Related papers: An algorithm for constructing principal geodesics …
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
Aerial imagery is increasingly used in Earth science and natural resource management as a complement to labor-intensive ground-based surveys. Aerial systems can collect overlapping images that provide multiple views of each location from…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
We present convincing empirical evidence for an effective and general strategy for building accurate small models. Such models are attractive for interpretability and also find use in resource-constrained environments. The strategy is to…
Latent variable models are an elegant framework for capturing rich probabilistic dependencies in many applications. However, current approaches typically parametrize these models using conditional probability tables, and learning relies…
We propose a flexible and multi-scale method for organizing, visualizing, and understanding datasets sampled from or near stratified spaces. The first part of the algorithm produces a cover tree using adaptive thresholds based on a…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
Bayesian approaches to reconstructing the evolutionary history of languages rely on the tree model, which assumes that these languages descended from a common ancestor and underwent modifications over time. However, this assumption can be…
We perform an experimental evaluation of algorithms for finding geodesic shortest paths between two points inside a simple polygon in the constant-workspace model. In this model, the input resides in a read-only array that can be accessed…
A key task in the study of networked systems is to derive local and global properties that impact connectivity, synchronizability, and robustness; computing shortest paths or geodesics yields measures of network connectivity that can…
Revealing hidden geometry and topology in noisy data sets is a challenging task. Elastic principal graph is a computationally efficient and flexible data approximator based on embedding a graph into the data space and minimizing the energy…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Stochastic mapping is a simulation-based method for probabilistically mapping substitution histories onto phylogenies according to continuous-time Markov models of evolution. This technique can be used to infer properties of the…
In 2019, Yoshida et al. introduced a notion of tropical principal component analysis (PCA). The output is a tropical polytope with a fixed number of vertices that best fits the data. We here apply tropical PCA to dimension reduction and…
Distance-based approaches in phylogenetics such as Neighbor-Joining are a fast and popular approach for building trees. These methods take pairs of sequences from them construct a value that, in expectation, is additive under a stochastic…
Statistical modeling of spatiotemporal phenomena often requires selecting a covariance matrix from a covariance class. Yet standard parametric covariance families can be insufficiently flexible for practical applications, while…