Artificial intelligence publications
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Beyond the Genome (BTG) Is a (PGDB) Pathway Genome Database: Humancyc
HumanCyc is a manually curated database of enzymatic reactions and metabolic pathways that can be used as a versatile reference resource or as a tool for analyzing 'omics' data sets…
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A Systematic Study of Genome Context Methods: Calibration, Normalization and Combination
We present a thorough study of the four main families of genome context methods found in the literature: phylogenetic profile, gene fusion, gene cluster, and gene neighbor.
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The BioPAX Community Standard for Pathway Data Sharing
BioPAX, which was created through a community process, solves this problem by making pathway data substantially easier to collect, index, interpret and share.
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Efficient Variable Elimination for Semi-Structured Simple Temporal Networks with Continuous Domains
We show that for an Simple Temporal Network, messages can be represented compactly as sub-STNs. We then present an efficient message-passing scheme for computing the minimal constraints of an STN.
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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.
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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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Convergence of a Least-Squares Monte Carlo Algorithm for Bounded Approximating Sets
We analyse the convergence properties of the Longstaff–Schwartz algorithm for approximately solving optimal stopping problems that arise in the pricing of American (Bermudan) financial options.
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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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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…