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153 Publications visible to you, out of a total of 153
The Free Lunch is not over yet – Systematic Exploration of Numerical Thresholds in Phylogenetic Inference

Abstract

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Authors: Julia Haag, Lukas Hübner, Alexey M. Kozlov, Alexandros Stamatakis

Date Published: 14th Jul 2022

Publication Type: Journal

From Easy to Hopeless - Predicting the Difficulty of Phylogenetic Analyses

Abstract

Not specified

Authors: Julia Haag, Dimitri Höhler, Ben Bettisworth, Alexandros Stamatakis

Date Published: 21st Jun 2022

Publication Type: Journal

Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade

Abstract

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Authors: Lucas Czech, Alexandros Stamatakis, Micah Dunthorn, Pierre Barbera

Date Published: 26th May 2022

Publication Type: Journal

Lagrange-NG: The next generation of Lagrange

Abstract

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Authors: Ben Bettisworth, Stephen A. Smith, Alexandros Stamatakis

Date Published: 20th Apr 2022

Publication Type: Journal

Core-Count Independent Reproducible Reduce

Abstract (Expand)

ecause of rounding errors, parallel floating-point summation can produce different results on different core-counts. For some algorithms like hill climbing, RAxML-NG [7] or greedy algorithms, this … implies that results may be irreproducible with different core-counts. We present the Binary Tree Reduction algorithm, which follows a distributed binary tree scheme that keeps the calculation order fixed and independent of the core-count 푝. A naive implementation requires up to (푝 − 1) ∗ (log2 ( 푁 −1 푝 ) + 1) messages to sum 푁 floating-point numbers. To reduce the message count, we introduce a message buffer and optimize data distribution across the cores, the latter results in a runtime decrease of 18 %. We find that for 푝 = 256, Binary Tree Reduction has a slowdown of less than 2 compared to a naive, irreproducible solution. It is able to compute the sum of 푁 ≈ 21 ∗ 106 summands on 푝 = 256 cores in about 248 μs.

Authors: Christoph Stelz, Lukas Hübner, Alexandros Stamatakis

Date Published: 1st Apr 2022

Publication Type: Bachelor's Thesis

Investigating the relationship between tree distance and model distance

Abstract

Not specified

Editor:

Date Published: 1st Feb 2022

Publication Type: Master's Thesis

SPART: A versatile and standardized data exchange format for species partition information

Abstract

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Authors: Aurélien Miralles, Jacques Ducasse, Sophie Brouillet, Tomas Flouri, Tomochika Fujisawa, Paschalia Kapli, L. Lacey Knowles, Sangeeta Kumari, Alexandros Stamatakis, Jeet Sukumaran, Sarah Lutteropp, Miguel Vences, Nicolas Puillandre

Date Published: 2022

Publication Type: Journal

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