Artificial intelligence publications
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Leveraging Curation Among Escherichia coli Pathway/Genome Databases Using Ortholog-Based Annotation Propagation
We have developed a method to automatically propagate multiple types of curated knowledge from genes and proteins in one genome database to their orthologs in uncurated databases for related strains,…
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Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in Porphyromonas gingivalis
We use bioinformatics tools to predict biosynthetic pathways for the production of the normal (O-type) lipopolysaccharide in the W50 strain Porphyromonas gingivalis and compare the pathway with other putative pathways…
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Pathway Tools Visualization of Organism-Scale Metabolic Networks
We have developed bioinformatics software tools that automatically generate a full metabolic-network diagram for an organism, and that enable searching and analyses of the network.
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Transformer Based Molecule Encoding for Property Prediction
We build a Transformer-based molecule encoder and property predictor network with novel input featurization that performs significantly better than existing methods.
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Interestingness Elements for Explainable Reinforcement Learning: Understanding Agents’ Capabilities and Limitations
We propose an explainable reinforcement learning (XRL) framework that analyzes an agent’s history of interaction with the environment to extract interestingness elements that explain its behavior.
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Learning Procedures by Augmenting Sequential Pattern Mining with Planning Knowledge
This paper explores the use of filtering heuristics based on action models for automated planning to augment sequence mining techniques.
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Exact Inference for Relational Graphical Models with Interpreted Functions: Lifted Probabilistic Inference Modulo Theories
In this paper, we expand PIMT to a lifted version that also processes random functions and relations.
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A Comparison of the Pathway Tools Software with the Reactome Software
This document compares SRI’s Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways.
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The MetaCyc Database of Metabolic Pathways and Enzymes – A 2019 Update
This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.
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Bridging the Gap: Converting Human Advice into Imagined Examples
We present an approach that converts human advice into synthetic or imagined training experiences, serving to scaffold the low-level representations of simple, reactive learning systems such as reinforcement learners.
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The MultiOmics Explainer: Explaining Omics Results in the Context of a Pathway/Genome Database
We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism’s metabolic and regulatory network to suggest explanations for…
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Privacy-Aware Adaptive Scheduling for Coalition Operations
We consider the use of an advanced cryptographic technique called secure multi-party computation to enable coalition members to achieve joint objectives while still meeting privacy requirements.