9,403 research outputs found
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
`The frozen accident' as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks. The approach to most of these questions involves using elements of Shannon's rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure in proteins. This leads to the suggestion that the frozen accident may have been a type of evolutionary adaptation
Synchronous Counting and Computational Algorithm Design
Consider a complete communication network on nodes, each of which is a
state machine. In synchronous 2-counting, the nodes receive a common clock
pulse and they have to agree on which pulses are "odd" and which are "even". We
require that the solution is self-stabilising (reaching the correct operation
from any initial state) and it tolerates Byzantine failures (nodes that
send arbitrary misinformation). Prior algorithms are expensive to implement in
hardware: they require a source of random bits or a large number of states.
This work consists of two parts. In the first part, we use computational
techniques (often known as synthesis) to construct very compact deterministic
algorithms for the first non-trivial case of . While no algorithm exists
for , we show that as few as 3 states per node are sufficient for all
values . Moreover, the problem cannot be solved with only 2 states per
node for , but there is a 2-state solution for all values .
In the second part, we develop and compare two different approaches for
synthesising synchronous counting algorithms. Both approaches are based on
casting the synthesis problem as a propositional satisfiability (SAT) problem
and employing modern SAT-solvers. The difference lies in how to solve the SAT
problem: either in a direct fashion, or incrementally within a counter-example
guided abstraction refinement loop. Empirical results suggest that the former
technique is more efficient if we want to synthesise time-optimal algorithms,
while the latter technique discovers non-optimal algorithms more quickly.Comment: 35 pages, extended and revised versio
Partition MCMC for inference on acyclic digraphs
Acyclic digraphs are the underlying representation of Bayesian networks, a
widely used class of probabilistic graphical models. Learning the underlying
graph from data is a way of gaining insights about the structural properties of
a domain. Structure learning forms one of the inference challenges of
statistical graphical models.
MCMC methods, notably structure MCMC, to sample graphs from the posterior
distribution given the data are probably the only viable option for Bayesian
model averaging. Score modularity and restrictions on the number of parents of
each node allow the graphs to be grouped into larger collections, which can be
scored as a whole to improve the chain's convergence. Current examples of
algorithms taking advantage of grouping are the biased order MCMC, which acts
on the alternative space of permuted triangular matrices, and non ergodic edge
reversal moves.
Here we propose a novel algorithm, which employs the underlying combinatorial
structure of DAGs to define a new grouping. As a result convergence is improved
compared to structure MCMC, while still retaining the property of producing an
unbiased sample. Finally the method can be combined with edge reversal moves to
improve the sampler further.Comment: Revised version. 34 pages, 16 figures. R code available at
https://github.com/annlia/partitionMCM
Dagstuhl Reports : Volume 1, Issue 2, February 2011
Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-HĂŒbner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro PezzĂ©, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn
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