Artificial intelligence publications
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A systematic comparison of the MetaCyc and KEGG pathway databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their…
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Query Answering in Object Oriented Knowledge Bases in Logic Programming: Description and Challenge for ASP
We give a description of this KB and ASP programs for a suite of queries that have been of practical interest.
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Automatic Strengthening of Graph-Structured Knowledge Bases
Keywords: Artificial Intelligence, Artificial Intelligence Center, AIC
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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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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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A corpus of online discussions for research into linguistic memes
We describe a 460-million word corpus of online discussions.
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Construction and completion of flux balance models from pathway databases
We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP).
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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.