相关论文: Efficient k-mer Dataset Compression Using Eulerian…

This paper introduces the de Bruijn graph edge minimization problem, which is related to the compression of de Bruijn graphs: find the order-k de Bruijn graph with minimum edge count among all orders. We describe an efficient algorithm that…

Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…

Learning-based probabilistic models can be combined with an entropy coder for data compression. However, due to the high complexity of learning-based models, their practical application as text compressors has been largely overlooked. To…

This study presents an efficient incremental/decremental approach for big streams based on Kernel Ridge Regression (KRR), a frequently used data analysis in cloud centers. To avoid reanalyzing the whole dataset whenever sensors receive new…

The de Bruijn graph plays an important role in bioinformatics, especially in the context of de novo assembly. However, the representation of the de Bruijn graph in memory is a computational bottleneck for many assemblers. Recent papers…

We introduce a Fourier-based fast algorithm for Gaussian process regression in low dimensions. It approximates a translationally-invariant covariance kernel by complex exponentials on an equispaced Cartesian frequency grid of $M$ nodes.…

K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of…

Minimum Bayes Risk (MBR) decoding is a powerful decoding strategy widely used for text generation tasks, but its quadratic computational complexity limits its practical application. This paper presents a novel approach for approximating MBR…

We present a novel lossless universal source coding algorithm that uses parallel computational units to increase the throughput. The length-$N$ input sequence is partitioned into $B$ blocks. Processing each block independently of the other…

De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…

In terms of signal samples, we propose and justify a new rank reduced multi-term transform, abbreviated as MTT, which, under certain conditions, may provide better-associated accuracy than that of known optimal rank reduced transforms. The…

Motivation: A Genomic Dictionary, i.e., the set of the k-mers appearing in a genome, is a fundamental source of genomic information: its collection is the first step in strategic computational methods ranging from assembly to sequence…

Machine learning interatomic potentials (MLIPs) balance high accuracy and lower costs compared to density functional theory calculations, but their performance often depends on the size and diversity of training datasets. Large datasets…

High-dimensional token embeddings underpin Large Language Models (LLMs), as they can capture subtle semantic information and significantly enhance the modelling of complex language patterns. However, this high dimensionality also introduces…

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…

Recent works have proven the effectiveness of k-nearest-neighbor machine translation(a.k.a kNN-MT) approaches to produce remarkable improvement in cross-domain translations. However, these models suffer from heavy retrieve overhead on the…

Retrieval augmentation addresses many critical problems in large language models such as hallucination, staleness, and privacy leaks. However, running retrieval-augmented language models (LMs) is slow and difficult to scale due to…

Cryogenic electron microscopy (Cryo-EM) has become an essential tool for capturing high-resolution biological structures. Despite its advantage in visualizations, the large storage size of Cryo-EM data file poses significant challenges for…

Robust tensor completion (RTC) aims to recover a low-rank tensor from its incomplete observation with outlier corruption. The recently proposed tensor ring (TR) model has demonstrated superiority in solving the RTC problem. However, the…

Discrete trigonometric transforms (DTTs), such as the DCT-2 and the DST-7, are widely used in video codecs for their balance between coding performance and computational efficiency. In contrast, data-dependent transforms, such as the…