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Calculating the length of a longest common subsequence (LCS) of two strings $A$ and $B$ of length $n$ and $m$ is a classic research topic, with many worst-case oriented results known. We present two algorithms for LCS length calculation…
Fast, efficient and reliable algorithms for pairwise alignment of protein structures are in ever increasing demand for analyzing the rapidly growing data of protein structures. CLePAPS is a tool developed for this purpose. It distinguishes…
We give a near-optimal quantum algorithm for the longest common substring (LCS) problem between two run-length encoded (RLE) strings, with the assumption that the prefix-sums of the run-lengths are given. Our algorithm costs…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Spatially coupled low-density parity-check (SC-LDPC) codes are sparse graph codes that have recently become of interest due to their capacity-approaching performance on memoryless binary input channels. In this paper, we unify all existing…
As the most powerful tool in discrepancy theory, the partial coloring method has wide applications in many problems including the Beck-Fiala problem and Spencer's celebrated result. Currently, there are two major algorithmic methods for the…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological…
Mining dense subgraphs on multi-layer graphs is an interesting problem, which has witnessed lots of applications in practice. To overcome the limitations of the quasi-clique-based approach, we propose d-coherent core (d-CC), a new notion of…
This paper proposes two coherent broadband focusing algorithms for spatial correlation estimation using sparse linear arrays. Both algorithms decompose the time-domain array data into disjoint frequency bands through discrete Fourier…
Let G be a simple connected graph with vertex set V(G) and edge set E(G. Each vertex of V(G) is colored by a color from the set of colors {c_1, c_2,\dots, c_{\alpha}}. We take a subset S of V(G), such that for every vertex v in V(G)\S, at…
Scaling test-time computation--generating and analyzing multiple or sequential outputs for a single input--has become a promising strategy for improving the reliability and quality of large language models (LLMs), as evidenced by advances…
Sparse superimposed coding (SSC) has emerged as a promising technique for short-packet transmission in ultra-reliable low-latency communication scenarios. However, conventional SSC schemes often suffer from high encoding and decoding…
The 2-LCPS problem, first introduced by Chowdhury et al. [Fundam. Inform., 129(4):329-340, 2014], asks one to compute (the length of) a longest palindromic common subsequence between two given strings $A$ and $B$. We show that the 2-LCPS…
We consider the problem of low-rank approximation of massive dense non-negative tensor data, for example to discover latent patterns in video and imaging applications. As the size of data sets grows, single workstations are hitting…
Semi-supervised learning has demonstrated great potential in medical image segmentation by utilizing knowledge from unlabeled data. However, most existing approaches do not explicitly capture high-level semantic relations between distant…
The Minimum Sum Coloring Problem (MSCP) is derived from the Graph Coloring Problem (GCP) by associating a weight to each color. The aim of MSCP is to find a coloring solution of a graph such that the sum of color weights is minimum. MSCP…
Exemplar-based colorization approaches rely on reference image to provide plausible colors for target gray-scale image. The key and difficulty of exemplar-based colorization is to establish an accurate correspondence between these two…
In this paper, we propose new coupled codes constructed by overlapping circular spatially-coupled low-density parity-check (SC-LDPC) codes, which show better asymptotic and finite-length decoding performance compared to the conventional…
Encoding long sequences in Natural Language Processing (NLP) is a challenging problem. Though recent pretraining language models achieve satisfying performances in many NLP tasks, they are still restricted by a pre-defined maximum length,…
A novel code construction based on spatially coupled low-density parity-check (SC-LDPC) codes is presented. The proposed code ensembles are described by protographs, comprised of several protograph-based chains characterizing individual…