Application of Graph Neural Networks and graph descriptors for graph classification

Graph classification is an important area in both modern research and industry. Multiple applications, especially in chemistry and novel drug discovery, encourage rapid development of machine learning models in this area. To keep up with the pace of new research, proper experimental design, fair evaluation, and independent benchmarks are essential. Design of strong baselines is an indispensable element of such works. In this thesis, we explore multiple approaches to graph classification. We focus on Graph Neural Networks (GNNs), which emerged as a de facto standard deep learning technique for graph representation learning. Classical approaches, such as graph descriptors and molecular fingerprints, are also addressed. We design fair evaluation experimental protocol and choose proper datasets collection. This allows us to perform numerous experiments and rigorously analyze modern approaches. We arrive to many conclusions, which shed new light on performance and quality of novel algorithms. We investigate application of Jumping Knowledge GNN architecture to graph classification, which proves to be an efficient tool for improving base graph neural network architectures. Multiple improvements to baseline models are also proposed and experimentally verified, which constitutes an important contribution to the field of fair model comparison.Comment: Master's thesis submitted at AGH University of Science and Technolog

Principles of Security and Trust: 7th International Conference, POST 2018, Held as Part of the European Joint Conferences on Theory and Practice of Software, ETAPS 2018, Thessaloniki, Greece, April 14-20, 2018, Proceedings

authentication; computer science; computer software selection and evaluation; cryptography; data privacy; formal logic; formal methods; formal specification; internet; privacy; program compilers; programming languages; security analysis; security systems; semantics; separation logic; software engineering; specifications; verification; world wide we

International Symposium on Mathematics, Quantum Theory, and Cryptography

This open access book presents selected papers from International Symposium on Mathematics, Quantum Theory, and Cryptography (MQC), which was held on September 25-27, 2019 in Fukuoka, Japan. The international symposium MQC addresses the mathematics and quantum theory underlying secure modeling of the post quantum cryptography including e.g. mathematical study of the light-matter interaction models as well as quantum computing. The security of the most widely used RSA cryptosystem is based on the difficulty of factoring large integers. However, in 1994 Shor proposed a quantum polynomial time algorithm for factoring integers, and the RSA cryptosystem is no longer secure in the quantum computing model. This vulnerability has prompted research into post-quantum cryptography using alternative mathematical problems that are secure in the era of quantum computers. In this regard, the National Institute of Standards and Technology (NIST) began to standardize post-quantum cryptography in 2016. This book is suitable for postgraduate students in mathematics and computer science, as well as for experts in industry working on post-quantum cryptography

International Symposium on Mathematics, Quantum Theory, and Cryptography

This open access book presents selected papers from International Symposium on Mathematics, Quantum Theory, and Cryptography (MQC), which was held on September 25-27, 2019 in Fukuoka, Japan. The international symposium MQC addresses the mathematics and quantum theory underlying secure modeling of the post quantum cryptography including e.g. mathematical study of the light-matter interaction models as well as quantum computing. The security of the most widely used RSA cryptosystem is based on the difficulty of factoring large integers. However, in 1994 Shor proposed a quantum polynomial time algorithm for factoring integers, and the RSA cryptosystem is no longer secure in the quantum computing model. This vulnerability has prompted research into post-quantum cryptography using alternative mathematical problems that are secure in the era of quantum computers. In this regard, the National Institute of Standards and Technology (NIST) began to standardize post-quantum cryptography in 2016. This book is suitable for postgraduate students in mathematics and computer science, as well as for experts in industry working on post-quantum cryptography

Cellular Automata

Modelling and simulation are disciplines of major importance for science and engineering. There is no science without models, and simulation has nowadays become a very useful tool, sometimes unavoidable, for development of both science and engineering. The main attractive feature of cellular automata is that, in spite of their conceptual simplicity which allows an easiness of implementation for computer simulation, as a detailed and complete mathematical analysis in principle, they are able to exhibit a wide variety of amazingly complex behaviour. This feature of cellular automata has attracted the researchers' attention from a wide variety of divergent fields of the exact disciplines of science and engineering, but also of the social sciences, and sometimes beyond. The collective complex behaviour of numerous systems, which emerge from the interaction of a multitude of simple individuals, is being conveniently modelled and simulated with cellular automata for very different purposes. In this book, a number of innovative applications of cellular automata models in the fields of Quantum Computing, Materials Science, Cryptography and Coding, and Robotics and Image Processing are presented

The anthropometric, environmental and genetic determinants of right ventricular structure and function

BACKGROUND Measures of right ventricular (RV) structure and function have significant prognostic value. The right ventricle is currently assessed by global measures, or point surrogates, which are insensitive to regional and directional changes. We aim to create a high-resolution three-dimensional RV model to improve understanding of its structural and functional determinants. These may be particularly of interest in pulmonary hypertension (PH), a condition in which RV function and outcome are strongly linked. PURPOSE To investigate the feasibility and additional benefit of applying three-dimensional phenotyping and contemporary statistical and genetic approaches to large patient populations. METHODS Healthy subjects and incident PH patients were prospectively recruited. Using a semi-automated atlas-based segmentation algorithm, 3D models characterising RV wall position and displacement were developed, validated and compared with anthropometric, physiological and genetic influences. Statistical techniques were adapted from other high-dimensional approaches to deal with the problems of multiple testing, contiguity, sparsity and computational burden. RESULTS 1527 healthy subjects successfully completed high-resolution 3D CMR and automated segmentation. Of these, 927 subjects underwent next-generation sequencing of the sarcomeric gene titin and 947 subjects completed genotyping of common variants for genome-wide association study. 405 incident PH patients were recruited, of whom 256 completed phenotyping. 3D modelling demonstrated significant reductions in sample size compared to two-dimensional approaches. 3D analysis demonstrated that RV basal-freewall function reflects global functional changes most accurately and that a similar region in PH patients provides stronger survival prediction than all anthropometric, haemodynamic and functional markers. Vascular stiffness, titin truncating variants and common variants may also contribute to changes in RV structure and function. CONCLUSIONS High-resolution phenotyping coupled with computational analysis methods can improve insights into the determinants of RV structure and function in both healthy subjects and PH patients. Large, population-based approaches offer physiological insights relevant to clinical care in selected patient groups.Open Acces