35,439 research outputs found
Adaptive just-in-time code diversification
We present a method to regenerate diversified code dynamically in a Java bytecode JIT compiler, and to update the diversification frequently during the execution of the program. This way, we can significantly reduce the time frame in which attackers can let a program leak useful address space information and subsequently use the leaked information in memory exploits. A proof of concept implementation is evaluated, showing that even though code is recompiled frequently, we can achieved smaller overheads than the previous state of the art, which generated diversity only once during the whole execution of a program
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Combinatorial optimization and metaheuristics
Today, combinatorial optimization is one of the youngest and most active areas of discrete mathematics. It is a branch of optimization in applied mathematics and computer science, related to operational research, algorithm theory and computational complexity theory. It sits at the intersection of several fields, including artificial intelligence, mathematics and software engineering. Its increasing interest arises for the fact that a large number of scientific and industrial problems can be formulated as abstract combinatorial optimization problems, through graphs and/or (integer) linear programs. Some of these problems have polynomial-time (“efficient”) algorithms, while most of them are NP-hard, i.e. it is not proved that they can be solved in polynomial-time. Mainly, it means that it is not possible to guarantee that an exact solution to the problem can be found and one has to settle for an approximate solution with known performance guarantees. Indeed, the goal of approximate methods is to find “quickly” (reasonable run-times), with “high” probability, provable “good” solutions (low error from the real optimal solution). In the last 20 years, a new kind of algorithm commonly called metaheuristics have emerged in this class, which basically try to combine heuristics in high level frameworks aimed at efficiently and effectively exploring the search space. This report briefly outlines the components, concepts, advantages and disadvantages of different metaheuristic approaches from a conceptual point of view, in order to analyze their similarities and differences. The two very significant forces of intensification and diversification, that mainly determine the behavior of a metaheuristic, will be pointed out. The report concludes by exploring the importance of hybridization and integration methods
Phylogenetic and phenotypic divergence of an insular radiation of birds
Evolutionary divergence of lineages is one of the key mechanisms underpinning large scale
patterns in biogeography and biodiversity. Island systems have been highly influential in shaping
theories of evolutionary diversification and here I use the insular Zosteropidae of the south west
Pacific to investigate the roles of ecology and biogeography in promoting evolutionary
divergence.
Initially I build a phylogenetic tree of the study group and use it to reveal the pattern of
colonisation and diversification. My results suggest a complex history of dispersal with the
observed pattern most likely a result of repeated bouts of colonisation and extinction. I then use
the new phylogeny to quantify the diversification rates of the Zosteropidae. I find a very high rate
of lineage divergence and suggest the most likely explanation relates to extensive niche
availability in the south west Pacific. I also find evidence for an overall slowdown in diversification
combined with repeated bursts of accelerated speciation, consistent with a model of taxon
cycles. I do not find evidence for sympatric speciation, however. Finally I combine morphological
and phylogenetic data to investigate the mode of evolution, evidence for character displacement
and influence of biogeography on trait evolution. I find little support for the traditional theory of
character displacement in sympatric species. I do, however, find some support for biogeographic
theories.
Taken together my results do not support traditional theories on the ecological and
biogeographical basis of divergence, even in those cases where Zosterops have been used as
exemplars. This appears to be because those theories assume rather simple patterns of
colonisation and a static ecological system. Instead, my results suggest that evolutionary
diversification is dominated by recurrent waves of colonisation and extinction, which, viewed at
any particular moment, tend to obscure any underlying ecological rules
Trade-offs drive resource specialization and the gradual establishment of ecotypes
Speciation is driven by many different factors. Among those are trade-offs
between different ways an organism utilizes resources, and these trade-offs can
constrain the manner in which selection can optimize traits. Limited migration
among allopatric populations and species interactions can also drive
speciation, but here we ask if trade-offs alone are sufficient to drive
speciation in the absence of other factors. We present a model to study the
effects of trade-offs on specialization and adaptive radiation in asexual
organisms based solely on competition for limiting resources, where trade-offs
are stronger the greater an organism's ability to utilize resources. In this
model resources are perfectly substitutable, and fitness is derived from the
consumption of these resources. The model contains no spatial parameters, and
is therefore strictly sympatric. We quantify the degree of specialization by
the number of ecotypes formed and the niche breadth of the population, and
observe that these are sensitive to resource influx and trade-offs. Resource
influx has a strong effect on the degree of specialization, with a clear
transition between minimal diversification at high influx and multiple species
evolving at low resource influx. At low resource influx the degree of
specialization further depends on the strength of the trade-offs, with more
ecotypes evolving the stronger trade-offs are. The specialized organisms
persist through negative frequency-dependent selection. In addition, by
analyzing one of the evolutionary radiations in greater detail we demonstrate
that a single mutation alone is not enough to establish a new ecotype, even
though phylogenetic reconstruction identifies that mutation as the branching
point. Instead, it takes a series of additional mutations to ensure the stable
coexistence of the new ecotype in the background of the existing ones,
reminiscent of a recent observaComment: 19 pages, 3 figure
Parallel local search for solving Constraint Problems on the Cell Broadband Engine (Preliminary Results)
We explore the use of the Cell Broadband Engine (Cell/BE for short) for
combinatorial optimization applications: we present a parallel version of a
constraint-based local search algorithm that has been implemented on a
multiprocessor BladeCenter machine with twin Cell/BE processors (total of 16
SPUs per blade). This algorithm was chosen because it fits very well the
Cell/BE architecture and requires neither shared memory nor communication
between processors, while retaining a compact memory footprint. We study the
performance on several large optimization benchmarks and show that this
achieves mostly linear time speedups, even sometimes super-linear. This is
possible because the parallel implementation might explore simultaneously
different parts of the search space and therefore converge faster towards the
best sub-space and thus towards a solution. Besides getting speedups, the
resulting times exhibit a much smaller variance, which benefits applications
where a timely reply is critical
Bifurcation into functional niches in adaptation
One of the central questions in evolutionary biology concerns the dynamics of adaptation and diversification. This issue can be addressed experimentally if replicate populations adapting to identical environments Call be investigated in detail. We have studied 501 such replicas Using digital organisms adapting to at least two fundamentally different functional niches (survival strategies) present in the same environment: one in which fast replication is the way to live, and another where exploitation of the environment's complexity leads to complex organisms with longer life spans and smaller replication rates. While these two modes of survival are closely analogous to those expected to emerge in so-called r and K selection scenarios respectively, the bifurcation of evolutionary histories according to these functional niches occurs in identical environments, under identical selective pressures. We find that the branching occurs early, and leads to drastic phenotypic differences (in fitness, sequence length, and gestation time) that are permanent and irreversible. This study confirms an earlier experimental effort using microorganisms, in that diversification can be understood at least in part in terms of bifurcations on saddle points leading to peak shifts, as in the picture drawn by Sewall Wright
Repeated Evolution of Digital Adhesion in Geckos: A Reply to Harrington and Reeder
We published a phylogenetic comparative analysis that found geckos had gained and lost adhesive toepads multiple times over their long evolutionary history (Gamble et al., PLoS One, 7, 2012, e39429). This was consistent with decades of morphological studies showing geckos had evolved adhesive toepads on multiple occasions and that the morphology of geckos with ancestrally padless digits can be distinguished from secondarily padless forms. Recently, Harrington & Reeder (J. Evol. Biol., 30, 2017, 313) reanalysed data from Gamble et al. (PLoS One, 7, 2012, e39429) and found little support for the multiple origins hypothesis. Here, we argue that Harrington and Reeder failed to take morphological evidence into account when devising ancestral state reconstruction models and that these biologically unrealistic models led to erroneous conclusions about the evolution of adhesive toepads in geckos
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