121,035 research outputs found
Abstract State Machines 1988-1998: Commented ASM Bibliography
An annotated bibliography of papers which deal with or use Abstract State
Machines (ASMs), as of January 1998.Comment: Also maintained as a BibTeX file at http://www.eecs.umich.edu/gasm
Static Safety for an Actor Dedicated Process Calculus by Abstract Interpretation
The actor model eases the definition of concurrent programs with non uniform
behaviors. Static analysis of such a model was previously done in a data-flow
oriented way, with type systems. This approach was based on constraint set
resolution and was not able to deal with precise properties for communications
of behaviors. We present here a new approach, control-flow oriented, based on
the abstract interpretation framework, able to deal with communication of
behaviors. Within our new analyses, we are able to verify most of the previous
properties we observed as well as new ones, principally based on occurrence
counting
What's unusual in online disease outbreak news?
Background: Accurate and timely detection of public health events of
international concern is necessary to help support risk assessment and response
and save lives. Novel event-based methods that use the World Wide Web as a
signal source offer potential to extend health surveillance into areas where
traditional indicator networks are lacking. In this paper we address the issue
of systematically evaluating online health news to support automatic alerting
using daily disease-country counts text mined from real world data using
BioCaster. For 18 data sets produced by BioCaster, we compare 5 aberration
detection algorithms (EARS C2, C3, W2, F-statistic and EWMA) for performance
against expert moderated ProMED-mail postings. Results: We report sensitivity,
specificity, positive predictive value (PPV), negative predictive value (NPV),
mean alerts/100 days and F1, at 95% confidence interval (CI) for 287
ProMED-mail postings on 18 outbreaks across 14 countries over a 366 day period.
Results indicate that W2 had the best F1 with a slight benefit for day of week
effect over C2. In drill down analysis we indicate issues arising from the
granular choice of country-level modeling, sudden drops in reporting due to day
of week effects and reporting bias. Automatic alerting has been implemented in
BioCaster available from http://born.nii.ac.jp. Conclusions: Online health news
alerts have the potential to enhance manual analytical methods by increasing
throughput, timeliness and detection rates. Systematic evaluation of health
news aberrations is necessary to push forward our understanding of the complex
relationship between news report volumes and case numbers and to select the
best performing features and algorithms
Experimental Biological Protocols with Formal Semantics
Both experimental and computational biology is becoming increasingly
automated. Laboratory experiments are now performed automatically on
high-throughput machinery, while computational models are synthesized or
inferred automatically from data. However, integration between automated tasks
in the process of biological discovery is still lacking, largely due to
incompatible or missing formal representations. While theories are expressed
formally as computational models, existing languages for encoding and
automating experimental protocols often lack formal semantics. This makes it
challenging to extract novel understanding by identifying when theory and
experimental evidence disagree due to errors in the models or the protocols
used to validate them. To address this, we formalize the syntax of a core
protocol language, which provides a unified description for the models of
biochemical systems being experimented on, together with the discrete events
representing the liquid-handling steps of biological protocols. We present both
a deterministic and a stochastic semantics to this language, both defined in
terms of hybrid processes. In particular, the stochastic semantics captures
uncertainties in equipment tolerances, making it a suitable tool for both
experimental and computational biologists. We illustrate how the proposed
protocol language can be used for automated verification and synthesis of
laboratory experiments on case studies from the fields of chemistry and
molecular programming
Mechanized semantics
The goal of this lecture is to show how modern theorem provers---in this
case, the Coq proof assistant---can be used to mechanize the specification of
programming languages and their semantics, and to reason over individual
programs and over generic program transformations, as typically found in
compilers. The topics covered include: operational semantics (small-step,
big-step, definitional interpreters); a simple form of denotational semantics;
axiomatic semantics and Hoare logic; generation of verification conditions,
with application to program proof; compilation to virtual machine code and its
proof of correctness; an example of an optimizing program transformation (dead
code elimination) and its proof of correctness
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