Artificial intelligence publications
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GIGA: a Simple, Efficient Algorithm for Gene Tree Inference in the Genomic Age
We describe a simple, fast algorithm for inferring gene phylogenies, which makes use of information that was not available prior to the genomic age: namely, a reliable species tree spanning…
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Discounted Deterministic Markov Decision Processes and Discounted All-Pairs Shortest Paths
We present algorithms for finding optimal strategies for discounted, infinite-horizon, Determinsitc Markov Decision Processes (DMDPs).
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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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Learning to Ask the Right Questions
Asking questions can clarify concepts, test hypotheses, add missing information, or provide additional knowledge to facilitate learning. The last item motivates the work described in this paper.
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A World Wider than the Web: End User Programming Across Multiple Domains
This chapter presents Integrated Task Learning (ITL), an approach for learning procedures across domains using end-user programming (EUP).
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Using Data Mining Findings to Aid Searching for Better Cognitive Models
We propose a hybrid approach in which we leverage findings from our previous educational data mining work to aid the search for a better cognitive model and thus, improve the…