Related papers: Burrows-Wheeler transform for terabases

The automation of ab initio simulations is essential in view of performing high-throughput (HT) computational screenings oriented to the discovery of novel materials with desired physical properties. In this work, we propose algorithms and…

This paper presents a new modeling strategy for joint unsupervised analysis of multiple high-throughput biological studies. As in Multi-study Factor Analysis, our goals are to identify both common factors shared across studies and…

Neural information retrieval architectures based on transformers such as BERT are able to significantly improve system effectiveness over traditional sparse models such as BM25. Though highly effective, these neural approaches are very…

Knowledge-intensive tasks such as question answering often require assimilating information from different sections of large inputs such as books or article collections. We propose ReadTwice, a simple and effective technique that combines…

The field of unsupervised machine translation has seen significant advancement from the marriage of the Transformer and the back-translation algorithm. The Transformer is a powerful generative model, and back-translation leverages…

For years the model performance in machine learning obeyed a power-law relationship with the model size. For the consideration of parameter efficiency, recent studies focus on increasing model depth rather than width to achieve better…

Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

Binary relations are commonly used in Computer Science for modeling data. In addition to classical representations using matrices or lists, some compressed data structures have recently been proposed to represent binary relations in compact…

As the global need for large-scale data storage is rising exponentially, existing storage technologies are approaching their theoretical and functional limits in terms of density and energy consumption, making DNA based storage a potential…

Bayesian deep learning (BDL) is a promising approach to achieve well-calibrated predictions on distribution-shifted data. Nevertheless, there exists no large-scale survey that evaluates recent SOTA methods on diverse, realistic, and…

Near-term noisy intermediate-scale quantum circuits can efficiently implement implicit probabilistic models in discrete spaces, supporting distributions that are practically infeasible to sample from using classical means. One of the…

Transformer architectures, underpinned by the self-attention mechanism, have achieved state-of-the-art results across numerous natural language processing (NLP) tasks by effectively modeling long-range dependencies. However, the…

We present a novel neural network for processing sequences. The ByteNet is a one-dimensional convolutional neural network that is composed of two parts, one to encode the source sequence and the other to decode the target sequence. The two…

Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…

Standard Byte-Pair Encoding (BPE) tokenization compresses text by pairing a learned token vocabulary with a detailed merge list. Recent work has shown that this merge list exposes a potential attack surface for extracting information about…

Many NLP models operate over sequences of subword tokens produced by hand-crafted tokenization rules and heuristic subword induction algorithms. A simple universal alternative is to represent every computerized text as a sequence of bytes…

The task of accumulating a portion of a list of values, whose values may be updated at any time, is widely used throughout various applications in computer science. While it is trivial to accomplish this task without any constraints,…

Code-switching (CSW) text generation has been receiving increasing attention as a solution to address data scarcity. In light of this growing interest, we need more comprehensive studies comparing different augmentation approaches. In this…

With the development of gene sequencing technology, an explosive growth of gene data has been witnessed. And the storage of gene data has become an important issue. Traditional gene data compression methods rely on general software like…