Automating Program Verification and Repair Using Invariant Analysis and Test Input Generation

Software bugs are a persistent feature of daily life---crashing web browsers, allowing cyberattacks, and distorting the results of scientific computations. One approach to improving software uses program invariants---mathematical descriptions of program behaviors---to verify code and detect bugs. Current invariant generation techniques lack support for complex yet important forms of invariants, such as general polynomial relations and properties of arrays. As a result, we lack the ability to conduct precise analysis of programs that use this common data structure. This dissertation presents DIG, a static and dynamic analysis framework for discovering several useful classes of program invariants, including (i) nonlinear polynomial relations, which are fundamental to many scientific applications; disjunctive invariants, (ii) which express branching behaviors in programs; and (iii) properties about multidimensional arrays, which appear in many practical applications. We describe theoretical and empirical results showing that DIG can efficiently and accurately find many important invariants in real-world uses, e.g., polynomial properties in numerical algorithms and array relations in a full AES encryption implementation. Automatic program verification and synthesis are long-standing problems in computer science. However, there has been a lot of work on program verification and less so on program synthesis. Consequently, important synthesis tasks, e.g., generating program repairs, remain difficult and time-consuming. This dissertation proves that certain formulations of verification and synthesis are equivalent, allowing for direct applications of techniques and tools between these two research areas. Based on these ideas, we develop CETI, a tool that leverages existing verification techniques and tools for automatic program repair. Experimental results show that CETI can have higher success rates than many other standard program repair methods

Density-dependent effects on the weight of female Ascaris lumbricoides infections of humans and its impact on patterns of egg production

<p>Abstract</p> <p>Background</p> <p><it>Ascaris lumbricoides </it>exhibits density-dependent egg production, a process which has a marked impact on both the transmission dynamics and the stability of the parasite population. Evidence suggests that the egg production of female <it>Ascaris </it>is also associated with the size of the worm. If worm size is mediated by density-dependent processes then the size of female worms may have a causal impact upon patterns of <it>Ascaris </it>egg production.</p> <p>Results</p> <p>We analyse data collected from a cohort of human hosts, and demonstrate that the per host mean weight (a proxy for size) of female <it>Ascaris </it>is dependent on the number of infecting females (worm burden) following a pattern of initial facilitation followed by limitation. Applying a negative binomial (NB) generalized linear model (GLM) and a zero-inflated negative binomial (ZINB) model we confirm that the per host female mean weight is significantly associated with per host egg production. Despite these associations, the mean weight of female <it>Ascaris </it>has little causal impact on patterns of density-dependent egg output. The ZINB model is able to account for the disproportionately large number of zero egg counts within the data and is shown to be a consistently better fit than the NB model. The probability of observing a zero egg count is demonstrated as being negatively associated with both female worm burden and female mean weight.</p> <p>Conclusion</p> <p>The mean weight of female <it>Ascaris </it>is statistically significantly associated with egg output, and follows a consistent pattern of facilitation preceding limitation with increasing female worm burden. Despite these relationships, incorporation of female <it>Ascaris </it>mean weight into models of egg output has little effect on patterns of density dependence. The ZINB model is a superior fit to the data than the NB model and provides additional information regarding the mechanisms that result in a zero egg count. The ZINB model is shown to be a useful tool for the analysis of individual-based egg output data.</p

Data Requirements for Developing Growth Models for Tropical Moist Forests

Permanent sample plots provide the basis for growth modelling, yield prediction and sustained yield management, and the reliability of the data is crucial to these and many other aspects of forest management. To obtain reliable data, it is necessary to ensure consistent standards and that a wide range of stand and site conditions are sampled using both passive monitoring and experimental plots. Individual trees should be numbered, marked and mapped. Remeasurement frequency should be determined to facilitate plot relocation and ensure that growth is greater than measurement errors. Measurement records should be unambiguous and secure

2013 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

URC Schedule and Abstract Book for the Fifth Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: November 16-17, 2013Plenary Speaker: Mariel Vazquez, Associate Professor of Mathematics at San Francisco State UniversityFeatured Speaker: Andrew Liebhold, Research Entomologist for the USDA Forest Servic

Nondestructive evaluation of wood properties by stress wave spectral analysis

The influence of selected properties on the propagation of stress waves in wood was investigated. Waveform analysis of the stress waves was performed using spectral analysis techhniques developed for stationary random processes. Information analyzed from the stress waves included wave velocity, energy spectra, and the frequency response function. Three wood properties investigated as to their influence on stress waves propagation were grain angle, moisture content, and weight loss caused by decay. Significant relationships between grain angle and the wave properties of velocity, amplitude gain, and total gain were obtained. Significant damping of the stress waves was observed at large grain angles and moisture content values above the fiber saturation point. No significant equations were found for consistent prediction of moisture content. The results of the decay study showed that as weight loss increased, the ratio of energy of the stress wave to that input to the specimen decreased for the perpendicular to grain case. Two approaches toward prediction of wood strength were investigated. The first method employed prediction of wood properties from the stress wave spectral characteristics. Known relationships between these wood properties and strength were then utilized. The second approach involved direct correlation of the stress wave spectral properties with strength. Significant correlatlons with strength were obtained using both approaches. Application of basic results are discussed as to their applicability toward development of an [sic] nondestructive evaluatlon (NOE) procedure for wood poles used in transmission line structures