Artificial intelligence publications
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Metabolic Route Computation in Organism Communities
We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms.
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Using pathway covering to explore connections among metabolites
Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites…
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Lucid Explanations Help: Using a Human-AI Image-Guessing Game to Evaluate Machine Explanation Helpfulness
We propose a Twenty-Questions style collaborative image retrieval game as a method of evaluating the efficacy of explanations (visual evidence or textual justification) in the context of Visual Question Answering.
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Interestingness Elements for Explainable Reinforcement Learning through Introspection
The framework uses introspective analysis of an agent’s history of interaction with its environment to extract several interestingness elements regarding its behavior.
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A Comparison of Microbial Genome Web Portals
This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.
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Explanation to Avert Surprise
We present an explanation framework based on the notion of explanation drivers —i.e., the intent or purpose behind agent explanations. We focus on explanations meant to reconcile expectation violations and…
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Application of Text Analytics to Extract and Analyze Material–Application Pairs from a Large Scientific Corpus
In this work, we have successfully extracted material–application pairs and ranked them on their importance. This method provides a novel way to map scientific advances in a particular material to…
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How accurate is automated gap filling of metabolic models?
Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model.
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Evaluation of reaction gap-filling accuracy by randomization
We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model.
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The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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Semantic Instrumentation of Virtual Environments for Training
We discuss an approach in which the virtual environment is semantically instrumented in order to allow for the tracking of and reasoning about open-ended learner activity therein.