lattice mismatch present between the two materials, this requires straining the Cu overlayer. This analysis confirmed once again that Cu(110) and Cu(111) are the most stable surfaces when de- posited on ZnO(10-10). During this thesis a number of new algorithm and programs were developed. Of particular interest is the bin and hash algorithm, which was designed to aid in the construction and curating of reference sets for the neural network potential, and can also be used to evaluate the quality of atomic descriptor sets.2021-10-0

Computational Approaches to Drug Profiling and Drug-Protein Interactions

Despite substantial increases in R&D spending within the pharmaceutical industry, denovo drug design has become a time-consuming endeavour. High attrition rates led to a long period of stagnation in drug approvals. Due to the extreme costs associated with introducing a drug to the market, locating and understanding the reasons for clinical failure is key to future productivity. As part of this PhD, three main contributions were made in this respect. First, the web platform, LigNFam enables users to interactively explore similarity relationships between ‘drug like’ molecules and the proteins they bind. Secondly, two deep-learning-based binding site comparison tools were developed, competing with the state-of-the-art over benchmark datasets. The models have the ability to predict offtarget interactions and potential candidates for target-based drug repurposing. Finally, the open-source ScaffoldGraph software was presented for the analysis of hierarchical scaffold relationships and has already been used in multiple projects, including integration into a virtual screening pipeline to increase the tractability of ultra-large screening experiments. Together, and with existing tools, the contributions made will aid in the understanding of drug-protein relationships, particularly in the fields of off-target prediction and drug repurposing, helping to design better drugs faster