One of the core classical problems in computational biology is that of constructing the most parsimonious phylogenetic tree interpreting an input set of sequences from the genomes of evolutionarily related organisms. We reexamine the classical maximum parsimony (MP) optimization problem for the general (asymmetric) scoring matrix case, where rooted phylogenies are implied, and analyze the worst case bounds of three approaches to MP: The approach of Cavalli-Sforza and Edwards, the approach of Hendy and Penny, and a new agglomerative, "bottom-up" approach we present in this article. We show that the second and third approaches are faster than the first one by a factor of Θ(√n) and Θ(n), respectively, where n is the number of species.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224053 | PMC |
| http://dx.doi.org/10.1089/cmb.2014.0128 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Assessing Long-Term Outcomes after Operative Management of Elbow Stiffness Secondary to Heterotopic Ossification.
J Shoulder Elbow Surg
January 2025
Department of Orthopaedic Surgery and Rehabilitation, Loyola University Health System, Maywood, IL, USA.
Article Synopsis
- Heterotopic ossification (HO) in the elbow leads to limited movement and is often caused by injuries like burns or trauma; this study analyzes the long-term outcomes of 51 elbows treated surgically.
- The study followed 48 patients over an average of 8 years, assessing metrics such as elbow movement arcs, pain levels, and functional performance scores post-surgery.
- Results showed significant improvement in elbow functionality, but patients with type II diabetes experienced the lowest movement range and higher complication rates, indicating potential risk factors for poorer outcomes.
High-resolution assessment of climate change impacts on the surface energy and water balance in the glaciated Naryn River basin, Central Asia.
J Environ Manage
January 2025
Mountain Societies Research Institute, University of Central Asia, Bishkek, Kyrgyzstan.
Mountain regions of Central Asia are experiencing strong influences from climate change, with significant reductions in snow cover and glacial reserves. A comprehensive assessment of the potential consequences under the worst-case climate scenario is vital for adaptation measures throughout the region. Water balance analysis in the Naryn River basin was conducted for the baseline period of 1981-2000 including potential changes under the worst-case SSP5-8.
View Article and Find Full Text PDFNeural network surrogate and projected gradient descent for fast and reliable finite element model calibration: A case study on an intervertebral disc.
Comput Biol Med
January 2025
Institute for Neuroradiology, TUM University Hospital, School of Medicine and Health, Technical University of Munich (TUM), Munich, Germany.
Accurate calibration of finite element (FE) models is essential across various biomechanical applications, including human intervertebral discs (IVDs), to ensure their reliability and use in diagnosing and planning treatments. However, traditional calibration methods are computationally intensive, requiring iterative, derivative-free optimization algorithms that often take days to converge. This study addresses these challenges by introducing a novel, efficient, and effective calibration method demonstrated on a human L4-L5 IVD FE model as a case study using a neural network (NN) surrogate.
View Article and Find Full Text PDFStochastic Filtering of the Attitude Quaternion.
Sensors (Basel)
December 2024
Mechanical Engineering Department, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.
Several stochastic H∞ filters for estimating the attitude of a rigid body from line-of-sight measurements and rate gyro readings are developed. The measurements are corrupted by white noise with unknown variances. Our approach consists of estimating the quaternion while attenuating the transmission gain from the unknown variances and initial errors to the current estimation error.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!