Reconstructing Biological and Digital Phylogenetic Trees in Parallel

  title={Reconstructing Biological and Digital Phylogenetic Trees in Parallel},
  author={Ramtin Afshar and Michael T. Goodrich and Pedro A. Matias and Martha C. Osegueda},
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer security settings, which can be abstracted in terms of two parties, a responder, Alice, who must correctly answer queries of a given type regarding a degree-d tree, T, and a querier, Bob, who issues batches of queries, with each query in a batch being independent of… 

Exact Learning of Multitrees and Almost-Trees Using Path Queries

This paper provides e-cient learning algorithms, as well as lower bounds, for multitrees and almost-trees, including butter-y networks, and studies the query complexity of exact learning for cases when learning G is possible using path queries.

Mapping Networks via Parallel kth-Hop Traceroute Queries

This paper provides efficient network mapping algorithms, that are based on kth-hop traceroute queries, and introduces a number of new algorithmic techniques, including a high-probability parametric parallelization of a graph clustering technique of Thorup and Zwick, which may be of independent interest.

A Simple Algorithm for Graph Reconstruction

This work shows that, on random Δ-regular graphs, the reconstruction algorithm based on multi-phase Voronoi-cell decomposition and using O(n^{3/2}) distance queries uses O( n) distance queries, and has a very simple structure, and is highly parallelizable.

Parallel Network Mapping Algorithms

These methods use a high-probability parametric parallelization of a graph clustering technique of Thorup and Zwick to provide efficient query complexity and round complexity bounds for graph reconstruction using distance queries.



Space-Efficient Data Structures, Streams, and Algorithms Papers in Honor of J. Ian Munro, on the Occasion of His 66th Birthday

The Query Complexity of Finding a Hidden Permutation, Bounds for Scheduling Jobs on Grid Processors, and a Survey of Algorithms and Models for List Update are presented.

Reconstructing Binary Trees in Parallel

It is shown that a querier can efficiently reconstruct a binary tree with a logarithmic number of rounds and quasilinear number of queries, with high probability, for various types of queries.

Methods for Computing Wagner Trees

The concept of a Wagner Network is formalized and a number of algorithms for calculating such networks are discussed and the rationale for the methods described is discussed.

Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology

A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented.

Algorithm Design and Applications

Algorithm Design and Applications, by Michael T. Goodrich & Roberto Tamassia teaches students about designing and using algorithms, illustrating connections between topics being taught and their potential applications, increasing engagement.

Introduction to Algorithms

  • Xin-She Yang
  • Computer Science
    Nature-Inspired Optimization Algorithms
  • 2021

Generating Pylogenetic Tree of Homogeneous Source Code in a Plagiarism Detection System

The proposed phylogeny construction algorithm is quite successful in reconstructing the evolutionary direction, which enables us to identify plagiarized codes more accurately and reliably and is successfully implemented on top of the plagiarism detection system of an automatic program evaluation system.

Practical Text Phylogeny for Real-World Settings

Experimental results show that word embeddings are competitive with other feature sets for the published benchmarks, and are highly effective for creative writing, when used in text phylogeny tree reconstruction.

Graph Reconstruction and Verification

This work provides a randomized algorithm for reconstruction using Õ(n3/2) distance queries, based on Voronoi cell decomposition, and analyzes natural greedy algorithms for reconstructionUsing a shortest path oracle and also for verification using either oracle, and shows that their query complexity is n1+o(1).