Artificial intelligence publications
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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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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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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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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.
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An Annotated Corpus and Method for Analysis of Ad-Hoc Structures Embedded in Text
We describe a method for identifying and performing functional analysis of structured regions that are embedded in natural language documents, such as tables or key-value lists.
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Assessing Problem-Solving Process At Scale
This paper describes a hybrid approach to assessing process at scale in the context of the use of computational thinking practices during programming.
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Can we replace curation with information extraction software?
Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are…
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Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.