Counting, generating and sampling tree alignments

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical sets of matches between identical pairs of trees. This ambiguity is uninformative, and detrimental to any probabilistic analysis.In this work, we consider tree alignments up to equivalence. Our first result is a precise asymptotic enumeration of tree alignments, obtained from a context-free grammar by mean of basic analytic combinatorics. Our second result focuses on alignments between two given ordered trees $S$ and $T$. By refining our grammar to align specific trees, we obtain a decomposition scheme for the space of alignments, and use it to design an efficient dynamic programming algorithm for sampling alignments under the Gibbs-Boltzmann probability distribution. This generalizes existing tree alignment algorithms, and opens the door for a probabilistic analysis of the space of suboptimal RNA secondary structures alignments.Comment: ALCOB - 3rd International Conference on Algorithms for Computational Biology - 2016, Jun 2016, Trujillo, Spain. 201

Approximately Sampling Elements with Fixed Rank in Graded Posets

Graded posets frequently arise throughout combinatorics, where it is natural to try to count the number of elements of a fixed rank. These counting problems are often $\#\textbf{P}$-complete, so we consider approximation algorithms for counting and uniform sampling. We show that for certain classes of posets, biased Markov chains that walk along edges of their Hasse diagrams allow us to approximately generate samples with any fixed rank in expected polynomial time. Our arguments do not rely on the typical proofs of log-concavity, which are used to construct a stationary distribution with a specific mode in order to give a lower bound on the probability of outputting an element of the desired rank. Instead, we infer this directly from bounds on the mixing time of the chains through a method we call $\textit{balanced bias}$. A noteworthy application of our method is sampling restricted classes of integer partitions of $n$. We give the first provably efficient Markov chain algorithm to uniformly sample integer partitions of $n$ from general restricted classes. Several observations allow us to improve the efficiency of this chain to require $O(n^{1/2}\log(n))$ space, and for unrestricted integer partitions, expected $O(n^{9/4})$ time. Related applications include sampling permutations with a fixed number of inversions and lozenge tilings on the triangular lattice with a fixed average height.Comment: 23 pages, 12 figure

Liquid crystal films on curved surfaces: An entropic sampling study

The confining effect of a spherical substrate inducing anchoring (normal to the surface) of rod-like liquid crystal molecules contained in a thin film spread over it has been investigated with regard to possible changes in the nature of the isotropic-to-nematic phase transition as the sample is cooled. The focus of these Monte Carlo simulations is to study the competing effects of the homeotropic anchoring due to the surface inducing orientational ordering in the radial direction and the inherent uniaxial order promoted by the intermolecular interactions. By adopting entropic sampling procedure, we could investigate this transition with a high temperature precision, and we studied the effect of the surface anchoring strength on the phase diagram for a specifically chosen geometry. We find that there is a threshold anchoring strength of the surface below which uniaxial nematic phase results, and above which the isotropic fluid cools to a radially ordered nematic phase, besides of course expected changes in the phase transition temperature with the anchoring strength. In the vicinity of the threshold anchoring strength we observe a bistable region between these two structures, clearly brought out by the characteristics of the corresponding microstates constituting the entropic ensemble.Comment: 14 pages, 5 figure

Polynomial tuning of multiparametric combinatorial samplers

Boltzmann samplers and the recursive method are prominent algorithmic frameworks for the approximate-size and exact-size random generation of large combinatorial structures, such as maps, tilings, RNA sequences or various tree-like structures. In their multiparametric variants, these samplers allow to control the profile of expected values corresponding to multiple combinatorial parameters. One can control, for instance, the number of leaves, profile of node degrees in trees or the number of certain subpatterns in strings. However, such a flexible control requires an additional non-trivial tuning procedure. In this paper, we propose an efficient polynomial-time, with respect to the number of tuned parameters, tuning algorithm based on convex optimisation techniques. Finally, we illustrate the efficiency of our approach using several applications of rational, algebraic and P\'olya structures including polyomino tilings with prescribed tile frequencies, planar trees with a given specific node degree distribution, and weighted partitions.Comment: Extended abstract, accepted to ANALCO2018. 20 pages, 6 figures, colours. Implementation and examples are available at [1] https://github.com/maciej-bendkowski/boltzmann-brain [2] https://github.com/maciej-bendkowski/multiparametric-combinatorial-sampler