Artificial intelligence publications
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The Pathway Tools Pathway Prediction Algorithm
The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes.
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Metabolic Pathway Databases for 1,000 Organisms
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EcoCyc: a Comprehensive Database of Escherichia Coli Biology
Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein…
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Discovering Semantic Web Services Using Sparql and Intelligent Agents
This paper describes a novel approach to the description and discovery of Semantic Web services.
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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).