Related papers: Time and Memory Efficient Lempel-Ziv Compression U…
Lossless model compression holds tremendous promise for alleviating the memory and bandwidth bottlenecks in bit-exact Large Language Model (LLM) serving. However, existing approaches often result in substantial inference slowdowns due to…
There are two major approaches for sequence labeling. One is the probabilistic gradient-based methods such as conditional random fields (CRF) and neural networks (e.g., RNN), which have high accuracy but drawbacks: slow training, and no…
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…
The deployment of Large Language Models is constrained by the memory and bandwidth demands of static weights and dynamic Key-Value cache. SVD-based compression provides a hardware-friendly solution to reduce these costs. However, existing…
An algorithm is presented that solves the Minimum Dominating Set problem exactly using polynomial space based on dynamic programming for a tree decomposition. A direct application of dynamic programming based on a tree decomposition would…
For both the Lempel Ziv 77- and 78-factorization we propose algorithms generating the respective factorization using $(1+\epsilon) n \lg n + O(n)$ bits (for any positive constant $\epsilon \le 1$) working space (including the space for the…
The rapid growth of digital data has heightened the demand for efficient lossless compression methods. However, existing algorithms exhibit trade-offs: some achieve high compression ratios, others excel in encoding or decoding speed, and…
Can we analyze data without decompressing it? As our data keeps growing, understanding the time complexity of problems on compressed inputs, rather than in convenient uncompressed forms, becomes more and more relevant. Suppose we are given…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…
We study the complexity of constructing an optimal parsing $\varphi$ of a string ${\bf s} = s_1 \dots s_n$ under the constraint that given a position $p$ in the original text, and the LZ76-like (Lempel Ziv 76) encoding of $T$ based on…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
Storing and archiving data produced by next-generation sequencing (NGS) is a huge burden for research institutions. Reference-based compression algorithms are effective in dealing with these data. Our work focuses on compressing FASTQ…
Bitmap indexes are frequently used to index multidimensional data. They rely mostly on sequential input/output. Bitmaps can be compressed to reduce input/output costs and minimize CPU usage. The most efficient compression techniques are…
The {\em wavelet tree} is a flexible data structure that permits representing sequences $S[1,n]$ of symbols over an alphabet of size $\sigma$, within compressed space and supporting a wide range of operations on $S$. When $\sigma$ is…
Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of…
Retrieval-Augmented Generation (RAG) enhances coding tasks by incorporating retrieved code examples into prompts. However, lengthy prompts, often exceeding tens of thousands of tokens, introduce challenges related to limited context windows…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…
Efficient solution of the single source shortest path (SSSP) problem on road networks is an important requirement for numerous real-world applications. This paper introduces an algorithm for the SSSP problem using compression method. Owning…