Related papers: Nucleotide String Indexing using Range Matching

This paper introduces a new kernel-based classifier by viewing kernel matrices as generalized graphs and leveraging recent progress in graph embedding techniques. The proposed method facilitates fast and scalable kernel matrix embedding,…

Kernel methods are powerful tools in machine learning. They have to be computationally efficient. In this paper, we present a novel Geometric-based approach to compute efficiently the string subsequence kernel (SSK). Our main idea is that…

Neural radiance field (NeRF) has shown remarkable performance in generating photo-realistic novel views. Among recent NeRF related research, the approaches that involve the utilization of explicit structures like grids to manage features…

Advances in novel hardware devices and architectures allow Spiking Neural Network evaluation using ultra-low power, mixed-signal, memristor crossbar arrays. As individual network sizes quickly scale beyond the dimensional capabilities of…

The adoption of deep neural networks (DNNs) in safety-critical domains has engendered serious reliability concerns. A prominent example is hardware transient faults that are growing in frequency due to the progressive technology scaling,…

Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to…

Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…

We propose MRU (Multi-Range Reasoning Units), a new fast compositional encoder for machine comprehension (MC). Our proposed MRU encoders are characterized by multi-ranged gating, executing a series of parameterized contract-and-expand…

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…

Deep neural networks have achieved significant improvements in information retrieval (IR). However, most existing models are computational costly and can not efficiently scale to long documents. This paper proposes a novel End-to-End neural…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…

Indexing intervals is a fundamental problem, finding a wide range of applications. Recent work on managing large collections of intervals in main memory focused on overlap joins and temporal aggregation problems. In this paper, we propose…

In this paper, we introduce Ranger - a toolkit to facilitate the easy use of effect-size-based meta-analysis for multi-task evaluation in NLP and IR. We observed that our communities often face the challenge of aggregating results over…

DNA sequence alignment is an important workload in computational genomics. Reference-guided DNA assembly involves aligning many read sequences against candidate locations in a long reference genome. To reduce the computational load of this…

The need for scalable concurrent ordered set data structures with linearizable range query support is increasing due to the rise of multicore computers, data processing platforms and in-memory databases. This paper presents a new concurrent…

The advent of next-generation sequencing (NGS) has revolutionized genomic research by enabling cost-effective, high-throughput sequencing of a diverse range of organisms. This breakthrough has unleashed a "Cambrian explosion" in genomic…

FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…

We revisit various string indexing problems with range reporting features, namely, position-restricted substring searching, indexing substrings with gaps, and indexing substrings with intervals. We obtain the following main results.…

Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and…