Artificial intelligence publications
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An Advanced Web Query Interface for Biological Databases
We present a web interface for building precise queries for biological DBs that can construct much more precise queries than most web-based query forms, yet that is user friendly enough…
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Goal-directed Metacontrol for Integrated Procedure Learning
We describe a metalevel framework for coordinating the activities of a community of learners to create an integrated learning system. The metalevel framework is organized around learning goals, which are…
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality...
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Language Analytics for Assessing Brain Health: Cognitive Impairment, Depression and Pre-Symptomatic Alzheimers Disease
We present data demonstrating how brain health may be assessed by applying data-mining and text analytics to patient language.
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Recommendations for End-User Development
We provide an overview of the state of the art in end-user development, focusing on the different kinds of recommendations made to users. We identify four classes of suggestion that…
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Machine Learning Methods for Metabolic Pathway Prediction
ML methods for pathway prediction perform as well as existing methods, and have qualitative advantages in terms of extensibility, tunability, and explainability.
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Creation of a Genome-Wide Metabolic Pathway Database for Populus trichocarpa Using a New Approach for Reconstruction and Curation of Metabolic Pathways for Plants
We developed a general approach for reconstructing metabolic pathway complements of plant genomes. Two new reference databases were created and added to the core of the infrastructure: PlantCyc, and RESD.
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Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).
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Pathway Tools Version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology
Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB).
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The Metacyc Database of Metabolic Pathways and Enzymes and the Biocyc Collection of Pathway/Genome Databases
Each BioCyc PGDB contains the predicted metabolic network of one organism, including metabolic pathways, enzymes, metabolites and reactions predicted by the Pathway Tools software using MetaCyc as a reference database.
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Evaluating User-Adaptive Systems: Lessons from Experiences with a Personalized Meeting Scheduling Assistant
We discuss experiences from evaluating the learning performance of a user-adaptive personal assistant agent.
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Task Assistant: Personalized Task Management for Military Environments
We describe an AI-enhanced task management tool developed for a military environment, which differs from office environments in important ways: differing time scales, a focus on teams collaborating on tasks…