Related papers: Another virtue of wavelet forests?
Motivated by challenges in pangenomic read alignment, we propose a generalization of Wheeler graphs that we call Wheeler maps. A Wheeler map stores a text $T[1..n]$ and an assignment of tags to the characters of $T$ such that we can…
Decision forests (Forests), in particular random forests and gradient boosting trees, have demonstrated state-of-the-art accuracy compared to other methods in many supervised learning scenarios. In particular, Forests dominate other methods…
The task of accumulating a portion of a list of values, whose values may be updated at any time, is widely used throughout various applications in computer science. While it is trivial to accomplish this task without any constraints,…
The selection of grouped variables using the random forest algorithm is considered. First a new importance measure adapted for groups of variables is proposed. Theoretical insights into this criterion are given for additive regression…
We show how to use a balanced wavelet tree as a data structure that stores a list of numbers and supports efficient {\em range quantile queries}. A range quantile query takes a rank and the endpoints of a sublist and returns the number with…
Wavelets are well known for data compression, yet have rarely been applied to the compression of neural networks. This paper shows how the fast wavelet transform can be used to compress linear layers in neural networks. Linear layers still…
A weight based dynamic compression method has recently been proposed, which is especially suitable for the encoding of files with locally skewed distributions. Its main idea is to assign larger weights to closer to be encoded symbols by…
Behavior trees (BTs) are an optimally modular framework to assemble hierarchical hybrid control policies from a set of low-level control policies using a tree structure. Many robotic tasks are naturally decomposed into a hierarchy of…
A dynamic forest data structure maintains a forest (and associated data like edge weights) under edge insertions and deletions. Dynamic forests are widely used to solve online and offline graph problems. Well-known examples of dynamic…
We prove a square-root space simulation for deterministic multitape Turing machines, showing $\mathrm{TIME}[t]\subseteq \mathrm{SPACE}[O(\sqrt{t})]$ \emph{measured in tape cells over a fixed finite alphabet}. The key step is a Height…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use…
In order to avoid the reference bias introduced by mapping reads to a reference genome, bioinformaticians are investigating reference-free methods for analyzing sequenced genomes. With large projects sequencing thousands of individuals,…
In this article we extend the elegant in-place Burrows-Wheeler transform (BWT) algorithm proposed by Crochemore et al. (Crochemore et al., 2015). Our extension is twofold: we first show how to compute simultaneously the longest common…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
The Block Tree (BT) is a novel compact data structure designed to compress sequence collections. It obtains compression ratios close to Lempel-Ziv and supports efficient direct access to any substring. The BT divides the text recursively…
We show how to construct a dynamic ordered dictionary, supporting insert/delete/rank/select on a set of $n$ elements from a universe of size $U$, that achieves the optimal amortized expected time complexity of $O(1 + \log n / \log \log U)$,…
We identify string corrections to the EM memory effect. Though largely negligible in the low-energy limit, the effect become relevant in high-energy collisions and in extreme events. We illustrate our findings in a simple unoriented bosonic…
We show how a collection of Euler-tour trees for a forest on $n$ vertices can be stored in $2 n + o (n)$ bits such that simple queries take constant time, more complex queries take logarithmic time and updates take polylogarithmic amortized…
We present an extension of the in-place BWT algorithm of Crochemore et al. [8] that enables the construction of the Lyndon array using O(1) extra space. Our approach incrementally maintains the lexicographic ranks of the suffixes during the…