Related papers: Species tree estimation using Neighbor Joining
We revisit the classical problem of exact inference on probabilistic graphical models (PGMs). Our algorithm is based on recent worst-case optimal database join algorithms, which can be asymptotically faster than traditional data processing…
In this letter, a novel method for change detection is proposed using neighborhood structure correlation. Because structure features are insensitive to the intensity differences between bi-temporal images, we perform the correlation…
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…
In an extant population, how much information do extant individuals provide on the pedigree of their ancestors? Recent work by Kim, Mossel, Ramnarayan and Turner (2020) studied this question under a number of simplifying assumptions,…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
We propose a new data-structure, the generalized randomized kd forest, or kgeraf, for approximate nearest neighbor searching in high dimensions. In particular, we introduce new randomization techniques to specify a set of independently…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
Nearest neighbor is a popular nonparametric method for classification and regression with many appealing properties. In the big data era, the sheer volume and spatial/temporal disparity of big data may prohibit centrally processing and…
This work presents novel algorithms for learning Bayesian network structures with bounded treewidth. Both exact and approximate methods are developed. The exact method combines mixed-integer linear programming formulations for structure…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein.…
Approximate K Nearest Neighbor (AKNN) search in high-dimensional spaces is a critical yet challenging problem. In AKNN search, distance computation is the core task that dominates the runtime. Existing approaches typically use approximate…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Modeling forests using historical data allows for more accurately evolution analysis, thus providing an important basis for other studies. As a recognized and effective tool, remote sensing plays an important role in forestry analysis. We…
Extracting complex structures from grid-based data is a common key step in automated medical image analysis. The conventional solution to recovering tree-structured geometries typically involves computing the minimal cost path through…
K-Nearest Neighbors (KNN) search is a fundamental algorithm in artificial intelligence software with applications in robotics, and autonomous vehicles. These wide-ranging applications utilize KNN either directly for simple classification or…
A recent proposal of data dependent similarity called Isolation Kernel/Similarity has enabled SVM to produce better classification accuracy. We identify shortcomings of using a tree method to implement Isolation Similarity; and propose a…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
We present a same-level comparison of the most prominent inversion methods for the reconstruction of the matter density field in the quasi-linear regime from the Ly$\alpha$ forest flux. Moreover, we present a pathway for refining the…
Ren et al. recently introduced a method for aggregating multiple decision trees into a strong predictor by interpreting a path taken by a sample down each tree as a binary vector and performing linear regression on top of these vectors…