Determining the underlying regulatory mechanism of genetic networks is one of the central challenges of computational biology. Numerous methods have been developed and applied to the important but complex task of reve...
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ISBN:
(纸本)9783540738466
Determining the underlying regulatory mechanism of genetic networks is one of the central challenges of computational biology. Numerous methods have been developed and applied to the important but complex task of reverse engineering regulatory networks from high-throughput gene expression data. However, many challenges remain. In this paper, we are interested in learning rules that will reveal the causal genes for the expression variation from various relational data sources in addition to gene expression data. Following our previous work where we showed that time series gene expression data could potentially uncover causal effects, we describe an application of an inductivelogicprogramming (ILP) system, to the task of identifying important regulatory relationships from discretized time series gene expression data, protein-protein interaction, protein phosphorylation and transcription factor data about the organism. Specifically, we learn rules for predicting gene expression levels at the next time step based on the available relational data and then generalize the learned theory to visualize a pruned network of important interactions. We evaluate and present experimental results on microarray experiments from Gasch et al on Saccharomyces cerevisiae.
OFDM Wireless LANs based on the IEEE 802.11 standard are complex systems in themselves. When smart antennas are used in such systems, boththe MAC and the PHY layers must be redefined in order to achieve application-s...
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ISBN:
(纸本)9781424412501
OFDM Wireless LANs based on the IEEE 802.11 standard are complex systems in themselves. When smart antennas are used in such systems, boththe MAC and the PHY layers must be redefined in order to achieve application-specific goals. As a result, the development of such systems can become impressively heavy. A complete development framework is presented here. It makes use of hardware/software codesign in order to implement all required layers to develop a wireless access point. the entire framework is targeted at an FPGA platform, providing full flexibility and processing power for the development of PHY layers.
A consequence of ILP systems being implemented in Prolog or using Prolog libraries is that, usually, these systems use a Prolog internal database to store and manipulate data. However, in real-world problems, the orig...
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ISBN:
(纸本)9783540738466
A consequence of ILP systems being implemented in Prolog or using Prolog libraries is that, usually, these systems use a Prolog internal database to store and manipulate data. However, in real-world problems, the original data is rarely in Prolog format. In fact, the data is often kept in Relational Database Management Systems (RDBMS) and then converted to a format acceptable by the ILP system. therefore, a more interesting approach is to link the ILP system to the RDBMS and manipulate the data without converting it. this scheme has the advantage of being more scalable since the whole data does not need to be loaded into memory by the ILP system. In this paper we study several approaches of coupling ILP systems with RDBMS systems and evaluate their impact on performance. We propose to use a Deductive Database (DDB) system to transparently translate the hypotheses to relational algebra expressions. the empirical evaluation performed shows that the execution time of ILP algorithms can be effectively reduced using a DDB and that the size of the problems can be increased due to a non-memory storage of the data.
Here we present the logic-programming language XCentric, discuss design issues, and show its adequacy for XML processing. Distinctive features of XCentric are a powerful unification algorithm for terms with functors o...
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ISBN:
(纸本)9781595938299
Here we present the logic-programming language XCentric, discuss design issues, and show its adequacy for XML processing. Distinctive features of XCentric are a powerful unification algorithm for terms with functors of arbitrary arity (which correspond closely to XML documents) and a rich type language that uses operators such as repetition (*), alternation, etc, as types allowing a compact representation of terms with functors with an arbitrary number of arguments (closely related to standard type languages for XML). this new form of unification together with an appropriate use of types yields a substantial degree of flexibility in programming. Copyright 2007 ACM.
It is commonly agreed that the success of future proof assistants will rely on their ability to incorporate computations within deduction in order to mimic the mathematician when replacing the proof of a proposition P...
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ISBN:
(纸本)9783540749141
It is commonly agreed that the success of future proof assistants will rely on their ability to incorporate computations within deduction in order to mimic the mathematician when replacing the proof of a proposition P by the proof of an equivalent proposition P' obtained from P thanks to possibly complex calculations. In this paper, we investigate a new version of the calculus of inductive constructions which incorporates arbitrary decision procedures into deduction via the conversion rule of the calculus. the novelty of the problem in the context of the calculus of inductive constructions lies in the fact that the computation mechanism varies along proof-checking: goals are sent to the decision procedure together withthe set of user hypotheses available from the current context. Our main result shows that this extension of the calculus of constructions does not compromise its main properties: confluence, subject reduction, strong normalization and consistency are all preserved.
We introduce a sequent calculus for bilattice-based annotated logic (BAL). We show that this logic can be syntactically and semantically translated into a fragment MSL* of conventional many-sorted logic MSL. We show d...
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ISBN:
(纸本)9783540730989
We introduce a sequent calculus for bilattice-based annotated logic (BAL). We show that this logic can be syntactically and semantically translated into a fragment MSL* of conventional many-sorted logic MSL. We show deductive equivalence of sequent calculus for BAL and sequent calculus for MSL*.
One promising family of search strategies to alleviate runtime and storage requirements of ILP systems is that of stochastic local search methods, which have been successfully applied to hard propositional tasks such ...
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the identification of the correct sense of a word is necessary for many tasks in automatic natural language processing like machine translation, information retrieval, speech and text processing. Automatic Word Sense ...
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the proceedings contain 19 papers. the topics discussed include: nonmonotonic description logics-requirements, theory, and implementations;our quest for the holy grail of agent verification;an abstract framework for s...
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ISBN:
(纸本)9783540730989
the proceedings contain 19 papers. the topics discussed include: nonmonotonic description logics-requirements, theory, and implementations;our quest for the holy grail of agent verification;an abstract framework for satisfiability modulo theories;axiom pinpointing in general tableaux;proof theory for first order Lukasiewicz logic;a tableau method for public announcement logics;bounded model checking with description logic reasoning;tableau systems for logics of subinterval structures over dense orderings;a cut-free sequent calculus for bi-intuitionistic logic;tableaux with dynamic filtration for layered modal logics;the neighbourhood of S0.9 and S1;EXPTIME tableaux with global caching for description logics with transition roles, inverse roles and role hierarchies;and tree-sequent methods for subintuitionistic predicate logics.
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