Artificial intelligence publications
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Database Editing Metrics for Pattern Matching
This paper introduces a family of metrics to measure the degree of qualitative match between a database and a pattern, that is, an elastic constraint on database objects and their…
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The SPARK Agent Framework
We describe the SRI Procedural Agent Realization Kit (SPARK), a new BDI agent framework that combines scaleability and the clean semantic underpinning of more formal agent frameworks.
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Using Functional and Organizational Information to Improve Genome-Wide Computational Prediction of Transcription Units on Pathway/Genome Databases
We implemented a TU predictor that uses only intergenic distance and functional classification of genes to predict TU boundaries, and applied it to EcoCyc, our PGDB of Escherichia coli.
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Designing a System for Structured Assessment of Compliance Risk
A formal reasoning technique known as structured argumentation has been explored by the IRS LMSB Research to improve compliance risk assessment. The IRS together with SRI International evaluated the use…
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Balancing Formal and Practical Concerns in Agent Design
In this paper, we discuss a number of both formal and practical requirements that must be met to satisfy the demands of large-scale applications. We also briefly describe work on…
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Call for an enzyme genomics initiative
I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically.
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Identifying Terrorist Activity with AI Plan Recognition Technology
We describe the application of plan recognition techniques to support human intelligence analysts in processing national security alert sets by automatically identifying the hostile intent behind them. Identifying the intent…
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The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database
No longer restricted to metabolic pathways, this curated database includes data on genomics, molecular biology, and more.
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Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. We also add 956 additional annotations to proteins annotated as “hypothetical” using the GeneQuiz annotation system.
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Toward a Theory of Qualitative Reasoning about Plans
We define a qualitative framework for reasoning about plan structure, defining a set of plan relations that characterize key interactions among plan components and a calculus for reasoning qualitatively about…
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Computational Prediction of Human Metabolic Pathways from the Complete Human Genome
We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways.
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MetaCyc: a multiorganism database of metabolic pathways and enzymes
In the past 2 years the data content and the Pathway Tools software used to query, visualize and edit MetaCyc have been expanded significantly. These enhancements are described in this…