Artificial intelligence publications
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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research.
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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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The Time Is Right to Focus on Model Organism Metabolomes
We propose a grand challenge for metabolomics studies of model organisms: to identify and map all metabolites onto metabolic pathways, to develop quantitative metabolic models for model organisms, and to…
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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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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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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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The EcoCyc Database
This review outlines the data content of EcoCyc and of the procedures by which this content is generated.