Barrier Trees of Degenerate Landscapes
This method paper introduces the concept of barrier trees, a convenient approach to describe the landscape of an optimization function. Barrier trees represent the toplogical characteristics of an energy landscape, such as a unique partitioning into local minima as leaves of the tree and saddle points as internal nodes connecting different minima.
The decomposition of non-degenerate landscapes into basins surrounding local minima connected by saddle points is straightforward. This paper extends the concept to degenerate landscapes, where the situation is more complex. We present the program 'barriers' that efficiently computes barrier trees for degenerate landscapes. This approach involves discretizing the search space, and constructing the barrier tree from i) a a set of states, ii) a neighborhood relation between states, and iii) an energy of fitness function assigned to each state. The resulting topology is visualized as a tree, and made accessible for further processing.
Citation
Barrier Trees of Degenerate Landscapes
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger
Z. Phys. Chem. 216: 155–73 (2002) | doi:10.1524/zpch.2002.216.2.155 | Preprint PDF
See Also
Memory Efficient RNA Energy Landscape Exploration
Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger
Bioinformatics 30: 2584–91 (2014) | doi:10.1093/bioinformatics/btu337 | PDF
BarMap: RNA Folding on Dynamic Energy Landscapes
Ivo L. Hofacker, Christoph Flamm, Michael Heine, Michael T. Wolfinger, Gerik Scheuermann, Peter F. Stadler
RNA 16:1308–16 (2010) | doi:10.1261/rna.2093310 | PDF
Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen, Peter F. Stadler
Europhys. Lett. 74(4): 726–32 (2006) | doi:10.1209/epl/i2005-10577-0 | Preprint PDF
Efficient Computation of RNA Folding Dynamics
Michael T. Wolfinger, W. Andreas Svrcek-Seiler, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
J. Phys. A: Math. Gen. 37(17): 4731–41 (2004) | doi:10.1088/0305-4470/37/17/005 | PDF