Thomas (Tom) J Lee

Current Projects

Pathway Tools Pathway Tools is a systems biology software system that supports several use cases: Development of organism-specific database that integrate many bioinformatics datatypes, from genomes to pathways. Development of metabolic-flux models using flux-balance analysis. Scientific visualization, web publishing, and querying of organism-specific databases. Analysis of omics datasets. Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons. Comparative analyses.

Past Projects

	Advisable Planners The Advisable Planners project sought to make AI planning technology more accessible and controllable through the metaphor of advisability. User-provided advice specifies characteristics for both the desired solution and the problem-solving process to be employed during plan generation. Such advice is specified in a high-level language that is natural and intuitive for users, then operationalized into constraints that direct the underlying planning technology.
	Automating Exception Handing with Dynamic, Collaborative Scheduling This project will integrate flight scheduling, execution management, and distributed coordination capabilities to provide an integrated basis for generating and updating flight schedules in response to new requirements, negotiating adjustments to resource assignments, immediately detecting schedule deviations during execution and alerting users about them, and dynamically reoptimizing flight schedules. Joint work with Carnegie Mellon University on problems at the Air Mobility Command.
	Coordination of Distributed Activities (CODA) The CODA system provides targeted information dissemination among distributed planners as a way of improving team coordination. In CODA, an individual planner declares interest in different types of plan changes that could impact his local plan development. As a team of distributed users develop plans with a plan authoring tool, their activities are monitored; changes that match declared interests are forwarded automatically to the person who declared interest in them.
	JFACC Continuous Planning and Execution The main result of this project was the development of the Continuous Planning and Execution Framework (CPEF), which provides plan generation and replanning capabilities for situated agents in highly dynamic environments. Within CPEF, plans are treated as dynamic, open-ended artifacts that evolve in response to an ever-changing environment. In particular, plans must be updated in response to new information and requirements in a timely fashion to ensure their relevance and viability.
	Plan Authoring System based on Sketches, Advice, and Templates (PASSAT) PASSAT is a user-centric plan-authoring system grounded in the concepts of plan sketches, advice, and templates. PASSAT enables users to quickly develop plans that draw upon past experience encoded in templates, but that are customized to their individual preferences of a given user. The PASSAT core consists of an interactive plan authoring capability; tools for task management, constraint reasoning, plan sketching and causal reasoning provide provide complementary automated capabilities.
	Planning and Decision Aids for Small Unit Operations We developed a planning and decision aid (PDA) for the DARPA Small Unit Operations (SUO) program, to show the feasibility of using advanced planning technologies in SUO. The PDA monitors the execution of machine-understandable plans, using events as they are realistically reported in the battlespace, and alerts the user when the situation requires his attention.
	TransPAL: Transitioning PAL Technologies The TransPAL project is transitioning a number of technologies developed on the DARPA PAL program for use by various members of the Armed Services.

Software

	Plan Authoring System based on Sketches, Advice and Templates PASSAT is a user-centric plan-authoring system grounded in the concepts of plan sketches, advice, and templates.
	SIPE-2: System for Interactive Planning and Execution SIPE-2 efficiently reasons about actions to generate a novel sequence of actions that responds precisely to the situation at hand. Supports interactive mixed-initiative planning with powerful GUI; Allows giving of advice to the planner; Plans hierarchically at different levels of abstraction.

Selected Publications

The following publications are selected by the author. They are listed in reverse chronological order.
[View All 17 Publications]

• Gervasio, M., Haines, W., Morley, D., Lee, T. J., Overholtzer, C. A., Saadati, S., and Spaulding A. How to Serve Soup: Interleaving Demonstration and Assisted Editing to Support Non-Programmers, in Proceedings of the 15th International Conference on Intelligent User Interfaces, 2011.  [Details]

• Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.. Brief Bioinform., vol. 11, no. 1, pp. 40-79, Jan 2010.  [PDF, Details]

• Lee T.J., Pouliot Y., Wagner V., Gupta P., Stringer-Calvert D.W.J, Tenenbaum J.D., Karp P.D. BioWarehouse: a bioinformatics database warehouse toolkit. BMC Bioinformatics, vol. 7, p. 170, 2006.  [PDF, Details]