Evolutionary improvement of programs

Most applications of genetic programming (GP) involve the creation of an entirely new function, program or expression to solve a specific problem. In this paper, we propose a new approach that applies GP to improve existing software by optimizing its non-functional properties such as execution time, memory usage, or power consumption. In general, satisfying non-functional requirements is a difficult task and often achieved in part by optimizing compilers. However, modern compilers are in general not always able to produce semantically equivalent alternatives that optimize non-functional properties, even if such alternatives are known to exist: this is usually due to the limited local nature of such optimizations. In this paper, we discuss how best to combine and extend the existing evolutionary methods of GP, multiobjective optimization, and coevolution in order to improve existing software. Given as input the implementation of a function, we attempt to evolve a semantically equivalent version, in this case optimized to reduce execution time subject to a given probability distribution of inputs. We demonstrate that our framework is able to produce non-obvious optimizations that compilers are not yet able to generate on eight example functions. We employ a coevolved population of test cases to encourage the preservation of the function's semantics. We exploit the original program both through seeding of the population in order to focus the search, and as an oracle for testing purposes. As well as discussing the issues that arise when attempting to improve software, we employ rigorous experimental method to provide interesting and practical insights to suggest how to address these issues

An experimental evaluation of error seeding as a program validation technique

A previously reported experiment in error seeding as a program validation technique is summarized. The experiment was designed to test the validity of three assumptions on which the alleged effectiveness of error seeding is based. Errors were seeded into 17 functionally identical but independently programmed Pascal programs in such a way as to produce 408 programs, each with one seeded error. Using mean time to failure as a metric, results indicated that it is possible to generate seeded errors that are arbitrarily but not equally difficult to locate. Examination of indigenous errors demonstrated that these are also arbitrarily difficult to locate. These two results support the assumption that seeded and indigenous errors are approximately equally difficult to locate. However, the assumption that, for each type of error, all errors are equally difficult to locate was not borne out. Finally, since a seeded error occasionally corrected an indigenous error, the assumption that errors do not interfere with each other was proven wrong. Error seeding can be made useful by taking these results into account in modifying the underlying model

Research in computer science

Synopses are given for NASA supported work in computer science at the University of Virginia. Some areas of research include: error seeding as a testing method; knowledge representation for engineering design; analysis of faults in a multi-version software experiment; implementation of a parallel programming environment; two computer graphics systems for visualization of pressure distribution and convective density particles; task decomposition for multiple robot arms; vectorized incomplete conjugate gradient; and iterative methods for solving linear equations on the Flex/32

A comprehensive evaluation of alignment algorithms in the context of RNA-seq.

Transcriptome sequencing (RNA-Seq) overcomes limitations of previously used RNA quantification methods and provides one experimental framework for both high-throughput characterization and quantification of transcripts at the nucleotide level. The first step and a major challenge in the analysis of such experiments is the mapping of sequencing reads to a transcriptomic origin including the identification of splicing events. In recent years, a large number of such mapping algorithms have been developed, all of which have in common that they require algorithms for aligning a vast number of reads to genomic or transcriptomic sequences. Although the FM-index based aligner Bowtie has become a de facto standard within mapping pipelines, a much larger number of possible alignment algorithms have been developed also including other variants of FM-index based aligners. Accordingly, developers and users of RNA-seq mapping pipelines have the choice among a large number of available alignment algorithms. To provide guidance in the choice of alignment algorithms for these purposes, we evaluated the performance of 14 widely used alignment programs from three different algorithmic classes: algorithms using either hashing of the reference transcriptome, hashing of reads, or a compressed FM-index representation of the genome. Here, special emphasis was placed on both precision and recall and the performance for different read lengths and numbers of mismatches and indels in a read. Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete

Particle Image Velocimetry Design & Installation

This work will mainly focus on the design, construction, and installation of the Particle Image Velocimetry (PIV) system in the Chemical Hazards Research Center wind tunnel. The PIV system utilizes a Class IV (double pulsed) laser, optics to produce a light sheet, timing circuitry, and a high-resolution camera (with buffered output) to measure a system’s velocity (two-dimensional) field by determining the displacement of particles over the time between laser pulses. For maximum mobility and functionality, the PIV system was installed in the center of the tunnel on a moveable cart with the laser and camera mounted to an adjustable support. The instrument support will allow for a variety of obstacle configurations to be studied. Based on the conditions during a recent set of field dispersion trials, basic experiments were performed to demonstrate the viability and versatility of the system. These experiments discussed here consider the fluid dynamics directly behind three different (model) CONEX containers

Development and optimization of a miniaturized western blot-based screening platform to identify regulators of post-translational modifications

Post-translational modifications (PTMs) are fundamental traits of protein functionality and their study has been addressed using several approaches over the past years. However, screening methods developed to detect regulators of PTMs imply many challenges and are usually based on expensive techniques. Herein, we described the development and optimization of a western blot-based platform for identification of regulators of a specific PTM—mono-ubiquitylation of proliferating cell nuclear antigen (PCNA). This cell-based method does not require specific equipment, apart from the basic western blot (WB) devices and minor accessories, which are accessible for most research labs. The modifications introduced to the classical WB protocol allow the performance of PTM analysis from a single well of a 96-well plate with minimal sample manipulation and low intra- and inter-plate variability, making this method ideal to screen arrayed compound libraries in a 96-well format. As such, our experimental pipeline provides the proof of concept to design small screenings of PTM regulators by improving the quantitative accuracy and throughput capacity of classical western blots.Fil: Villafañez, Florencia. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentina. Universidad Nacional de Córdoba; ArgentinaFil: Gottifredi, Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Soria, Ramiro Gaston. Universidad Nacional de Córdoba; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Centro de Investigaciones en Bioquímica Clínica e Inmunología; Argentin

On the use of testability measures for dependability assessment

Program “testability” is informally, the probability that a program will fail under test if it contains at least one fault. When a dependability assessment has to be derived from the observation of a series of failure free test executions (a common need for software subject to “ultra high reliability” requirements), measures of testability can-in theory-be used to draw inferences on program correctness. We rigorously investigate the concept of testability and its use in dependability assessment, criticizing, and improving on, previously published results. We give a general descriptive model of program execution and testing, on which the different measures of interest can be defined. We propose a more precise definition of program testability than that given by other authors, and discuss how to increase testing effectiveness without impairing program reliability in operation. We then study the mathematics of using testability to estimate, from test results: the probability of program correctness and the probability of failures. To derive the probability of program correctness, we use a Bayesian inference procedure and argue that this is more useful than deriving a classical “confidence level”. We also show that a high testability is not an unconditionally desirable property for a program. In particular, for programs complex enough that they are unlikely to be completely fault free, increasing testability may produce a program which will be less trustworthy, even after successful testin

NPEFix: Automatic Runtime Repair of Null Pointer Exceptions in Java

Null pointer exceptions, also known as null dereferences are the number one exceptions in the field. In this paper, we propose 9 alternative execution semantics when a null pointer exception is about to happen. We implement those alternative execution strategies using code transformation in a tool called NPEfix. We evaluate our prototype implementation on 11 field null dereference bugs and 519 seeded failures and show that NPEfix is able to repair at runtime 10/11 and 318/519 failures

Modeling software design diversity

Design diversity has been used for many years now as a means of achieving a degree of fault tolerance in software-based systems. Whilst there is clear evidence that the approach can be expected to deliver some increase in reliability compared with a single version, there is not agreement about the extent of this. More importantly, it remains difficult to evaluate exactly how reliable a particular diverse fault-tolerant system is. This difficulty arises because assumptions of independence of failures between different versions have been shown not to be tenable: assessment of the actual level of dependence present is therefore needed, and this is hard. In this tutorial we survey the modelling issues here, with an emphasis upon the impact these have upon the problem of assessing the reliability of fault tolerant systems. The intended audience is one of designers, assessors and project managers with only a basic knowledge of probabilities, as well as reliability experts without detailed knowledge of software, who seek an introduction to the probabilistic issues in decisions about design diversity