Artificial intelligence publications
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An Evidence Ontology for use in Pathway/Genome Databases
This paper presents an ontology for encoding the type of support and the degree of support for DB assertions, and for encoding the literature source in which that support is…
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A Multimodal Learning Interface for Sketch, Speak and Point Creation of a Schedule Chart
We present a video demonstration of an agent-based test bed application for ongoing research into multi-user, multimodal, computer-assisted meetings.
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Trained Named Entity Recognition Using Distributional Clusters
This work applies boosted wrapper induction (BWI), a machine learning algorithm for information extraction from semi-structured documents, to the problem of named entity recognition.
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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.