2D Hybrid Analytical Model Based Performance Optimization for Linear Induction Motors

In this thesis the domain of double-layer, single-sided, 3-phase, integral slot winding, linear induction motor (LIM)s is analyzed. Motor meta parameters such as slots and poles are difficult to optimize since they drastically effect the configuration of the motor and require heuristic optimization implementations. A non-dominated sorting genetic algorithm II (NSGAII) was implemented with the Platypus-Opt Python library. It serves as a robust, yet flexible integration while maximizing thrust and minimizing the mass of each motor iteration. Each iteration was accurately modelled using the hybrid analytical model (HAM), producing the necessary performance parameters for the NSGAII’s objective function. Field plotting capability of the processed HAM allowed for the feasibility check on postprocessing constraints, increasing the robustness of the optimization. Validation between the HAM to finite element analysis (FEA) and HAM to the baseline proved the accuracy of the modelling algorithm within the objective function. The optimization concluded that the optimal motor had 36 slots and 4 poles within the domain of 12-54 slots and 4-12 poles, where 9 feasible motors were objectively compared. The proposed design tool lacks the ability to produce a fully functional optimized motor due to domain and complexity constraints. However, it saved significant time and effort while generating reproducible results within a constrained domain. The entire optimization was completed in 5 minutes, whereas the total time for configuring all motors via FEA within the domain took 4.5 hours, proving its worth

Optimization for Image Segmentation

Image segmentation, i.e., assigning each pixel a discrete label, is an essential task in computer vision with lots of applications. Major techniques for segmentation include for example Markov Random Field (MRF), Kernel Clustering (KC), and nowadays popular Convolutional Neural Networks (CNN). In this work, we focus on optimization for image segmentation. Techniques like MRF, KC, and CNN optimize MRF energies, KC criteria, or CNN losses respectively, and their corresponding optimization is very different. We are interested in the synergy and the complementary benefits of MRF, KC, and CNN for interactive segmentation and semantic segmentation. Our first contribution is pseudo-bound optimization for binary MRF energies that are high-order or non-submodular. Secondly, we propose Kernel Cut, a novel formulation for segmentation, which combines MRF regularization with Kernel Clustering. We show why to combine KC with MRF and how to optimize the joint objective. In the third part, we discuss how deep CNN segmentation can benefit from non-deep (i.e., shallow) methods like MRF and KC. In particular, we propose regularized losses for weakly-supervised CNN segmentation, in which we can integrate MRF energy or KC criteria as part of the losses. Minimization of regularized losses is a principled approach to semi-supervised learning, in general. Our regularized loss method is very simple and allows different kinds of regularization losses for CNN segmentation. We also study the optimization of regularized losses beyond gradient descent. Our regularized losses approach achieves state-of-the-art accuracy in semantic segmentation with near full supervision quality

Radiogenomics in non-small-cell lung cancer

Ο μη μικροκυτταρικός καρκίνος του πνεύμονα είναι ο πιο συχνά συναντώμενος υποτύπος καρκίνου του πνεύμονα, ο οποίος αποτελείται από ένα φάσμα υποτύπων. Το NSCLC είναι ένας θανατηφόρος, ετερογενής συμπαγής όγκος με μια εκτεταμένη σειρά μοριακών χαρακτηριστικών. Η πάθηση έχει γίνει ένα αξιοσημείωτο παράδειγμα ιατρικής ακριβείας καθώς το ενδιαφέρον για το θέμα συνεχίζει να επεκτείνεται. Ο απώτερος στόχος της τρέχουσας έρευνας είναι να χρησιμοποιήσει συγκεκριμένα γονίδια ως βιοδείκτες για την πρόγνωση, την έγκαιρη διάγνωση και την εξατομικευμένη θεραπεία, τα οποία διευκολύνονται από τη χρήση εξελισσόμενων τεχνικών αλληλούχισης επόμενης γενιάς που επιτρέπουν την ταυτόχρονη ανίχνευση μεγάλου αριθμού γενετικές ανωμαλίες. Γνωστές μεταλλάξεις ενός αριθμού γονιδίων, όπως τα EGFR, ALK και KRAS, επηρεάζουν ήδη τις αποφάσεις θεραπείας και νέα βασικά γονίδια και μοριακές υπογραφές διερευνώνται για την προγνωστική τους αξία καθώς και για την πιθανή συμβολή τους στην ανοσοθεραπεία και τη θεραπεία της υποτροπής στην αντίσταση στις υπάρχουσες θεραπείες. Οι τύποι δειγμάτων που χρησιμοποιούνται για μελέτες NGS, όπως αναρροφήσεις με λεπτή βελόνα, ιστός ενσωματωμένος σε παραφίνη σταθεροποιημένος με φορμαλίνη και DNA χωρίς κύτταρα, έχουν ο καθένας τα δικά του πλεονεκτήματα και μειονεκτήματα που πρέπει να ληφθούν υπόψηNon-small cell lung cancer is the most often encountered subtype of lung cancer, which consists of a spectrum of subtypes. NSCLC is a lethal, heterogeneous solid tumor with an extensive array of molecular features. The condition has become a notable example of precision medicine as interest in the topic continues to expand. The ultimate goal of the current research is to use specific genes as biomarkers for its prognosis, timely diagnosis, and personalized therapy, all of which are facilitated by the use of evolving next-generation sequencing techniques that permit the simultaneous detection of a large number of genetic abnormalities. Known mutations of a number of genes, such as EGFR, ALK, and KRAS, already influence treatment decisions, and new key genes and molecular signatures are being investigated for their prognostic value as well as their potential contribution to immunotherapy and the treatment of recurrence due to resistance to existing therapies. The sample types utilized for NGS studies, such as fine-needle aspirates, formalin-fixed paraffin-embedded tissue, and cell-free DNA, each have their own advantages and disadvantages that must be taken into accoun

Consensus Network Inference of Microarray Gene Expression Data

Genetic and protein interactions are essential to regulate cellular machinery. Their identification has become an important aim of systems biology research. In recent years, a variety of computational network inference algorithms have been employed to reconstruct gene regulatory networks from post-genomic data. However, precisely predicting these regulatory networks remains a challenge. We began our study by assessing the ability of various network inference algorithms to accurately predict gene regulatory interactions using benchmark simulated datasets. It was observed from our analysis that different algorithms have strengths and weaknesses when identifying regulatory networks, with a gene-pair interaction (edge) predicted by one algorithm not always necessarily consistent with the other. An edge not predicted by most inference algorithms may be an important one, and should not be missed. The naïve consensus (intersection) method is perhaps the most conservative approach and can be used to address this concern by extracting the edges consistently predicted across all inference algorithms; however, it lacks credibility as it does not provide a quantifiable measure for edge weights. Existing quantitative consensus approaches, such as the inverse-variance weighted method (IVWM) and the Borda count election method (BCEM), have been previously implemented to derive consensus networks from diverse datasets. However, the former method was biased towards finding local solutions in the whole network, and the latter considered species diversity to build the consensus network. In this thesis we proposed a novel consensus approach, in which we used Fishers Combined Probability Test (FCPT) to combine the statistical significance values assigned to each network edge by a number of different networking algorithms to produce a consensus network. We tested our method by applying it to a variety of in silico benchmark expression datasets of different dimensions and evaluated its performance against individual inference methods, Bayesian models and also existing qualitative and quantitative consensus techniques. We also applied our approach to real experimental data from the yeast (S. cerevisiae) network as this network has been comprehensively elucidated previously. Our results demonstrated that the FCPT-based consensus method outperforms single algorithms in terms of robustness and accuracy. In developing the consensus approach, we also proposed a scoring technique that quantifies biologically meaningful hierarchical modular networks.University of Exeter studentshi

Generating and auto-tuning parallel stencil codes

In this thesis, we present a software framework, Patus, which generates high performance stencil codes for different types of hardware platforms, including current multicore CPU and graphics processing unit architectures. The ultimate goals of the framework are productivity, portability (of both the code and performance), and achieving a high performance on the target platform. A stencil computation updates every grid point in a structured grid based on the values of its neighboring points. This class of computations occurs frequently in scientific and general purpose computing (e.g., in partial differential equation solvers or in image processing), justifying the focus on this kind of computation. The proposed key ingredients to achieve the goals of productivity, portability, and performance are domain specific languages (DSLs) and the auto-tuning methodology. The Patus stencil specification DSL allows the programmer to express a stencil computation in a concise way independently of hardware architecture-specific details. Thus, it increases the programmer productivity by disburdening her or him of low level programming model issues and of manually applying hardware platform-specific code optimization techniques. The use of domain specific languages also implies code reusability: once implemented, the same stencil specification can be reused on different hardware platforms, i.e., the specification code is portable across hardware architectures. Constructing the language to be geared towards a special purpose makes it amenable to more aggressive optimizations and therefore to potentially higher performance. Auto-tuning provides performance and performance portability by automated adaptation of implementation-specific parameters to the characteristics of the hardware on which the code will run. By automating the process of parameter tuning — which essentially amounts to solving an integer programming problem in which the objective function is the number representing the code's performance as a function of the parameter configuration, — the system can also be used more productively than if the programmer had to fine-tune the code manually. We show performance results for a variety of stencils, for which Patus was used to generate the corresponding implementations. The selection includes stencils taken from two real-world applications: a simulation of the temperature within the human body during hyperthermia cancer treatment and a seismic application. These examples demonstrate the framework's flexibility and ability to produce high performance code

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

NETWORK ANALYTICS FOR THE MIRNA REGULOME AND MIRNA-DISEASE INTERACTIONS

miRNAs are non-coding RNAs of approx. 22 nucleotides in length that inhibit gene expression at the post-transcriptional level. By virtue of this gene regulation mechanism, miRNAs play a critical role in several biological processes and patho-physiological conditions, including cancers. miRNA behavior is a result of a multi-level complex interaction network involving miRNA-mRNA, TF-miRNA-gene, and miRNA-chemical interactions; hence the precise patterns through which a miRNA regulates a certain disease(s) are still elusive. Herein, I have developed an integrative genomics methods/pipeline to (i) build a miRNA regulomics and data analytics repository, (ii) create/model these interactions into networks and use optimization techniques, motif based analyses, network inference strategies and influence diffusion concepts to predict miRNA regulations and its role in diseases, especially related to cancers. By these methods, we are able to determine the regulatory behavior of miRNAs and potential causal miRNAs in specific diseases and potential biomarkers/targets for drug and medicinal therapeutics