21 papers · ranked by Valyu relevance
Tao Sun, Linzheng Chai, Jian Yang, Yuwei Yin + 5 more
'Jiaheng Liu' 'Bing Wang' 'Liqun Yang' 'Zhoujun Li'] Intermediate reasoning or acting steps have successfully improved large language models (LLMs) for handling various downstream natural language processing (NLP) tasks. When applying LLMs for code generation, recent works mainly focus on directing the models to…
Lloyd Allison, Arun S. Konagurthu, Daniel F. Schmidt
A universal code for the (positive) integers can be used to store or compress a sequence of integers. Every universal code implies a probability distribution on integers. This implied distribution may be a reasonable choice when the true distribution of a source of integers is unknown. Wallace Tree Code (WTC) is a…
Krishnamurthy Kirthi, Subhash Kak
A universal code maps positive integers which represent the source messages into codewords of different lengths. The codeword elements are a set of digits that are constructed according to a specified rule, and they may be binary. There are various universal codes including the Elias codes, the Fibonacci universal…
Wei Yan, Sian-Jheng Lin
In entropy coding, universal coding of integers (UCI) is a binary universal prefix code, such that the ratio of the expected codeword length to max { 1, H ( P ) } is less than or equal to a constant expansion factor KC for any probability distribution P, where H ( P ) is the Shannon entropy of P . K ∗C is the infimum…
Jung Hoon Kim, Sunmi Yeo, Jong Won Kim, Kyeongsoon Kim + 3 more
'Tai-Kyong Song' 'Changhan Yoon' 'Joohon Sung'] Software-based ultrasound imaging systems provide high flexibility that allows easy and fast adoption of newly developed algorithms. However, the extremely high data rate required for data transfer from sensors (e.g., transducers) to the ultrasound imaging systems is a…
John-Antonio Argyriadis, Yang-Hui He, Vishnu Jejjala, Djordje Minic
We study the dynamics of genetic code evolution. The algorithm of Vetsigian et al. [1] provides a solution that is both optimal and universal. We reproduce and analyze the algorithm as a dynamical system. All the parameters used in the model are varied to assess their impact on achieving universality. We show that by…
Jun Lu, Zhuo Zhang, Juan Mo
The conception of universal combinatorial coding is proposed. Relations exist more or less in many coding methods. It means that a kind of universal coding method is objectively existent. It can be a bridge connecting many coding methods. Universal combinatorial coding is lossless and it is based on the combinatorics…
Miloje Rakočević
In some previous works (2018a,b; 2019, 2021a,b, 2022) we presented a new type of mirror symmetry, expressed in the set of protein amino acids; such a symmetry, that it simultaneously represents the semiotic essence of the genetic code. In this paper we provide new evidences that the genetic code represents the unity of…
Simone Giannerini, Alberto Danielli, Diego Luis Gonzalez, Greta Goracci
Circular codes represent a form of coding allowing detection/correction of frameshift errors. Building on recent theoretical advances on circular codes, we provide evidence that protein coding sequences exhibit in-frame circular code marks, that are absent in introns and are intimately linked to the keto-amino…
Pawel M. Mordaka, Kitty Clouston, Jing Cui, Andre Holzer + 3 more
Genome scale engineering has enabled codon compression of the universal genetic code of up to three codons in E. coli, providing the means for genetic code expansion. To go much beyond this number, smaller and simpler genetic systems are needed to avoid significant technical challenges. Chloroplast genomes offer…
Tapan Kumar Mohanta, Yugal Kishore Mohanta, Ahmed Al-Harrasi, Nanaocha Sharma
The chloroplast genome of 5959 species was analyzed to construct the anticodon table of the chloroplast genome. Analysis of the chloroplast transfer ribonucleic acid (tRNA) revealed the presence of a putative quadruplet anticodon containing tRNAs in the chloroplast genome. The tRNAs with putative quadruplet anticodons…
Paweł Błażej, Dariusz R. Kowalski, Dorota Mackiewicz, Małgorzata Wnetrzak + 2 more
The standard genetic code (SGC) is the set of rules by which genetic information is translated into proteins, from codons, i.e. triplets of nucleotides, to amino acids. The questions about the origin and the main factor responsible for the present structure of the code are still under a hot debate. Various…
Julie D. Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch + 1 more
The X circular code is a set of 20 trinucleotides (codons) that has been identified in the protein-coding genes of most organisms (bacteria, archaea, eukaryotes, plasmids, viruses). It has been shown previously that the X circular code has the important mathematical property of being an error-correcting code. Thus…
Lei M. Li, Boris Ryabko
We consider the lossless compression bound of any individual data sequence. Conceptually, its Kolmogorov complexity is such a bound yet uncomputable. According to Shannon’s source coding theorem, the average compression bound is $nH$, where n is the number of words and H is the entropy of an oracle probability…
Pushpa Sree Potluri
Unary coding has found applications in data compression, neural network training, and in explaining the production mechanism of birdsong. Unary coding is redundant; therefore it should have inherent error correction capacity. An expression for the error correction capability of unary coding for the correction of single…
Vadim A. Nenashev, Aleksandr R. Bestugin, Alexey V. Rabin, Sergei V. Solenyi + 2 more
'Sergei V. Solenyi' 'Sergey A. Nenashev' 'Hsiao-Chun Wu'] Currently, various applications of ultra-wideband signal-code constructions are among the most vibrant technologies, being implemented in very different fields. The purpose of this research consists of analyzing Barker codes and searching for the optimal nested…
Stephan Rafler
A code is presented for fast, easy and efficient communication over channels that allow only two signal types: a single sound (e.g. a knock), or no sound (i.e. silence). This is a true binary code while Morse code is a ternary code and does not work in such situations. Thus the presented code is more universal than…
Andrzej Chmielowiec, Paweł Litwin, Philip Broadbridge, Raúl Alcaraz
This article deals with compression of binary sequences with a given number of ones, which can also be considered as a list of indexes of a given length. The first part of the article shows that the entropy H of random n-element binary sequences with exactly k elements equal one satisfies the inequalities…
Pieter Floris Jacobs, Robert Pollice
Scientists across domains are often challenged to master domain-specific languages (DSLs) for their research, which are merely a means to an end but are pervasive in fields like computational chemistry. Automated code generation promises to overcome this barrier, allowing researchers to focus on their core expertise.…
Authors not listed
Synthetic biology's central goal is to create new forms and functions of genetic material by increasing the information a cell can store and retrieve. Wang and co-workers reached a significant milestone by engineering the dTAT1-dNaM unnatural base pair that is significantly more photo- and thermostable than dTPT3-dNaM…
David Kracht, Steffen Schober
Background Barcode multiplexing is a key strategy for sharing the rising capacity of next-generation sequencing devices: Synthetic DNA tags, called barcodes, are attached to natural DNA fragments within the library preparation procedure. Different libraries, can individually be labeled with barcodes for a joint…