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The hypothesis that similar chemicals exert similar biological activities has been widely adopted in the field of drug discovery and development. Quantitative Structure-Activity Relationship (QSAR) models have been used ubiquitously in drug discovery to understand the function of chemicals in biological systems. A common QSAR modeling method calculates similarity scores between chemicals to assess their biological function. However, due to the fact that some chemicals can be similar and yet have different biological activities, or conversely can be structurally different yet have similar biological functions, various methods have instead been developed to quantify chemical similarity at the functional level. Quantmap is one such method, which utilizes biological databases to quantify the biological similarity between chemicals. Quantmap uses quantitative molecular network topology analysis to cluster chemical substances based on their bioactivities. This method by itself, unfortunately, cannot assign new chemicals (those which may not yet have biological data) to the derived clusters. Owing to the fact that there is a lack of biological data for many chemicals, deep learning models were explored in this project with respect to their ability to correctly assign unknown chemicals to Quantmap clusters. The deep learning methods explored included both convolutional and recurrent neural networks. Transfer learning/pretraining based approaches and data augmentation methods were also investigated. The best performing model, among those considered, was the Seq2seq model (a recurrent neural network containing two joint networks, a perceiver and an interpreter network) without pretraining, but including data augmentation.

Цель работы – разработка автоматической системы распознавания номерных знаков автомобилей, в естественных дорожных условиях, в том числе в сложных погодных и физических условиях, таких как недостаточная видимость, загрязнение, умышленное или непреднамеренное частичное скрытие символов. Объектом исследования являются цифровые изображения автомобилей в естественной среде. Методы исследования: сверточные нейронные сети, в том числе одноэтапные детекторы (SSOD), комбинации сетей с промежуточными связями между слоями - Cross Stage Partial Network (CSPNet) и сети, объединяющей информацию с разных уровней сети – Path Aggregation Network (PANet), преобразования изображений с помощью библиотеки OpenCV, включая фильтры Собеля и Гауса, преобразование Кэнни, методы глубокого машинного обучения для обработки последовательностей LSTM, CRNN, CRAFT. В рамках данной работы разработана система распознавания автомобильных номеров, переводящая графические данные из цифрового изображения или видеопотока в текст в виде файлов различных форматов. Задача детекции автомобильных номеров на изображениях решена с помощью глубокой нейронной сети YoLo v5, представляющая собой современную модель обнаружения объектов, основанную на архитектуре с использованием CSPNet и PANet. Она обеспечивает высокую скорость и точность при обнаружении объектов на изображениях. Благодаря своей эффективности и масштабируемости, YoLov5 стала популярным выбором для решения задач компьютерного зрения в различных областях. Для решения задачи распознавания текса на обнаруженных объектах используется алгоритм детектирования объектов, основанный на преобразованиях Кэнни, фильтрах Собеля и Гаусса и нейронная сеть keras-ocr, на основе фреймворка keras, представляющая собой комбинацию сверточной нейронной сети (CNN) и рекуррентной нейронной сети (RNN), решающая задачу распознавания печатного текста. Созданный метод способен безошибочно распознавать 85 % предоставленных номеров, преимущественно российского стандарта. Полученный функционал может быть внедрен в существующую системы фото- или видео-фиксации трафика и использоваться в рамках цифровизации систем трекинга и контроля доступа и безопасности на дорогах и объектах транспортной инфраструктуры. Выпускная квалификационная работа в теоретической и описательной части выполнена в текстовом редакторе Microsoft Word и представлена в электронном формате. Практическая часть выполнялась в jupiter-ноутбуке на платформе облачных вычислений Google Collaboratory. / The goal of the work is to develop an automatic system for recognizing car license plates in natural road conditions, including difficult weather and physical conditions, such as insufficient visibility, pollution, intentional or unintentional partial hiding of symbols. The object of the study is digital images of cars in their natural environment. Research methods: convolutional neural networks, including single-stage detectors (SSOD), combinations of networks with intermediate connections between layers - Cross Stage Partial Network (CSPNet) and networks that combine information from different levels of the network - Path Aggregation Network (PANet), image transformations using the OpenCV library, including Sobel and Gauss filters, Canny transform, deep machine learning methods for processing LSTM, CRNN, CRAFT sequences. As part of this work, a license plate recognition system has been developed that converts graphic data from a digital image or video stream into text in the form of files in various formats. The problem of detecting license plates in images is solved using the YoLo v5 deep neural network, which is a modern object detection model based on an architecture using CSPNet and PANet. It provides high speed and accuracy in detecting objects in images. Due to its efficiency and scalability, YoLov5 has become a popular choice for solving computer vision problems in various fields. To solve the problem of text recognition on detected objects, an object detection algorithm is used, based on Canny transforms, Sobel and Gaussian filters, and the keras-ocr neural network, based on the keras framework, which is a combination of a convolutional neural network (CNN) and a recurrent neural network (RNN) , which solves the problem of recognizing printed text. The created method is capable of accurately recognizing 85% of the provided numbers, mainly of the Russian standard. The resulting functionality can be implemented into existing systems for photo or video recording of traffic and used as part of the digitalization of tracking systems and access control and security on roads and transport infrastructure facilities. The final qualifying work in the theoretical and descriptive parts was completed in the text editor Microsoft Word and presented in electronic format. The practical part was carried out on a jupiter laptop on the Google Collaboratory cloud computing platform.

[pt] Este trabalho propõe e avalia arquiteturas profundas para o reconhecimento de culturas agrícolas a partir de seqüências de imagens multitemporais de sensoriamento remoto. Essas arquiteturas combinam a capacidade de modelar contexto espacial prórpia de redes totalmente convolucionais com a capacidade de modelr o contexto temporal de redes recorrentes para a previsão prever culturas agrícolas em cada data de uma seqüência de imagens multitemporais. O desempenho destes métodos é avaliado em dois conjuntos de dados públicos. Ambas as áreas apresentam alta dinâmica espaçotemporal devido ao clima tropical/subtropical e a práticas agrícolas locais, como a rotação de culturas. Nos experimentos verificou-se que as arquiteturas propostas superaram os métodos recentes baseados em redes recorrentes em termos de Overall Accuracy (OA) e F1-score médio por classe. / [en] This work proposes and evaluates deep learning architectures for multi-date agricultural crop recognition from remote sensing image sequences. These architectures combine the spatial modelling capabilities of fully convolutional networks and the sequential modelling capabilities of recurrent networks into end-to-end architectures so-called fully convolutional recurrent networks, configured to predict crop type at multiple dates from a multitemporal image sequence. Their performance is assessed over two publicly available datasets. Both datasets present highly spatio-temporal dynamics due to their tropical/sub-tropical climate and local agricultural practices such as crop rotation. The experiments indicated that the proposed architectures outperformed state of the art methods based on recurrent networks in terms of Overall Accuracy (OA) and per-class average F1 score.

<p>The numerical simulation of physical systems plays a key role in different fields of science and engineering. The popularity of numerical methods stems from their ability to simulate complex physical phenomena for which analytical solutions are only possible for limited combinations of geometry, boundary, and initial conditions. Despite their flexibility, the computational demand of classical numerical methods quickly escalates as the size and complexity of the model increase. To address this limitation, and motivated by the unprecedented success of Deep Learning (DL) in computer vision, researchers started exploring the possibility of developing computationally efficient DL-based algorithms to simulate the response of complex systems. To date, DL techniques have been shown to be effective in simulating certain physical systems. However, their practical application faces an important common constraint: trained DL models are limited to a predefined set of configurations. Any change to the system configuration (e.g., changes to the domain size or boundary conditions) entails updating the underlying architecture and retraining the model. It follows that existing DL-based simulation approaches lack the flexibility offered by classical numerical methods. An important constraint that severely hinders the widespread application of these approaches to the simulation of physical systems.</p> <p><br></p> <p>In an effort to address this limitation, this dissertation explores DL models capable of combining the conceptual flexibility typical of a numerical approach for structural analysis, the finite element method, with the remarkable computational efficiency of trained neural networks. Specifically, this dissertation introduces the novel concept of <em>“Finite Element Network Analysis”</em> (FENA), a physics-informed, DL-based computational framework for the simulation of physical systems. FENA leverages the unique transfer knowledge property of bidirectional recurrent neural networks to provide a uniquely powerful and flexible computing platform. In FENA, each class of physical systems (for example, structural elements such as beams and plates) is represented by a set of surrogate DL-based models. All classes of surrogate models are pre-trained and available in a library, analogous to the finite element method, alleviating the need for repeated retraining. Another remarkable characteristic of FENA is the ability to simulate assemblies built by combining pre-trained networks that serve as surrogate models of different components of physical systems, a functionality that is key to modeling multicomponent physical systems. The ability to assemble pre-trained network models, dubbed <em>network concatenation</em>, places FENA in a new category of DL-based computational platforms because, unlike existing DL-based techniques, FENA does not require <em>ad hoc</em> training for problem-specific conditions.</p> <p><br></p> <p>While FENA is highly general in nature, this work focuses primarily on the development of linear and nonlinear static simulation capabilities of a variety of fundamental structural elements as a benchmark to demonstrate FENA's capabilities. Specifically, FENA is applied to linear elastic rods, slender beams, and thin plates. Then, the concept of concatenation is utilized to simulate multicomponent structures composed of beams and plate assemblies (stiffened panels). The capacity of FENA to model nonlinear systems is also shown by further applying it to nonlinear problems consisting in the simulation of geometrically nonlinear elastic beams and plastic deformation of aluminum beams, an extension that became possible thanks to the flexibility of FENA and the intrinsic nonlinearity of neural networks. The application of FENA to time-transient simulations is also presented, providing the foundation for linear time-transient simulations of homogeneous and inhomogeneous systems. Specifically, the concepts of Super Finite Network Element (SFNE) and network concatenation in time are introduced. The proposed concepts enable training SFNEs based on data available in a limited time frame and then using the trained SFNEs to simulate the system evolution beyond the initial time window characteristic of the training dataset. To showcase the effectiveness and versatility of the introduced concepts, they are applied to the transient simulation of homogeneous rods and inhomogeneous beams. In each case, the framework is validated by direct comparison against the solutions available from analytical methods or traditional finite element analysis. Results indicate that FENA can provide highly accurate solutions, with relative errors below 2 % for the cases presented in this work and a clear computational advantage over traditional numerical solution methods. </p> <p><br></p> <p>The consistency of the performance across diverse problem settings substantiates the adaptability and versatility of FENA. It is expected that, although the framework is illustrated and numerically validated only for selected classes of structures, the framework could potentially be extended to a broad spectrum of structural and multiphysics applications relevant to computational science.</p>

Dynamic Spectrum Access (DSA) has strong potential to address the need for improved spectrum efficiency. Unfortunately, traditional DSA approaches such as simple "sense-and-avoid" fail to provide sufficient performance in many scenarios. Thus, the combination of sensing with deep reinforcement learning (DRL) has been shown to be a promising alternative to previously proposed simplistic approaches. DRL does not require the explicit estimation of transition probability matrices and prohibitively large matrix computations as compared to traditional reinforcement learning methods. Further, since many learning approaches cannot solve the resulting online Partially-Observable Markov Decision Process (POMDP), Deep Recurrent Q-Networks (DRQN) have been proposed to determine the optimal channel access policy via online learning. The fundamental goal of this dissertation is to develop DRL-based solutions to address this POMDP-DSA problem. We mainly consider three aspects in this work: (1) optimal transmission strategies, (2) combined intelligent sensing and transmission strategies, and (c) learning efficiency or online convergence speed. Four key challenges in this problem are (1) the proposed DRQN-based node does not know the other nodes' behavior patterns a priori and must to predict the future channel state based on previous observations; (2) the impact to primary user throughput during learning and even after learning must be limited; (3) resources can be wasted the sensing/observation; and (4) convergence speed must be improved without impacting performance performance. We demonstrate in this dissertation, that the proposed DRQN can learn: (1) the optimal transmission strategy in a variety of environments under partial observations; (2) a sensing strategy that provides near-optimal throughput in different environments while dramatically reducing the needed sensing resources; (3) robustness to imperfect observations; (4) a sufficiently flexible approach that can accommodate dynamic environments, multi-channel transmission and the presence of multiple agents; (5) in an accelerated fashion utilizing one of three different approaches. / Doctor of Philosophy / With the development of wireless communication, such as 5G, global mobile data traffic has experienced tremendous growth, which makes spectrum resources even more critical for future networks. However, the spectrum is an exorbitant and scarce resource. Dynamic Spectrum Access (DSA) has strong potential to address the need for improved spectrum efficiency. Unfortunately, traditional DSA approaches such as simple "sense-and-avoid" fail to provide sufficient performance in many scenarios. Thus, the combination of sensing with deep reinforcement learning (DRL) has been shown to be a promising alternative to previously proposed simplistic approaches. Compared with traditional reinforcement learning methods, DRL does not require explicit estimation of transition probability matrices and extensive matrix computations. Furthermore, since many learning methods cannot solve the resulting online partially observable Markov decision process (POMDP), a deep recurrent Q-network (DRQN) is proposed to determine the optimal channel access policy through online learning. The basic goal of this paper is to develop a DRL-based solution to this POMDP-DSA problem. This paper mainly focuses on improving performance from three directions. 1. Find the optimal (or sub-optimal) channel access strategy based on fixed partial observation mode; 2. Based on work 1, propose a more intelligent way to dynamically and efficiently find more reasonable (higher efficiency) sensing/observation policy and corresponding channel access strategy; 3. On the premise of ensuring performance, use different machine learning algorithms or structures to improve learning efficiency and avoid users waiting too long for expected performance. Through the research in these three main directions, we have found an efficient and diverse solution, namely DRQN-based technology.

Online quality assurance is crucial for elevating product quality and boosting process productivity in advanced manufacturing. However, the inherent complexity of advanced manufacturing, including nonlinear process dynamics, multiple process attributes, and low signal/noise ratio, poses severe challenges for both maintaining stable process operations and establishing efficacious online quality assurance schemes. To address these challenges, four different advanced manufacturing processes, namely, fused filament fabrication (FFF), binder jetting, chemical mechanical planarization (CMP), and the slicing process in wafer production, are investigated in this dissertation for applications of online quality assurance, with utilization of various sensors, such as thermocouples, infrared temperature sensors, accelerometers, etc. The overarching goal of this dissertation is to develop innovative integrated methodologies tailored for these individual manufacturing processes but addressing their common challenges to achieve satisfying performance in online quality assurance based on heterogeneous sensor data. Specifically, three new methodologies are created and validated using actual sensor data, namely, (1) Real-time process monitoring methods using Dirichlet process (DP) mixture model for timely detection of process changes and identification of different process states for FFF and CMP. The proposed methodology is capable of tackling non-Gaussian data from heterogeneous sensors in these advanced manufacturing processes for successful online quality assurance. (2) Spatial Dirichlet process (SDP) for modeling complex multimodal wafer thickness profiles and exploring their clustering effects. The SDP-based statistical control scheme can effectively detect out-of-control wafers and achieve wafer thickness quality assurance for the slicing process with high accuracy. (3) Augmented spatiotemporal log Gaussian Cox process (AST-LGCP) quantifying the spatiotemporal evolution of porosity in binder jetting parts, capable of predicting high-risk areas on consecutive layers. This work fills the long-standing research gap of lacking rigorous layer-wise porosity quantification for parts made by additive manufacturing (AM), and provides the basis for facilitating corrective actions for product quality improvements in a prognostic way. These developed methodologies surmount some common challenges of advanced manufacturing which paralyze traditional methods in online quality assurance, and embody key components for implementing effective online quality assurance with various sensor data. There is a promising potential to extend them to other manufacturing processes in the future. / Ph. D.

Background – Feeding horses round bale hay (RBH) has been associated with airway inflammation. The purpose of this study was to determine if horses fed RBH for a 6-week period demonstrated more evidence of airway inflammation than horses fed square bale hay (SBH) of comparable quality. Hypothesis - The respiratory health of horses fed RBH will not differ from horses fed SBH of comparable quality. Animals – Two feeding groups of 15 healthy horses (mixed ages, breeds) from the University riding program. Methods – This was a prospective study performed during fall of 2009. At the beginning and end of a 6- week feeding trial, horses were examined (physical, upper airway endoscopic) and samples (tracheal aspirate (TA), bronchoalveolar lavage (BAL)) collected for cytology and/or bacterial/fungal culture. Hay was analyzed for nutritional value and bacterial/fungal content. Results – Horses fed RBH demonstrated an increase in pharyngeal lymphoid hyperplasia (p=0.0143) and percentage neutrophils (p=0.0078) in the TA samples post-feeding as compared to pre-feeding values. Nutritional analysis of hay and measurements of bacterial/fungal load did not differ over time and/or between hay types. Conclusions and clinical importance – The identification of airway inflammation in the horses fed RBH indicates that factors associated with the manner in which the hay is fed and consumed contribute to the development of subclinical airway inflammation. RBH affords horses continuous daily exposure to hay and as horses bury their muzzles in the bale, exposure to particulate matter is likely increased. These factors may partially explain the response in horses fed RBH. Further studies are required to confirm these predictions. / Master of Science

Objective - evaluate horses with acute airway obstruction using three treatment regimens: tapering doses of dexamethasone (DEX), environmental modification (ENV), and a combination of both treatments (DEX + ENV) by analyzing clinical parameters, pulmonary function testing, bronchoalveolar lavage fluid (BALF) cytology and BALF cell expression of the cytokines IFN-? and IL-4 Animals - 6 horses with recurrent airway obstruction (RAO) Procedures - Clinical examination, pulmonary function test, and collection of BALF prior to treatment and during 22 day treatment period Hypothesis - Alterations in clinical parameters, pulmonary function and airway inflammation in acute equine RAO will return to remission values by treating with DEX, ENV or DEX + ENV Results - All horses demonstrated clinical disease, reduced pulmonary dynamic compliance (Cdyn) and an increased maximum change in pleural pressures (?Pplmax) when in a challenge environment. All treatments improved clinical parameters, ?Pplmax and Cdyn. BALF cytology during an RAO crisis demonstrated neutrophilic inflammation. ENV or DEX + ENV resulted in a significant decrease in airway neutrophilia that was maintained throughout the treatment period. In contrast, treatment with DEX caused a reduction in airway neutrophilia initially followed by a rebound neutrophilia as the period between administrations of dexamethasone (0.05mg/kg) was increased to 72 hours. The rebound neutrophilia was not accompanied by equivalent deterioration in clinical parameters or pulmonary function. Conclusions - Environmental modification is important in the management of RAO horses. Treatment of clinical RAO with a decreasing dosage protocol of corticosteroids in the absence of environmental modification results in the persistence of airway inflammation without recrudescence of clinical disease. / Master of Science