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PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out…

Quantitative Methods · Quantitative Biology 2021-12-15 Jordan Douglas , David Welch

We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR process, a diffusion widely used in…

Probability · Mathematics 2007-05-23 Thomas Lepage , Stephan Lawi , Paul Tupper , David Bryant

Tree-based models are increasingly popular due to their ability to identify complex relationships that are beyond the scope of parametric models. Survival tree methods adapt these models to allow for the analysis of censored outcomes, which…

Machine Learning · Computer Science 2020-12-09 Dimitris Bertsimas , Jack Dunn , Emma Gibson , Agni Orfanoudaki

Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for…

Data Structures and Algorithms · Computer Science 2023-01-16 Alessio Conte , Nicola Cotumaccio , Travis Gagie , Giovanni Manzini , Nicola Prezza , Marinella Sciortino

The Li-Chao tree (LICT) was first introduced in lecture as an efficient data structure for dynamic lower envelope maintenance. In the years since, it has achieved widespread adoption within the competitive programming community, yet no…

Data Structures and Algorithms · Computer Science 2026-03-10 Chao Li

We have incorporated star formation algorithms into a hybrid N-body/smoothed particle hydrodynamics code (TREESPH) in order to describe the star forming properties of disk galaxies over timescales of a few billion years. The models employ a…

Astrophysics · Physics 2007-05-23 Chris Mihos , Lars Hernquist

A scaling law developed by Amraoui et al. is a powerful technique to estimate the block error probability of finite length low-density parity-check (LDPC) codes. Solving a system of differential equations called covariance evolution is a…

Information Theory · Computer Science 2016-05-31 Takayuki Nozaki , Kenta Kasai , Kohichi Sakaniwa

Materials discovery requires navigating vast chemical and structural spaces while satisfying multiple, often conflicting, objectives. We present LLM-guided Evolution for MAterials discovery (LLEMA), a unified framework that couples the…

Machine Learning · Computer Science 2026-03-06 Nikhil Abhyankar , Sanchit Kabra , Saaketh Desai , Chandan K. Reddy

Algorithms that use Large Language Models (LLMs) to evolve code arrived on the Genetic Programming (GP) scene very recently. We present LLM GP, a formalized LLM-based evolutionary algorithm designed to evolve code. Like GP, it uses…

Neural and Evolutionary Computing · Computer Science 2024-01-17 Erik Hemberg , Stephen Moskal , Una-May O'Reilly

I review the basic concepts for the spectrophotometric and chemical evolution of galaxies, contrast various approaches and discuss their respective advantages and shortcomings, both for the interpretation of nearby and high redshift…

Astrophysics · Physics 2007-05-23 U. Fritze-v. Alvensleben

We propose a consistently algebraic formulation of the extended KP (supersymmetric) integrable -hierarchy systems. We exploit the results already established in [14] and which consist in a framework suspected to unify in a fascinating way…

High Energy Physics - Theory · Physics 2008-01-30 B. Maroufi , M. Nazah , M. B. Sedra

The major difficulty in Multi-objective Optimization Evolutionary Algorithms (MOEAs) is how to find an appropriate solution that is able to converge towards the true Pareto Front with high diversity. Most existing methodologies, which have…

Optimization and Control · Mathematics 2020-04-30 Jeisson Prieto , Jonatan Gomez

Chemical evolution models are useful for understanding the formation and evolution of stars and galaxies. Model predictions will be more robust as more observational constraints are used. We present chemical evolution models for the dwarf…

Cosmology and Nongalactic Astrophysics · Physics 2011-08-31 Liliana Hernandez-Martinez , Leticia Carigi , Miriam Peña , Manuel Peimbert

A freely available Python code for modelling SNR evolution has been created. This software is intended for two purposes: to understand SNR evolution; and to use in modelling observations of SNR for obtaining good estimates of SNR…

High Energy Astrophysical Phenomena · Physics 2017-05-10 Denis A. Leahy , Jacqueline Williams

We show that in the continuum limit watersheds dividing drainage basins are Schramm-Loewner Evolution (SLE) curves, being described by one single parameter $\kappa$. Several numerical evaluations are applied to ascertain this. All…

Statistical Mechanics · Physics 2012-12-04 E. Daryaei , N. A. M. Araujo , K. J. Schrenk , S. Rouhani , H. J. Herrmann

We describe PTreeSPH, a gravity treecode combined with an SPH hydrodynamics code designed for massively parallel supercomputers having distributed memory. Our computational algorithm is based on the popular TreeSPH code of Hernquist & Katz…

Astrophysics · Physics 2016-08-30 Romeel Dave' , John Dubinski , Lars Hernquist

Low-rank adaptation (LoRA) has been demonstrated effective in reducing the trainable parameter number when fine-tuning a large foundation model (LLM). However, it still encounters computational and memory challenges when scaling to larger…

Computer Vision and Pattern Recognition · Computer Science 2025-02-11 Yixian Shen , Qi Bi , Jia-Hong Huang , Hongyi Zhu , Andy D. Pimentel , Anuj Pathania

We present EvoL, the new release of the Padova N-body code for cosmological simulations of galaxy formation and evolution. In this paper, the basic Tree + SPH code is presented and analysed, together with an overview on the software…

Cosmology and Nongalactic Astrophysics · Physics 2015-05-14 Emiliano Merlin , Umberto Buonomo , Tommaso Grassi , Lorenzo Piovan , Cesare Chiosi

The results, obtained with evolutionary synthesis code package, developed by the author, for spectral properties of stellar populations with different initial metallicities Z, are presented and discussed . Also, their contributions to the…

Astrophysics · Physics 2007-05-23 Peeter Traat

The Schramm-Loewner evolution (SLE) can be simulated by dividing the time interval into N subintervals and approximating the random conformal map of the SLE by the composition of N random, but relatively simple, conformal maps. In the usual…

Probability · Mathematics 2010-10-27 Tom Kennedy
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