Publications and Manuscripts

Recent publications and manuscripts

Machine Learning Models for Phenotype Classification and Biomarker Discovery

C.F. Aliferis, A. Statnikov, I. Tsamardinos "Challenges in the Analysis of Mass-Throughput Data: A Technical Commentary from the Statistical Machine Learning Perspective" Cancer Informatics, 2006 [Article]
Levy S, Statnikov A, Aliferis C.F., "Biomarker Selection from High-Dimensionality Data. Pharmaceutical Discovery." 2005 Microarray Supplement, September 2005: 37-44.
A. Statnikov, C.F. Aliferis, I. Tsamardinos, D. Hardin, S. Levy. " A Comprehensive Evaluation of Multicategory Classification Methods for Microarray Gene Expression Cancer Diagnosis", Bioinformatics, 2005 Mar 1;21(5):631-43 [Pubmed] [Appendix] [Supplement]
A. Sboner, C.F. Aliferis, "Modeling Clinical Judgment and Implicit Guideline Compliance in the Diagnosis of Melanomas Using Machine Learning", AMIA Symposium, 2005 [Article]
C.F. Aliferis, I. Tsamardinos, P. Massion, A. Statnikov, D. Hardin. "Why Classification Models Using Array Gene Expression Data Perform So Well: A Preliminary Investigation Of Explanatory Factors" In Proceedings of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), June 23-26, 2003, Las Vegas, Nevada, USA, CSREA Press [Article]
C.F. Aliferis, I. Tsamardinos, P. Massion, A. Statnikov, N. Fananapazir, D. Hardin. "Machine Learning Models For Classification Of Lung Cancer and Selection of Genomic Markers Using Array Gene Expression Data" In Proceedings of the 16th International Florida Artificial Intelligence Research Society (FLAIRS) Conference, May 12-14, 2003, St. Augustine, Florida, USA, AAAI Press, pages 67-71 [Article] [Supplement]
C.F. Aliferis, D. Hardin, P. Massion, "Machine Learning Models For Lung Cancer Classification Using Array Comparative Genomic Hybridization" In Proceedings of the 2002 American Medical Informatics Association (AMIA) Annual Symposium, November 9-13, 2002, San Antonio, Texas, USA, pages 7-11 [Article]

Local Causal Discovery, Markov Blanket Induction, and Feature Selection

D. Hardin, I. Tsamardinos, C.F. Aliferis, "A Theoretical Characterization of Linear SVM-Based Feature Selection", In the Twenty-First International Conference on Machine Learning (ICML), 2004 [Article] [Supplement]
L. Frey, D. Fisher, I. Tsamardinos, C.F. Aliferis, A. Statnikov. "Identifying Markov Blankets with Decision Tree Induction" In Proceedings of the Third IEEE International Conference on Data Mining (ICDM), November 19-22, 2003, Melbourne, Florida, USA, IEEE Computer Society Press, pages 59-66 [Article]
C. F. Aliferis, I. Tsamardinos, A. Statnikov. "HITON, A Novel Markov Blanket Algorithm for Optimal Variable Selection" In Proceedings of the 2003 American Medical Informatics Association (AMIA) Annual Symposium, November 8-12, 2003, Washington, DC, USA, pages 21-25 [Article]
I. Tsamardinos, C.F. Aliferis, A. Statnikov. "Time and Sample Efficient Discovery of Markov Blankets and Direct Causal Relations" DSL TR-03-04, September 3, 2003, Vanderbilt University, Nashville, TN, USA [Article]
I. Tsamardinos, C.F. Aliferis, A. Statnikov. "Time and Sample Efficient Discovery of Markov Blankets and Direct Causal Relations" In Proceedings of the 9th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, August 24-27, 2003, Washington, DC, USA, ACM Press, pages 673-678 [Article]
I. Tsamardinos, C.F. Aliferis, A. Statnikov. "Algorithms for Large Scale Markov Blanket Discovery" In Proceedings of the 16th International Florida Artificial Intelligence Research Society (FLAIRS) Conference, May 12-14, 2003, St. Augustine, Florida, USA, AAAI Press, pages 376-380 [Article]
I. Tsamardinos and C.F. Aliferis. "Towards Principled Feature Selection: Relevance, Filters, and Wrappers" In Proceedings of the Ninth International Workshop on Artificial Intelligence and Statistics, January 3-6, 2003, Key West, Florida, USA [Article]
C.F. Aliferis, I. Tsamardinos, A. Statnikov, "Large-Scale Feature Selection Using Markov Blanket Induction for the Prediction of Protein-Drug Binding" DSL TR-02-06, June 1, 2002, Vanderbilt University, Nashville, TN, USA [Article]
C.F. Aliferis and I. Tsamardinos. "Algorithms for Large-Scale Local Causal Discovery And Feature Selection In the Presence of Limited Sample Or Large Local Neighborhoods" DSL TR-02-08, 2002 [Article]

Global Causal Discovery and Reverse Engineering of Regulatory Networks

I. Tsamardinos, L.E. Brown, C.F. Aliferis. "The Max-Min Hill-Climbing Bayesian Network Structure Learning Algorithm" Machine Learning, 2006 [Article] [Supplement]
L.E. Brown, I. Tsamardinos, C.F. Aliferis. "A Comparison of Novel and State-of-the-Art Polynomial Bayesian Network Learning Algorithms" In the Proceedings of the Twentieth National Conference on Artificial Intelligence (AAAI), 2005 [Article]
L.E. Brown, I. Tsamardinos, C.F. Aliferis. "A Novel Algorithm for Scalable and Accurate Bayesian Network Learning" In Proceedings of the 11th World Congress on Medical Informatics (MEDINFO), September 7-11, 2004, San Francisco, California, USA [Article] [Supplement]
I. Tsamardinos, C. F. Aliferis, A. Statnikov, L. E. Brown. "Scaling-Up Bayesian Network Learning to Thousands of Variables Using Local Learning Technique" DSL TR-03-02, March 12, 2003, Vanderbilt University, Nashville, TN, USA [Article]

Publicly Available Tools and Software

N. Fananapazir, M. Li, D. Spentzos, C.F. Aliferis, "Formative Evaluation of a Prototype System for Automated Analysis of Mass Spectrometry Data", AMIA Symposium, 2005 [Article] [Supplement]
A. Statnikov, I. Tsamardinos, Y. Dosbayev, C.F. Aliferis, "GEMS: A System for Automated Cancer Diagnosis and Biomarker Discovery from Microarray Gene Expression Data", International Journal of Medical Informatics, 2005 [Pubmed] [Supplement]
A. Statnikov, C.F. Aliferis, I. Tsamardinos. "Methods for Multi-Category Cancer Diagnosis from Gene Expression Data: A Comprehensive Evaluation to Inform Decision Support System Development", Medinfo, 2004;2004:813-7 [Article] [Appendix] [Supplement]
C. Aliferis, I. Tsamardinos, A. Statnikov, L.E. Brown. "Causal Explorer: A Probabilistic Network Learning Toolkit for Biomedical Discovery" In Proceedings of the 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS), June 23-26, 2003, Las Vegas, Nevada, USA, CSREA Press [Article] [Supplement]

Text Categorization and Information Retrieval

Y. Aphinyanaphongs, A. Statnikov, C.F. Aliferis "A Comparison of Citation Metrics to Machine Learning Filters for the Identification of High Quality MEDLINE Documents." J Am Med Inform Assoc., 2006 [Pubmed]
E.V.Bernstam, J.R.Herskovic, Y. Aphinyanaphons, C.F.Aliferis, M.G.Sriram, W.R. Hersh, "Using citation data to improve retrieval from MEDLINE" J Am Med Inform Assoc. 2006 Jan-Feb;13(1):96-105. [Pubmed]
S. Duda, C.F. Aliferis, R.A. Miller, A. Statnikov, K.B.Johnson, "Extracting Drug-Drug Interaction Articles from MEDLINE to Improve the Content of Drug Databases", AMIA Symposium, 2005 [Article]
Y. Aphinyanaphongs, I. Tsamardinos, A. Statnikov, D. Hardin, C. F. Aliferis "Text Categorization Models for High-Quality Article Retrieval in Internal Medicine" J Am Med Inform Assoc 2005; 12: 207-216. , USA [Pubmed] [Supplement]
Y. Aphinyanaphongs, C.F. Aliferis. "Learning Boolean Queries for Article Quality Filtering" In Proceedings of the 11th World Congress on Medical Informatics (MEDINFO), September 7-11, 2004, San Francisco, California, USA [Article]
Y. Aphinyanaphongs, C.F. Aliferis. "Text Categorization Models for Retrieval of High Quality Articles in Internal Medicine" In Proceedings of the 2003 American Medical Informatics Association (AMIA) Annual Symposium, November 8-12, 2003, Washington, DC, USA, pages 31-35 [Article]

Planning and Temporal Reasoning

M. E. Pollack, I. Tsamardinos, "Efficiently Dispatching Plans Encoded as Simple Temporal Problems", In Intelligent Techniques for Planning, Idea Group Publishing, Editors: Ioannis Vlahavas and Dimitris Vrakas, 2004
M. E. Pollack, L. Brown, D. Colbry, C. E. McCarthy, C. Orosz, B. Peintner, S. Ramakrishnan, and I. Tsamardinos, "Autominder: An Intelligent Cognitive Orthotic System for People with Memory Impairment" Robotics and Autonomous Systems, 44(3-4):273-282, 2003 [Article]
I. Tsamardinos and M. E. Pollack, "Efficient Solution Techniques for Disjunctive Temporal Reasoning Problems" Artificial Intelligence, 151(1-2):43-90, 2003 [Article]
I. Tsamardinos, T. Vidal, M. E. Pollack, "CTP: A New Constraint-Based Formalism for Conditional, Temporal Planning" Special Issue of Constraints Journal on Planning, 8(4):365-388, 2003 [Article]
I. Tsamardinos, M. E. Pollack, S. Ramakrishnan, "Assessing the Probability of Legal Execution of Plans with Temporal Uncertainty" In Proceedings of the International Conference on Automated Planning and Scheduling (ICAPS), Workshop on Planning under Uncertainty and Incomplete Information, June 9-13, 2003, Trento, Italy [Article]
Ioannis Tsamardinos, "A Probabilistic Approach to Robust Execution ofTemporal Plans with Uncertainty" Proceedings of the 2nd Greek National Conference on Artificial Intelligence, Thessaloniki, Greece, April 2002, p. 97108 [Article]
Martha E. Pollack, Colleen E. McCarthy, Sailesh Ramakrishnan, Ioannis Tsamardinos, "Execution Time Plan Management for a Cognitive Orthotic System" eds. M. Beetz and J. Hertzberg, Plan-Based Control of Robotic Agents, 2002 [Article]
M. E. Pollack, C. E .McCarthy, S. Ramakrishnan, I. Tsamardinos, L. Brown, S. Carrion, D. Colbry, C. Orosz, and B. Peintner, "Autominder: A Planning, Monitoring, and Reminding Assistive Agent" Proceedings of the 7th International Conference on Intelligent Autonomous Systems (IAS), March, 2002 [Article]
Alan Berfield, Panos K. Chrysanthis, Ioannis Tsamardinos, Martha E. Pollack, Sujata Banerjee, "A Scheme for Integrating e-Services in Establishing Virtual Enterprises" 12th International Workshop on Research Issues on Data Engineering, (RIDE-02) [Article]
I. Tsamardinos, "Constraint-based Temporal Reasoning Algorithms and Applications to Planning" Ph.D. Thesis: Intelligent Systems Program, August 2001, University of Pittsburgh, PA, USA [Thesis]
I. Tsamardinos, M. Pollack, P. Ganchev, "Flexible Dispatch of Disjunctive Temporal Plans" in Proceedings of Sixth European Conference on Planning, 2001 (ECP-01), Toledo, Spain, pp. 417—422 [Article]
I. Tsamardinos, M. E. Pollack, J. F. Horty, "Merging Plans with Quantitative Temporal Constraints, Temporally Extended Actions, and Conditional Branches" Proceedings of the 5th International Conference on AI Planning and Scheduling (AIPS 2000), Breckenridge, CO, April, 2000, pp264-272. Winner of the Outstanding Student Paper Award [Article]
M. E. Pollack, I. Tsamardinos and J. F. Horty, "Adjustable Autonomy for a Plan Management Agent" 1999 AAAI Spring Symposium on Adjustable Autonomy, Stanford, CA, March, 1999 [Article]
I. Tsamardinos, N. Muscettola, and P. Morris, "Fast Transformation of Temporal Plans for Efficient Execution" in Proceedings of the 15th National Conference on Artificial Intelligence, (AAAI'98), pp254-261 [Article]
N. Muscettola, P. Morris, and I. Tsamardinos, "Reformulation of Temporal Plans for Efficient Execution" in Proceedings of the 6th Conference Principles of Knowledge Representation and Reasoning (KR), 1998, pp444-452 [Article]
C. Bicchieri, M. Pollack, C. Rovelli, and I. Tsamardinos, "The Potential for the Evolution of Cooperation among Web Agents" in International Journal of Computer-Human Systems, 48(1): 9-29, 1998 [Article]
I. Tsamardinos, "Reformulating Temporal Plans for Efficient Execution" M.Sc. Dissertation; Intelligent Systems Program, July 1998, University of Pittsburgh, PA, USA [Thesis]

Generation of Bayesian Networks

I. Tsamardinos, A. Statnikov, L.E. Brown, C.F. Aliferis. "Generating Realistic Large Bayesian Networks by Tiling" In Proceedings of the 19th International Florida Artificial Intelligence Research Society (FLAIRS) Conference, 2006 [Article]

Other Articles

A. Statnikov, E. Kasparova, C.F. Aliferis. "Applying Decision Support Models in the Presence of Incomplete Evidence" , DSL TR-06-02, June 23, 2006, Vanderbilt University, Nashville, TN, USA [Article]
G.F. Cooper, V. Abraham , C.F. Aliferis, J. Aronis, B.G. Buchanan , R.Caruana, M. J. Fine, J.E. Janosky, G. Livingston, S. Monti, T. Mitchell, P. Spirtes, "Predicting Dire Outcomes of Patients with Community Acquired Pneumonia", Journal of Biomedical Informatics, 2005 [Pubmed]

Other Publications are available upon request. All DSL member publications listed in their CVs (including theses) are available electronically or in reprint/copy form by request.