4,181 research outputs found
Lifted Variable Elimination for Probabilistic Logic Programming
Lifted inference has been proposed for various probabilistic logical
frameworks in order to compute the probability of queries in a time that
depends on the size of the domains of the random variables rather than the
number of instances. Even if various authors have underlined its importance for
probabilistic logic programming (PLP), lifted inference has been applied up to
now only to relational languages outside of logic programming. In this paper we
adapt Generalized Counting First Order Variable Elimination (GC-FOVE) to the
problem of computing the probability of queries to probabilistic logic programs
under the distribution semantics. In particular, we extend the Prolog Factor
Language (PFL) to include two new types of factors that are needed for
representing ProbLog programs. These factors take into account the existing
causal independence relationships among random variables and are managed by the
extension to variable elimination proposed by Zhang and Poole for dealing with
convergent variables and heterogeneous factors. Two new operators are added to
GC-FOVE for treating heterogeneous factors. The resulting algorithm, called
LP for Lifted Probabilistic Logic Programming, has been implemented by
modifying the PFL implementation of GC-FOVE and tested on three benchmarks for
lifted inference. A comparison with PITA and ProbLog2 shows the potential of
the approach.Comment: To appear in Theory and Practice of Logic Programming (TPLP). arXiv
admin note: text overlap with arXiv:1402.0565 by other author
The PITA System: Tabling and Answer Subsumption for Reasoning under Uncertainty
Many real world domains require the representation of a measure of
uncertainty. The most common such representation is probability, and the
combination of probability with logic programs has given rise to the field of
Probabilistic Logic Programming (PLP), leading to languages such as the
Independent Choice Logic, Logic Programs with Annotated Disjunctions (LPADs),
Problog, PRISM and others. These languages share a similar distribution
semantics, and methods have been devised to translate programs between these
languages. The complexity of computing the probability of queries to these
general PLP programs is very high due to the need to combine the probabilities
of explanations that may not be exclusive. As one alternative, the PRISM system
reduces the complexity of query answering by restricting the form of programs
it can evaluate. As an entirely different alternative, Possibilistic Logic
Programs adopt a simpler metric of uncertainty than probability. Each of these
approaches -- general PLP, restricted PLP, and Possibilistic Logic Programming
-- can be useful in different domains depending on the form of uncertainty to
be represented, on the form of programs needed to model problems, and on the
scale of the problems to be solved. In this paper, we show how the PITA system,
which originally supported the general PLP language of LPADs, can also
efficiently support restricted PLP and Possibilistic Logic Programs. PITA
relies on tabling with answer subsumption and consists of a transformation
along with an API for library functions that interface with answer subsumption
Towards Incremental Parsing of Natural Language using Recursive Neural Networks
In this paper we develop novel algorithmic ideas for building a natural language
parser grounded upon the hypothesis of incrementality. Although widely accepted
and experimentally supported under a cognitive perspective as a model of the human
parser, the incrementality assumption has never been exploited for building automatic
parsers of unconstrained real texts. The essentials of the hypothesis are that words are
processed in a left-to-right fashion, and the syntactic structure is kept totally connected
at each step.
Our proposal relies on a machine learning technique for predicting the correctness of
partial syntactic structures that are built during the parsing process. A recursive neural
network architecture is employed for computing predictions after a training phase on
examples drawn from a corpus of parsed sentences, the Penn Treebank. Our results
indicate the viability of the approach andlay out the premises for a novel generation of
algorithms for natural language processing which more closely model human parsing.
These algorithms may prove very useful in the development of eÆcient parsers
Logic-Based Decision Support for Strategic Environmental Assessment
Strategic Environmental Assessment is a procedure aimed at introducing
systematic assessment of the environmental effects of plans and programs. This
procedure is based on the so-called coaxial matrices that define dependencies
between plan activities (infrastructures, plants, resource extractions,
buildings, etc.) and positive and negative environmental impacts, and
dependencies between these impacts and environmental receptors. Up to now, this
procedure is manually implemented by environmental experts for checking the
environmental effects of a given plan or program, but it is never applied
during the plan/program construction. A decision support system, based on a
clear logic semantics, would be an invaluable tool not only in assessing a
single, already defined plan, but also during the planning process in order to
produce an optimized, environmentally assessed plan and to study possible
alternative scenarios. We propose two logic-based approaches to the problem,
one based on Constraint Logic Programming and one on Probabilistic Logic
Programming that could be, in the future, conveniently merged to exploit the
advantages of both. We test the proposed approaches on a real energy plan and
we discuss their limitations and advantages.Comment: 17 pages, 1 figure, 26th Int'l. Conference on Logic Programming
(ICLP'10
Chromatin dynamics of the developmentally regulated P. lividus neural alpha tubulin gene
Over 40 years ago, Allfrey and colleagues (1964) suggested that two histone modifications, namely acetylation and methylation, might regulate RNA synthesis. Nowadays it is universally accepted that activation of gene expression strictly depends on enzymatic mechanisms able to dynamically modify chromatin structure. Here, using techniques including DNaseI hypersensitive site analysis, chomatin immunoprecipitation and quantitative PCR analysis, we have analyzed the dynamics of histone post-translation modifications involved in developmentally/spatially controlled activation of the sea urchin PlTalpha2 tubulin gene. We have demonstrated that only when the PlTalpha2 core promoter chromatin is acetylated on H3K9, tri-methylated on H3K4 and not di-methylated on H3K27, RNA pol II can be enrolled. In contrast, we have shown that when chromatin is methylated both on H3K9 (me2/3) and H3K27 (me2) and mono methylated on H3K4 the promoter is not accessible to RNA pol II. Our results suggest that, during P. lividus embryogenesis, both HAT/HDAC and HMT/HDM activities, which are able to regulate accessibility of the PlTalpha2 basal promoter to RNA polymerase II, are coordinately switched-on
GraphProt: modeling binding preferences of RNA-binding proteins
We present GraphProt, a computational framework for learning sequence- and structure-binding preferences of RNA-binding proteins (RBPs) from high-throughput experimental data. We benchmark GraphProt, demonstrating that the modeled binding preferences conform to the literature, and showcase the biological relevance and two applications of GraphProt models. First, estimated binding affinities correlate with experimental measurements. Second, predicted Ago2 targets display higher levels of expression upon Ago2 knockdown, whereas control targets do not. Computational binding models, such as those provided by GraphProt, are essential for predicting RBP binding sites and affinities in all tissues. GraphProt is freely available at http://www.bioinf.uni-freiburg.de/Software/GraphProt
Quality Evaluation and Nonuniform Compression of Geometrically Distorted Images Using the Quadtree Distortion Map
The paper presents an analysis of the effects of lossy compression algorithms applied to images affected by geometrical distortion. It will be shown that the encoding-decoding process results in a nonhomogeneous image degradation in the geometrically corrected image, due to the different amount of information associated to each pixel. A distortion measure named quadtree distortion map (QDM) able to quantify this aspect is proposed. Furthermore, QDM is exploited to achieve adaptive compression of geometrically distorted pictures, in order to ensure a uniform quality on the final image. Tests are performed using JPEG and JPEG2000 coding standards in order to quantitatively and qualitatively assess the performance of the proposed method
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