Related papers: Local Decodability of the Burrows-Wheeler Transfor…
This paper addresses the problem of data compression with local decoding and local update. A compression scheme has worst-case local decoding $d_{wc}$ if any bit of the raw file can be recovered by probing at most $d_{wc}$ bits of the…
High-throughput DNA sequencers are becoming indispensable in our understanding of diseases at molecular level, in marker-assisted selection in agriculture and in microbial genetics research. These sequencing instruments produce enormous…
Text encoding is one of the most important steps in Natural Language Processing (NLP). It has been done well by the self-attention mechanism in the current state-of-the-art Transformer encoder, which has brought about significant…
In this paper, we develop a method of performing the one-point statistics of a perturbed density field with a multiresolutional decomposition based on the discrete wavelet transform (DWT). We establish the algorithm of the one-point…
There are currently plenty of programs available for mapping short sequences (reads) to a genome. Most of them, however, including such popular and actively developed programs as Bowtie, BWA, TopHat and many others, are based on…
Chinese word segmentation (CWS) is a fundamental task for Chinese language understanding. Recently, neural network-based models have attained superior performance in solving the in-domain CWS task. Last year, Bidirectional Encoder…
Optimal transport (OT), which provides a distance between two probability distributions by considering their spatial locations, has been applied to widely diverse applications. Computing an OT problem requires solution of linear programming…
We consider decoding of binary Tanner codes using message-passing iterative decoding and linear programming (LP) decoding in MBIOS channels. We present new certificates that are based on a combinatorial characterization for local-optimality…
The Binary Iterative Hard Thresholding (BIHT) algorithm is a popular reconstruction method for one-bit compressed sensing due to its simplicity and fast empirical convergence. There have been several works about BIHT but a theoretical…
The Fourier Transform is one of the most important linear transformations used in science and engineering. Cooley and Tukey's Fast Fourier Transform (FFT) from 1964 is a method for computing this transformation in time $O(n\log n)$.…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
Transforming an input sequence into its constituent k-mers is a fundamental operation in computational genomics. To reduce storage costs associated with k-mer datasets, we introduce and formally analyze MCTR, a novel two-stage algorithm for…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…
We apply the influence-adaptive Walsh geometry of a companion theory paper (arXiv:2605.01637) to extreme low-bit weight-only LLM quantization. The recipe is one math-invariant transformation: WHT-rotate each linear layer's weight matrix and…
Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string $S$, it produces a dictionary $D$ and a parse $P$ of…
We present a new scalable, lightweight algorithm to incrementally construct the BWT and FM-index of large string sets such as those produced by Next Generation Sequencing. The algorithm is designed for massive parallelism and can…
Long-term location tracking, where trajectory compression is commonly used, has gained high interest for many applications in transport, ecology, and wearable computing. However, state-of-the-art compression methods involve high space-time…
Real-time decoding plays a crucial role in practical fault-tolerant quantum computing. Window decoding, in which the decoding problem is divided into windows, is a promising approach. While reducing the window size is desirable for faster…
Minimum Bayes risk (MBR) decoding is a decision rule of text generation, which selects the hypothesis that maximizes the expected utility and robustly generates higher-quality texts than maximum a posteriori (MAP) decoding. However, it…
The so-called block-term decomposition (BTD) tensor model has been recently receiving increasing attention due to its enhanced ability of representing systems and signals that are composed of \emph{blocks} of rank higher than one, a…