相关论文: Species Tree Estimation Using ASTRAL: Practical Co…
Tree-based ensemble methods, as Random Forests and Gradient Boosted Trees, have been successfully used for regression in many applications and research studies. Furthermore, these methods have been extended in order to deal with uncertainty…
The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…
Tree-based ensemble methods such as random forests, gradient-boosted trees, and Bayesianadditive regression trees have been successfully used for regression problems in many applicationsand research studies. In this paper, we study ensemble…
We are totally immersed in the Big Data era and reliable algorithms and methods for data classification are instrumental for astronomical research. Random Forest and Support Vector Machines algorithms have become popular over the last few…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Accurate tree height estimation is vital for ecological monitoring and biomass assessment. We apply quantile regression to existing tree height estimation models based on satellite data to incorporate uncertainty quantification. Most…
Incomplete lineage sorting (ILS) is a common source of gene tree incongruence in multilocus analyses. A large number of methods have been developed to infer species trees in the presence of ILS. Here we provide a mathematical analysis of…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
Analysis of sample survey data often requires adjustments to account for missing data in the outcome variables of principal interest. Standard adjustment methods based on item imputation or on propensity weighting factors rely heavily on…
One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…
Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations:…
Random forests are an ensemble method relevant for many problems, such as regression or classification. They are popular due to their good predictive performance (compared to, e.g., decision trees) requiring only minimal tuning of…
The prevailing mindset is that a single decision tree underperforms classic random forests in testing accuracy, despite its advantages in interpretability and lightweight structure. This study challenges such a mindset by significantly…
We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates…
Based on decision trees, many fields have arguably made tremendous progress in recent years. In simple words, decision trees use the strategy of "divide-and-conquer" to divide the complex problem on the dependency between input features and…
We study graph estimation and density estimation in high dimensions, using a family of density estimators based on forest structured undirected graphical models. For density estimation, we do not assume the true distribution corresponds to…
Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree…
Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…