Related papers: Reconstructing Biological and Digital Phylogenetic…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
We consider the following graph reconstruction problem: given an unweighted connected graph $G = (V,E)$ with visible vertex set $V$ and an oracle which takes two vertices $u,v \in V$ and returns the shortest path distance between $u$ and…
We describe a new implementation of a parallel N-body tree code. The code is load-balanced using the method of orthogonal recursive bisection to subdivide the N-body system into independent rectangular volumes each of which is mapped to a…
Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
The dynamic trees problem is to maintain a forest undergoing edge insertions and deletions while supporting queries for information such as connectivity. There are many existing data structures for this problem, but few of them are capable…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
The wavelet tree has become a very useful data structure to efficiently represent and query large volumes of data in many different domains, from bioinformatics to geographic information systems. One problem with wavelet trees is their…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
We introduce Tree D-fusion, featuring the first collection of 600,000 environmentally aware, 3D simulation-ready tree models generated through Diffusion priors. Each reconstructed 3D tree model corresponds to an image from Google's Auto…
Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…
Reading comprehension models are based on recurrent neural networks that sequentially process the document tokens. As interest turns to answering more complex questions over longer documents, sequential reading of large portions of text…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
We initiate a study of a query-driven approach to designing partition trees for range-searching problems. Our model assumes that a data structure is to be built for an unknown query distribution that we can access through a sampling oracle,…
The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf…