T. Hartmann, M. Bernt, M. Middendorf
An Exact Algorithm for Sorting by Weighted Preserving Genome Rearrangements
accepted for the Sixtheenth Asia Pacific Bioinformatics Conference (APBC2018)

T. Hartmann, N. Wieseke, R. Sharan, M. Middendorf, M. Bernt
Genome Rearrangement with ILP
accepted for the Fifteenth Asia Pacific Bioinformatics Conference (APBC2017)

S. Volke, G. Scheuermann, M. Middendorf
Coarse-Graining Large Search Landscapes using Massive Edge Collapse
accepted for TopoInVis 2017

Y.-C. Cheng, T. Hartmann, P.-Y. Tsai, M. Middendorf
Population Based Ant Colony Optimization for Reconstructing ECG Signals
Proc. 19th European Conference on Applications of Evolutionary Computation (EvoApplications 2016), LNCS 9597, 770-785, 2016.

R. L. V. Moritz, E. Reich, M. Bernt, M. Middendorf
A Property Preserving Method for Extending a Single-objective Problem Instance to Multiple Objectives with Specific Correlations
Proc. 16th European Conference on Evolutionary Computation in Combinatorial Optimization (EvoCOP 2016), LNCS 9595, 18-33, 2016.

Martin Clauß, Lydia Lotzmann, Martin Middendorf
A Population Based ACO Algorithm for the Combined Tours TSP Problem
accepted for BICT 2015

T. Gernat, W. Deng, V. Rao, M. Middendorf, N.D. Goldenfeld, H. Dankowicz, G.E. Robinson
Automated tracking of individuals reveals temporal structure and resiliency of honey bee social networks
accepted for Conference on Complex systems (CCS 2015), Tempe Arizona, 2015

S. Volke, D. Zeckzer, G. Scheuermann, M. Middendorf
A Visual Method for Analysis and Comparison of Search Landscapes
Proc. Genetic and Evolutionary Computation Conference (GECCO 2015), 497-504, 2015.

R. L. V. Moritz, M. Middendorf
Evolutionary Mechanisms in Multi-Objective Multi-Agent Systems Solving Multi-Agent Tasks
Proc. Genetic and Evolutionary Computation Conference (GECCO 2015), 65-72, 2015.

S. Volke, D. Zeckzer, M. Middendorf, G. Scheuermann
Visualizing Topological Properties of the Search Landscape of Combinatorial Optimization Problems
accpeted for TopoInVis 2015 workshop

N. Wieseke, T. Hartmann, M. Bernt, M. Middendorf
Cophylogenetic Reconciliation with ILP
Thirteenth Asia-Pacific Bioinformatics Conference (APBC 2015), Hsinchu, Taiwan, 2015.

S. Bin, S. Volke, G. Scheuermann, M. Middendorf
Comparing the Optimization Behaviour of Heuristics with Topology Based Visualization
Proc. 3rd International Conference on the Theory and Practice of Natural Computing (TPNC 2014), LNCS 8890, 47 - 58, 2014

R. L.V. Moritz, E. Reich, M. Bernt, M. Middendorf
The Influence of Correlated Objectives on Different Types of P-ACO Algorithms
Proc. 14th European Conference on Evolutionary Computation in Combinatorial Optimisation (EvoCOP 2014), LNCS 8600,230-241.

M. Bernt, N. Wieseke, and M. Middendorf
On Weighting Schemes for Gene Order Analysis
Proc. of the German Conference on Bioinformatics (GCB 2013), OASIcs Vol. 34, 14-23, 2013
link

N. Wieseke, M. Bernt, M. Middendorf
Unifying Parsimonious Tree Reconciliation
Proc. 13th Workshop on Algorithms in Bioinformatics (WABI 2013), LNBI 8126, 200-214, 2013
link

R. L. V. Moritz, M. Middendorf
Self-adaptable Group Formation of Reconfigurable Agents in Dynamic Environments
Proceedings of the Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2013), Springer, Studies in Computational Intelligence, Vol. 512, 287 - 301, 2013

R. L. V. Moritz, E. Reich, M. Schwarz, M. Bernt, and M. Middendorf
Refined Ranking Relations for Multi Objective Optimization and Application to P-ACO
Proceedings of the Fifteenth Annual Conference on Genetic and Evolutionary Computation (GECCO '13), 65-72, 2013
link

Y.-C. Lin. Martin Middendorf
Simple Probabilistic Population Based Optimization for Combinatorial Optimization
Proc. IEEE Symposium on Swarm Intelligence, 213-220, 2013

M. Clauß, M. Bernt. M. Middendorf
A Common Interval Guided ACO Algorithm for Permutation Problems
Proc. IEEE Symposium on Swarm Intelligence, 64-71, 2013

R. L. V. Moritz, M. Middendorf
Self-Organized Cooperation between Agents that have to Solve Resource Collection Tasks
Proc. IEEE Symposium on Swarm Intelligence, 206-212, 2013

R. L. V. Moritz, M. Bernt, and M. Middendorf
Annotation Guided Local Similarity Search in Multiple Sequences and its Application to Mitochondrial Genomes
Proc. 12th IEEE International Conference on Bioinformatics & Bioengineering (BIBE),157-162, 2012
Link

M. Bernt, K.-M. Chao, J.-W. Kao, M. Middendorf, E. Tannier
Preserving Inversion Phylogeny Reconstruction
Algorithms in Bioinformatics 2012, Lecture Notes in Computer Science, Vol. 7534, Springer, pp. 1-13
appendix
link

M. Bernt, M. Middendorf
A Method for Computing an Inventory of Metazoan Mitochondrial Gene Order Rearrangements.
Ninth Annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB CG), 2011.

K. Diwold, D. Himmelbach, R. Meier, C. Baldauf, M. Middendorf
Bonding as a Swarm: Applying Bee Nest-Site Selection Behaviour to Protein Docking
Proc. 13th Annual Conference on Genetic and Evolutionary Computation (GECCO 2011), 2011.

R. Moritz, K. Ramsch, M. Middendorf
Trophallaxis-Inspired Self-Organised Task Exchange in Heterogeneous Swarms
Proc. IEEE Swarm Intelligence Symposium (SIS2011), pp. 8, 2011.

W. Cheng, M. Middendorf, B. Scheuermann
Quick-ACO: Accelerating Ant Decisions and Pheromone Updates in ACO
Proc. EvoCOP'11, LNCS 6622, 238-249, 2011.

K. Diwold, T. Ruhnke, M. Middendorf
Sensor Placement in Water Networks Using a Population-Based Ant Colony Optimization Algorithm
Proc. Second International Conference on Computational Collective Intelligence - Technologies and Applications (ICCCI-2010), Springer, LNAI 6423, 426-437, 2010.

K. Diwold, M. Beekman, M. Middendorf
Bee Nest Site Selection as an Optimization Process
Proc. 12th International Conference on the Synthesis and Simulation of Living Systems (Alife XII), The MIT Press, 626-633, 2010.

M. Middendorf, B. Scheuermann
Perspectives of Extending Runtime Reconfigurable Computing to the Enterprise Application Domain
Accepted for 8th IEEE International Conference on Indutstrial Informatics (INDIN 2010), July 13-16, Osaka, Japan.

A. Aderhold, K. Diwold, A. Scheidler, and M. Middendorf
Artificial Bee Colony Optimization: A new Selection Scheme and its Performance
Proc. International Workshop on Nature Inspired Cooperative Strategies for Optimization (NICSO 2010), Springer, Studies in Computational Intelligence, Vol. 284/2010, 283-294, 2010.

A. Scheidler, M. Middendorf
Invited Talk: Communication Patterns in Decentralized Learning Classifier Systems
Proc. Autonomics 2009, Lecture Notes of ICST (LNICST)

K. Diwold, A. Scheidler, M. Middendorf
The Effect of Spatial Organisation in Response Threshold Models for Social Insects
accpeted for European Conference on Complex Systems (ECCS’09), 21-25 September 2009, University of Warwick, UK

M. Hellmuth, D. Merkle, M. Middendorf
On the Design of RNA Sequences for Realizing Extended Shapes
Proc. International Joint Conferences on System Biology, Bioinformatics and Intelligent Computing (IJCBS 2009), IEEE,167 - 173, 2009.

A. Scheidler, M. Middendorf
Evolved cooperation and emergent communication structures in learning classifier based organic computing systems
Proc. 11th Annual Conference Companion on Genetic and Evolutionary Computation Conference: Late Breaking Papers, 2633-2640, 2009.

M. Bernt, M.-C. Chen, D. Merkle, H.-L. Wang, K.-M. Chao, M. Middendorf
Finding All Sorting Tandem Duplication Random Loss Operations
Proc. 20th Annual Symposium on Combinatorial Pattern Matching (CPM 2009), LNCS 5577, 301-313, 2009.

H. Hernandez, C. Blum, M. Middendorf, K. Ramsch, A, Scheidler
Self-Synchronized Duty-Cycling for Mobile Sensor Networks with Energy Harvesting Capabilities: A Swarm Intelligence Study
Proc. IEEE Swarm Intelligence Symposium (SIS 2009), 153 – 159, 2009.

M. Bernt, D. Merkle, M. Middendorf
An Algorithm for Inferring Mitochondrial Genome Rearrangements in a Phylogenetic Tree
Proc. 6th Annual RECOMB Satellite Meeting on Comparative Genomics, LNCS 5267, 143-157, 2008.
link

S. Lange, M. Middendorf
SPP1148 booth: Hyperreconfigurable architectures
Proc. International Conference on Field Programmable Logic and Applications (FPL 2008), 353, 2008.

A. Brutschy, A. Scheidler, D. Merkle, M. Middendorf
Learning from House-Hunting Ants: Collective Decision-Making in Organic Computing Systems
Proc. 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008), LNCS 5217, 96-107, 2008. This paper won the Best Paper Award of ANTS 2008.

A. Scheidler, C. Blum, D. Merkle, M. Middendorf
Emergent Sorting in Networks of Router Agents
Proc. 6th International Conference on Ant Colony Optimization and Swarm Intelligence (ANTS 2008),LNCS 5217, 299-306, 2008.

K. Diwold, D. Merkle, M. Middendorf
The Influence of Dynamic Environments on Polyethism in Response Threshold Models for Social Insects
Proc. 8th German Workshop on Artificial Life (GWAL-8 2008), Leipzig, Germany, July 30 - August 01, 2008.

A. Scheidler, D. Merkle, M. Middendorf
Congestion Control in Ant Like Moving Agent Systems
Accepted for 2nd IFIP Conference on Biologically Inspired Collaborative Computing (BICC), Springer, 33-44, 2008

T. Basuki Kurniawan, N. Khafifah Khalid, Z. Ibrahim, M. Khalid, M. Middendorf
Evaluation of Ordering Methods for DNA Sequence Design Based on Ant Colony System
Asia International Conference on Modelling and Simulation 2008: 905-910.

T. Thalheim, D. Merkle, M. Middendorf
A Hybrid Population based ACO Algorithm for Protein Folding
Proc. 2008 IAENG International Conference on Bioinformatics Hong Kong, 19-21 March, 2008

S. Lange, M. Middendorf
On the Reconfiguration Costs of Models for Partially Reconfigurable FPGAs
Proc. IV Southern Programmable Logic Conference (SPL'08), IEEE, 111-118, 2008.

A. Scheidler, D. Merkle, M. Middendorf
Stability and Performance of Ant Queue Inspired Task Division Methods
Proc. European Conference on Complex Systems 2007 (ECCS 2007), Dresden, October 1-5, 2007.

M. Geis, M. Middendorf
An Ant Colony Optimizer for Melody Creation with Baroque Harmony
Proc. IEEE Congress on Evolutionary Computation (CEC 2007), Singapore, 2007.

M. Bernt, D. Merkle, M. Middendorf
A Fast and Exact Algorithm for the Perfect Reversal Median Problem
Proc. International Symposium on Bioinformatics Research and Applications (ISBRA), Georgia, USA, May 7-10, 2007.
link

S. Lange, M. Middendorf
Online Strategies for the Reconfiguration of Two-Level Reconfigurable Architectures
Proc. Workshop Workshop on Dynamically Reconfigurable Systems (DRS), Zurich, 2007.

D. Merkle, M. Middendorf, A. Scheidler
Swarm Controlled Emergence - Designing an Anti-Clustering Ant System
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

S. Janson, M. Middendorf
On Trajectories of Particles in PSO
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

M. Geis, M. Middendorf
A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures
Proc. IEEE Swarm Intelligence Symposium, Honolulu, Hawaii, 2007.

S. Lange, M. Middendorf
Granularity Aspects for the Design of Multi-level Reconfigurable Architectures
Proc. IEEE International Conference on Field Programmable Technology (ICFPT 06), IEEE, 2006

M. Bernt, D. Merkle, M. Middendorf
The Reversal Median Problem, Common Intervals, and Mitochondrial Gene Orders
Computational Life Sciences II: Second International Symposium CompLife 2006, Cambridge (UK), Sept. 2006, Lecture Notes in Bioinformatics, M.R. Berthold, R. Glen, I. Fischer (eds.), Vol. 4216, Springer, pp. 52-63, 2006
link

D. Merkle, M. Middendorf, A. Scheidler
Using Decentralized Clustering for Task Allocation in Networks with Reconfigurable Helper Units
Proc. International Workshop on Self-Organizing Systems 2006 (IWSOS 2006), LNCS 4124, 137-147, 2006.

A. Scheidler, D. Merkle, M. Middendorf
Emergent Sorting Patterns and Individual Differences of Randomly Moving Ant Like Agents
Proc. 7th German Workshop on Artificial Life (GWAL-7), IOS Press, 11 pp., 2006.

S. Lange, M. Middendorf
Cache Architectures for Reconfigurable Hardware
Proc. 2006 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'06), IEEE, Las Vegas, USA.

D. Merkle, M. Middendorf, A. Scheidler
Self-Organized Task Allocation for Computing Systems with Reconfigurable Components
Proc. 9th International Workshop on Nature Inspired Distributed Computing (NIDISC'06), IEEE, 8 pp., 2006.

S. Lange, M. Middendorf
On Multi-level Reconfigurable Architectures
Proc. 13th Reconfigurable Architectures Workshop (RAW 2006), IEEE, 8 pp., 2006.

S.Janson, E. Alba, B. Dorronsoro, M. Middendorf
Hierarchical Cellular Genetic Algorithm
Proc. 6th European Conference on Evolutionary Computation in Combinatorial Optimization, Springer, LNCS 3906, 111-122, 2006.
Paper

S. Lange, M. Middendorf
Heuristics for Context-Caches in 2-Level Reconfigurable Architectures
Proc. of IEEE 2005 Conference on Field-Programmable Technology (FPT' 05), 293-294, 2005.

M. Bernt, D. Merkle, M. Middendorf
A Parallel Algorithm for Solving the Reversal Median Problem
Proc. Parallel Processing and Applied Mathematics - Bio-Computing Workshop (PBC'5), LNCS 3911, 1089-1096, 2005.
link

S. Lange, M. Middendorf
On the Design of Two-Level Reconfigurable Architectures
Proceedings of the 2005 International Conference on Reconfigurable Computing and FPGAs (ReConFig05), IEEE Computer Society, 9 p., 2005.

S. Janson, D. Merkle
A New Multi-Objective Particle Swarm Optimization Algorithm Using Clustering Applied to Automated Docking
Proc. Second Int. Workshop on Hybrid Metaheuristics (HM 2005), Springer, LNCS 3636, 128-140, 2005.

S. Janson, D. Merkle, M. Middendorf
Decentralized Packet Clustering in Networks Applied to Particle Swarm Optimization
Proc. of the Conference on Design, Analysis, and Simulation of Distributed Systems 2005 (DASD 2005), 3-10, 2005

S. Janson, M. Middendorf
Flexible Particle Swarm Optimization Tasks for Reconfigurable Processor Arrays
Proc. 8th International Workshop on Nature Inspired Distributed Computing (NIDISC’05), IEEE Computer Society , 8 p., 2005.
Paper

D. Merkle, M. Middendorf, A. Scheidler
Dynamic Decentralized Packet Clustering in Networks
Proc. EvoWorkkshops 2005, 2nd European Workshop on Evolutionary Algorithms in Stochastic and Dynamic Environments, Springer, LNCS 3449, 574-583, 2005

B. Scheuermann, M. Middendorf
Counter-based Ant Colony Optimization as a Hardware-oriented Meta-Heuristic
Proc. EvoWorkkshops 2005, 2nd European Workshop on Evolutionary Computation in Hardware Optimisation, Springer, LNCS 3449, 235-244, 2005

S. Lange, M. Middendorf
The Partition into Hypercontexts Problem for Hyperreconfigurable Architectures
Proc. of the International Conference on Field Programmable Logic and Applications (FPL 2004), Springer Verlag, LNCS 3205, 2004, 251-260.
Paper

D. Merkle, M. Middendorf
Competition Controlled Pheromone Update for Ant Colony Optimization
Proc. Fourth International Workshop ANTS 2004, Springer, LNCS 3172, 95-105, 2004

B. Scheuermann, M. Guntsch, M. Middendorf, H. Schmeck
Time-Scattered Heuristic Guidance for a Hardware Implementation of ACO
Proc. Fourth International Workshop ANTS 2004, Springer, LNCS 3172, 250-261, 2004

S. Lange, M. Middendorf
Hyperreconfigurable Architectures for Fast Runtime Reconfiguration
Proc. 2004 IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM´04), 304-305, 2004.
Paper

S. Lange, M. Middendorf
Hyperreconfigurable Architectures as Flexible Control Systems
ARCS 2004 Workshop "Dynamically Reconfigurable Systems", Lecture Notes in Informatics, Vol. P-41, 175-184, 2004.
Paper

S. Janson, M. Middendorf
A Hierarchical Particle Swarm Optimizer for Dynamic Optimization Problems
Proc. Evoworkshops 2004: 1st European Workshop on Evolutionary Algorithms in Stochastic and Dynamic Environments, LNCS 3005, 2004, 513-524.

S. Lange, M. Middendorf
Models and Reconfiguration Problems for Multi Task Hyperreconfigurable Architectures
Proc. International Parallel and Distributed Processing Symposium (IPDPS-2004), Reconfigurable Architectures Workshop (RAW-2004), IEEE-CS Press, 8 pp., 2004.
Paper

D. Merkle, 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, Georgia Institute of Technology, 99-106, 2003.

M. Guntsch, M. Middendorf
Solving Multi-Objective Permutation Problems with Population Based ACO
Proceedings of the Second International Conference on Evolutionary Multi-Criterion Optimization (EMO 2003), C.M. Fonseca, P.J. Fleming, E. Zitzler, K. Deb, L. Thiele (Eds.), Springer, LNCS 2636, 2003, 464-478.
Paper

M. Guntsch, M. Middendorf, B. Scheuermann, O. Diessel, H. ElGindy, H. Schmeck, K. So
Population based Ant Colony Optimization on FPGA
Proceedings 2002 IEEE International Conference on Field-Programmable Technology (FPT'02), P. Leong, W. Luk (Eds.), IEEE, Hong Kong, 2002, 125-132.

D. Merkle, M. Middendorf
Modelling ACO: Composed Permutation Problems
Ant Algorithms, Proceedings of Third International Workshop ANTS 2002, Brussels, Belgium, Springer Verlag, LNCS 2463, 2002, 149-162.

M. Guntsch, M. Middendorf
Applying Population Based ACO to Dynamic Optimization Problems
Ant Algorithms, Proceedings of Third International Workshop ANTS 2002, Brussels, Belgium, Springer Verlag, LNCS 2463, 2002, 111-122.
Paper

J. Branke, M. Decker, D. Merkle and H. Schmeck
Coevolutionary Ant Algorithms Playing Games
Proceedings of Third International Workshop ANTS 2002, Springer Verlag, LNCS 2463, 2002, 298-299.

D. Merkle and M. Middendorf
Modelling the Dynamics of Ant Colony Optimization Algorithms
Proceedings of the Genetic and Evolutionary Computation Conference (GECCO-2002), New York, 2002, 105-112.

M. Guntsch and M. Middendorf
A Population Based Approach for ACO
Proc. 2nd European Workshop on Evolutionary Computation in Combinatorial Optimization (EvoCOP-2002), Kinsale, Ireland, Springer Verlag, LNCS 2279, 2002, 72-81.
Paper

D. Merkle and M. Middendorf
Ant Colony Optimization with the Relative Pheromone Evaluation Method
Proc. 3rd European Workshop on Scheduling and Timetabling and 3rd European Workshop on Evolutionary Methods for AI Planning (EvoSTIM/EvoPLAN-2002), Kinsale, Ireland, LNCS 2279, 2002, 325-333.
Paper