Related papers: Space-efficient merging of succinct de Bruijn grap…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
Analysing Web graphs has applications in determining page ranks, fighting Web spam, detecting communities and mirror sites, and more. This study is however hampered by the necessity of storing a major part of huge graphs in the external…
We describe an algorithm for compressing a partially ordered set, or \emph{poset}, so that it occupies space matching the information theory lower bound (to within lower order terms), in the worst case. Using this algorithm, we design a…
Real-world optimization problems are generally not just black-box problems, but also involve mixed types of inputs in which discrete and continuous variables coexist. Such mixed-space optimization possesses the primary challenge of modeling…
We explored an uncharted part of the solution space for sorting algorithms: the role of symmetry in divide&conquer algorithms. We found/designed novel simple binary Quicksort and Mergesort algorithms operating in contiguous space which…
Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…
For the first time we provide a succinct pattern matching index for arbitrary graphs that can be built in polynomial time, which requires less space and answers queries more efficiently than the one in [SODA 2021]. We show that, given an…
This paper presents primarily two Euclidean embeddings of the quotient space generated by matrices that are identified modulo arbitrary row permutations. The original application is in deep learning on graphs where the learning task is…
In this article, we show how to transform a colored de Bruijn graph (dBG) into a practical index for processing massive sets of sequencing reads. Similar to previous works, we encode an instance of a colored dBG of the set using BOSS and a…
We prove that a fractional perfect matching in a non-bipartite graph can be written, in polynomial time, as a convex combination of perfect matchings. This extends the Birkhoff-von Neumann Theorem from bipartite to non-bipartite graphs. The…
We propose a space-efficient algorithm for hidden surface removal that combines one of the fastest previous algorithms for that problem with techniques based on bit manipulation. Such techniques had been successfully used in other settings,…
We describe an efficient method for drawing any n-vertex simple graph G in the hyperbolic plane. Our algorithm produces greedy drawings, which support greedy geometric routing, so that a message M between any pair of vertices may be routed…
Matching nodes in a graph G = (V, E) is a well-studied algorithmic problem with many applications. The b-matching problem is a generalizati on that allows to match a node with up to b neighbors. This allows more flexible connectivity…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running…
In this paper, we introduce a graph matching method that can account for constraints of arbitrary order, with arbitrary potential functions. Unlike previous decomposition approaches that rely on the graph structures, we introduce a…
We propose a weighted common subgraph (WCS) matching algorithm to find the most similar subgraphs in two labeled weighted graphs. WCS matching, as a natural generalization of the equal-sized graph matching or subgraph matching, finds wide…
The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy.…
Given a weighted bipartite graph $G = (L, R, E, w)$, the maximum weight matching (MWM) problem seeks to find a matching $M \subseteq E$ that maximizes the total weight $\sum_{e \in M} w(e)$. This paper presents a novel algorithm with a time…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…