Artificial intelligence publications
-
Expansion of the BioCyc Collection of Pathway/Genome Databases to 160 Genomes
This paper discusses the computational methodology by which the BioCyc collection has been expanded, and presents an aggregate analysis of the collection that includes the range of number of pathways…
-
Genome Annotation Errors in Pathway Databases Due to Semantic Ambiguity in Partial EC Numbers
We report on a new type of systematic annotation error in genome and pathway databases that results from the misinterpretation of partial Enzyme Commission (EC) numbers such as ‘1.1.1.-’.
-
Database Editing Metrics for Pattern Matching
This paper introduces a family of metrics to measure the degree of qualitative match between a database and a pattern, that is, an elastic constraint on database objects and their…
-
The SPARK Agent Framework
We describe the SRI Procedural Agent Realization Kit (SPARK), a new BDI agent framework that combines scaleability and the clean semantic underpinning of more formal agent frameworks.
-
Designing a System for Structured Assessment of Compliance Risk
A formal reasoning technique known as structured argumentation has been explored by the IRS LMSB Research to improve compliance risk assessment. The IRS together with SRI International evaluated the use…
-
Balancing Formal and Practical Concerns in Agent Design
In this paper, we discuss a number of both formal and practical requirements that must be met to satisfy the demands of large-scale applications. We also briefly describe work on…
-
Call for an enzyme genomics initiative
I propose an Enzyme Genomics Initiative, the goal of which is to obtain at least one protein sequence for each enzyme that has previously been characterized biochemically.
-
Identifying Terrorist Activity with AI Plan Recognition Technology
We describe the application of plan recognition techniques to support human intelligence analysts in processing national security alert sets by automatically identifying the hostile intent behind them. Identifying the intent…
-
The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database
No longer restricted to metabolic pathways, this curated database includes data on genomics, molecular biology, and more.
-
Computational analysis of Plasmodium falciparum metabolism: Organizing genomic information to facilitate drug discovery
We have constructed PlasmoCyc, a PGDB for Plasmodium falciparum 3D7, using its annotated genomic sequence. We also add 956 additional annotations to proteins annotated as “hypothetical” using the GeneQuiz annotation system.
-
Toward a Theory of Qualitative Reasoning about Plans
We define a qualitative framework for reasoning about plan structure, defining a set of plan relations that characterize key interactions among plan components and a calculus for reasoning qualitatively about…
-
Computational Prediction of Human Metabolic Pathways from the Complete Human Genome
We present a computational pathway analysis of the human genome that assigns enzymes encoded therein to predicted metabolic pathways.