22 papers · ranked by Valyu relevance
Kees Schouhamer Immink, Jos H. Weber, Tuan Thanh Nguyen, Kui Cai + 2 more
The design of low-complexity and efficient constrained codes has been a major research item for many years. This paper reports on a versatile method named concatenated constrained codes for designing efficient fixed-length constrained codes with small complexity. A concatenated constrained code comprises two (or more)…
Daniella Bar-Lev, Adir Kobovich, Orian Leitersdorf, Eitan Yaakobi
Constrained coding is a fundamental field in coding theory that tackles efficient communication through constrained channels. While channels with fixed constraints (e.g., a fixed set of substrings may not appear in transmitted messages) have a general optimal solution, there is increasing demand for supporting…
James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan
Deep catalogs of genetic variation collected from many thousands of humans enable the detection of intraspecies constraint by revealing coding regions with a scarcity of variation. While existing techniques summarize constraint for entire genes, single metrics cannot capture the fine-scale variability in constraint…
Boris Ryabko
Nowadays there are several classes of constrained codes intended for different applications. The following two large classes can be distinguished. The first class contains codes with local constraints; for example, the source data must be encoded by binary sequences containing no sub-words 00 and 111. The second class…
Kallie Whritenour, Mete Civelek, Farzad Farnoud
DNA has been proposed as an alternative to magnetic and solid-state devices for storing digital data. In DNA data storage, writing data is performed through DNA synthesis, and reading is done via sequencing. Nanopore devices for sequencing DNA, like those produced by Oxford Nanopore Technologies, allow long reads and…
Yuanting Shen, Chong Shangguan, Zhicong Lin, Gennian Ge
Motivated by applications in DNA-based data storage, constrained codes have attracted a considerable amount of attention from both academia and industry. We study the maximum cardinality of constrained codes for which the constraints can be characterized by a set of forbidden substrings, where by a substring we mean…
Ahmed Hareedy, Beyza Dabak, Robert Calderbank
Constrained codes are used to prevent errors from occurring in various data storage and data transmission systems. They can help in increasing the storage density of magnetic storage devices, in managing the lifetime of electronic storage devices, and in increasing the reliability of data transmission over wires. Over…
Yimin Zhao, Song Xiao, Hongping Gan, Lizhao Li + 1 more
In wireless multi-hop networks, instead of using the traditional store-and-forward method, the relay nodes can exploit the network coding idea to encode and transmit the packets in the distributed coding-aware routing (DCAR) mechanisms, which can decrease the transmission number and achieve higher throughput. However…
Prachi Mishra, Navin Kashyap
—A weakly constrained code is a collection of finitelength strings over a finite alphabet in which certain substrings or patterns occur according to some prescribed frequencies. Buzaglo and Siegel (ITW 2017) gave a construction of weakly constrained codes based on row-by-row coding, that achieved the capacity of the…
Paridhi Latawa, Nuh Aydın
| 1 | Abstract | | 2 | | --- | --- | --- | --- | | 2 | | Introduction | 2 | | 3 | | Convolutional Codes | 3 | | | 3.1 | Encoding of Binary Convolutional Codes | 3 | | | 3.2 | Decoding Convolutional Codes | 11 | | | 3.3 | Truncated Viterbi Decoding | 13 | | 4 | | DNA Codes | 17 | | | 4.1 | Constraints for the…
Matthew J. Christmas, Irene M. Kaplow, Diane P. Genereux, Michael X. Dong + 72 more
Evolutionary constraint and acceleration are powerful, cell-type agnostic measures of functional importance. Previous studies in mammals were limited by species number and reliance on human-referenced alignments. We explore the evolution of placental mammals, including humans, through reference-free whole-genome…
Siwei Chen, Laurent C. Francioli, Julia K. Goodrich, Ryan L. Collins + 41 more
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders, but attempts to assess constraint for non-protein-coding regions have proven more difficult. Here we aggregate, process, and release a dataset of…
Jarek Duda
Barcodes like QR Codes have made that encoded messages have entered our everyday life, what suggests to attach them a second layer of information: directly available to human receiver for informational or marketing purposes. We will discuss a general problem of using codes with chosen statistical constrains, for…
Jasmina Ponjavic, Peter L. Oliver, Gerton Lunter, Chris P. Ponting + 1 more
'Yoshihide Hayashizaki'] Besides protein-coding mRNAs, eukaryotic transcriptomes include many long non-protein-coding RNAs (ncRNAs) of unknown function that are transcribed away from protein-coding loci. Here, we have identified 659 intergenic long ncRNAs whose genomic sequences individually exhibit evolutionary…
Martin Danner, Matthias Begemann, Florian Kraft, Miriam Elbracht + 2 more
'Ingo Kurth' 'Jeremias Krause'] Understanding the dark genome is a priority task following the complete sequencing of the human genome. Short open reading frames (sORFs) are a group of largely unexplored elements of the dark genome with the potential for being translated into microproteins. The definitive number of…
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…
Kees Schouhamer Immink, Jos H. Weber, Kui Cai, Olgiça Milenković + 1 more
'Jin Sima'] Low-weight codes have been proposed for efficiently synthesizing deoxyribonucleic acid (DNA) for massive data storage, where a multiple of DNA strands are synthesized in parallel. We report on the redundancy and information rate of maxentropic low-weight codes for asymptotically large codeword length. We…
Riley Hickman, Matteo Aldeghi, Alán Aspuru-Guzik
Model-based optimization strategies, such as Bayesian optimization (BO), have been deployed across the natural sciences in design and discovery campaigns due to their sample efficiency and flexibility. The combination of such strategies with automated laboratory equipment and/or high-performance computing in a…
Jie Lin, Mingyuan Xu, Hongming Chen
Shape-based virtual screening is a widely utilized method in ligand-based de novo drug design, aiming to identify molecules in chemical libraries that share similar 3D shapes but simultaneously possess novel 2D chemical structures compared to the reference compound. As an emerging technology, generative model is an…
Andre KY Low, Flore Mekki-Berrada, Aleksandr Ostudin, Jiaxun Xie + 7 more
The development of automated high-throughput experimental platforms has enabled fast sampling of high-dimensional decision spaces. To reach target properties efficiently, these platforms are increasingly paired with intelligent experimental design. When solving optimization problems, Bayesian-based optimizers are often…
Romain Brette
“Neural coding” is a popular metaphor in neuroscience, where objective properties of the world are communicated to the brain in the form of spikes. Here I argue that this metaphor is often inappropriate and misleading. First, when neurons are said to encode experimental parameters, the implied communication channel…
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…