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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Gibbs Sampling in Open-Universe Stochastic Languages
This paper goes some way to remedying this deficit by introducing, and proving correct, a generalization of Gibbs sampling to partial worlds with possibly varying model structure.
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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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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…