Artificial intelligence publications
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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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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…
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Deductive Formation of Recursive Workflows
We present an action theory with the power to represent recursive plans and the capability to reason about and synthesize recursive workflow control structures.
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Box Invariance in Biologically-Inspired Dynamical Systems
We show that box invariance can be checked in cubic time for linear and affine systems, and that it remains decidable for classes of nonlinear systems of interest (with polynomial…
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Efficient Online Learning and Prediction of Users’ Desktop Actions
We show that simple efficient many-class learning can perform well for action prediction, significantly improving over previously published results and baselines.