Application of digital interferogram evaluation techniques to the measurement of 3-D flow fields

A system for digitally evaluating interferograms, based on an image processing system connected to a host computer, was implemented. The system supports one- and two-dimensional interferogram evaluations. Interferograms are digitized, enhanced, and then segmented. The fringe coordinates are extracted, and the fringes are represented as polygonal data structures. Fringe numbering and fringe interpolation modules are implemented. The system supports editing and interactive features, as well as graphic visualization. An application of the system to the evaluation of double exposure interferograms from the transonic flow field around a helicopter blade and the reconstruction of the three dimensional flow field is given

Efficient design and evaluation of countermeasures against fault attacks using formal verification

This paper presents a formal verification framework and tool that evaluates the robustness of software countermeasures against fault-injection attacks. By modeling reference assembly code and its protected variant as automata, the framework can generate a set of equations for an SMT solver, the solutions of which represent possible attack paths. Using the tool we developed, we evaluated the robustness of state-of-the-art countermeasures against fault injection attacks. Based on insights gathered from this evaluation, we analyze any remaining weaknesses and propose applications of these countermeasures that are more robust

A compiler level intermediate representation based binary analysis system and its applications

Analyzing and optimizing programs from their executables has received a lot of attention recently in the research community. There has been a tremendous amount of activity in executable-level research targeting varied applications such as security vulnerability analysis, untrusted code analysis, malware analysis, program testing, and binary optimizations. The vision of this dissertation is to advance the field of static analysis of executables and bridge the gap between source-level analysis and executable analysis. The main thesis of this work is scalable static binary rewriting and analysis using compiler-level intermediate representation without relying on the presence of metadata information such as debug or symbolic information. In spite of a significant overlap in the overall goals of several source-code methods and executables-level techniques, several sophisticated transformations that are well-understood and implemented in source-level infrastructures have yet to become available in executable frameworks. It is a well known fact that a standalone executable without any meta data is less amenable to analysis than the source code. Nonetheless, we believe that one of the prime reasons behind the limitations of existing executable frameworks is that current executable frameworks define their own intermediate representations (IR) which are significantly more constrained than an IR used in a compiler. Intermediate representations used in existing binary frameworks lack high level features like abstract stack, variables, and symbols and are even machine dependent in some cases. This severely limits the application of well-understood compiler transformations to executables and necessitates new research to make them applicable. In the first part of this dissertation, we present techniques to convert the binaries to the same high-level intermediate representation that compilers use. We propose methods to segment the flat address space in an executable containing undifferentiated blocks of memory. We demonstrate the inadequacy of existing variable identification methods for their promotion to symbols and present our methods for symbol promotion. We also present methods to convert the physically addressed stack in an executable to an abstract stack. The proposed methods are practical since they do not employ symbolic, relocation, or debug information which are usually absent in deployed executables. We have integrated our techniques with a prototype x86 binary framework called \emph{SecondWrite} that uses LLVM as the IR. The robustness of the framework is demonstrated by handling executables totaling more than a million lines of source-code, including several real world programs. In the next part of this work, we demonstrate that several well-known source-level analysis frameworks such as symbolic analysis have limited effectiveness in the executable domain since executables typically lack higher-level semantics such as program variables. The IR should have a precise memory abstraction for an analysis to effectively reason about memory operations. Our first work of recovering a compiler-level representation addresses this limitation by recovering several higher-level semantics information from executables. In the next part of this work, we propose methods to handle the scenarios when such semantics cannot be recovered. First, we propose a hybrid static-dynamic mechanism for recovering a precise and correct memory model in executables in presence of executable-specific artifacts such as indirect control transfers. Next, the enhanced memory model is employed to define a novel symbolic analysis framework for executables that can perform the same types of program analysis as source-level tools. Frameworks hitherto fail to simultaneously maintain the properties of correct representation and precise memory model and ignore memory-allocated variables while defining symbolic analysis mechanisms. We exemplify that our framework is robust, efficient and it significantly improves the performance of various traditional analyses like global value numbering, alias analysis and dependence analysis for executables. Finally, the underlying representation and analysis framework is employed for two separate applications. First, the framework is extended to define a novel static analysis framework, \emph{DemandFlow}, for identifying information flow security violations in program executables. Unlike existing static vulnerability detection methods for executables, DemandFlow analyzes memory locations in addition to symbols, thus improving the precision of the analysis. DemandFlow proposes a novel demand-driven mechanism to identify and precisely analyze only those program locations and memory accesses which are relevant to a vulnerability, thus enhancing scalability. DemandFlow uncovers six previously undiscovered format string and directory traversal vulnerabilities in popular ftp and internet relay chat clients. Next, the framework is extended to implement a platform-specific optimization for embedded processors. Several embedded systems provide the facility of locking one or more lines in the cache. We devise the first method in literature that employs instruction cache locking as a mechanism for improving the average-case run-time of general embedded applications. We demonstrate that the optimal solution for instruction cache locking can be obtained in polynomial time. Since our scheme is implemented inside a binary framework, it successfully addresses the portability concern by enabling the implementation of cache locking at the time of deployment when all the details of the memory hierarchy are available

Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins

<p>Abstract</p> <p>Background</p> <p>Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs) or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships.</p> <p>Results</p> <p>A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein's primary sequence into a group of functionally non-disruptive amino acids and a second group of functionally deleterious amino acids.</p> <p>Conclusions</p> <p>With this approach, not only conserved amino acid positions in a protein family can be labeled as functionally relevant, but also non-conserved amino acid positions can be identified to have a physicochemically meaningful functional effect. These results become a discriminative tool in the selection and elaboration of rational mutagenesis strategies for the protein. They can also be used to predict if a given nsSNP, identified, for instance, in a genomic-scale analysis, can have a functional implication for a particular protein and which nsSNPs are most likely to be functionally silent for a protein. This analytical tool could be used to rapidly and automatically discard any irrelevant nsSNP and guide the research focus toward functionally significant mutations. Based on preliminary results and applications, this technique shows promising performance as a valuable bioinformatics tool to aid in the development of new protein variants and in the understanding of function-structure relationships in proteins.</p

Towards Personal Virtual Traffic Lights

Traffic control management at intersections, a challenging and complex field of study, aims to strike a balance between safety and efficient traffic control. Nowadays, traffic control at intersections is typically done by traffic light systems which are not optimal and exhibit several drawbacks, such as poor efficiency and real-time adaptability. With the advent of Intelligent Transportation Systems (ITS), vehicles are being equipped with state-of-the-art technology, enabling cooperative decision-making which will certainly overwhelm the available traffic control systems. This solution strongly penalizes users without such capabilities, namely pedestrians, cyclists, and other legacy vehicles. Therefore, in this work, a prototype based on an alternative technology to the standard vehicular communications, Bluetooth Low Energy (BLE), is presented. The proposed framework aims to integrate legacy and modern vehicular communication systems into a cohesive management system. In this framework, the movements of users at intersections are managed by a centralized controller which, through the use of networked retransmitters deployed at intersections, broadcasts alerts and virtual light signalization orders. Users receive the aforementioned information on their own smart devices, discarding the need for dedicated light signalization infrastructures. Field tests, carried out with a real-world implementation, validate the correct operation of the proposed framework. Document type: Articl

Automatic Performance Optimization of Stencil Codes

A widely used class of codes are stencil codes. Their general structure is very simple: data points in a large grid are repeatedly recomputed from neighboring values. This predefined neighborhood is the so-called stencil. Despite their very simple structure, stencil codes are hard to optimize since only few computations are performed while a comparatively large number of values have to be accessed, i.e., stencil codes usually have a very low computational intensity. Moreover, the set of optimizations and their parameters also depend on the hardware on which the code is executed. To cut a long story short, current production compilers are not able to fully optimize this class of codes and optimizing each application by hand is not practical. As a remedy, we propose a set of optimizations and describe how they can be applied automatically by a code generator for the domain of stencil codes. A combination of a space and time tiling is able to increase the data locality, which significantly reduces the memory-bandwidth requirements: a standard three-dimensional 7-point Jacobi stencil can be accelerated by a factor of 3. This optimization can target basically any stencil code, while others are more specialized. E.g., support for arbitrary linear data layout transformations is especially beneficial for colored kernels, such as a Red-Black Gauss-Seidel smoother. On the one hand, an optimized data layout for such kernels reduces the bandwidth requirements while, on the other hand, it simplifies an explicit vectorization. Other noticeable optimizations described in detail are redundancy elimination techniques to eliminate common subexpressions both in a sequence of statements and across loop boundaries, arithmetic simplifications and normalizations, and the vectorization mentioned previously. In combination, these optimizations are able to increase the performance not only of the model problem given by Poisson’s equation, but also of real-world applications: an optical flow simulation and the simulation of a non-isothermal and non-Newtonian fluid flow

Reconfiguration for Fault Tolerance and Performance Analysis

Architecture reconfiguration, the ability of a system to alter the active interconnection among modules, has a history of different purposes and strategies. Its purposes develop from the relatively simple desire to formalize procedures that all processes have in common to reconfiguration for the improvement of fault-tolerance, to reconfiguration for performance enhancement, either through the simple maximizing of system use or by sophisticated notions of wedding topology to the specific needs of a given process. Strategies range from straightforward redundancy by means of an identical backup system to intricate structures employing multistage interconnection networks. The present discussion surveys the more important contributions to developments in reconfigurable architecture. The strategy here is in a sense to approach the field from an historical perspective, with the goal of developing a more coherent theory of reconfiguration. First, the Turing and von Neumann machines are discussed from the perspective of system reconfiguration, and it is seen that this early important theoretical work contains little that anticipates reconfiguration. Then some early developments in reconfiguration are analyzed, including the work of Estrin and associates on the fixed plus variable restructurable computer system, the attempt to theorize about configurable computers by Miller and Cocke, and the work of Reddi and Feustel on their restructable computer system. The discussion then focuses on the most sustained systems for fault tolerance and performance enhancement that have been proposed. An attempt will be made to define fault tolerance and to investigate some of the strategies used to achieve it. By investigating four different systems, the Tandern computer, the C.vmp system, the Extra Stage Cube, and the Gamma network, the move from dynamic redundancy to reconfiguration is observed. Then reconfiguration for performance enhancement is discussed. A survey of some proposals is attempted, then the discussion focuses on the most sustained systems that have been proposed: PASM, the DC architecture, the Star local network, and the NYU Ultracomputer. The discussion is organized around a comparison of control, scheduling, communication, and network topology. Finally, comparisons are drawn between fault tolerance and performance enhancement, in order to clarify the notion of reconfiguration and to reveal the common ground of fault tolerance and performance enhancement as well as the areas in which they diverge. An attempt is made in the conclusion to derive from this survey and analysis some observations on the nature of reconfiguration, as well as some remarks on necessary further areas of research