相关论文: High-performance BWT-based Encoders
Transformer-based models, exemplified by GPT-3, ChatGPT, and GPT-4, have recently garnered considerable attention in both academia and industry due to their promising performance in general language tasks. Nevertheless, these models…
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheeler Transform (BWT), and for this problem various in-memory…
It was estimated that the world produced $59 ZB$ ($5.9 \times 10^{13} GB$) of data in 2020, resulting in the enormous costs of both data storage and transmission. Fortunately, recent advances in deep generative models have spearheaded a new…
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…
Popular sequence alignment tools such as BWA convert a reference genome to an indexing data structure based on the Burrows-Wheeler Transform (BWT), from which matches to individual query sequences can be rapidly determined. However the…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
This paper presents a new solution to address the challenge of increasing memory usage in high-performance computing simulations of Lattice-Bolzmann or Finite-Volume schemes.Our approach utilises a lossy compression scheme based on the…
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…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
In a system that performs both encryption and lossy compression, the conventional way is to compress first and then encrypt the compressed data. This separation approach proves to be optimal. In certain applications where sensitive…
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…
We present an end-to-end trainable wavelet video coder based on motion-compensated temporal filtering (MCTF). Thereby, we introduce a different coding scheme for learned video compression, which is currently dominated by residual and…
Due to the speed limitation of the conventional bit-chosen strategy in the existing weighted bit flipping algorithms, a high-speed LDPC decoder cannot be realized. To solve this problem, we propose a fast weighted bit flipping (FWBF)…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
Inspired by recent work on compression with and for young humans, the success of transform-based approaches to information processing, and the rise of powerful language-based AI, we propose \emph{textual transform coding}. It shares some of…
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in $O (r)$ space and $O ((r + L) \log (m + n))$ time, where $m$ and $n$ are the…
Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external…
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes…
A variety of new and powerful algorithms have been developed for image compression over the years. Among them the wavelet-based image compression schemes have gained much popularity due to their overlapping nature which reduces the blocking…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…