相关论文: Simulating the DNA String Graph in Succinct Space

A quest to determine the complete sequence of a human DNA from telomere to telomere started three decades ago and was finally completed in 2021. This accomplishment was a result of a tremendous effort of numerous experts who engineered…

Graph analysis is a critical component of applications such as online social networks, protein interactions in biological networks, and Internet traffic analysis. The arrival of massive graphs with hundreds of millions of nodes, e.g. social…

The merging of succinct data structures is a well established technique for the space efficient construction of large succinct indexes. In the first part of the paper we propose a new algorithm for merging succinct representations of de…

Identifying near duplicates within large, noisy text corpora has a myriad of applications that range from de-duplicating training datasets, reducing privacy risk, and evaluating test set leakage, to identifying reproduced news articles and…

Deep learning is widely used to uncover hidden patterns in large code corpora. To achieve this, constructing a format that captures the relevant characteristics and features of source code is essential. Graph-based representations have…

Given a graph G and the desired size k in bits, how can we summarize G within k bits, while minimizing the information loss? Large-scale graphs have become omnipresent, posing considerable computational challenges. Analyzing such large…

We propose a new compression scheme for genomic data given as sequence fragments called reads. The scheme uses a reference genome at the decoder side only, freeing the encoder from the burdens of storing references and performing…

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…

Graphs and networks are a key research tool for a variety of science fields, most notably chemistry, biology, engineering and social sciences. Modeling and generation of graphs with efficient sampling is a key challenge for graphs. In…

A retrieval data structure stores a static function f : S -> {0,1}^r . For all x in S, it returns the r-bit value f(x), while for other inputs it may return an arbitrary result. The structure cannot answer membership queries, so it does not…

Graphs are a powerful tool for analyzing large data sets, but many real-world phenomena involve interactions that go beyond the simple pairwise relationships captured by a graph. In this paper we introduce and study a simple combinatorial…

We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…

A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…

In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…

A number of bioinformatic or biostatistical methods are available for analyzing DNA copy number profiles measured from microarray or sequencing technologies. In the absence of rich enough gold standard data sets, the performance of these…

The field of succinct data structures has flourished over the last 16 years. Starting from the compressed suffix array (CSA) by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations…

The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…

Frequent pattern mining is a flagship problem in data mining. In its most basic form, it asks for the set of substrings of a given string $S$ of length $n$ that occur at least $\tau$ times in $S$, for some integer $\tau\in[1,n]$. We…

Graphs play an increasingly important role in various big data applications. However, existing graph data structures cannot simultaneously address the performance bottlenecks caused by the dynamic updates, large scale, and high query…

We present CREST (Compact Retrieval-Based Speculative Decoding), a redesign of REST that allows it to be effectively "compacted". REST is a drafting technique for speculative decoding based on retrieving exact n-gram matches of the most…