Related papers: BWT construction and search at the terabase scale

GPU-based fast Fourier transform (FFT) is extremely important for scientific computing and signal processing. However, we find the inefficiency of existing FFT libraries and the absence of fault tolerance against soft error. To address…

Data stalls are a major overhead in main-memory database engines due to the use of pointer-rich data structures. Lightweight coroutines ease the implementation of software prefetching to hide data stalls by overlapping computation and…

While modern biotechnologies allow synthesizing new proteins and function measurements at scale, efficiently exploring a protein sequence space and engineering it remains a daunting task due to the vast sequence space of any given protein.…

We extract an optimal subset of architectural parameters for the BERT architecture from Devlin et al. (2018) by applying recent breakthroughs in algorithms for neural architecture search. This optimal subset, which we refer to as "Bort", is…

Various networks are broadly and deeply applied in real-life applications. Reliability is the most important index for measuring the performance of all network types. Among the various algorithms, only implicit enumeration algorithms, such…

Adapting large pre-trained models (PTMs) through fine-tuning imposes prohibitive computational and storage burdens. Recent studies of parameter-efficient tuning (PET) find that only optimizing a small portion of parameters conditioned on…

Motivation: Over the past decade, network-based approaches have proven useful in identifying disease modules within the human interactome, often providing insights into key mechanisms and guiding the quest for therapeutic targets. This is…

Indexes can significantly improve search performance in relational databases. However, if the query workload changes frequently or new data updates occur continuously, it may not be worthwhile to build a conventional index upfront for query…

This paper presents a novel approach to the acquisition of language models from corpora. The framework builds on Cobweb, an early system for constructing taxonomic hierarchies of probabilistic concepts that used a tabular, attribute-value…

Language models are trained mainly on massive text data from the Internet, and it becomes increasingly important to understand this data source. Exact-match search engines enable searching in large text corpora - counting string appearances…

Protein structure prediction helps to understand gene translation and protein function, which is of growing interest and importance in structural biology. The AlphaFold model, which used transformer architecture to achieve atomic-level…

The rapid growth in biological sequence data is revolutionizing our understanding of genotypic diversity and challenging conventional approaches to informatics. With the increasing availability of genomic data, traditional bioinformatic…

Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…

We describe an algorithm to find maximal exact matches (MEMs) among HiFi reads with homopolymer errors. The main novelty in our work is that we resort to run-length compression to help deal with errors. Our method receives as input a…

Index structures are one of the most important tools that DBAs leverage to improve the performance of analytics and transactional workloads. However, building several indexes over large datasets can often become prohibitive and consume…

The sort transform (ST) is a modification of the Burrows-Wheeler transform (BWT). Both transformations map an arbitrary word of length n to a pair consisting of a word of length n and an index between 1 and n. The BWT sorts all rotation…

Neural Machine Translation (MT) has reached state-of-the-art results. However, one of the main challenges that neural MT still faces is dealing with very large vocabularies and morphologically rich languages. In this paper, we propose a…

Docker is a tool for lightweight OS-level virtualization. Docker images are created by performing a build, controlled by a source-level artifact called a Dockerfile. We studied Dockerfiles on GitHub, and -- to our great surprise -- found…

Biomedical question-answering (QA) systems require effective retrieval and generation components to ensure accuracy, efficiency, and scalability. This study systematically examines a Retrieval-Augmented Generation (RAG) system for…

Database-search algorithms, that deduce peptides from Mass Spectrometry (MS) data, have tried to improve the computational efficiency to accomplish larger, and more complex systems biology studies. Existing serial, and high-performance…