18 papers · ranked by Valyu relevance
Xutan Peng, Yi Zhang, Dejia Peng, Jiafa Zhu
Run-Length Encoding (RLE) is one of the most fundamental tools in data compression. However, its compression power drops significantly if there lacks consecutive elements in the sequence. In extreme cases, the output of the encoder may require more space than the input (aka size inflation). To alleviate this issue…
Akiyoshi Kawamoto, I Tomohiro
Let ST (k) denote the set of distinct substrings of length k in a string T, then the k-th substring complexity is defined by its cardinality |ST (k)|. Recently, δ = max{|ST (k)|/k : k ≥ 1} is shown to be a good compressibility measure of highly-repetitive strings. In this paper, given T of length n in the run-length…
Yaohua Zhu, Ya Liu, Yanghang Zhu, Mingsheng Huang + 3 more
'Yong Zhang' 'Bogdan Smolka'] Infrared line-scanning images have high redundancy and large file sizes. In JPEG2000 compression, the MQ arithmetic encoder’s complexity slows down processing. Huffman coding can achieve O(1) complexity based on a code table, but its integer-bit encoding mechanism and ignorance of the…
Mukesh Mishra, Gourab Sen Gupta, Xiang Gui, Óscar García
The exponential growth in remote sensing, coupled with advancements in integrated circuits (IC) design and fabrication technology for communication, has prompted the progress of Wireless Sensor Networks (WSN). WSN comprises of sensor nodes and hubs fit for detecting, processing, and communicating remotely. Sensor nodes…
Tzu-Ching Lee, Han-Hsuan Lin
between Run-Length Encoded Strings Authors: ['Tzu-Ching Lee' 'Han-Hsuan Lin'] 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 O˜ (n 2/3…
Rohan Choudhury, Guanglei Zhu, Sihan Liu, Koichiro Niinuma + 2 more
'Kris Kitani' 'László A. Jeni'] Transformers are slow to train on videos due to extremely large numbers of input tokens, even though many video tokens are repeated over time. Existing methods to remove such uninformative tokens either have significant overhead, negating any speedup, or require tuning for different…
Lily Major, Amanda Clare, Jacqueline W. Daykin, Benjamin Mora + 1 more
'Christine Zarges'] The Burrows-Wheeler Transform (BWT) is a string transformation technique widely used in areas such as bioinformatics and file compression. Many applications combine a run-length encoding (RLE) with the BWT in a way which preserves the ability to query the compressed data efficiently. However, these…
Tzu-Ching Lee, Han-Hsuan Lin
We give a sublinear quantum algorithm for the longest common substring (LCS) problem on the run-length encoded (RLE) inputs, under the assumption that the prefix-sums of the runs are given. Our algorithm costs O˜ (n 5/6 ) · O(polylog(˜n)) time, where n and n˜ are the encoded and decoded length of the inputs…
Fabio Cunial, Olgert Denas, Djamal Belazzougui, Yann Ponty
Even though $ms_{S,T}$ takes just $2|S|$ bits, storing the bitvector of every pair of genomes in a large dataset for later analysis and querying might still require too much space overall. Real $\text{ms}$ bitvectors, however, have several features that could be exploited for lossless compression. Specifically, if S…
Fabian Müntefering, Yeremia Gunawan Adhisantoso, Shubham Chandak, Jörn Ostermann + 2 more
'Jörn Ostermann' 'Mikel Hernaez' 'Jan Voges'] For the last two decades, the amount of genomic data produced by scientific and medical applications has been growing at a rapid pace. To enable software solutions that analyze, process, and transmit these data in an efficient and interoperable way, ISO and IEC released the…
Ahsan Sanaullah, Nathaniel K. Brown, Pramesh Shakya, Arun Deegutla + 4 more
Lossless full text indexes are utilized in a myriad of applications in bioinformatics. The continuously decreasing cost of generating biological data has resulted in the need to build full text indexes on biological datasets of increasing size. Many compressed full text indexes have been developed to address this…
Leah Woldemariam, Hang Liu, Anna Scaglione
In this paper, we propose a source coding scheme that represents data from unknown distributions through frequency and support information. Existing encoding schemes often compress data by sacrificing computational efficiency or by assuming the data follows a known distribution. We take advantage of the structure that…
Hideo Bannai, I Tomohiro, Yuto Nakashima
The Burrows-Wheeler transform (BWT) is a reversible transform that converts a string w into another string BWT(w). The size of the run-length encoded BWT (RLBWT) can be interpreted as a measure of repetitiveness in the class of representations called dictionary compression which are essentially representations based on…
Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Dominik Köppl + 2 more
The positional Burrows-Wheeler Transform (PBWT) has been introduced as a key data structure for indexing haplotype sequences with the main purpose of finding maximal haplotype matches in h sequences containing w variation sites in -time with a significant improvement over classical quadratic time approaches. However…
Fajia Sun, Long Qian
DNA has been pursued as a compelling medium for digital data storage during the past decade. While large-scale data storage and random access have been achieved in artificial DNA, the synthesis cost keeps hindering DNA data storage from popularizing into daily life. In this study, we proposed a more efficient paradigm…
Authors not listed
Sequence is the critical determinant of macromolecular function, yet current polymer design approaches often optimize monomer composition and ratios while ignoring sequence. This creates poorly defined design spaces for active learning that miss the vast combinatorial landscape of sequence possibilities. We introduce…
Roland Wittler
To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σ^k^ k-mers and the interval [0, σ^k^ −1], where σ is the alphabet size. In many…
Ignas Galminas, Omer Sabary, Hadas Abraham, Kornelija Kaminskaitė + 8 more
DNA data storage allows sequences to be defined without biological constraints, yet readout workflows still depend on generic end-repair/dA-tailing chemistry. We developed NinjaSeq, a type IIS restriction endonuclease library-preparation strategy that incorporates recognition sites into primer flanks, enabling…