Artificial intelligence publications
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Preliminary Steps Towards a Knowledge Factory Process
In this demo/poster session, we will demonstrate the biology knowledge base created using AURA, the electronic textbook application Inquire, and discuss the knowledge engineering process we used to construct the…
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BioCyc: Microbial Genomes and Cellular Networks
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Learning by Demonstration Technology for Military Planning and Decision Making: A Deployment Story
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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Introduction to the Special Issue on Question Answering
This special issue issue of AI Magazine presents six articles on some of the most interesting question answering systems in development today.
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Discovering Semantic Web Services Using Sparql and Intelligent Agents
This paper describes a novel approach to the description and discovery of Semantic Web services.
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EcoCyc: a Comprehensive Database of Escherichia Coli Biology
Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein…
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Beyond the Genome (BTG) Is a (PGDB) Pathway Genome Database: Humancyc
HumanCyc is a manually curated database of enzymatic reactions and metabolic pathways that can be used as a versatile reference resource or as a tool for analyzing 'omics' data sets…
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A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor.
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The BioPAX Community Standard for Pathway Data Sharing
BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share.
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Efficient Variable Elimination for Semi-Structured Simple Temporal Networks with Continuous Domains
We show that for an Simple Temporal Network, messages can be represented compactly as sub-STNs. We then present an efficient message-passing scheme for computing the minimal constraints of an STN.
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Creation of a Genome-Wide Metabolic Pathway Database for Populus Trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes.
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GIGA: a Simple, Efficient Algorithm for Gene Tree Inference in the Genomic Age
We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning…