979 research outputs found
Approximations from Anywhere and General Rough Sets
Not all approximations arise from information systems. The problem of fitting
approximations, subjected to some rules (and related data), to information
systems in a rough scheme of things is known as the \emph{inverse problem}. The
inverse problem is more general than the duality (or abstract representation)
problems and was introduced by the present author in her earlier papers. From
the practical perspective, a few (as opposed to one) theoretical frameworks may
be suitable for formulating the problem itself. \emph{Granular operator spaces}
have been recently introduced and investigated by the present author in her
recent work in the context of antichain based and dialectical semantics for
general rough sets. The nature of the inverse problem is examined from
number-theoretic and combinatorial perspectives in a higher order variant of
granular operator spaces and some necessary conditions are proved. The results
and the novel approach would be useful in a number of unsupervised and semi
supervised learning contexts and algorithms.Comment: 20 Pages. Scheduled to appear in IJCRS'2017 LNCS Proceedings,
Springe
A syntax for semantics in P-Lingua
P-Lingua is a software framework for Membrane Computing, it includes a
programming language, also called P-Lingua, for writting P system de nitions using a
syntax close to standard scienti c notation. The rst line of a P-Lingua le is an unique
identi er de ning the variant or model of P system to be used, i.e, the semantics of the
P system. Software tools based on P-Lingua use this identi er to select a simulation
algorithm implementing the corresponding derivation mode. Derivation modes de ne
how to obtain a con guration Ct+1 from a con guration Ct. This information is usually
hard-coded in the simulation algorithm.
The P system model also de nes what types or rules can be used, the P-Lingua
compiler uses the identi er to select an speci c parser for the le. In this case, a set of
parsers is codi ed within the compiler tool. One for each unique identi er.
P-Lingua has grown during the last 12 years, including more and more P system
models. From a software engineering point of view, this approximation implies a continous
development of the framework, leading to a monolithic software which is hard to debug
and maintain.
In this paper, we propose a new software approximation for the framework, including
a new syntax for de ning rule patterns and derivation modes. The P-Lingua users can
now de ne custom P system models instead of hard-coding them in the software. This
approximation leads to a more
exible solution which is easier to maintain and debug.
Moreover, users could de ne and play with new/experimental P system models
A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances
Spaced seeds have been recently shown to not only detect more alignments, but
also to give a more accurate measure of phylogenetic distances (Boden et al.,
2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower
misclassification rate when used with Support Vector Machines (SVMs) (On-odera
and Shibuya, 2013), We confirm by independent experiments these two results,
and propose in this article to use a coverage criterion (Benson and Mak, 2008,
Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both
cases in order to design better seed patterns. We show first how this coverage
criterion can be directly measured by a full automaton-based approach. We then
illustrate how this criterion performs when compared with two other criteria
frequently used, namely the single-hit and multiple-hit criteria, through
correlation coefficients with the correct classification/the true distance. At
the end, for alignment-free distances, we propose an extension by adopting the
coverage criterion, show how it performs, and indicate how it can be
efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017
A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances
Spaced seeds have been recently shown to not only detect more alignments, but
also to give a more accurate measure of phylogenetic distances (Boden et al.,
2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower
misclassification rate when used with Support Vector Machines (SVMs) (On-odera
and Shibuya, 2013), We confirm by independent experiments these two results,
and propose in this article to use a coverage criterion (Benson and Mak, 2008,
Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both
cases in order to design better seed patterns. We show first how this coverage
criterion can be directly measured by a full automaton-based approach. We then
illustrate how this criterion performs when compared with two other criteria
frequently used, namely the single-hit and multiple-hit criteria, through
correlation coefficients with the correct classification/the true distance. At
the end, for alignment-free distances, we propose an extension by adopting the
coverage criterion, show how it performs, and indicate how it can be
efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017
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