Artificial intelligence publications
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CyanoCyc Cyanobacterial Web Portal
Abstract CyanoCyc is a web portal that integrates an exceptionally rich database collection of information about cyanobacterial genomes with an extensive suite of bioinformatics tools. It was developed to address…
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The Omics Dashboard for Interactive Exploration of Metabolomics and Multi-Omics Data
The Omics Dashboard is a software tool for interactive exploration and analysis of metabolomics, transcriptomics, proteomics, and multi-omics datasets.
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Human Body Model Based ID using Shape and Pose Parameters
We present a Human Body model-based IDentification system (HMID) system that is jointly trained for shape, pose, and biometric identification.
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SynRoute: A Retrosynthetic Planning Software
SynRoute is a new retrosynthetic planning software tool that uses a relatively small number of general reaction templates, currently 263, along with a literature-based reaction database to find short, practical…
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IxDRL: A Novel Explainable Deep Reinforcement Learning Toolkit based on Analyses of Interestingness
Our tool provides various measures of RL agent competence stemming from interestingness analysis and is applicable to a wide range of RL algorithms, natively supporting the popular RLLib toolkit.
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The EcoCyc Database (2023)
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to…
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Notes on Refactoring Exponential Macros in Common Lisp Or: Multiple @Body Considered Harmful
I will first illuminate the problem, and then demonstrate two potential solutions in terms of macro refactoring techniques. These techniques can be applied in related scenarios.
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BioCyc: Metabolic Pathway Databases and Informatics Tools
This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways.
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Multiagent Inverse Reinforcement Learning via Theory of Mind Reasoning
We approach the problem of understanding how people interact with each other in collaborative settings via Multiagent Inverse Reinforcement Learning (MIRL), where the goal is to infer the reward functions…
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Reviewing Knowledgebase and Database Grant Proposals in the Life Sciences: The Role of Innovation
This article offers thoughts on reviewing grant proposals for biological knowledgebases and databases (KDs) in the hope of aiding grant reviewers and applicants in addressing the issue of innovation.
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Sensor Control for Information Gain in Dynamic, Sparse and Partially Observed Environments
We present an approach for autonomous sensor control for information gathering under partially observable, dynamic and sparsely sampled environments.
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Global and Local Analysis of Interestingness for Competency-Aware Deep Reinforcement Learning
Our new framework provides various measures of RL agent competence stemming from interestingness analysis and is applicable to a wide range of RL algorithms.