Related papers: Indexing arbitrary-length $k$-mers in sequencing r…
The Shortest Superstring Problem (SSP) consists, for a set of strings S = {s_1,...,s_n}, to find a minimum length string that contains all s_i, 1 <= i <= k, as substrings. This problem is proved to be NP-Complete and APX-hard. Guaranteed…
While short read aligners, which predominantly use the FM-index, are able to easily index one or a few human genomes, they do not scale well to indexing databases containing thousands of genomes. To understand why, it helps to examine the…
(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…
Sparse matrix-matrix multiplication (SpGEMM) is a computational primitive that is widely used in areas ranging from traditional numerical applications to recent big data analysis and machine learning. Although many SpGEMM algorithms have…
The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…
The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…
We address the problem of building an index for a set $D$ of $n$ strings, where each string location is a subset of some finite integer alphabet of size $\sigma$, so that we can answer efficiently if a given simple query string (where each…
It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
The compressed indexing problem is to preprocess a string $S$ of length $n$ into a compressed representation that supports pattern matching queries. That is, given a string $P$ of length $m$ report all occurrences of $P$ in $S$. We present…
This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and…
Applications in domains ranging from bioinformatics to advertising feature strings that come with numerical scores (utilities). The utilities quantify the importance, interest, profit, or risk of the letters occurring at every position of a…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data. In particular, we show that the recent idea of pseudoalignment introduced in the RNA-Seq context is suitable in the…
The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we…
Top-k Nearest Neighbors (kNN) problem on road network has numerous applications on location-based services. As direct search using the Dijkstra's algorithm results in a large search space, a plethora of complex-index-based approaches have…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
In this paper, we first propose a new iterative algorithm, called the K-sets+ algorithm for clustering data points in a semi-metric space, where the distance measure does not necessarily satisfy the triangular inequality. We show that the…