Artificial intelligence publications
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Deductive Response to Geographic Queries
They may reside on different machines in diverse locations. Knowledge may be represented according to different frameworks, notations, or coordinate systems. The answer may not exist anywhere explicitly; it may…
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Reflections on Godel’s and Gandy’s Reflections on Turing’s Thesis
We sketch the historical and conceptual context of Turing’s analysis of algorithmic or mechanical computation and then discuss two responses to that analysis.
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Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
We seek to determine the accuracy of computational methods for predicting metabolic pathways in sequenced genomes, and to understand the contributions of both the prediction algorithms, and the reference pathway…
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The Pathway Tools Software
The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB).
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Active Coordination of Distributed Human Planners
This paper presents a framework called CODA that provides targeted information dissemination among distributed human planners as a way of improving coordination.
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Self-consistency, Stereo, MDL, and Change detection
Our main goal is to predict the accuracy of an output element of an existing stereo algorithm
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A 50-kb Plasmid Rich in Mobile Gene Sequences Isolated from a Marine Micrococcus
A 50,709-bp cryptic plasmid isolated from a marine Micrococcus has been sequenced and found to contain a number of putative mobile genetic elements.
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Resolving Conflicts in Agent Guidance
This paper considers the problem of conflicting guidance for agents, making contributions in two areas: (a) outlining a space of conflict types, and (b) defining resolution methods that provide robust…
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Conflict Management for Agent Guidance
This paper considers the problem of conflicting guidance for agents, making contributions in two areas: outlining a space of conflict types, and defining resolution methods that provide robust agent operation…
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The past, present and future of genome-wide re-annotation
We define the process of annotating a previously annotated genome sequence as 're-annotation', and examine the strengths and weaknesses of current manual and automatic genome-wide re-annotation approaches.
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The MetaCyc Database
MetaCyc is a metabolic-pathway database that describes 445 pathways and 1115 enzymes occurring in 158 organisms.
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Capturing Analytic Thought
We are developing a new methodology that retains the ease of use, the familiarity, and (some of) the free-form nature of informal methods, while benefiting from the rigor, structure, and…