Artificial intelligence publications
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The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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How accurate is automated gap filling of metabolic models?
Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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Semantic Instrumentation of Virtual Environments for Training
We discuss an approach in which the virtual environment is semantically instrumented in order to allow for the tracking of and reasoning about open-ended learner activity therein.
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Approximate Graph Matching for Mistake-tolerant Skill Assessment
This paper presents an approach to automated assessment for online training based on approximate graph matching.
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Demonstration-based Solution Authoring for Skill Assessment
This paper reports on an approach to creating solution models for automated skill assessment using an example-based methodology, specifically targeting domains for which solution models must support robustness to learner…
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An Ontology-Based Dialogue Management System for Virtual Personal Assistants
The features of OntoVPA are offered as potential solutions to core DM problems. We illustrate OntoVPA’s solutions to these problems by means of a running VPA example domain.
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Update notifications for the BioCyc collection of databases
The BioCyc update notifications service is a new mechanism to keep researchers informed of the latest developments in their areas of interest.
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The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12
New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.
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The BioCyc collection of microbial genomes and metabolic pathways
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by…
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Feature Derivation for Exploitation of Distant Annotation via Pattern Induction against Dependency Parses
We consider the use of distant supervision for biological information extraction, and introduce two understudied corpora of this form, the Biological Expression Language (BEL) Large Corpus and the Pathway Logic…
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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.