Books
-
BLUM, C. D. MERKLE (editors):
Swarm
Intelligence - Introduction and Application.
- Springer, 2007 or 2008.
to be published.
-
MERKLE, D.: Ameisenalgorithmen -- Optimierung und
Modellierung.
- Institut für Angewandte Informatik und Formale
Beschreibungsverfahren, Universität Karlsruhe (TH), 2002.
211 pages.
International Journals
-
PERSEKE, M., G. FRIZSCH, K. RAMSCH, M. BERNT, D. MERKLE, M. MIDDENDORF, D. BERNHARD, P.F. STADLER M. SCHLEGEL: Phylogenetic analyses of mitochondrial genomes of
echinoderms challenge the monophyly of Eleutherozoa.
- accepted subject to minor changes for Molecular Phylogenetics and Evolution, 2007.
-
BERNT, M., D. MERKLE, K. RAMSCH, G. FRIZSCH, M. PERSEKE, D. BERNHARD, M. SCHLEGEL, P.F. STADLER, M. MIDDENDORF: CREx: Inferring Genomic Rearrangements Based on Common Intervals.
- accepted subject to minor changes for Bioinformatics, 2007.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Self-Organized Task Allocation for Service Tasks in Computing Systems with
Reconfigurable Components.
- accepted for Journal of Mathematical Modelling and Algorithms, 2007.
-
JANSON, S., D. MERKLE M. MIDDENDORF: Molecular Docking with Multi-Objective Particle Swarm Optimization.
- Applied Soft Computing, 2007.
to be published.
-
BERNT, M., D. MERKLE M. MIDDENDORF:
Using
Median Sets for Inferring Phylogenetic Trees.
- Bioinformatics, 23:e129-e135, 2007.
-
BERNT, M., D. MERKLE M. MIDDENDORF:
Genome Rearrangement Based on Reversals that Preserve Conserved Intervals.
- IEEE/ACM Transactions on Computational Biology and Bioinformatics,
3(3):275-288, 2006.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Modelling Ant Brood Tending Behaviour with Cellular Automata.
- Journal of Cellular Automata, 2(2):183-194, 2006.
-
MERKLE, D. C. BLUM: Swarm
Intelligence - An
optimization-based introduction.
- Künstliche Intelligenz, 4:5-10, 2005.
-
MERKLE, D. M. MIDDENDORF: Reconstruction of the
Cophylogenetic History of Related Phylogenetic Tree with Divergence Timing
Information.
- Theory in Biosciences, 123(4):277-299, 2005.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Decentralized Packet Clustering in Router-based Networks.
- International Journal of Foundations of Computer Science,
16(2):321-341, 2005.
-
MERKLE, D. M. MIDDENDORF: On solving
permutation scheduling problems with ant colony optimization.
- International Journal of Systems Science, 36(5):255-266, 2005.
-
MERKLE, D. M. MIDDENDORF: Dynamic
Polyethism
and Competition for Tasks in Threshold Reinforcement Models of Social
Insects.
- Adaptive Behavior, 12:251-262, 2004.
-
MERKLE, D. M. MIDDENDORF: Modelling
the
dynamics of ant colony optimization.
- Evolutionary Computation, 10(3):235-265, 2002.
-
MERKLE, D, M. MIDDENDORF H. SCHMECK:
- Ant colony optimization for resource-constrained project scheduling.
IEEE Transactions on Evolutionary Computation, 6(4):333-346,
2002.
-
MERKLE, D. M. MIDDENDORF: Fast ant
colony
optimization on runtime reconfigurable processor arrays.
- Genetic Programming and Evolvable Machines, 3(4):345-361, 2002.
-
MERKLE, D. and TH. WORSCH
- Formal language recognition by stochastic cellular
automata.
Fundamenta Informaticae, 52(1-3):183-201, 2002.
-
JANSON, S., D. MERKLE, M. MIDDENDORF, H. ELGINDY
H. SCHMECK: On enforced convergence of ACO
and its implementation on the reconfigurable mesh architecture using size
reduction tasks.
- Journal of Supercomuting, 26(3): 221-238,2003.
-
MERKLE, D M. MIDDENDORF: An ant
algorithm with
global pheromone evaluation for scheduling a single machine.
- Applied Intelligence., 18(1):105-111, 2002.
- submitted to International Journals
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Task Allocation in Organic Computing Systems: Networks with Reconfigurable
Helper Units.
- submitted.
- Book Chapters
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Swarm Intelligence in Organic Computing.
- BLUM, C. D. MERKLE (editors): Swarm Intelligence, Natural Computing. Springer,
2007.
to be published.
-
PETZOLD, E., A. VON HAESELER, D. MERKLE, M. MIDDENDORF
H.A. SCHMIDT: Phylogenetic Parameter Estimation on
COWs.
- ZOMAYA, A. (editor): Parallel
Computing in Bioinformatics and Computational Biology, 347-368. Wiley, 2006.
-
MERKLE, D. M. MIDDENDORF: Swarm Intelligence.
- BURKE, E. G. KENDALL (editors): Introductory Tutorials in Optimisation, Search and
Decision Support Methodology, 401-435. Springer, 2005.
-
JANSON, S., D. MERKLE M. MIDDENDORF: Parallel Ant Colony Algorithms.
- ALBA, E. (editors): Parallel
Metaheuristics, Wiley Book Series on Parallel and Distributed Computing,
171 - 201. Wiley, 2005.
-
MERKLE, D. M. MIDDENDORF: On the behaviour of
ant algorithms: Studies on simple problems.
- RESENDE, M.G.C. J.P.
DE SOUSA (editors): Metaheuristics: Computer
Decision-Making. page 465-480, Kluwer Academic Publisher, 2003.
- Publications in Conference Proceedings
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Swarm Controlled Emergence - Designing an Anti-Clustering Ant System.
- Proc. of the IEEE Swarm Intelligence Symposium
2007, 242-249. IEEE Press, 2007.
-
SCHEIDLER, A., D. MERKLE M. MIDDENDORF: Stability and Performance of Ant Queue Inspired Task Division Methods.
- Proc. of the European Conference on Complex
Systems, 2007.
accepted.
-
BERNT, M., D. MERKLE M. MIDDENDORF:
A
Fast and Exact Algorithm for the Perfect Reversal Median Problem.
- MANDOIU, ION ALEXANDER
ZELIKOVSKY (editors): Bioinformatics Research and
Applications, 4463 Lecture Notes
in Bioinformatics (LNBI), 305-316, 2007.
-
BERNT, M., D. MERKLE M. MIDDENDORF:
The
Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders.
- BERTHOLD, M.R., R. GLEN I. FISCHER (editors): Computational Life Sciences II - Proc.
2nd International Symposium CompLife, 4216
Lecture Notes in Bioinformatics (LNBI),
52-63, 2006.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Using Decentralized Clustering for Task Allocation in Networks with
Reconfigurable Helper Units.
- Proceedings of the International Workshop on
Self-Organizing Systems 2006 (IWSOS 2006), 4124
LNCS, 137-147. Springer, Berlin,
2006.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Self-Organized Task Allocation for Computing Systems with Reconfigurable
Components.
- Proceedings of the 9th International Workshop on
Nature Inspired Distributed Computing (NIDISC'06), 2006.
-
SCHEIDLER, A., D. MERKLE M. MIDDENDORF: Emergent Sorting Patterns and Individual Differences of Randomly Moving Ant
Like Agents.
- Proceedings of the 7th German Workshop on
Artificial Life (GWAL-7), 2006.
-
JANSON, S., D. MERKLE:
A New Multi-Objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking.
- Proc. of Hybrid Metaheuristics: Second International Workshop, HM 2005,
3636 Lecture Notes in Computer
Science (LNCS), 128-141. Springer Verlag, 2005.
-
BERNT, M., D. MERKLE M. MIDDENDORF: A
Parallel Algorithm for Solving the Reversal Median Problem.
- Proceedings of the Parallel Processing and Applied
Mathematics - Bio-Computing Workshop (PBC 2005), 3911
LNCS, 1089-1096, Berlin, 2006.
Springer.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Dynamic Decentralized Packet Clustering in Networks.
- ROTHLAUF ET AL., F. (editors):
Proceedings of the 2nd European Workshop on Evolutionary Algorithms in
Stochastic and Dynamic Environments, 3449
LNCS, 574-583, Berlin, 2005.
Springer.
-
JANSON, S., D. MERKLE M. MIDDENDORF: Decentralized Packet Clustering in Networks Applied to Particle Swarm
Optimization.
- Proceedings of the Conference on Design, Analysis,
and Simulation of Distributed Systems 2005 (DASD 2005), 3-10, 2005.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Modelling Ant Brood Tending with Cellular Automata.
- Proceedings of the Workshop on Modelling of
Complex Systems by Cellular Automata 2005 (ICCS 2005), 3515 LNCS, 412-419. Springer,
Berlin, 2005.
-
MERKLE, D. M. MIDDENDORF: Ant Colony
Optimization: Biological Motivation, Phase Structure, and Modelling.
- Proceedings of the first International Symposium
on Mathematical and Computational Biology (BIOMAT 2004), 2005.
-
MERKLE, D., M. MIDDENDORF A. SCHEIDLER: Decentralized Packet Clustering in Networks.
- Proceedings of the International Parallel and
Distributed Processing Symposium (IPDPS-2004), Sixth International Workshop
on Nature Inspired Distributed Computing (NIDISC'04). IEEE-CS Press, 9
pages, 2004.
-
MERKLE, D. M. MIDDENDORF: Competition
Controlled Pheromone Update for Ant Colony Optimization.
- DORIGO, M., M. BIRATTARI, C. BLUM,
L. M. GAMBARDELLA, F. MONDADA T. STÜTZLE (editors): Proceedings of the Fourth International Workshop on
Ant Colony and Swarm Intelligence (ANTS 2004), 3172
LNCS, 95-105, Berlin, 2004.
Springer.
-
MERKLE, D. M. MIDDENDORF: Dynamic Polyethism
in
Social Insect Societies - A Simulation Study.
- BALCH, T. C. ANDERSON. (editors): Proceedings of the 2nd International Workshop on
the Mathematics and Algorithms of Social Insects, 99-106,
Georgia Institute of Technology, Atlanta, 2003.
-
MERKLE, D., M. MIDDENDORF H. SCHMECK: Ant
colony optimization for resource-constrained project scheduling.
- WHITLEY, D., D. GOLDBERG, E. CANTU-PAZ, L. SPECTOR, I. PARMEE H.-G.
BEYER (editors): Proceedings of the Genetic and Evolutionary
Computation Conference (GECCO 2000), 893-900, San
Francisco, CA, USA, 2000. Morgan Kaufmann.
-
MERKLE, D. M. MIDDENDORF: An ant algorithm
with
a new pheromone evaluation rule for total tardiness problems.
- Proceeding of the EvoWorkshops 2000,
1803 Lecture Notes in Computer
Science (LNCS), 287-296. Springer Verlag, 2000.
-
IREDI, S., D. MERKLE M. MIDDENDORF: Bi-criterion optimization with multi colony ant algorithms.
- ZITZLER, E., K. DEB, L. THIELE, C.A. COELLO COELLO D. CORNE (editors):
First International Conference on Evolutionary Multi-Criterion
Optimization (EMO'01), 1993 Lecture Notes in Computer Science (LNCS), 359-372, Berlin,
2001. Springer.
-
MERKLE, D. M. MIDDENDORF: Studies on the
dynamics of ant colony optimization algorithms.
- Proceedings of the Genetic and Evolutionary
Computation Conference (GECCO-2002), 105-112, San
Francisco, CA, USA, 2002. Morgan Kaufmann.
-
MERKLE, D. M. MIDDENDORF: Modelling
ACO:
Composed permutation problems.
- DORIGO, M, G. DI CARO M. SAMPELS (editors): Proceedings of 3rd International
Workshop on Ant Algorithms (ANTS'2002),12.-14. September Brssel, Belgien,
2463 Lecture Notes in Computer
Science (LNCS), 149-162, Berlin, 2002. Springer.
-
MERKLE, D. M. MIDDENDORF: A new approach to
solve permutation scheduling problems with ant colony optimization.
- Second European Workshop on Scheduling and
Timetabling (EvoStim2001), 2037 Lecture Notes in Computer Science (LNCS), 484-493.
Springer Verlag, 2001.
-
MERKLE, D. M. MIDDENDORF: Ant colony
optimization with the relative pheromone evaluation method.
- Proceedings of the 3rd European Workshop on
Scheduling and Timetabling and 3rd European Workshop on
Evolutionary Methods for AI Planning, 2279
Lecture Notes in Computer Science (LNCS),
325-333, 2002.
-
BRANKE, J., M. DECKER D. MERKLE: Coevolutionary Ant Algorithms for Playing Games.
- DORIGO, M, G. DI CARO M. SAMPELS (editors): Proceedings of 3rd International
Workshop on Ant Algorithms (ANTS'2002),12.-14. September Brssel, Belgien,
2463 Lecture Notes in Computer
Science (LNCS), 298-299, Berlin, 2002. Springer.
-
JANSON, S., D. MERKLE, M. MIDDENDORF, H. ELGINDY
H. SCHMECK: On enforced convergence of ACO
and its implementation on the reconfigurable mesh architecture using size
reduction tasks.
- Proceedings of the Second International Conference
on Engineering of Reconfigurable Systems and Algorithms (ERSA'02),
3-9, 2002.
-
MERKLE, D. M. MIDDENDORF: Dynamic
Polyethism in Social Insect Societies - A Simulation Study.
- Proceedings of the 2nd International Workshop on the Mathematics
and Algorithms of Social Insects, Atlanta, USA, 2003.
-
MERKLE, D. M. MIDDENDORF: Collective
optimization: The artificial ants way.
- Abstracts of the Workshop From Worker to
Colony: Understanding the Organisation of Insect Societies,
Cambridge, UK, 2001. Isaac Newton Institute for Mathematical
Sciences.
-
MERKLE, D. M. MIDDENDORF: Fast ant colony
optimization on reconfigurable processor arrays.
- Proceedings of the 15th International Parallel and
Distributed Processing Symposium (IPDPS-01). IEEE Computer Society Press,
2001.
-
MERKLE, D. M. MIDDENDORF: On the behaviour of
ant algorithms: Studies on simple problems.
- Proceedings of the 4th Metaheuristics
International Conference (MIC' 2001), Porto, Portugal,
573-577, 2001.
-
MERKLE, D. M. MIDDENDORF: Prospects for
dynamic
algorithm control: Lessons from the phase structure of ant scheduling
algorithms.
- HECKENDORN, R.B. (editors): Proceedings of the 2001 Genetic and Evolutionary Computation Conference -
Workshop Program, 121-126, San Francisco, CA, USA, 2001.
Morgan Kaufmann.
-
MERKLE, D., M. MIDDENDORF H. SCHMECK: Ant
colony optimization for the RCPSP using weighted summation
evaluation.
- Abstract Proceedings of the ANTS'2000 - From
Ant Colonies to Artificial Ants: Second International Workshop
on Ant Algorithms, 84-87, 2000.
-
MERKLE, D., M. MIDDENDORF H. SCHMECK: Pheromone evaluation in ant colony optimization.
- Proceedings of the 26th Annual Conference of
the IEEE Electronics Society IECON-2000 (2000 IEEE International
Conference on Industrial Electronics, Control and Instrumentation),
Third Asia-Pacific Conference on Simulated Evolution and
Learning (SEAL2000), 2726-2731, Piscataway, USA,
2000. IEEE Press.
- Book Review
-
MERKLE, D. M. MIDDENDORF: Bookreview on ``Ant
Colony Optimization'' by M. Dorigo, T. Stützle.
- European Journal of Operations Research, 168(1):269-271, 2005.
- Other Publications
-
JANSON, S., D. MERKLE M. MIDDENDORF: Solving Molecular Docking Problems with Particle Swarm Optimization.
- Abstracts of 3rd Biotechnolgy Symposium 2006,
Center of Biotechnolgy and Biomedicine, University of Leipzig,
77, 2006.
-
BERNT, M., D. MERKLE M. MIDDENDORF: From
Genome Rearrangements to Phylogenies.
- Abstracts of 3rd Biotechnolgy Symposium 2006,
Center of Biotechnolgy and Biomedicine, University of Leipzig,
59, 2006.
-
PETZOLD, E., A. VON HAESELER, D. MERKLE M. MIDDENDORF: Efficient Parallel Parameter Estimation for Maximum
Likelihood Reconstruction of Phylogenetic Trees.
- Abstracts of 3rd Biotechnolgy Symposium 2004,
Center of Biotechnolgy and Biomedicine, University of Leipzig,
228, 2004.
-
MERKLE, D., M. MIDDENDORF R. LEGAT: Reconstruction of Host-Parasite Phylognies with Extinction Events.
- Abstracts of 3rd Biotechnolgy Symposium 2004,
Center of Biotechnolgy and Biomedicine, University of Leipzig,
227, 2004.
-
BERNT, M., D. MERKLE M. MIDDENDORF: Solving the Multiple Genome Rearrangement Problem.
- Abstract Proceedings of the 19th Dubrovnik
International Course and Conference on the Interfaces Among Mathematics,
Chemistry and Computer Sciences (MCC 2004), 6. 2004.
-
MERKLE, D. M. MIDDENDORF: Combined
Phylogenies:
Hosts and Their Parasites.
- Abstract Proceedings of the 19th Dubrovnik
International Course and Conference on the Interfaces Among Mathematics,
Chemistry and Computer Sciences (MCC 2004), 46, 2004.
-
MERKLE, D. M. MIDDENDORF: Modelling the
dynamics of ant colony optimization.
- TechReport 412, Institut AIFB, Universitt Karlsruhe, 2001.
-
MERKLE, D., M. MIDDENDORF H. SCHMECK: Ant
colony optimization for resource-constrained project scheduling.
- TechReport 409, Institut AIFB, Universitt Karlsruhe, 2001.
-
MERKLE, D. TH. WORSCH: Formal language
recognition by stochastic cellular automata.
- TechReport 392, Institut AIFB, Universitt Karlsruhe, 1999.