Artificial intelligence publications
-
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 organismās metabolic and regulatory network to suggest explanations for…
-
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.
-
Metabolic Route Computation in Organism Communities
We developed an efficient software tool to search for metabolicĀ routesĀ that include metabolic reactions from multiple organisms.
-
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…
-
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.
-
Interestingness Elements for Explainable Reinforcement Learning through Introspection
The framework uses introspective analysis of an agentās history of interaction with its environment to extract several interestingness elements regarding its behavior.
-
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.
-
Explanation to Avert Surprise
We present an explanation framework based on the notion of explanation drivers āi.e., the intent or purpose behind agent explanations. We focus on explanations meant to reconcile expectation violations and…
-
Application of Text Analytics to Extract and Analyze MaterialāApplication Pairs from a Large Scientific Corpus
In this work, we have successfully extracted materialāapplication pairs and ranked them on their importance. This method provides a novel way to map scientific advances in a particular material to…
-
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.
-
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.
-
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.