Artificial intelligence publications
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Identifying Candidate Genes Using The BioWarehouse: A Case Study
The BioWarehouse is an open source data warehousing environment focused on supporting bioinformatics databases (DBs). BioWarehouse integrates public source DBs such as Swiss-Prot and GenBank into a unified normalized schema…
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EcoCyc: a comprehensive database resource for Escherichia coli
The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli.
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Supporting the Pattern Development Cycle in Intelligence Gathering
This paper discusses the cycle through a use case of the Link Analysis Workbench (LAW), a tool for discovering and analyzing situations of interest in large relational data sets.
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A Collaborative Framework for Managing Uncertainty and Cognitive Bias
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Execution Monitoring and Replanning with Incremental and Collaborative Scheduling
We describe the Flight Manager Assistant (FMA), a prototype system, designed to support real-time management of airlift operations at the USAF Air Mobility Command (AMC).
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Querying and Computing with BioCyc Databases
We describe multiple methods for accessing and querying the complex and integrated cellular data in the BioCyc family of databases.
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The Role of Higher-Order Constructs in the Inexact Matching of Semantic Graphs
This paper reports the results of an experimental analysis of higher-order constructs in graphical patterns and their effect on pattern matching efficiency.
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Expansion of the BioCyc Collection of Pathway/Genome Databases to 160 Genomes
This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways…
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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…