Dynamic Algorithms for the Massively Parallel Computation Model

The Massive Parallel Computing (MPC) model gained popularity during the last decade and it is now seen as the standard model for processing large scale data. One significant shortcoming of the model is that it assumes to work on static datasets while, in practice, real-world datasets evolve continuously. To overcome this issue, in this paper we initiate the study of dynamic algorithms in the MPC model. We first discuss the main requirements for a dynamic parallel model and we show how to adapt the classic MPC model to capture them. Then we analyze the connection between classic dynamic algorithms and dynamic algorithms in the MPC model. Finally, we provide new efficient dynamic MPC algorithms for a variety of fundamental graph problems, including connectivity, minimum spanning tree and matching.Comment: Accepted to the 31st ACM Symposium on Parallelism in Algorithms and Architectures (SPAA 2019

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