The Collatz conjecture and De Bruijn graphs

We study variants of the well-known Collatz graph, by considering the action of the 3n+1 function on congruence classes. For moduli equal to powers of 2, these graphs are shown to be isomorphic to binary De Bruijn graphs. Unlike the Collatz graph, these graphs are very structured, and have several interesting properties. We then look at a natural generalization of these finite graphs to the 2-adic integers, and show that the isomorphism between these infinite graphs is exactly the conjugacy map previously studied by Bernstein and Lagarias. Finally, we show that for generalizations of the 3n+1 function, we get similar relations with 2-adic and p-adic De Bruijn graphs.Comment: 9 pages, 8 figure

Boltzmann samplers for random generation of lambda terms

Randomly generating structured objects is important in testing and optimizing functional programs, whereas generating random $'l$-terms is more specifically needed for testing and optimizing compilers. For that a tool called QuickCheck has been proposed, but in this tool the control of the random generation is left to the programmer. Ten years ago, a method called Boltzmann samplers has been proposed to generate combinatorial structures. In this paper, we show how Boltzmann samplers can be developed to generate lambda-terms, but also other data structures like trees. These samplers rely on a critical value which parameters the main random selector and which is exhibited here with explanations on how it is computed. Haskell programs are proposed to show how samplers are actually implemented

Counting and Generating Terms in the Binary Lambda Calculus (Extended version)

In a paper entitled Binary lambda calculus and combinatory logic, John Tromp presents a simple way of encoding lambda calculus terms as binary sequences. In what follows, we study the numbers of binary strings of a given size that represent lambda terms and derive results from their generating functions, especially that the number of terms of size n grows roughly like 1.963447954. .. n. In a second part we use this approach to generate random lambda terms using Boltzmann samplers.Comment: extended version of arXiv:1401.037

A representation of a compressed de Bruijn graph for pan-genome analysis that enables search

Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de Bruijn graph to describe the relationship between the genomes of many individuals/strains of the same or closely related species. They devised an $O(n \log g)$ time algorithm called splitMEM that constructs this graph directly (i.e., without using the uncompressed de Bruijn graph) based on a suffix tree, where $n$ is the total length of the genomes and $g$ is the length of the longest genome. In this paper, we present a construction algorithm that outperforms their algorithm in theory and in practice. Moreover, we propose a new space-efficient representation of the compressed de Bruijn graph that adds the possibility to search for a pattern (e.g. an allele - a variant form of a gene) within the pan-genome.Comment: Submitted to Algorithmica special issue of CPM201