Reconstructing pedigrees: some identifiability questions for a recombination-mutation model

Pedigrees are directed acyclic graphs that represent ancestral relationships between individuals in a population. Based on a schematic recombination process, we describe two simple Markov models for sequences evolving on pedigrees - Model R (recombinations without mutations) and Model RM (recombinations with mutations). For these models, we ask an identifiability question: is it possible to construct a pedigree from the joint probability distribution of extant sequences? We present partial identifiability results for general pedigrees: we show that when the crossover probabilities are sufficiently small, certain spanning subgraph sequences can be counted from the joint distribution of extant sequences. We demonstrate how pedigrees that earlier seemed difficult to distinguish are distinguished by counting their spanning subgraph sequences.Comment: 40 pages, 9 figure

An Algorithmic Proof of the Lovasz Local Lemma via Resampling Oracles

The Lovasz Local Lemma is a seminal result in probabilistic combinatorics. It gives a sufficient condition on a probability space and a collection of events for the existence of an outcome that simultaneously avoids all of those events. Finding such an outcome by an efficient algorithm has been an active research topic for decades. Breakthrough work of Moser and Tardos (2009) presented an efficient algorithm for a general setting primarily characterized by a product structure on the probability space. In this work we present an efficient algorithm for a much more general setting. Our main assumption is that there exist certain functions, called resampling oracles, that can be invoked to address the undesired occurrence of the events. We show that, in all scenarios to which the original Lovasz Local Lemma applies, there exist resampling oracles, although they are not necessarily efficient. Nevertheless, for essentially all known applications of the Lovasz Local Lemma and its generalizations, we have designed efficient resampling oracles. As applications of these techniques, we present new results for packings of Latin transversals, rainbow matchings and rainbow spanning trees.Comment: 47 page