Theodore J. Perkins

According to our database, Theodore J. Perkins authored at least 36 papers between 1998 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

A Model of Cell Population Dynamics in Skeletal Muscle Regeneration.

Renad Al-Ghazawi, Theodore J. Perkins, Xiaojian Shao

Proceedings of the 14th ACM International Conference on Bioinformatics, 2023

2022

BATL: Bayesian annotations for targeted lipidomics.

Justin G. Chitpin, Anuradha Surendra, Thao T. Nguyen, Graeme Taylor, Hongbin Xu, Irina Alecu, Roberto Ortega, Julianna J. Tomlinson, Angela M. Crawley, Michaeline McGuinty, Michael G. Schlossmacher, Rachel Saunders-Pullman, Miroslava Cuperlovic-Culf, Steffany A. L. Bennett, Theodore J. Perkins

Bioinform., 2022

2021

WACS: improving ChIP-seq peak calling by optimally weighting controls.

Aseel Awdeh, Marcel Turcotte, Theodore J. Perkins

BMC Bioinform., 2021

2019

RECAP reveals the true statistical significance of ChIP-seq peak calls.

Justin G. Chitpin, Aseel Awdeh, Theodore J. Perkins

Bioinform., 2019

Optimal Risk in Multiagent Blind Tournaments.

Theodore J. Perkins

Proceedings of the 18th International Conference on Autonomous Agents and MultiAgent Systems, 2019

2018

Dynamics in Epistasis Analysis.

Aseel Awdeh, Hilary Phenix, Mads Kærn, Theodore J. Perkins

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

2017

Fully polynomial-time computation of maximum likelihood trajectories in Markov chains.

Yuri Grinberg, Theodore J. Perkins

Inf. Process. Lett., 2017

Learning-based interactive segmentation using the maximum mean cycle weight formalism.

Sharmin Nilufar, Dao Sen Wang, John Girgis, Carmen G. Palii, D. Yang, A. Blais, M. Brand, Doina Precup, Theodore J. Perkins

Proceedings of the Medical Imaging 2017: Image Processing, 2017

Analysis of Controls in ChIP-seq.

Aseel Awdeh, Theodore J. Perkins

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Super-enhancer Dynamics Throughout Myogenesis.

Basma Abdelkarim, Theodore J. Perkins

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

On cross-conditional and fluctuation correlations in competitive RNA networks.

Daniel Sánchez-Taltavull, Matthew MacLeod, Theodore J. Perkins

Bioinform., 2016

2015

Gene selection for the reconstruction of stem cell differentiation trees: a linear programming approach.

Mohamed A. Ghadie, Nathalie Japkowicz, Theodore J. Perkins

Bioinform., 2015

State Sequence Analysis in Hidden Markov Models.

Yuri Grinberg, Theodore J. Perkins

Proceedings of the Thirty-First Conference on Uncertainty in Artificial Intelligence, 2015

The potential power of dynamics in epistasis analysis.

Aseel Awdeh, Hilary Phenix, Mads Kærn, Theodore J. Perkins

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Learning to Detect Contours with Dynamic Programming Snakes.

Sharmin Nilufar, Theodore J. Perkins

Proceedings of the 22nd International Conference on Pattern Recognition, 2014

Learning a cost function for microscope image segmentation.

Sharmin Nilufar, Theodore J. Perkins

Proceedings of the 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2014

Learning a Cost Function for Interactive Microscope Image Segmentation.

Sharmin Nilufar, Theodore J. Perkins

Proceedings of the Modern Artificial Intelligence for Health Analytics, 2014

2013

FiloDetect: automatic detection of filopodia from fluorescence microscopy images.

Sharmin Nilufar, Anne Morrow, Jonathan Lee, Theodore J. Perkins

BMC Syst. Biol., 2013

MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data.

Parameswaran Ramachandran, Gareth A. Palidwor, Christopher J. Porter, Theodore J. Perkins

Bioinform., 2013

Automatic Detection of Filopodia from Fluorescence Microscopy Images.

Sharmin Nilufar, Theodore J. Perkins, Anne Morrow, Jonathan Lee

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

2011

Quantitative Epistasis Analysis and Pathway Inference from Genetic Interaction Data.

Hilary Phenix, Katy Morin, Cory Batenchuk, Jacob Parker, Vida Abedi, Liu Yang, Lioudmila Tepliakova, Theodore J. Perkins, Mads Kærn

PLoS Comput. Biol., 2011

2010

A Trade-Off between Sample Complexity and Computational Complexity in Learning Boolean Networks from Time-Series Data.

Theodore J. Perkins, Michael T. Hallett

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

Estimating the Stochastic Bifurcation Structure of Cellular Networks.

Carl Song, Hilary Phenix, Vida Abedi, Matthew Scott, Brian P. Ingalls, Mads Kærn, Theodore J. Perkins

PLoS Comput. Biol., 2010

2009

Statistical lower bounds on protein copy number from fluorescence expression images.

Lee Zamparo, Theodore J. Perkins

Bioinform., 2009

Maximum likelihood trajectories for continuous-time Markov chains.

Theodore J. Perkins

Proceedings of the Advances in Neural Information Processing Systems 22: 23rd Annual Conference on Neural Information Processing Systems 2009. Proceedings of a meeting held 7-10 December 2009, 2009

2008

Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation.

Sean M. Cory, Theodore J. Perkins

PLoS Comput. Biol., 2008

2006

Reverse Engineering the Gap Gene Network of <i>Drosophila melanogaster</i>.

Theodore J. Perkins, Johannes Jaeger, John Reinitz, Leon Glass

PLoS Comput. Biol., 2006

2002

Lyapunov Design for Safe Reinforcement Learning.

Theodore J. Perkins, Andrew G. Barto

J. Mach. Learn. Res., 2002

A Convergent Form of Approximate Policy Iteration.

Theodore J. Perkins, Doina Precup

Proceedings of the Advances in Neural Information Processing Systems 15 [Neural Information Processing Systems, 2002

On the Existence of Fixed Points for Q-Learning and Sarsa in Partially Observable Domains.

Theodore J. Perkins, Mark D. Pendrith

Proceedings of the Machine Learning, 2002

Reinforcement Learning for POMDPs Based on Action Values and Stochastic Optimization.

Theodore J. Perkins

Proceedings of the Eighteenth National Conference on Artificial Intelligence and Fourteenth Conference on Innovative Applications of Artificial Intelligence, July 28, 2002

Scheduling Contract Algorithms on Multiple Processors.

Daniel S. Bernstein, Theodore J. Perkins, Shlomo Zilberstein, Lev Finkelstein

Proceedings of the Eighteenth National Conference on Artificial Intelligence and Fourteenth Conference on Innovative Applications of Artificial Intelligence, July 28, 2002

2001

Heuristic Search in Infinite State Spaces Guided by Lyapunov Analysis.

Theodore J. Perkins, Andrew G. Barto

Proceedings of the Seventeenth International Joint Conference on Artificial Intelligence, 2001

Lyapunov-Constrained Action Sets for Reinforcement Learning.

Theodore J. Perkins, Andrew G. Barto

Proceedings of the Eighteenth International Conference on Machine Learning (ICML 2001), Williams College, Williamstown, MA, USA, June 28, 2001

2000

Machine Learning for Subproblem Selection.

Robert Moll, Theodore J. Perkins, Andrew G. Barto

Proceedings of the Seventeenth International Conference on Machine Learning (ICML 2000), Stanford University, Stanford, CA, USA, June 29, 2000

1998

Learning Instance-Independent Value Functions to Enhance Local Search.

Robert Moll, Andrew G. Barto, Theodore J. Perkins, Richard S. Sutton

Proceedings of the Advances in Neural Information Processing Systems 11, [NIPS Conference, Denver, Colorado, USA, November 30, 1998