Reconstruction of Random Colourings

Reconstruction problems have been studied in a number of contexts including biology, information theory and and statistical physics. We consider the reconstruction problem for random $k$-colourings on the $\Delta$-ary tree for large $k$. Bhatnagar et. al. showed non-reconstruction when $\Delta \leq \frac12 k\log k - o(k\log k)$ and reconstruction when $\Delta \geq k\log k + o(k\log k)$. We tighten this result and show non-reconstruction when $\Delta \leq k[\log k + \log \log k + 1 - \ln 2 -o(1)]$ and reconstruction when $\Delta \geq k[\log k + \log \log k + 1+o(1)]$.Comment: Added references, updated notatio

Necessary and sufficient conditions for consistent root reconstruction in Markov models on trees

We establish necessary and sufficient conditions for consistent root reconstruction in continuous-time Markov models with countable state space on bounded-height trees. Here a root state estimator is said to be consistent if the probability that it returns to the true root state converges to 1 as the number of leaves tends to infinity. We also derive quantitative bounds on the error of reconstruction. Our results answer a question of Gascuel and Steel and have implications for ancestral sequence reconstruction in a classical evolutionary model of nucleotide insertion and deletion.Comment: 30 pages, 3 figures, title of reference [FR] is update

Global Alignment of Molecular Sequences via Ancestral State Reconstruction

Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on substitution-only models of sequence evolution. In practice these methods are extended beyond this simplified setting with the use of heuristics that produce global alignments of the input sequences--an important problem which has no rigorous model-based solution. In this paper we consider a new version of the multiple sequence alignment in the context of stochastic indel models. More precisely, we introduce the following {\em trace reconstruction problem on a tree} (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves of the tree. We give a recursive procedure for this problem with strong reconstruction guarantees at low mutation rates, providing also an alignment of the sequences at the leaves of the tree. The TRPT problem without indels has been studied in previous work (Mossel 2004, Daskalakis et al. 2006) as a bootstrapping step towards obtaining optimal phylogenetic reconstruction methods. The present work sets up a framework for extending these works to evolutionary models with indels

Reconstruction threshold for the hardcore model

"Vegeu el resum a l'inici del document del fitxer adjunt"

Phase transition for the mixing time of the Glauber dynamics for coloring regular trees

We prove that the mixing time of the Glauber dynamics for random k-colorings of the complete tree with branching factor b undergoes a phase transition at $k=b(1+o_b(1))/\ln{b}$. Our main result shows nearly sharp bounds on the mixing time of the dynamics on the complete tree with n vertices for $k=Cb/\ln{b}$ colors with constant C. For $C\geq1$ we prove the mixing time is $O(n^{1+o_b(1)}\ln{n})$. On the other side, for $C<1$ the mixing time experiences a slowing down; in particular, we prove it is $O(n^{1/C+o_b(1)}\ln{n})$ and $\Omega(n^{1/C-o_b(1)})$. The critical point C=1 is interesting since it coincides (at least up to first order) with the so-called reconstruction threshold which was recently established by Sly. The reconstruction threshold has been of considerable interest recently since it appears to have close connections to the efficiency of certain local algorithms, and this work was inspired by our attempt to understand these connections in this particular setting.Comment: Published in at http://dx.doi.org/10.1214/11-AAP833 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org