Matsen, Frederick A.
- 19 dubious ways to compute the marginal likelihood of a phylogenetic\n tree topology
2018/11/28 by Mathieu Fourment, Andrew F. Magee, Fourment, Mathieu +9 · 4 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #Computation (stat.CO) #Evolution and Paleontology Studies #FOS: Biological sciences #FOS: Computer and information sciences #Genomics and Phylogenetic Studies #Morphological variations and asymmetry #Populations and Evolution (q-bio.PE)
- Quantifying MCMC Exploration of Phylogenetic Tree Space
2014/05/08 by Chris Whidden, Whidden, Christopher, F. A. Matsen +1 · 3 citations
Earth and Planetary Sciences · Computer Science · Biochemistry, Genetics and Molecular Biology · #Evolution and Paleontology Studies #Bayesian Methods and Mixture Models #Genomics and Phylogenetic Studies
- Generalizing Tree Probability Estimation via Bayesian Networks
2018/05/20 by Cheng Zhang, Zhang, Cheng, F. A. Matsen +1 · 3 citations
Computer Science · #Applications (stat.AP) #Bayesian Modeling and Causal Inference #Data Management and Algorithms #FOS: Computer and information sciences #Time Series Analysis and Forecasting
- Non-bifurcating phylogenetic tree inference via the adaptive LASSO
2018/05/28 by Cheng Zhang, Zhang, Cheng, Vu Dinh +3 · 2 citations
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · #Evolution and Paleontology Studies #FOS: Biological sciences #FOS: Computer and information sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Machine Learning (stat.ML) #Populations and Evolution (q-bio.PE)
- Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies
2018/11/27 by Whidden, Chris, Claywell, Brian C., Fisher, Thayer +3 · 2 citations
#Data Structures and Algorithms (cs.DS) #FOS: Biological sciences #FOS: Computer and information sciences #Populations and Evolution (q-bio.PE)
- The phylogenetic Kantorovich-Rubinstein metric for environmental sequence samples
2010/05/10 by Steven N. Evans, Evans, Steven N., Frederick A. Matsen +2 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Bayesian Methods and Mixture Models #Bioinformatics and Genomic Networks #FOS: Biological sciences #Gene expression and cancer classification #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE)
- Minimizing the average distance to a closest leaf in a phylogenetic tree
2012/05/31 by F. A. Matsen, Aaron Gallagher, Matsen, Frederick A. +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Genomics and Phylogenetic Studies #Genetic diversity and population structure #Bioinformatics and Genomic Networks
- Calculating the Unrooted Subtree Prune-and-Regraft Distance
2015/11/24 by Whidden, Chris, Matsen, Frederick A. · 1 citation
#Data Structures and Algorithms (cs.DS) #FOS: Biological sciences #FOS: Computer and information sciences #Populations and Evolution (q-bio.PE)
- Consistency and convergence rate of phylogenetic inference via\n regularization
2016/06/09 by Vu Dinh, Dinh, Vu, Lam Tung Ho +5 · 1 citation
Biochemistry, Genetics and Molecular Biology · Earth and Planetary Sciences · Mathematics · #05C05 #62F12 (Primary) #92B10 #92D15 (Secondary) #Evolution and Paleontology Studies #FOS: Biological sciences #FOS: Mathematics #Genetic diversity and population structure #Morphological variations and asymmetry #Populations and Evolution (q-bio.PE) #Statistics Theory (math.ST)
- Probabilistic Path Hamiltonian Monte Carlo
2017/02/25 by Vu Dinh, Dinh, Vu, Arman Bilge +5 · 2 citations
Biochemistry, Genetics and Molecular Biology · Computer Science · Mathematics · #05C05 #65J99 #92B10 #92D15 #Bioinformatics and Genomic Networks #FOS: Biological sciences #Markov Chains and Monte Carlo Methods #Populations and Evolution (q-bio.PE) #Topological and Geometric Data Analysis
- The Bayesian optimist's guide to adaptive immune receptor repertoire\n analysis
2018/04/29 by Branden J Olson, Olson, Branden J., Frederick A. Matsen +1 · 1 citation
Immunology and Microbiology · #Atherosclerosis and Cardiovascular Diseases #FOS: Biological sciences #Immune Cell Function and Interaction #Populations and Evolution (q-bio.PE) #T-cell and B-cell Immunology
- On the importance of assessing topological convergence in Bayesian phylogenetic inference
2024/02/18 by Marius Brusselmans, Brusselmans, Marius, Luiz Max Carvalho +17 · 2 voices · 2 citations
#q-bio.PE #q-bio.GN #q-bio.QM
- How trustworthy is your tree? Bayesian phylogenetic effective sample size through the lens of Monte Carlo error
2021/09/16 by Magee, Andrew F., Karcher, Michael D., Matsen, Frederick A. +1 · 1 citation
#FOS: Biological sciences #FOS: Computer and information sciences #Methodology (stat.ME) #Populations and Evolution (q-bio.PE)
- Vector encoding of phylogenetic trees by ordered leaf attachment
2025/03/13 by Richman, Harry, Zhang, Cheng, Matsen, Frederick A. · 4 citations
#05C05 #05C85 #68W40 #92B10 #Combinatorics (math.CO) #FOS: Biological sciences #FOS: Mathematics #Populations and Evolution (q-bio.PE)
- A Variational Approach to Bayesian Phylogenetic Inference
2022/04/16 by Cheng Zhang, Zhang, Cheng, Frederick A. Matsen +1 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Genomics and Phylogenetic Studies #Bayesian Methods and Mixture Models #Biomedical Text Mining and Ontologies
- Many-core algorithms for high-dimensional gradients on phylogenetic trees
2023/03/08 by Karthik Gangavarapu, Gangavarapu, Karthik, Xiang Ji +11 · 1 citation
Biochemistry, Genetics and Molecular Biology · #Computation (stat.CO) #FOS: Biological sciences #FOS: Computer and information sciences #Genetic diversity and population structure #Genomics and Phylogenetic Studies #Populations and Evolution (q-bio.PE) #RNA and protein synthesis mechanisms