Prediction of Oxidation States of Cysteines and Disulphide Connectivity

Knowledge on cysteine oxidation state and disulfide bond connectivity is of great importance to protein chemistry and 3-D structures. This research is aimed at finding the most relevant features in prediction of cysteines oxidation states and the disulfide bonds connectivity of proteins. Models predicting the oxidation states of cysteines are developed with machine learning techniques such as Support Vector Machines (SVMs) and Associative Neural Networks (ASNNs). A record high prediction accuracy of oxidation state, 95%, is achieved by incorporating the oxidation states of N-terminus cysteines, flanking sequences of cysteines and global information on the protein chain (number of cysteines, length of the chain and amino acids composition of the chain etc.) into the SVM encoding. This is 5% higher than the current methods. This indicates to us that the oxidation states of amino terminal cysteines infer the oxidation states of other cysteines in the same protein chain. Satisfactory prediction results are also obtained with the newer and more inclusive SPX dataset, especially for chains with higher number of cysteines. Compared to literature methods, our approach is a one-step prediction system, which is easier to implement and use. A side by side comparison of SVM and ASNN is conducted. Results indicated that SVM outperform ASNN on this particular problem. For the prediction of correct pairings of cysteines to form disulfide bonds, we first study disulfide connectivity by calculating the local interaction potentials between the flanking sequences of the cysteine pairs. The obtained interaction potential is further adjusted by the coefficients related to the binding motif of enzymes during disulfide formation and also by the linear distance between the cysteine pairs. Finally, maximized weight matching algorithm is applied and performance of the interaction potentials evaluated. Overall prediction accuracy is unsatisfactory compared with the literature. SVM is used to predict the disulfide connectivity with the assumption that oxidation states of cysteines on the protein are known. Information on binding region during disulfide formation, distance between cysteine pairs, global information of the protein chain and the flanking sequences around the cysteine pairs are included in the SVM encoding. Prediction results illustrate the advantage of using possible anchor region information

Intelligent approaches to VLSI routing

Very Large Scale Integrated-circuit (VLSI) routing involves many large-size and complex problems and most of them have been shown to be NP-hard or NP-complete. As a result, conventional approaches, which have been successfully used to handle relatively small-size routing problems, are not suitable to be used in tackling large-size routing problems because they lead to \u27combinatorial explosion\u27 in search space. Hence, there is a need for exploring more efficient routing approaches to be incorporated into today\u27s VLSI routing system. This thesis strives to use intelligent approaches, including symbolic intelligence and computational intelligence, to solve three VLSI routing problems: Three-Dimensional (3-D) Shortest Path Connection, Switchbox Routing and Constrained Via Minimization. The 3-D shortest path connection is a fundamental problem in VLSI routing. It aims to connect two terminals of a net that are distributed in a 3-D routing space subject to technological constraints and performance requirements. Aiming at increasing computation speed and decreasing storage space requirements, we present a new A* algorithm for the 3-D shortest path connection problem in this thesis. This new A*algorithm uses an economical representation and adopts a novel back- trace technique. It is shown that this algorithm can guarantee to find a path if one exists and the path found is the shortest one. In addition, its computation speed is fast, especially when routed nets are spare. The computational complexities of this A* algorithm at the best case and the worst case are O(Ɩ) and 0(Ɩ3), respectively, where Ɩ is the shortest path length between the two terminals. Most importantly, this A\u27 algorithm is superior to other shortest path connection algorithms as it is economical in terms of storage space requirement, i.e., 1 bit/grid. The switchbox routing problem aims to connect terminals at regular intervals on the four sides of a rectangle routing region. From a computational point of view, the problem is NP-hard. Furthermore, it is extremely complicated and as the consequence no existing algorithm can guarantee to find a solution even if one exists no matter how high the complexity of the algorithm is. Previous approaches to the switch box routing problem can be divided into algorithmic approaches and knowledge-based approaches. The algorithmic approaches are efficient in computational time, but they are unsucessful at achieving high routing completion rate, especially for some dense and complicated switchbox routing problems. On the other hand, the knowledge-based approaches can achieve high routing completion rate, but they are not efficient in computation speed. In this thesis we present a hybrid approach to the switchbox routing problem. This hybrid approach is based on a new knowledge-based routing technique, namely synchronized routing, and combines some efficient algorithmic routing techniques. Experimental results show it can achieve the high routing completion rate of the knowledge-based approaches and the high efficiency of the algorithmic approaches. The constrained via minimization is an important optimization problem in VLSI routing. Its objective is to minimize the number of vias introduced in VLSI routing. From computational perspective, the constrained via minimization is NP-complete. Although for a special case where the number of wire segments splits at a via candidate is not more than three, elegant theoretical results have been obtained. For a general case in which there exist more than three wire segment splits at a via candidate few approaches have been proposed, and those approaches are only suitable for tackling some particular routing styles and are difficult or impossible to adjust to meet practical requirements. In this thesis we propose a new graph-theoretic model, namely switching graph model, for the constrained via minimization problem. The switching graph model can represent both grid-based and grid less routing problems, and allows arbitrary wire segments split at a via candidate. Then on the basis of the model, we present the first genetic algorithm for the constrained via minimization problem. This genetic algorithm can tackle various kinds of routing styles and be configured to meet practical constraints. Experimental results show that the genetic algorithm can find the optimal solutions for most cases in reasonable time

Advanced Trends in Wireless Communications

Physical limitations on wireless communication channels impose huge challenges to reliable communication. Bandwidth limitations, propagation loss, noise and interference make the wireless channel a narrow pipe that does not readily accommodate rapid flow of data. Thus, researches aim to design systems that are suitable to operate in such channels, in order to have high performance quality of service. Also, the mobility of the communication systems requires further investigations to reduce the complexity and the power consumption of the receiver. This book aims to provide highlights of the current research in the field of wireless communications. The subjects discussed are very valuable to communication researchers rather than researchers in the wireless related areas. The book chapters cover a wide range of wireless communication topics

Analog Spiking Neuromorphic Circuits and Systems for Brain- and Nanotechnology-Inspired Cognitive Computing

Human society is now facing grand challenges to satisfy the growing demand for computing power, at the same time, sustain energy consumption. By the end of CMOS technology scaling, innovations are required to tackle the challenges in a radically different way. Inspired by the emerging understanding of the computing occurring in a brain and nanotechnology-enabled biological plausible synaptic plasticity, neuromorphic computing architectures are being investigated. Such a neuromorphic chip that combines CMOS analog spiking neurons and nanoscale resistive random-access memory (RRAM) using as electronics synapses can provide massive neural network parallelism, high density and online learning capability, and hence, paves the path towards a promising solution to future energy-efficient real-time computing systems. However, existing silicon neuron approaches are designed to faithfully reproduce biological neuron dynamics, and hence they are incompatible with the RRAM synapses, or require extensive peripheral circuitry to modulate a synapse, and are thus deficient in learning capability. As a result, they eliminate most of the density advantages gained by the adoption of nanoscale devices, and fail to realize a functional computing system. This dissertation describes novel hardware architectures and neuron circuit designs that synergistically assemble the fundamental and significant elements for brain-inspired computing. Versatile CMOS spiking neurons that combine integrate-and-fire, passive dense RRAM synapses drive capability, dynamic biasing for adaptive power consumption, in situ spike-timing dependent plasticity (STDP) and competitive learning in compact integrated circuit modules are presented. Real-world pattern learning and recognition tasks using the proposed architecture were demonstrated with circuit-level simulations. A test chip was implemented and fabricated to verify the proposed CMOS neuron and hardware architecture, and the subsequent chip measurement results successfully proved the idea. The work described in this dissertation realizes a key building block for large-scale integration of spiking neural network hardware, and then, serves as a step-stone for the building of next-generation energy-efficient brain-inspired cognitive computing systems

Vidutinių dažnių 5G belaidžių tinklų galios stiprintuvų tyrimas

This dissertation addresses the problems of ensuring efficient radio fre-quency transmission for 5G wireless networks. Taking into account, that the next generation 5G wireless network structure will be heterogeneous, the device density and their mobility will increase and massive MIMO connectivity capability will be widespread, the main investigated problem is formulated – increasing the efficiency of portable mid-band 5G wireless network CMOS power amplifier with impedance matching networks. The dissertation consists of four parts including the introduction, 3 chapters, conclusions, references and 3 annexes. The investigated problem, importance and purpose of the thesis, the ob-ject of the research methodology, as well as the scientific novelty are de-fined in the introduction. Practical significance of the obtained results, defended state-ments and the structure of the dissertation are also included. The first chapter presents an extensive literature analysis. Latest ad-vances in the structure of the modern wireless network and the importance of the power amplifier in the radio frequency transmission chain are de-scribed in detail. The latter is followed by different power amplifier archi-tectures, parameters and their improvement techniques. Reported imped-ance matching network design methods are also discussed. Chapter 1 is concluded distinguishing the possible research vectors and defining the problems raised in this dissertation. The second chapter is focused around improving the accuracy of de-signing lumped impedance matching network. The proposed methodology of estimating lumped inductor and capacitor parasitic parameters is dis-cussed in detail provi-ding complete mathematical expressions, including a summary and conclusions. The third chapter presents simulation results for the designed radio fre-quency power amplifiers. Two variations of Doherty power amplifier archi-tectures are presented in the second part, covering the full step-by-step de-sign and simulation process. The latter chapter is concluded by comparing simulation and measurement results for all designed radio frequency power amplifiers. General conclusions are followed by an extensive list of references and a list of 5 publications by the author on the topic of the dissertation. 5 papers, focusing on the subject of the discussed dissertation, have been published: three papers are included in the Clarivate Analytics Web of Sci-ence database with a citation index, one paper is included in Clarivate Ana-lytics Web of Science database Conference Proceedings, and one paper has been published in unreferred international conference preceedings. The au-thor has also made 9 presentations at 9 scientific conferences at a national and international level.Dissertatio

Neural text line extraction in historical documents: a two-stage clustering approach

Accessibility of the valuable cultural heritage which is hidden in countless scanned historical documents is the motivation for the presented dissertation. The developed (fully automatic) text line extraction methodology combines state-of-the-art machine learning techniques and modern image processing methods. It demonstrates its quality by outperforming several other approaches on a couple of benchmarking datasets. The method is already being used by a wide audience of researchers from different disciplines and thus contributes its (small) part to the aforementioned goal.Das Erschließen des unermesslichen Wissens, welches in unzähligen gescannten historischen Dokumenten verborgen liegt, bildet die Motivation für die vorgelegte Dissertation. Durch das Verknüpfen moderner Verfahren des maschinellen Lernens und der klassischen Bildverarbeitung wird in dieser Arbeit ein vollautomatisches Verfahren zur Extraktion von Textzeilen aus historischen Dokumenten entwickelt. Die Qualität wird auf verschiedensten Datensätzen im Vergleich zu anderen Ansätzen nachgewiesen. Das Verfahren wird bereits durch eine Vielzahl von Forschern verschiedenster Disziplinen genutzt