Related papers: From H&M to Gap for Lightweight BWT Merging
The Burrows-Wheeler Transform (BWT) is often taught in undergraduate courses on algorithmic bioinformatics, because it underlies the FM-index and thus important tools such as Bowtie and BWA. Its admirers consider the BWT a thing of beauty…
At CPM 2017, Castelli et al. define and study a new variant of the Longest Common Subsequence Problem, termed the Longest Filled Common Subsequence Problem (LFCS). For the LFCS problem, the input consists of two strings $A$ and $B$ and a…
Recent large reasoning models (LRMs) have made substantial progress in complex reasoning tasks, yet they often generate lengthy reasoning paths for every query, incurring unnecessary computation and latency. Existing speed-up approaches…
We generalize the Brouwer-Zimmermann algorithm, which is the most efficient general algorithm for computing the minimum distance of a random linear code, to the case of generalized Hamming weights. We also adapt this algorithm to compute…
The Bag-of-Words (BoW) representation is well applied to recent state-of-the-art image retrieval works. Typically, multiple vocabularies are generated to correct quantization artifacts and improve recall. However, this routine is corrupted…
Given a weighted bipartite graph $G = (L, R, E, w)$, the maximum weight matching (MWM) problem seeks to find a matching $M \subseteq E$ that maximizes the total weight $\sum_{e \in M} w(e)$. This paper presents a novel algorithm with a time…
The Burrows-Wheeler Transform (BWT) serves as the basis for many important sequence indexes. On very large datasets (e.g. genomic databases), classical BWT construction algorithms are often infeasible because they usually need to have the…
The Burrows-Wheeler Transform (BWT) of a string is an invertible permutation of the string, which can be used for data compression and compact indexes for string pattern matching. Ganguly et al. [SODA, 2017] introduced the parameterized BWT…
The Lempel-Ziv factorization (LZ77) and the Run-Length encoded Burrows-Wheeler Transform (RLBWT) are two important tools in text compression and indexing, being their sizes $z$ and $r$ closely related to the amount of text…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
The Burrows-Wheeler Transform (BWT) is among the most influential discoveries in text compression and DNA storage. It is a reversible preprocessing step that rearranges an $n$-letter string into runs of identical characters (by exploiting…
The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…
Large language models (LLMs) have shown remarkable performance in various natural language processing tasks. However, a primary constraint they face is the context limit, i.e., the maximum number of tokens they can process. Previous works…
It is a consensus that feature maps in the shallow layer are more related to image attributes such as texture and shape, whereas abstract semantic representation exists in the deep layer. Meanwhile, some image information will be lost in…
Checkpoint merging is a technique for combining multiple model snapshots into a single superior model, potentially reducing training time for large language models. This paper explores checkpoint merging in the context of…
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string $w$ into another string $\mathsf{BWT}(w)$. The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of…
One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
For bin packing, the input consists of $n$ items with sizes $s_1,...,s_n \in [0,1]$ which have to be assigned to a minimum number of bins of size 1. Recently, the second author gave an LP-based polynomial time algorithm that employed…
Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem. Length-limited Huffman coding, useful for many…