Practical dynamic thermal management on Intel desktop computer

Fueled by increasing human appetite for high computing performance, semiconductor technology has now marched into the deep sub-micron era. As transistor size keeps shrinking, more and more transistors are integrated into a single chip. This has increased tremendously the power consumption and heat generation of IC chips. The rapidly growing heat dissipation greatly increases the packaging/cooling costs, and adversely affects the performance and reliability of a computing system. In addition, it also reduces the processor's life span and may even crash the entire computing system. Therefore, dynamic thermal management (DTM) is becoming a critical problem in modern computer system design. Extensive theoretical research has been conducted to study the DTM problem. However, most of them are based on theoretically idealized assumptions or simplified models. While these models and assumptions help to greatly simplify a complex problem and make it theoretically manageable, practical computer systems and applications must deal with many practical factors and details beyond these models or assumptions. The goal of our research was to develop a test platform that can be used to validate theoretical results on DTM under well-controlled conditions, to identify the limitations of existing theoretical results, and also to develop new and practical DTM techniques. This dissertation details the background and our research efforts in this endeavor. Specifically, in our research, we first developed a customized test platform based on an Intel desktop. We then tested a number of related theoretical works and examined their limitations under the practical hardware environment. With these limitations in mind, we developed a new reactive thermal management algorithm for single-core computing systems to optimize the throughput under a peak temperature constraint. We further extended our research to a multicore platform and developed an effective proactive DTM technique for throughput maximization on multicore processor based on task migration and dynamic voltage frequency scaling technique. The significance of our research lies in the fact that our research complements the current extensive theoretical research in dealing with increasingly critical thermal problems and enabling the continuous evolution of high performance computing systems.

Dynamic image precompensation for improving visual performance of computer users with ocular aberrations

With the progress of computer technology, computers are expected to be more intelligent in the interaction with humans, presenting information according to the user's psychological and physiological characteristics. However, computer users with visual problems may encounter difficulties on the perception of icons, menus, and other graphical information displayed on the screen, limiting the efficiency of their interaction with computers. In this dissertation, a personalized and dynamic image precompensation method was developed to improve the visual performance of the computer users with ocular aberrations. The precompensation was applied on the graphical targets before presenting them on the screen, aiming to counteract the visual blurring caused by the ocular aberration of the user's eye. A complete and systematic modeling approach to describe the retinal image formation of the computer user was presented, taking advantage of modeling tools, such as Zernike polynomials, wavefront aberration, Point Spread Function and Modulation Transfer Function. The ocular aberration of the computer user was originally measured by a wavefront aberrometer, as a reference for the precompensation model. The dynamic precompensation was generated based on the resized aberration, with the real-time pupil diameter monitored. The potential visual benefit of the dynamic precompensation method was explored through software simulation, with the aberration data from a real human subject. An "artificial eye'' experiment was conducted by simulating the human eye with a high-definition camera, providing objective evaluation to the image quality after precompensation. In addition, an empirical evaluation with 20 human participants was also designed and implemented, involving image recognition tests performed under a more realistic viewing environment of computer use. The statistical analysis results of the empirical experiment confirmed the effectiveness of the dynamic precompensation method, by showing significant improvement on the recognition accuracy. The merit and necessity of the dynamic precompensation were also substantiated by comparing it with the static precompensation. The visual benefit of the dynamic precompensation was further confirmed by the subjective assessments collected from the evaluation participants.

On-screen pre-deblurring of digital images using the wavefront aberration function of the human eye to improve computer access for the visually impaired

Traditional Optics has provided ways to compensate some common visual limitations (up to second order visual impairments) through spectacles or contact lenses. Recent developments in wavefront science make it possible to obtain an accurate model of the Point Spread Function (PSF) of the human eye. Through what is known as the "Wavefront Aberration Function" of the human eye, exact knowledge of the optical aberration of the human eye is possible, allowing a mathematical model of the PSF to be obtained. This model could be used to pre-compensate (inverse-filter) the images displayed on computer screens in order to counter the distortion in the user's eye. This project takes advantage of the fact that the wavefront aberration function, commonly expressed as a Zernike polynomial, can be generated from the ophthalmic prescription used to fit spectacles to a person. This allows the pre-compensation, or onscreen deblurring, to be done for various visual impairments, up to second order (commonly known as myopia, hyperopia, or astigmatism). The technique proposed towards that goal and results obtained using a lens, for which the PSF is known, that is introduced into the visual path of subjects without visual impairment will be presented. In addition to substituting the effect of spectacles or contact lenses in correcting the loworder visual limitations of the viewer, the significance of this approach is that it has the potential to address higher-order abnormalities in the eye, currently not correctable by simple means.

Radiotherapy Treatment Assessment using DCE-MRI

Abstract

The goal of modern radiotherapy is to precisely deliver a prescribed radiation dose to delineated target volumes that contain a significant amount of tumor cells while sparing the surrounding healthy tissues/organs. Precise delineation of treatment and avoidance volumes is the key for the precision radiation therapy. In recent years, considerable clinical and research efforts have been devoted to integrate MRI into radiotherapy workflow motivated by the superior soft tissue contrast and functional imaging possibility. Dynamic contrast-enhanced MRI (DCE-MRI) is a noninvasive technique that measures properties of tissue microvasculature. Its sensitivity to radiation-induced vascular pharmacokinetic (PK) changes has been preliminary demonstrated. In spite of its great potential, two major challenges have limited DCE-MRI’s clinical application in radiotherapy assessment: the technical limitations of accurate DCE-MRI imaging implementation and the need of novel DCE-MRI data analysis methods for richer functional heterogeneity information.

This study aims at improving current DCE-MRI techniques and developing new DCE-MRI analysis methods for particular radiotherapy assessment. Thus, the study is naturally divided into two parts. The first part focuses on DCE-MRI temporal resolution as one of the key DCE-MRI technical factors, and some improvements regarding DCE-MRI temporal resolution are proposed; the second part explores the potential value of image heterogeneity analysis and multiple PK model combination for therapeutic response assessment, and several novel DCE-MRI data analysis methods are developed.

I. Improvement of DCE-MRI temporal resolution. First, the feasibility of improving DCE-MRI temporal resolution via image undersampling was studied. Specifically, a novel MR image iterative reconstruction algorithm was studied for DCE-MRI reconstruction. This algorithm was built on the recently developed compress sensing (CS) theory. By utilizing a limited k-space acquisition with shorter imaging time, images can be reconstructed in an iterative fashion under the regularization of a newly proposed total generalized variation (TGV) penalty term. In the retrospective study of brain radiosurgery patient DCE-MRI scans under IRB-approval, the clinically obtained image data was selected as reference data, and the simulated accelerated k-space acquisition was generated via undersampling the reference image full k-space with designed sampling grids. Two undersampling strategies were proposed: 1) a radial multi-ray grid with a special angular distribution was adopted to sample each slice of the full k-space; 2) a Cartesian random sampling grid series with spatiotemporal constraints from adjacent frames was adopted to sample the dynamic k-space series at a slice location. Two sets of PK parameters’ maps were generated from the undersampled data and from the fully-sampled data, respectively. Multiple quantitative measurements and statistical studies were performed to evaluate the accuracy of PK maps generated from the undersampled data in reference to the PK maps generated from the fully-sampled data. Results showed that at a simulated acceleration factor of four, PK maps could be faithfully calculated from the DCE images that were reconstructed using undersampled data, and no statistically significant differences were found between the regional PK mean values from undersampled and fully-sampled data sets. DCE-MRI acceleration using the investigated image reconstruction method has been suggested as feasible and promising.

Second, for high temporal resolution DCE-MRI, a new PK model fitting method was developed to solve PK parameters for better calculation accuracy and efficiency. This method is based on a derivative-based deformation of the commonly used Tofts PK model, which is presented as an integrative expression. This method also includes an advanced Kolmogorov-Zurbenko (KZ) filter to remove the potential noise effect in data and solve the PK parameter as a linear problem in matrix format. In the computer simulation study, PK parameters representing typical intracranial values were selected as references to simulated DCE-MRI data for different temporal resolution and different data noise level. Results showed that at both high temporal resolutions (<1s) and clinically feasible temporal resolution (~5s), this new method was able to calculate PK parameters more accurate than the current calculation methods at clinically relevant noise levels; at high temporal resolutions, the calculation efficiency of this new method was superior to current methods in an order of 102. In a retrospective of clinical brain DCE-MRI scans, the PK maps derived from the proposed method were comparable with the results from current methods. Based on these results, it can be concluded that this new method can be used for accurate and efficient PK model fitting for high temporal resolution DCE-MRI.

II. Development of DCE-MRI analysis methods for therapeutic response assessment. This part aims at methodology developments in two approaches. The first one is to develop model-free analysis method for DCE-MRI functional heterogeneity evaluation. This approach is inspired by the rationale that radiotherapy-induced functional change could be heterogeneous across the treatment area. The first effort was spent on a translational investigation of classic fractal dimension theory for DCE-MRI therapeutic response assessment. In a small-animal anti-angiogenesis drug therapy experiment, the randomly assigned treatment/control groups received multiple fraction treatments with one pre-treatment and multiple post-treatment high spatiotemporal DCE-MRI scans. In the post-treatment scan two weeks after the start, the investigated Rényi dimensions of the classic PK rate constant map demonstrated significant differences between the treatment and the control groups; when Rényi dimensions were adopted for treatment/control group classification, the achieved accuracy was higher than the accuracy from using conventional PK parameter statistics. Following this pilot work, two novel texture analysis methods were proposed. First, a new technique called Gray Level Local Power Matrix (GLLPM) was developed. It intends to solve the lack of temporal information and poor calculation efficiency of the commonly used Gray Level Co-Occurrence Matrix (GLCOM) techniques. In the same small animal experiment, the dynamic curves of Haralick texture features derived from the GLLPM had an overall better performance than the corresponding curves derived from current GLCOM techniques in treatment/control separation and classification. The second developed method is dynamic Fractal Signature Dissimilarity (FSD) analysis. Inspired by the classic fractal dimension theory, this method measures the dynamics of tumor heterogeneity during the contrast agent uptake in a quantitative fashion on DCE images. In the small animal experiment mentioned before, the selected parameters from dynamic FSD analysis showed significant differences between treatment/control groups as early as after 1 treatment fraction; in contrast, metrics from conventional PK analysis showed significant differences only after 3 treatment fractions. When using dynamic FSD parameters, the treatment/control group classification after 1st treatment fraction was improved than using conventional PK statistics. These results suggest the promising application of this novel method for capturing early therapeutic response.

The second approach of developing novel DCE-MRI methods is to combine PK information from multiple PK models. Currently, the classic Tofts model or its alternative version has been widely adopted for DCE-MRI analysis as a gold-standard approach for therapeutic response assessment. Previously, a shutter-speed (SS) model was proposed to incorporate transcytolemmal water exchange effect into contrast agent concentration quantification. In spite of richer biological assumption, its application in therapeutic response assessment is limited. It might be intriguing to combine the information from the SS model and from the classic Tofts model to explore potential new biological information for treatment assessment. The feasibility of this idea was investigated in the same small animal experiment. The SS model was compared against the Tofts model for therapeutic response assessment using PK parameter regional mean value comparison. Based on the modeled transcytolemmal water exchange rate, a biological subvolume was proposed and was automatically identified using histogram analysis. Within the biological subvolume, the PK rate constant derived from the SS model were proved to be superior to the one from Tofts model in treatment/control separation and classification. Furthermore, novel biomarkers were designed to integrate PK rate constants from these two models. When being evaluated in the biological subvolume, this biomarker was able to reflect significant treatment/control difference in both post-treatment evaluation. These results confirm the potential value of SS model as well as its combination with Tofts model for therapeutic response assessment.

In summary, this study addressed two problems of DCE-MRI application in radiotherapy assessment. In the first part, a method of accelerating DCE-MRI acquisition for better temporal resolution was investigated, and a novel PK model fitting algorithm was proposed for high temporal resolution DCE-MRI. In the second part, two model-free texture analysis methods and a multiple-model analysis method were developed for DCE-MRI therapeutic response assessment. The presented works could benefit the future DCE-MRI routine clinical application in radiotherapy assessment.

Learning from Geometry

Subspaces and manifolds are two powerful models for high dimensional signals. Subspaces model linear correlation and are a good fit to signals generated by physical systems, such as frontal images of human faces and multiple sources impinging at an antenna array. Manifolds model sources that are not linearly correlated, but where signals are determined by a small number of parameters. Examples are images of human faces under different poses or expressions, and handwritten digits with varying styles. However, there will always be some degree of model mismatch between the subspace or manifold model and the true statistics of the source. This dissertation exploits subspace and manifold models as prior information in various signal processing and machine learning tasks.

A near-low-rank Gaussian mixture model measures proximity to a union of linear or affine subspaces. This simple model can effectively capture the signal distribution when each class is near a subspace. This dissertation studies how the pairwise geometry between these subspaces affects classification performance. When model mismatch is vanishingly small, the probability of misclassification is determined by the product of the sines of the principal angles between subspaces. When the model mismatch is more significant, the probability of misclassification is determined by the sum of the squares of the sines of the principal angles. Reliability of classification is derived in terms of the distribution of signal energy across principal vectors. Larger principal angles lead to smaller classification error, motivating a linear transform that optimizes principal angles. This linear transformation, termed TRAIT, also preserves some specific features in each class, being complementary to a recently developed Low Rank Transform (LRT). Moreover, when the model mismatch is more significant, TRAIT shows superior performance compared to LRT.

The manifold model enforces a constraint on the freedom of data variation. Learning features that are robust to data variation is very important, especially when the size of the training set is small. A learning machine with large numbers of parameters, e.g., deep neural network, can well describe a very complicated data distribution. However, it is also more likely to be sensitive to small perturbations of the data, and to suffer from suffer from degraded performance when generalizing to unseen (test) data.

From the perspective of complexity of function classes, such a learning machine has a huge capacity (complexity), which tends to overfit. The manifold model provides us with a way of regularizing the learning machine, so as to reduce the generalization error, therefore mitigate overfiting. Two different overfiting-preventing approaches are proposed, one from the perspective of data variation, the other from capacity/complexity control. In the first approach, the learning machine is encouraged to make decisions that vary smoothly for data points in local neighborhoods on the manifold. In the second approach, a graph adjacency matrix is derived for the manifold, and the learned features are encouraged to be aligned with the principal components of this adjacency matrix. Experimental results on benchmark datasets are demonstrated, showing an obvious advantage of the proposed approaches when the training set is small.

Stochastic optimization makes it possible to track a slowly varying subspace underlying streaming data. By approximating local neighborhoods using affine subspaces, a slowly varying manifold can be efficiently tracked as well, even with corrupted and noisy data. The more the local neighborhoods, the better the approximation, but the higher the computational complexity. A multiscale approximation scheme is proposed, where the local approximating subspaces are organized in a tree structure. Splitting and merging of the tree nodes then allows efficient control of the number of neighbourhoods. Deviation (of each datum) from the learned model is estimated, yielding a series of statistics for anomaly detection. This framework extends the classical {\em changepoint detection} technique, which only works for one dimensional signals. Simulations and experiments highlight the robustness and efficacy of the proposed approach in detecting an abrupt change in an otherwise slowly varying low-dimensional manifold.

Towards Proactive Context-aware Computing and Systems

A primary goal of context-aware systems is delivering the right information at the right place and right time to users in order to enable them to make effective decisions and improve their quality of life. There are three key requirements for achieving this goal: determining what information is relevant, personalizing it based on the users’ context (location, preferences, behavioral history etc.), and delivering it to them in a timely manner without an explicit request from them. These requirements create a paradigm that we term as “Proactive Context-aware Computing”. Most of the existing context-aware systems fulfill only a subset of these requirements. Many of these systems focus only on personalization of the requested information based on users’ current context. Moreover, they are often designed for specific domains. In addition, most of the existing systems are reactive - the users request for some information and the system delivers it to them. These systems are not proactive i.e. they cannot anticipate users’ intent and behavior and act proactively without an explicit request from them. In order to overcome these limitations, we need to conduct a deeper analysis and enhance our understanding of context-aware systems that are generic, universal, proactive and applicable to a wide variety of domains. To support this dissertation, we explore several directions. Clearly the most significant sources of information about users today are smartphones. A large amount of users’ context can be acquired through them and they can be used as an effective means to deliver information to users. In addition, social media such as Facebook, Flickr and Foursquare provide a rich and powerful platform to mine users’ interests, preferences and behavioral history. We employ the ubiquity of smartphones and the wealth of information available from social media to address the challenge of building proactive context-aware systems. We have implemented and evaluated a few approaches, including some as part of the Rover framework, to achieve the paradigm of Proactive Context-aware Computing. Rover is a context-aware research platform which has been evolving for the last 6 years. Since location is one of the most important context for users, we have developed ‘Locus’, an indoor localization, tracking and navigation system for multi-story buildings. Other important dimensions of users’ context include the activities that they are engaged in. To this end, we have developed ‘SenseMe’, a system that leverages the smartphone and its multiple sensors in order to perform multidimensional context and activity recognition for users. As part of the ‘SenseMe’ project, we also conducted an exploratory study of privacy, trust, risks and other concerns of users with smart phone based personal sensing systems and applications. To determine what information would be relevant to users’ situations, we have developed ‘TellMe’ - a system that employs a new, flexible and scalable approach based on Natural Language Processing techniques to perform bootstrapped discovery and ranking of relevant information in context-aware systems. In order to personalize the relevant information, we have also developed an algorithm and system for mining a broad range of users’ preferences from their social network profiles and activities. For recommending new information to the users based on their past behavior and context history (such as visited locations, activities and time), we have developed a recommender system and approach for performing multi-dimensional collaborative recommendations using tensor factorization. For timely delivery of personalized and relevant information, it is essential to anticipate and predict users’ behavior. To this end, we have developed a unified infrastructure, within the Rover framework, and implemented several novel approaches and algorithms that employ various contextual features and state of the art machine learning techniques for building diverse behavioral models of users. Examples of generated models include classifying users’ semantic places and mobility states, predicting their availability for accepting calls on smartphones and inferring their device charging behavior. Finally, to enable proactivity in context-aware systems, we have also developed a planning framework based on HTN planning. Together, these works provide a major push in the direction of proactive context-aware computing.

A Binary Classifier for Test Case Feasibility Applied to Automatically Generated Tests of Event-Driven Software

Modern software application testing, such as the testing of software driven by graphical user interfaces (GUIs) or leveraging event-driven architectures in general, requires paying careful attention to context. Model-based testing (MBT) approaches first acquire a model of an application, then use the model to construct test cases covering relevant contexts. A major shortcoming of state-of-the-art automated model-based testing is that many test cases proposed by the model are not actually executable. These \textit{infeasible} test cases threaten the integrity of the entire model-based suite, and any coverage of contexts the suite aims to provide. In this research, I develop and evaluate a novel approach for classifying the feasibility of test cases. I identify a set of pertinent features for the classifier, and develop novel methods for extracting these features from the outputs of MBT tools. I use a supervised logistic regression approach to obtain a model of test case feasibility from a randomly selected training suite of test cases. I evaluate this approach with a set of experiments. The outcomes of this investigation are as follows: I confirm that infeasibility is prevalent in MBT, even for test suites designed to cover a relatively small number of unique contexts. I confirm that the frequency of infeasibility varies widely across applications. I develop and train a binary classifier for feasibility with average overall error, false positive, and false negative rates under 5\%. I find that unique event IDs are key features of the feasibility classifier, while model-specific event types are not. I construct three types of features from the event IDs associated with test cases, and evaluate the relative effectiveness of each within the classifier. To support this study, I also develop a number of tools and infrastructure components for scalable execution of automated jobs, which use state-of-the-art container and continuous integration technologies to enable parallel test execution and the persistence of all experimental artifacts.

Top-K Query Processing in Edge-Labeled Graph Data

Edge-labeled graphs have proliferated rapidly over the last decade due to the increased popularity of social networks and the Semantic Web. In social networks, relationships between people are represented by edges and each edge is labeled with a semantic annotation. Hence, a huge single graph can express many different relationships between entities. The Semantic Web represents each single fragment of knowledge as a triple (subject, predicate, object), which is conceptually identical to an edge from subject to object labeled with predicates. A set of triples constitutes an edge-labeled graph on which knowledge inference is performed. Subgraph matching has been extensively used as a query language for patterns in the context of edge-labeled graphs. For example, in social networks, users can specify a subgraph matching query to find all people that have certain neighborhood relationships. Heavily used fragments of the SPARQL query language for the Semantic Web and graph queries of other graph DBMS can also be viewed as subgraph matching over large graphs. Though subgraph matching has been extensively studied as a query paradigm in the Semantic Web and in social networks, a user can get a large number of answers in response to a query. These answers can be shown to the user in accordance with an importance ranking. In this thesis proposal, we present four different scoring models along with scalable algorithms to find the top-k answers via a suite of intelligent pruning techniques. The suggested models consist of a practically important subset of the SPARQL query language augmented with some additional useful features. The first model called Substitution Importance Query (SIQ) identifies the top-k answers whose scores are calculated from matched vertices' properties in each answer in accordance with a user-specified notion of importance. The second model called Vertex Importance Query (VIQ) identifies important vertices in accordance with a user-defined scoring method that builds on top of various subgraphs articulated by the user. Approximate Importance Query (AIQ), our third model, allows partial and inexact matchings and returns top-k of them with a user-specified approximation terms and scoring functions. In the fourth model called Probabilistic Importance Query (PIQ), a query consists of several sub-blocks: one mandatory block that must be mapped and other blocks that can be opportunistically mapped. The probability is calculated from various aspects of answers such as the number of mapped blocks, vertices' properties in each block and so on and the most top-k probable answers are returned. An important distinguishing feature of our work is that we allow the user a huge amount of freedom in specifying: (i) what pattern and approximation he considers important, (ii) how to score answers - irrespective of whether they are vertices or substitution, and (iii) how to combine and aggregate scores generated by multiple patterns and/or multiple substitutions. Because so much power is given to the user, indexing is more challenging than in situations where additional restrictions are imposed on the queries the user can ask. The proposed algorithms for the first model can also be used for answering SPARQL queries with ORDER BY and LIMIT, and the method for the second model also works for SPARQL queries with GROUP BY, ORDER BY and LIMIT. We test our algorithms on multiple real-world graph databases, showing that our algorithms are far more efficient than popular triple stores.

Miradouro Virtual(R)

Esta tese pretende descrever o desenvolvimento e arquitectura do software que constitui o Miradouro Virtual@, mais especificamente do componente referente à interface. O Miradouro Virtual@ é um dispositivo cujo propósito à semelhança dos tradicionais binóculos turísticos, é observar a paisagem, mas cuja interacção não está limitada à simples observação individual. Recorre à realidade aumentada para sobrepôr imagens geradas por computador a imagens reais, capturadas por um dispositivo para aquisição de imagem real (tipicamente uma câmara de vídeo), e mostra-as num ecrã touchscreen, permitindo deste modo, combinar elementos virtuais e multimédia com a paisagem real. A imagem final, composta, dá ao utilizador uma nova dimensão do espaço envolvente, permitindo-lhe explorar uma nova camada de informação não visível anteriormente. Sendo sensíveis à orientação do Miradouro Virtual@, os elementos virtuais e multimédia adaptam-se de acordo com os movimentos do dispositivo. O Miradouro Virtual@ é um produto composto por diversos elementos de hardware e software. O foco desta tese recai apenas nos componentes de software, mais especificamente na interface. Pretende dar a conhecer as limitações da versão anterior do software e mostrar as soluções encontradas que permitiram ultrapassar algumas dessas limitações. ABSTRACT; This thesis focuses on the design and development of the Virtual Sightseeing™ software, more specifically on the interface component. The Virtual Sightseeing™ is a device similar to the traditional scenic viewers that takes advantage of its generally known and popularity to build an innovative system. It works by using augmented reality to superimpose, in real-time, images generated by a computer onto a live stream captured by a video camera and displaying them on a touchscreen display. It allows adding multimedia elements to the real scenery by composing them in the image that is presented to the user. The multimedia information and virtual elements that are displayed are sensitive to the orientation and position of the device. They change as the user manually changes the orientation of the device. The Virtual Sightseeing™ is comprised of several hardware and software components. The focus of this thesis is on the software part, more specifically on the interface component. It intends to show the known limitations of the previous software version and how they were overcome in this new version.

Implementação da rotina de unfolding para determinação de distribuição de tamanho de grãos esféricos via distribuição de interceptos lineares e de área de seção

Na unfolding method of linear intercept distributions and secction área distribution was implemented for structures with spherical grains. Although the unfolding routine depends on the grain shape, structures with spheroidal grains can also be treated by this routine. Grains of non-spheroidal shape can be treated only as approximation. A software was developed with two parts. The first part calculates the probability matrix. The second part uses this matrix and minimizes the chi-square. The results are presented with any number of size classes as required. The probability matrix was determined by means of the linear intercept and section area distributions created by computer simulation. Using curve fittings the probability matrix for spheres of any sizes could be determined. Two kinds of tests were carried out to prove the efficiency of the Technique. The theoretical tests represent ideal cases. The software was able to exactly find the proposed grain size distribution. In the second test, a structure was simulated in computer and images of its slices were used to produce the corresponding linear intercept the section area distributions. These distributions were then unfolded. This test simulates better reality. The results show deviations from the real size distribution. This deviations are caused by statistic fluctuation. The unfolding of the linear intercept distribution works perfectly, but the unfolding of section area distribution does not work due to a failure in the chi-square minimization. The minimization method uses a matrix inversion routine. The matrix generated by this procedure cannot be inverted. Other minimization method must be used

MINING AND VERIFICATION OF TEMPORAL EVENTS WITH APPLICATIONS IN COMPUTER MICRO-ARCHITECTURE RESEARCH

Computer simulation programs are essential tools for scientists and engineers to understand a particular system of interest. As expected, the complexity of the software increases with the depth of the model used. In addition to the exigent demands of software engineering, verification of simulation programs is especially challenging because the models represented are complex and ridden with unknowns that will be discovered by developers in an iterative process. To manage such complexity, advanced verification techniques for continually matching the intended model to the implemented model are necessary. Therefore, the main goal of this research work is to design a useful verification and validation framework that is able to identify model representation errors and is applicable to generic simulators. The framework that was developed and implemented consists of two parts. The first part is First-Order Logic Constraint Specification Language (FOLCSL) that enables users to specify the invariants of a model under consideration. From the first-order logic specification, the FOLCSL translator automatically synthesizes a verification program that reads the event trace generated by a simulator and signals whether all invariants are respected. The second part consists of mining the temporal flow of events using a newly developed representation called State Flow Temporal Analysis Graph (SFTAG). While the first part seeks an assurance of implementation correctness by checking that the model invariants hold, the second part derives an extended model of the implementation and hence enables a deeper understanding of what was implemented. The main application studied in this work is the validation of the timing behavior of micro-architecture simulators. The study includes SFTAGs generated for a wide set of benchmark programs and their analysis using several artificial intelligence algorithms. This work improves the computer architecture research and verification processes as shown by the case studies and experiments that have been conducted.

Dynamic Image Precompensation for Improving Visual Performance of Computer Users with Ocular Aberrations

With the progress of computer technology, computers are expected to be more intelligent in the interaction with humans, presenting information according to the user's psychological and physiological characteristics. However, computer users with visual problems may encounter difficulties on the perception of icons, menus, and other graphical information displayed on the screen, limiting the efficiency of their interaction with computers. In this dissertation, a personalized and dynamic image precompensation method was developed to improve the visual performance of the computer users with ocular aberrations. The precompensation was applied on the graphical targets before presenting them on the screen, aiming to counteract the visual blurring caused by the ocular aberration of the user's eye. A complete and systematic modeling approach to describe the retinal image formation of the computer user was presented, taking advantage of modeling tools, such as Zernike polynomials, wavefront aberration, Point Spread Function and Modulation Transfer Function. The ocular aberration of the computer user was originally measured by a wavefront aberrometer, as a reference for the precompensation model. The dynamic precompensation was generated based on the resized aberration, with the real-time pupil diameter monitored. The potential visual benefit of the dynamic precompensation method was explored through software simulation, with the aberration data from a real human subject. An "artificial eye'' experiment was conducted by simulating the human eye with a high-definition camera, providing objective evaluation to the image quality after precompensation. In addition, an empirical evaluation with 20 human participants was also designed and implemented, involving image recognition tests performed under a more realistic viewing environment of computer use. The statistical analysis results of the empirical experiment confirmed the effectiveness of the dynamic precompensation method, by showing significant improvement on the recognition accuracy. The merit and necessity of the dynamic precompensation were also substantiated by comparing it with the static precompensation. The visual benefit of the dynamic precompensation was further confirmed by the subjective assessments collected from the evaluation participants.

Symbolic dynamics generated by a hybrid chaotic systems

We consider piecewise defined differential dynamical systems which can be analysed through symbolic dynamics and transition matrices. We have a continuous regime, where the time flow is characterized by an ordinary differential equation (ODE) which has explicit solutions, and the singular regime, where the time flow is characterized by an appropriate transformation. The symbolic codification is given through the association of a symbol for each distinct regular system and singular system. The transition matrices are then determined as linear approximations to the symbolic dynamics. We analyse the dependence on initial conditions, parameter variation and the occurrence of global strange attractors.

Production Lot Detection through Synthetic Generated Data

Correctness of information gathered in production environments is an essential part of quality assurance processes in many industries, this task is often performed by human resources who visually take annotations in various steps of the production flow. Depending on the performed task the correlation between where exactly the information is gathered and what it represents is more than often lost in the process. The lack of labeled data places a great boundary on the application of deep neural networks aimed at object detection tasks, moreover supervised training of deep models requires a great amount of data to be available. Reaching an adequate large collection of labeled images through classic techniques of data annotations is an exhausting and costly task to perform, not always suitable for every scenario. A possible solution is to generate synthetic data that replicates the real one and use it to fine-tune a deep neural network trained on one or more source domains to a different target domain. The purpose of this thesis is to show a real case scenario where the provided data were both in great scarcity and missing the required annotations. Sequentially a possible approach is presented where synthetic data has been generated to address those issues while standing as a training base of deep neural networks for object detection, capable of working on images taken in production-like environments. Lastly, it compares performance on different types of synthetic data and convolutional neural networks used as backbones for the model.

Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.