Artificial intelligence publications
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Construction and completion of flux balance models from pathway databases
We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP).
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Accurate Atom-Mapping Computation for Biochemical Reactions
We introduce a new method for computing atom mappings called the minimum weighted edit-distance (MWED) metric.
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Browsing Metabolic and Regulatory Networks with BioCyc
The BioCyc database collection at BioCyc.org integrates genome and cellular network information for more than 1,100 organisms.
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A Survey of Metabolic Databases Emphasizing the Metacyc Family
The main families are the MetaCyc, KEGG, Reactome, Model SEED, and BiGG families. We survey these database families, as well as important individual metabolic databases, including multiple human metabolic databases.
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Analysis and comparison of recent MLP features for LVCSR systems
This paper aims at providing a fair comparison of these recent progresses including the use of different long/short temporal inputs and the use of complex architectures that go beyond the…
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Efficient Methods for Lifted Inference with Aggregate Factors
We propose an exact solution constant in n when k = 2 for certain aggregate operations such as AND, OR and SUM, and (b) a close approximation for inference with aggregate factors with time…
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Discovering Novel Subsystems Using Comparative Genomics
We propose a novel method for the discovery of subsystems from annotated genomes.
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Cancer: a Computational Disease That AI Can Cure
We discuss these in the context of Cancer Commons, a “rapid learning” community where patients, physicians, and researchers collect and analyze the molecular and clinical data from every cancer patient,…
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Web-Based Metabolic Network Visualization with a Zooming User Interface
We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling…
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Biocyc: Microbial Genomes and Cellular Networks
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A Collective Intelligence Based Business-Matching and Recommending System for Next Generation E-Marketplaces
The present work proposes and describes a novel approach to business-matching and recommending systems, for the next-generation e-marketplaces, with a focus on the needs and realities of small business.
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Deducing Answers to English Questions from Structured Data
We describe ongoing research using natural English text queries as an intelligent interface for inferring answers from structured data in a specific domain.