Publications by Kamran Karimi:
Thesis Works:
Refereed Journal Papers:
- Malcolm E Fisher, Christina James-Zorn, Virgilio Ponferrada, Andrew J Bell, Nivitha Sundararaj, Erik Segerdell, Praneet Chaturvedi, Nadia Bayyari,
Stanley Chu, Troy Pells, Vaneet Lotay, Sergei Agalakov, Dong Zhuo Wang, Bradley I Arshinoff, Saoirse Foley, Kamran Karimi, Peter D Vize, Aaron M Zorn,
Xenbase: key features and resources of the Xenopus model organism knowledgebase,
Genetics, Volume 224, Issue 1, iyad018, 2023
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- Malcolm E Fisher, Erik Segerdell, Nicolas Matentzoglu, Mardi J Nenni, Joshua D Fortriede, Stanley Chu, Troy J Pells, David Osumi-Sutherland, Praneet Chaturvedi,
Christina James-Zorn, Nivitha Sundararaj, Vaneet S Lotay, Virgilio Ponferrada, Dong Zhuo Wang, Eugene Kim, Sergei Agalakov, Bradley I Arshinoff, Kamran Karimi,
Peter D Vize, Aaron M Zorn,
The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development,
BMC Bioinformatics, 22;23(1):99, 2022
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- Bradley I Arshinoff, Gregory A Cary, Kamran Karimi, Saoirse Foley, Sergei Agalakov, Francisco Delgado, Vaneet S Lotay, Carolyn J Ku, Troy J Pells, Thomas R Beatman,
Eugene Kim, R Andrew Cameron, Peter D Vize, Cheryl A Telmer, Jenifer C Croce, Charles A Ettensohn, Veronica F Hinman,
Echinobase: leveraging an extant model organism database to build a knowledgebase supporting research on the genomics and biology of echinoderms,
Nucleic Acids Research, gkab1005, 2022
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- Kamran Karimi, Sergei Agalakov, Cheryl A Telmer, Thomas R Beatman, Troy J Pells, Bradley Im Arshinoff, Carolyn J Ku, Saoirse Foley, Veronica F Hinman, Charles A Ettensohn, Peter D Vize,
Classifying domain-specific text documents containing ambiguous keywords,
Database, Volume 2021, baab062, 2021
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- Saoirse Foley, Carolyn Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D. Vize, Veronica Hinman,
Integration of 1:1 orthology maps and updated datasets into Echinobase,
Database, Volume 2021, baab030, 2021
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- Joshua D. Fortriede, Troy J. Pells, Stanley Chu, Praneet Chaturvedi, DongZhuo Wang, Malcom E. Fisher, Christina James-Zorn, Ying Wang, Mardi J. Nenni,
Kevin A. Burns, Vaneet S. Lotay, Virgilio G. Ponferrada, Kamran Karimi, Aaron M. Zorn, Peter D. Vize,
Xenbase: deep integration of GEO & SRA RNA-seq and ChIP-seq data in a model organism database,
Nucleic Acids Research (NAR), Volume 48, Issue D1, pp. D776–D782, 2020
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- Daniel M. Wuitchik, DongZhuo Wang, Troy J. Pells, Kamran Karimi, Selina Ward, Peter D. Vize,
Seasonal temperature, the lunar cycle and diurnal rhythms interact in a combinatorial manner to modulate genomic responses to the environment in a reef-building coral,
Molecular Ecology, doi:10.1111/mec.15173, 2019
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- Mardi J. Nenni, Malcolm E. Fisher, Christina James-Zorn, Troy J. Pells, Virgilio Ponferrada, Stanley Chu, Joshua D. Fortriede, Kevin A. Burns, Ying Wang,
Vaneet S. Lotay, Dong Zhou Wang, Erik Segerdell, Praneet Chaturvedi, Kamran Karimi, Peter D. Vize, Aaron M. Zorn, Xenbase: Facilitating the Use of Xenopus to Model Human Disease,
Frontiers in physiology,Volume 10, Article 154, 2019
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- Kamran Karimi, Daniel M. Wuitchik, Matthew J. Oldach, Peter D. Vize, Distinguishing Species Using GC Contents in Mixed DNA or RNA Sequences,
Evolutionary Bioinformatics,Volume 14, Issue January 1, 2018, 2018
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- Kamran Karimi, Joshua D. Fortriede, Vaneet S. Lotay, Kevin A. Burns, Dong Zhou Wang, Malcom E. Fisher,
Troy J. Pells, Christina James-Zorn, Ying Wang, V.G. Ponferrada, Stanley Chu, Praneet Chaturvedi, Aaron M. Zorn,
Peter D. Vize, Xenbase: a genomic, epigenomic and transcriptomic model organism database,
Nucleic Acids Research (NAR),Volume 46, Issue D1, pp. D861-D868, 2018
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- A.M. Session, Y. Uno, T. Kwon, J.A. Chapman, A. Toyoda, S. Takahashi, A. Fukui, A. Hikosaka, A. Suzuki, M Kondo, S.J. van Heeringen,
I. Quigley, S. Heinz, H. Ogino, H. Ochi, U. Hellsten, J.B. Lyons, O. Simakov, N. Putnam, J. Stites,
Y. Kuroki, T. Tanaka, T. Michiue, M. Watanabe, O. Bogdanovic, R. Lister, G. Georgiou, S.S. Paranjpe, I. van Kruijsbergen,
S. Shu, J. Carlson, T. Kinoshita, Y. Ohta, S. Mawaribuchi, J. Jenkins, J. Grimwood, J. Schmutz, T. Mitros, S.V. Mozaffari,
Y. Suzuki, Y. Haramoto, T.S. Yamamoto, C. Takagi, R. Heald, K. Miller,
C. Haudenschild, J. Kitzman, T. Nakayama, Y. Izutsu, J. Robert, J. Fortriede,
K. Burns, V. Lotay, K. Karimi, Y. Yasuoka, D.S. Dichmann, M.F. Flajnik,
D.W. Houston, J. Shendure, L. DuPasquier, P.D. Vize, A.M. Zorn, M. Ito, E. Marcotte, J.B. Wallingford, Y. Ito, M. Asashima, N. Ueno,
Y. Matsuda, G.J.C. Veenstra, A. Fujiyama, R.M. Harland, M. Taira, D.S. Rokhsar,
Genome evolution in the allotetraploid frog Xenopus laevis,
Nature, Volume 538 Number 7625, 2016
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- Christina James-Zorn, Virgillio G. Ponferrada, Kevin A. Burns, Joshua D. Fortriede,
Vaneet S. Lotay, Yu Liu, J. Brad Karpinka, Kamran Karimi, Aaron M. Zorn, and Peter D. Vize,
Xenbase; core features, data acquisition and data processing,
genesis, The Journal of Genetics and Development, 53 (8), 486-497, 2015
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- Peter D. Vize, Yu Liu and Kamran Karimi,
Database and informatic challenges in representing both diploid and tetraploid Xenopus species in Xenbase,
Cytogenetic and Genome Research, 145:278-282, 2015
- J. Brad Karpinka, Joshua D. Fortriede, Kevin A. Burns, Christina James-Zorn, Virgilio
G. Ponferrada, Jacqueline Lee, Kamran Karimi, Aaron M. Zorn, and Peter D. Vize,
Xenbase, the Xenopus model organism database; new virtualized system, data types
and genomes,
Nucleic Acids Research (NAR), 43 (D1): D756-D763, 2015
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- Kamran Karimi and Peter D. Vize, The Virtual Xenbase: transitioning an
online bioinformatics resource to a private cloud,
Database, doi: 10.1093/database/bau108, 2014
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- Kamran Karimi, Aleks G. Pamir, M. Haris Afzal, Accelerating a
Cloud-Based Software GNSS Receiver,
International Journal of Grid and High Perfprmace
Computing (IJGHPC), Volum3 6, Number 3, 2014
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- N.G. Dickson, M.W. Johnson, M.H. Amin, R. Harris, F. Altomare, A.J.
Berkley, P. Bunyk, J. Cai, E.M. Chapple, P. Chavez, F. Cioata, T. Cirip,
P. deBuen, M. Drew-Brook, C. Enderud, S. Gildert, F. Hamze, J.P. Hilton,
E. Hoskinson, K. Karimi, E. Ladizinsky, N. Ladizinsky, T. Lanting, T.
Mahon, R. Neufeld, T. Oh, I. Perminov, C. Petroff, A. Przybysz, C. Rich, P.
Spear, A. Tcaciuc, M.C. Thom, E. Tolkacheva, S. Uchaikin, J. Wang, A.B.
Wilson, Z. Merali, G. Rose, Thermally assisted quantum annealing of
a 16-qubit problem,
Nature Communications 4, article number:1903,
doi:10.1038/ncomms2920, 2013
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- Kamran Karimi, Challenges of Upgrading a Virtual Appliance,
Journal of Emerging Trends in Computing and Information Sciences,
Volume 3, Number 7, 2012
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- Kamran Karimi, Neil G. Dickson, Firas Hamze, M.H.S. Amin, Marshall
Drew-Brook, Fabian A. Chudak, Paul I. Bunyk, William G. Macready, Geordie
Rose, Investigating the Performance of an Adiabatic Quantum Optimization
Processor,
Quantum Information Processing, Volume 11, Number 1, 2012
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- M.W. Johnson, M.H.S. Amin, S. Gildert, T. Lanting, F. Hamze, N.
Dickson, R.Harris, A.J. Berkley, J. Johansson, P. Bunyk, E.M. Chapple, C.
Enderud, J.P. Hilton, K. Karimi, E. Ladizinsky, N. Ladizinsky, T. Oh, I.
Perminov, C. Rich, M.C. Thom, E. Tolkacheva, C.J.S. Truncik, S.
Uchaikin, J.Wang, B.Wilson, G. Rose, Quantum annealing with
manufactured spins,
Nature, Volume 473 Number 7346, 2011
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- Neil G. Dickson, Kamran Karimi, Firas Hamze, Importance of
Explicit Vectorization for CPU and GPU Software Performance,
Journal of Computational Physics, Volume 230, Issue 13, 2011
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- Kamran Karimi, Neil G. Dickson, Firas Hamze, High-Performance Physics
Simulations Using Multi-Core CPUs and GPGPUs in a Volunteer Computing
Context,
International Journal of High Performance Computing Applications.,
Volume 25, issue 1, 2011
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- Kamran Karimi and Howard J. Hamilton, Generation and Interpretation of
Temporal Decision Rules,
International Journal of Computer Information Systems and Industrial
Management Applications(IJCISIM), Volume 3, pp. 314-323, 2011
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- Firas Hamze, Neil Dickson, Kamran Karimi, Robust Parameter Selection
for Parallel Tempering,
International Journal of Modern Physics C, Volume 21, issue 5,
2010.
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- R. Harris, M.W. Johnson, T. Lanting, A.J. Berkley, J. Johansson, P.
Bunyk, E. Tolkacheva, E. Ladizinsky, N. Ladizinsky, T. Oh, F. Cioata, I.
Perminov, P. Spear, C. Enderud, C. Rich, S. Uchaikin, M.C. Thom, E.M.
Chapple, J. Wang, B. Wilson, M.H.S. Amin, N. Dickson, K. Karimi, B.
Macready, C.J.S. Truncik, G. Rose, Experimental Investigation of an
Eight-Qubit Unit Cell in a Superconducting Optimization Processor,
Physical Review B 82 02411, 2010
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- Xing Li, Howard J. Hamilton, Kamran Karimi, Liqiang Geng, The
Multi-Tree Cubing Algorithm for Computing Iceberg Cubes,
Journal of Intelligent Information Systems (JIIS), Volume 33, Number
2, pp. 179-208, 2009
Book Chapters:
- Christina James-Zorn, Virgilio Ponferrada, Malcolm E. Fisher, Kevin Burns, Joshua Fortriede, Erik Segerdell,
Kamran Karimi, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy Pells, Ying Wang, Peter D. Vize, Aaron Zorn,
Navigating Xenbase: An Integrated Xenopus Genomics and Gene Expression Database,
In: Martin Kollmar (Ed.), Eukaryotic Genomic Databases. Methods in Molecular Biology, Volume 1757, Chapter 10, pp. 251-305, Humana Press, New York, 2018
Refereed Conference Papers:
- Kamran Karimi and Howard J. Hamilton,Using Dependence Diagrams to
Summarize Decision Rule Sets,
The Twenty-first Canadian Artificial Intelligence Conference
(AI'2008), Windsor, Canada, May 2008
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- Kamran Karimi and Mohsen Sharifi, Transparent Distributed Programming
under Linux,
The 20th International Symposium on High Performance Computing Systems
and Applications (HPCS'2006), St. John's, Canada, May 2006
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- Kamran Karimi, Mehran Mehrandezh, and Howard J. Hamilton, A Proposal
for Self-Recognition in Robot Programming,
The 18th Annual Canadian Conference on Electrical and Computer
Engineering (CCECE'2005) , Saskatoon, Canada, May 2005
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- Howard J. Hamilton and Kamran Karimi, The TIMERS II Algorithm for the
Discovery of Causality,
The Ninth Pacific-Asia Conference on Knowledge Discovery and Data Mining
(PAKDD'2005), Hanoi, Vietnam, May 2005
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- Kamran Karimi and Howard J. Hamilton, Discovering
Temporal/Causal Rules: A Comparison of Methods,
The Sixteenth Canadian Artificial Intelligence Conference (AI'2003),
Halifax, Nova Scotia, Canada, June 2003, pp. 175-189
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- Kamran Karimi, Back to the Future: Changing the Direction of Time for
the Discovery of Causality,
Student Paper at The Sixteenth Canadian Artificial Intelligence
Conference (AI'2003), Halifax, Nova Scotia, Canada, June 2003, pp.
624-626
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- Kamran Karimi and Howard J. Hamilton, Distinguishing Causal and
Acausal Temporal Relations,
The seventh Pacific-Asia Conference on Knowledge Discovery and Data
Mining (PAKDD'2003), Seoul, South Korea, April/May 2003, pp. 234-240
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- Kamran Karimi and Howard J. Hamilton, TimeSleuth: A Tool for
Discovering Causal and Temporal Rules,
14th IEEE International Conference On Tools with Artificial Intelligence
(ICTAI'2002), Washington DC, USA, November 2002, pp. 375-380
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- Kamran Karimi and Howard J. Hamilton, Discovering Temporal Rules from
Temporally Ordered Data,
The Third International Conference on Intelligent Data Engineering and
Automated Learning (IDEAL'2002), Manchester, UK, August 2002, pp.
25-30
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- Kamran Karimi and Howard J. Hamilton, RFCT: An Association-Based
Causality Miner,
The Fifteenth Canadian Conference on Artificial Intelligence (AI'2002)
, Calgary, Alberta, Canada, May 2002, pp. 334-338
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- Kamran Karimi and Howard J. Hamilton, Logical Decision Rules: Teaching
C4.5 to Speak Prolog,
The Second International Conference on Intelligent Data Engineering and
Automated Learning (IDEAL'2000), Hong Kong, December 2000, pp. 85-90
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- Kamran Karimi and Howard J. Hamilton, Learning With C4.5 in a
Situation Calculus Domain,
The Twentieth SGES International Conference on Knowledge Based Systems
and Applied Artificial Intelligence (ES'2000), Cambridge, UK, December
2000. pp. 73-85
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- Kamran Karimi, Julia A. Johnson and Howard J. Hamilton, A Proposal for
Including Behavior in the Process of Object Similarity Assessment with
Examples from Artificial Life,
The Second International Conference on Rough Sets and Current Trends in
Computing (RSCTC'2000), Banff, Alberta, Canada, October 2000, pp.
603-607
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- Kamran Karimi and Howard J. Hamilton, Finding Temporal Relations:
Causal Bayesian Networks vs. C4.5,
The Twelfth International Symposium on Methodologies for Intelligent
Systems (ISMIS'2000), Charlotte, North Carolina, USA, October 2000, pp.
266-273
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- Kamran Karimi, Howard Hamilton and Scott Goodwin, Divide and
(Iteratively) Conquer!,
The International Conference on Artificial Intelligence
(IC-AI'2000), Las Vegas, Nevada, USA, June 2000, pp. 595-601
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- Kamran Karimi, The Iterative Multi-Agent Method for Solving Complex
Search Problems,
The Thirteenth Canadian Conference on Artificial Intelligence
(AI'2000), Montréal, Québec, Canada, May 2000, pp. 369-378
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- Kamran Karimi, Michael Schmitz and Mohsen Sharifi, DIPC: A
Heterogeneous Distributed Programming System,
The Third International Annual Computer Society of Iran Computer
Conference (CSICC'97), Tehran, Iran, December 1997, pp. 126-130
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- Kamran Karimi and Mohsen Sharifi, DIPC: A System Software Solution for
Distributed Programming,
Parallel and Distributed Processing Techniques and Applications
Conference (PDPTA'97), Las Vegas, Nevada, USA, June/July 1997 pp.
218-221
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- Kamran Karimi and Mohsen Sharifi, DIPC: The Linux Way of Distributed
Programming,
The 4th International Linux Conference, Würzburg, Germany, May
1997
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Patents:
Richard Harris, Geordie Rose, Kamran Karimi,
Systems and Methods for Quantum Computation Using Real Physical
Hardware, WO/2010/151581 A3
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Workshop Proceedings:
- Kamran Karimi (Ed.), Proceedings of the Workshop on
Causality and Causal Discovery,
In Conjunction with the Seventeenth Canadian Conference on
Artificial Intelligence (AI'2004), London, Ontario, 2004
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Publicly Available Papers:
- Leonid Peshkin, Alexander Lukyanov, Marian Kalocsay, Robert Michael Gage, DongZhuo Wang, Troy J. Pells, Kamran Karimi, Peter D. Vize, Martin Wühr,
Marc W. Kirschner, The protein repertoire in early vertebrate embryogenesis,
https://www.biorxiv.org/content/10.1101/571174v1
- Kamran Karimi, A Brief Introduction to Temporality and
Causality,
http://arxiv.org/abs/1007.2449
- Kamran Karimi, Neil G. Dickson, Firas Hamze, A Performance
Comparison of CUDA and OpenCL,
http://arxiv.org/abs/1005.2581
- Kamran Karimi, The Feasibility of Using OpenCL Instead of OpenMP for Parallel CPU Programming,
http://arxiv.org/abs/1503.06532
Professional Journal Papers:
- Mohsen Sharifi and Kamran Karimi, DIPC: The Linux Way of Distributed
Programming,
Linux Journal,
Issue 57, January 1999, pp. 10-17
Workshop Papers:
- Kamran Karimi and Howard J. Hamilton, From Temporal Rules to One
Dimensional Rules,
Proceedings of the Workshop on Causality and Causal Discovery, Technical
Report CS-2004-02, Kamran Karimi (Ed.). Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, May 2004, pp 30-44
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Technical Reports:
- Kamran Karimi, Reversibility in Evolutionary Algorithms,
Technical Report 06-015, School of Computer Science, University of
Windsor, Windsor, Ontario, Canada, May 2006
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- Kamran Karimi and Howard J. Hamilton, An Extension to the TIMERS
Method,
Technical Report CS-2005-02, Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, March 2005
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- Kamran Karimi and Howard J. Hamilton, Problem Solving with Limited
Knowledge: Pruning Attributes in Classification Rules,
Technical Report CS-2004-04, Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, June 2004
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- Kamran Karimi and Howard J. Hamilton, Discovering Causality and
Acausality in Temporal Data,
Technical Report CS-2003-02, Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, February 2003
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- Kamran Karimi and Howard J. Hamilton, Learning Causal Rules,
Technical Report CS-2001-03, Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, December 2001
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- Kamran Karimi and Howard J. Hamilton, Temporal Rules and Temporal
Decision trees: A C4.5 Approach,
Technical Report CS-2001-02, Department of Computer Science,
University of Regina, Regina, Saskatchewan, Canada, December 2001
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