44,854 research outputs found
A Model to Estimate First-Order Mutation Coverage from Higher-Order Mutation Coverage
The test suite is essential for fault detection during software development.
First-order mutation coverage is an accurate metric to quantify the quality of
the test suite. However, it is computationally expensive. Hence, the adoption
of this metric is limited. In this study, we address this issue by proposing a
realistic model able to estimate first-order mutation coverage using only
higher-order mutation coverage. Our study shows how the estimation evolves
along with the order of mutation. We validate the model with an empirical study
based on 17 open-source projects.Comment: 2016 IEEE International Conference on Software Quality, Reliability,
and Security. 9 page
Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods
A number of studies have suggested using comparisons between DNA sequences of
closely related bacterial isolates to estimate the relative rate of
recombination to mutation for that bacterial species. We consider such an
approach which uses single-locus variants: pairs of isolates whose DNA differ
at a single gene locus. One way of deriving point estimates for the relative
rate of recombination to mutation from such data is to use composite likelihood
methods. We extend recent work in this area so as to be able to construct
confidence intervals for our estimates, without needing to resort to
computationally-intensive bootstrap procedures, and to develop a test for
whether the relative rate varies across loci. Both our test and method for
constructing confidence intervals are obtained by modeling the dependence
structure in the data, and then applying asymptotic theory regarding the
distribution of estimators obtained using a composite likelihood. We applied
these methods to multi-locus sequence typing (MLST) data from eight bacteria,
finding strong evidence for considerable rate variation in three of these:
Bacillus cereus, Enterococcus faecium and Klebsiella pneumoniae.Comment: Published at http://dx.doi.org/10.1214/14-AOAS795 in the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Predictions of the emergence of vaccine-resistant hepatitis B in The Gambia using a mathematical model
Vaccine escape variants of hepatitis B virus (HBV) have been identified world-wide. A mathematical model of HBV transmission is used to investigate the potential pattern of emergence of such variants. Attention is focused on The Gambia as a country with high quality epidemiological data, universal infant immunization and in which escape mutants after childhood infections have been observed. We predict that a variant cannot become dominant for at least 20 years from the start of vaccination, even when using a vaccine which affords no cross protection. The dominant factor responsible for this long time scale is the low rate of infectious contacts between infected and susceptible individuals (we estimate the basic reproduction number of hepatitis B in The Gambia to be 1·7). A variant strain that achieves high prevalence will also take many years to control, and it is questionable whether emergence will be identifiable by sero-surveillance until of high prevalence. The sensitivity of the model predictions to epidemiological and demographic factors is explored
Survival analysis of DNA mutation motifs with penalized proportional hazards
Antibodies, an essential part of our immune system, develop through an
intricate process to bind a wide array of pathogens. This process involves
randomly mutating DNA sequences encoding these antibodies to find variants with
improved binding, though mutations are not distributed uniformly across
sequence sites. Immunologists observe this nonuniformity to be consistent with
"mutation motifs", which are short DNA subsequences that affect how likely a
given site is to experience a mutation. Quantifying the effect of motifs on
mutation rates is challenging: a large number of possible motifs makes this
statistical problem high dimensional, while the unobserved history of the
mutation process leads to a nontrivial missing data problem. We introduce an
-penalized proportional hazards model to infer mutation motifs and
their effects. In order to estimate model parameters, our method uses a Monte
Carlo EM algorithm to marginalize over the unknown ordering of mutations. We
show that our method performs better on simulated data compared to current
methods and leads to more parsimonious models. The application of proportional
hazards to mutation processes is, to our knowledge, novel and formalizes the
current methods in a statistical framework that can be easily extended to
analyze the effect of other biological features on mutation rates
Predictions of the emergence of vaccine-resistant hepatitis B in The Gambia using a mathematical model
Vaccine escape variants of hepatitis B virus (HBV) have been identified world-wide. A mathematical model of HBV transmission is used to investigate the potential pattern of emergence of such variants. Attention is focused on The Gambia as a country with high quality epidemiological data, universal infant immunization and in which escape mutants after childhood infections have been observed. We predict that a variant cannot become dominant for at least 20 years from the start of vaccination, even when using a vaccine which affords no cross protection. The dominant factor responsible for this long time scale is the low rate of infectious contacts between infected and susceptible individuals (we estimate the basic reproduction number of hepatitis B in The Gambia to be 1·7). A variant strain that achieves high prevalence will also take many years to control, and it is questionable whether emergence will be identifiable by sero-surveillance until of high prevalence. The sensitivity of the model predictions to epidemiological and demographic factors is explored
LittleDarwin: a Feature-Rich and Extensible Mutation Testing Framework for Large and Complex Java Systems
Mutation testing is a well-studied method for increasing the quality of a
test suite. We designed LittleDarwin as a mutation testing framework able to
cope with large and complex Java software systems, while still being easily
extensible with new experimental components. LittleDarwin addresses two
existing problems in the domain of mutation testing: having a tool able to work
within an industrial setting, and yet, be open to extension for cutting edge
techniques provided by academia. LittleDarwin already offers higher-order
mutation, null type mutants, mutant sampling, manual mutation, and mutant
subsumption analysis. There is no tool today available with all these features
that is able to work with typical industrial software systems.Comment: Pre-proceedings of the 7th IPM International Conference on
Fundamentals of Software Engineerin
Bayesian co-estimation of selfing rate and locus-specific mutation rates for a partially selfing population
We present a Bayesian method for characterizing the mating system of
populations reproducing through a mixture of self-fertilization and random
outcrossing. Our method uses patterns of genetic variation across the genome as
a basis for inference about pure hermaphroditism, androdioecy, and gynodioecy.
We extend the standard coalescence model to accommodate these mating systems,
accounting explicitly for multilocus identity disequilibrium, inbreeding
depression, and variation in fertility among mating types. We incorporate the
Ewens Sampling Formula (ESF) under the infinite-alleles model of mutation to
obtain a novel expression for the likelihood of mating system parameters. Our
Markov chain Monte Carlo (MCMC) algorithm assigns locus-specific mutation
rates, drawn from a common mutation rate distribution that is itself estimated
from the data using a Dirichlet Process Prior (DPP) model. Among the parameters
jointly inferred are the population-wide rate of self-fertilization,
locus-specific mutation rates, and the number of generations since the most
recent outcrossing event for each sampled individual
The Progress, Challenges, and Perspectives of Directed Greybox Fuzzing
Most greybox fuzzing tools are coverage-guided as code coverage is strongly
correlated with bug coverage. However, since most covered codes may not contain
bugs, blindly extending code coverage is less efficient, especially for corner
cases. Unlike coverage-guided greybox fuzzers who extend code coverage in an
undirected manner, a directed greybox fuzzer spends most of its time allocation
on reaching specific targets (e.g., the bug-prone zone) without wasting
resources stressing unrelated parts. Thus, directed greybox fuzzing (DGF) is
particularly suitable for scenarios such as patch testing, bug reproduction,
and specialist bug hunting. This paper studies DGF from a broader view, which
takes into account not only the location-directed type that targets specific
code parts, but also the behaviour-directed type that aims to expose abnormal
program behaviours. Herein, the first in-depth study of DGF is made based on
the investigation of 32 state-of-the-art fuzzers (78% were published after
2019) that are closely related to DGF. A thorough assessment of the collected
tools is conducted so as to systemise recent progress in this field. Finally,
it summarises the challenges and provides perspectives for future research.Comment: 16 pages, 4 figure
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