Related papers: XORRO: Rapid Paired-End Read Overlapper

Genome sequencing has become a central focus in computational biology. A genome study typically begins with sequencing, which produces millions to billions of short DNA fragments known as reads. Read mapping aligns these reads to a…

Erasure coding (EC) affords data redundancy for large-scale systems. XOR-based EC is an easy-to-implement method for optimizing EC. This paper addresses a significant performance gap between the state-of-the-art XOR-based EC approach (with…

Code retrieval helps developers reuse the code snippet in the open-source projects. Given a natural language description, code retrieval aims to search for the most relevant code among a set of code. Existing state-of-the-art approaches…

Transformer-based pre-trained models, such as BERT, have achieved remarkable results on machine reading comprehension. However, due to the constraint of encoding length (e.g., 512 WordPiece tokens), a long document is usually split into…

Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…

Binary-source code matching plays an important role in many security and software engineering related tasks such as malware detection, reverse engineering and vulnerability assessment. Currently, several approaches have been proposed for…

Generative models have achieved remarkable success across various applications, driving the demand for multi-GPU computing. Inter-GPU communication becomes a bottleneck in multi-GPU computing systems, particularly on consumer-grade GPUs. By…

Regular expression matching is essential for many applications, such as finding patterns in text, exploring substrings in large DNA sequences, or lexical analysis. However, sequential regular expression matching may be time-prohibitive for…

The goal of co-clustering is to simultaneously identify a clustering of rows as well as columns of a two dimensional data matrix. A number of co-clustering techniques have been proposed including information-theoretic co-clustering and the…

Bitmap indexes are commonly used in databases and search engines. By exploiting bit-level parallelism, they can significantly accelerate queries. However, they can use much memory, and thus we might prefer compressed bitmap indexes.…

Detecting issue framing in text - how different perspectives approach the same topic - is valuable for social science and policy analysis, yet challenging for automated methods due to subtle linguistic differences. We introduce `paired…

In this paper, we propose a new method of applying the XOR and XNOR gates on exponentially large superpositions in Instantaneous Noise-Based Logic. These new gates are repeatable, and they can achieve an exponential speed up in computation…

In this paper, we consider the convergence of a very general asynchronous-parallel algorithm called ARock, that takes many well-known asynchronous algorithms as special cases (gradient descent, proximal gradient, Douglas Rachford, ADMM,…

While end-to-end models have shown great success on the Automatic Speech Recognition task, performance degrades severely when target sentences are long-form. The previous proposed methods, (partial) overlapping inference are shown to be…

Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous…

This paper presents a new, parallel implementation of clustering and demonstrates its utility in greatly speeding up the process of identifying homologous proteins. Clustering is a technique to reduce the number of comparison needed to find…

Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…

We propose to address online speaker diarization as a combination of incremental clustering and local diarization applied to a rolling buffer updated every 500ms. Every single step of the proposed pipeline is designed to take full advantage…

We propose smooth $q$-gram, the first variant of $q$-gram that captures $q$-gram pair within a small edit distance. We apply smooth $q$-gram to the problem of detecting overlapping pairs of error-prone reads produced by single molecule real…

This paper investigates the utilization of an end-to-end diarization model as post-processing of conventional clustering-based diarization. Clustering-based diarization methods partition frames into clusters of the number of speakers; thus,…