Artificial intelligence publications
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Conceptual Models of Structure and Function
We report our achievements in creating conceptual, multidimensional models of biological structure and function out of the linear text of an introductory biology textbook.
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Data Mining in the Metacyc Family of Pathway Databases
The MetaCyc family of pathway databases consists of thousands of databases that were derived through computational inference of metabolic pathways from the MetaCyc pathway/genome database (PGDB).
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KB_Bio_101: A challenge for OWL Reasoners
We describe the axiomatic content of a biology knowledge base that poses both theoretical and empirical challenges for OWL reasoning.
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EcoCyc: Fusing Model Organism Databases with Systems Biology
Updates to EcoCyc content continue to improve the comprehensive picture of E. coli biology. The utility of EcoCyc is enhanced by new tools available on the EcoCyc web site, and…
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On the Combination of Logical and Probabilistic Models for Information Analysis
We describe a framework for systems that incorporate the advantages of both Bayesian and logical systems. We define a formalism for the conversion of automatically generated natural deduction proof trees…
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Accurate Atom-Mapping Computation for Biochemical Reactions
We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric.
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The Use of Pattern Recognition Technology to Generate New Approaches to Prematurity Research
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Metabolomics Reveals Amino Acids Contribute to Variation in Response to Simvastatin Treatment
We used a gas chromatography-time-of-flight mass-spectrometry-based metabolomics platform to evaluate global effects of simvastatin on intermediary metabolism.
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Learning by Demonstration for a Collaborative Planning Environment
We describe the deployment of a learning by demonstration capability to support user creation of automated procedures in a collaborative planning environment that is used widely by the U.S. Army.
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Exact lifted inference with distinct soft evidence on every object
We show that both exact maximum a posteriori (MAP) and marginal inference can be lifted for the case of distinct soft evidence on a unary Markov Logic predicate.
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Regulatory Network Operations in the Pathway Tools Software
Pathway Tools provides a comprehensive environment for manipulating molecular regulatory interactions that integrates regulatory data with an organism’s genome and metabolic network.
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The 2012 SESAME Multimedia Event Detection (MED) and Multimedia Event Recounting (MER) Systems
The SESAME team submitted four runs for the MED12 pre-specified events, two runs for the ad hoc events, and a run for multimedia event recounting.