Artificial intelligence publications
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Solution Authoring via Demonstration and Annotation: An Empirical Study
This paper reports on a concept validation study that provides an empirical basis for the design of solution authoring frameworks based on end-user programming techniques.
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Representation and inference of cellular architecture for metabolic reconstruction and modeling
We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.
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Computational Metabolomics Operations at Biocyc.Org
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.
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Neural network joint modeling via context-dependent projection
We propose a context-dependent linear projection approach which considers neighboring words. Experimental results showed that the proposed approach further improves NNJM by 0.5 BLEU for English-Iraqi Arabic translation in N-best…
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Natural Language Access to Data: It Takes Common Sense!
In a deductive approach to this problem, language processing technology translates English queries into a first-order logical form, which is regarded as a conjecture to be established by a theorem…
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Pathway Tools version 19.0 update: Software for Pathway/Genome Informatics and Systems Biology
The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations.
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Optimal Metabolic Route Search Based on Atom Mappings
We present the algorithm used in the new RouteSearch tool within the Pathway Tools software.
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An Operational Semantics for the Goal Life-Cycle in BDI Agents
A fundamental feature of intelligent agents is their ability to deliberate over their goals. Operating in an environment that may change in unpredictable ways, an agent needs to regularly evaluate…
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Metabolic Pathways for the Whole Community
Here we adopt the MetaPathways annotation and analysis pipeline and Pathway Tools to construct environmental pathway/genome databases that describe microbial community metabolism using MetaCyc.
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The EcoCyc Database
This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs
Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV.
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A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network.