Bug Code Research Articles

Jeu de mots paronomasia: a StackOverflow-driven bug discovery approach

Locating bug code snippets (short for BugCode) has been a complex problem throughout the history of software security, mainly because the constraints that define BugCode are obscure and hard to summarize. Previously, security analysts attempted to define such constraints manually (e.g., limiting buffer size to detect overflow), but were limited to the types of BugCode. Recent researchers address this problem by extracting constraints from program documentation, which shows the potential for API misuse. But for bugs beyond the scope of API misuse, such an approach becomes less effective since the corresponding constraints are not defined in documents, not to mention the programs without documentation In this paper, inspired by the fact that expert programmers often correct the BugCode on open forums such as StackOverflow, we design an approach to automatically extract knowledge from StackOverflow and leverage it to detect BugCode. As we all know, the contexts in StackOverflow come from ordinary developers. Their writing tends to be loosely organized and in various styles, which are more challenging to analyze than program documentation. To address the challenges, we design a custom tokenization approach to segment sentences and employ sentiment analysis to find the Controversial Sentences (CSs) that typically contain the constraints we need for code analysis. Then we use constituency parsing to extract knowledge from CSs, which helps locate BugCode. We evaluated our system on 41,144 comments from the questions tagged with Java and Android. The results show that our approach achieves 95.5% precision in discovering CSs. We have discovered 276 pieces of BugCode proved to be true through manual validation including an assigned CVE. 89.3% of the discovered bugs remained in the current version of answers, which are unknown to users.

BIKE: Dietary Exposure Model for Foodborne Microbiological and Chemical Hazards.

BIKE is a Bayesian dietary exposure assessment model for microbiological and chemical hazards. A graphical user interface was developed for running the model and inspecting the results. It is based on connected Bayesian hierarchical models, utilizing OpenBUGS and R in tandem. According to occurrence and consumption data given as inputs, a specific BUGS code is automatically written for running the Bayesian model in the background. The user interface is based on shiny app. Chronic and acute exposures are estimated for chemical and microbiological hazards, respectively. Uncertainty and variability in exposures are visualized, and a few optional model structures can be used. Simulated synthetic data are provided with BIKE for an example, resembling real occurrence and consumption data. BIKE is open source and available from github.

A Bayesian approach to estimating variance components within a multivariate generalizability theory framework.

In many behavioral research areas, multivariate generalizability theory (mG theory) has been typically used to investigate the reliability of certain multidimensional assessments. However, traditional mG-theory estimation-namely, using frequentist approaches-has limits, leading researchers to fail to take full advantage of the information that mG theory can offer regarding the reliability of measurements. Alternatively, Bayesian methods provide more information than frequentist approaches can offer. This article presents instructional guidelines on how to implement mG-theory analyses in a Bayesian framework; in particular, BUGS code is presented to fit commonly seen designs from mG theory, including single-facet designs, two-facet crossed designs, and two-facet nested designs. In addition to concrete examples that are closely related to the selected designs and the corresponding BUGS code, a simulated dataset is provided to demonstrate the utility and advantages of the Bayesian approach. This article is intended to serve as a tutorial reference for applied researchers and methodologists conducting mG-theory studies.

Modeling false positive detections in species occurrence data under different study designs.

The occurrence of false positive detections in presence-absence data, even when they occur infrequently, can lead to severe bias when estimating species occupancy patterns. Building upon previous efforts to account for this source of observational error, we established a general framework to model false positives in occupancy studies and extend existing modeling approaches to encompass a broader range of sampling designs. Specifically, we identified three common sampling designs that are likely to cover most scenarios encountered by researchers. The different designs all included ambiguous detections, as well as some known-truth data, but their modeling differed in the level of the model hierarchy at which the known-truth information was incorporated (site level or observation level). For each model, we provide the likelihood, as well as R and BUGS code needed for implementation. We also establish a clear terminology and provide guidance to help choosing the most appropriate design and modeling approach.

A Comparison of Imputation Methods for Bayesian Factor Analysis Models

Imputation methods are popular for the handling of missing data in psychology. The methods generally consist of predicting missing data based on observed data, yielding a complete data set that is amiable to standard statistical analyses. In the context of Bayesian factor analysis, this article compares imputation under an unrestricted multivariate normal model (Multiple Imputation [MI]) to imputation under the statistical model of interest (Data Augmentation [DA]). The former method is popular in applied research, but the latter method is more straightforward from a Bayesian perspective. Simulations demonstrate that DA yields less-biased parameter estimates for moderate sample sizes and high missingness proportions. MI, however, yields less-biased parameter estimates for large sample sizes with misspecified models. The incorporation of auxiliary variables in DA is also addressed, and BUGS code is provided.

BUGSCode for Item Response Theory

I present BUGS code to fit common models from item response theory (IRT), such as the two parameter logistic model, three parameter logisitic model, graded response model, generalized partial credit model, testlet model, and generalized testlet models. I demonstrate how the code in this article can easily be extended to fit more complicated IRT models, when the data at hand require a more sophisticated approach. Specifically, I describe modifications to the BUGS code that accommodate longitudinal item response data.

Bayesian Animal Survival Estimation

We present the Bayesian approach to estimating parameters associated with animal survival on the basis of data arising from mark recovery and recapture studies. We provide two examples, beginning with a discussion of band-return models and examining data gathered from observations of blue winged teal (Aas discors), ringed as nestlings. We then look at open population recapture models, focusing on the Cormack- Jolly-Seber model, and examine this model in the context of a data set on European dippers (Cinclus cinclus). The Bayesian procedures are shown to be straightforward and provide a convenient framework for model-averaging, which incorporates the uncertainty due to model selection into the inference process. Sufficient detail is provided so that readers who wish to employ the Bayesian approach in this field can do so with ease. An example of BUGS code is also provided.

Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference

Introduction Stochastic simulation Introduction Generation of Discrete Random Quantities Generation of Continuous Random Quantities Generation of Random Vectors and Matrices Resampling Methods Exercises Bayesian Inference Introduction Bayes' Theorem Conjugate Distributions Hierarchical Models Dynamic Models Spatial Models Model Comparison Exercises Approximate methods of inference Introduction Asymptotic Approximations Approximations by Gaussian Quadrature Monte Carlo Integration Methods Based on Stochastic Simulation Exercises Markov chains Introduction Definition and Transition Probabilities Decomposition of the State Space Stationary Distributions Limiting Theorems Reversible Chains Continuous State Spaces Simulation of a Markov Chain Data Augmentation or Substitution Sampling Exercises Gibbs Sampling Introduction Definition and Properties Implementation and Optimization Convergence Diagnostics Applications MCMC-Based Software for Bayesian Modeling Appendix 5.A: BUGS Code for Example 5.7 Appendix 5.B: BUGS Code for Example 5.8 Exercises Metropolis-Hastings algorithms Introduction Definition and Properties Special Cases Hybrid Algorithms Applications Exercises Further topics in MCMC Introduction Model Adequacy Model Choice: MCMC Over Model and Parameter Spaces Convergence Acceleration Exercises References Author Index Subject Index

Analysing the relationship between treatment effect and underlying risk in meta-analysis: comparison and development of approaches

Three approaches for estimating the relationship between treatment effect and underlying risk in a meta-analysis of clinical trials have recently been published. The aim of each is to overcome the bias inherent in conventional regressions of treatment effect on control group risk, which arises from the measurement error in the observed control group risks in different trials. Here we describe these published approaches, and compare them with respect to their underlying models and methods of implementation. The underlying model for one of them is shown to be seriously flawed, while the other two are both statistically more appropriate than the conventional approaches, and differ from each other in only two assumptions. Both may be implemented using the Gibbs sampling algorithm in BUGS, and are exemplified here using a meta-analysis of mortality and bleeding data in trials of sclerotherapy for patients with cirrhosis. One approach is developed further; for the illustrative example considered, it is shown to be robust to different choices of prior distributions for the model parameters, and to the assumption of a linear relationship on a log-odds scale. It can also be used to estimate the level of underlying risk (and its standard error) at which the treatment effect crosses from benefit to harm, and other trial-level covariates may be included in the model as confounders. The BUGS code is provided in an Appendix, to enable applied researchers to perform the various analyses described.