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An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…

Data Structures and Algorithms · Computer Science 2018-03-28 Édouard Bonnet , Paweł Rzążewski , Florian Sikora

DNA-mediated computing is a novel technology that seeks to capitalize on the enormous informational capacity of DNA and has tremendous computational ability to compete with the current silicon-mediated computing, due to massive parallelism…

Emerging Technologies · Computer Science 2017-09-01 Jian-Jun Shu , Qi-Wen Wang , Kian-Yan Yong

DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…

Information Theory · Computer Science 2024-09-11 Guodong Wang , Hongwei Liu , Xueyan Chen

Vector multiplication is a fundamental operation for AI acceleration, responsible for over 85% of computational load in convolution tasks. While essential, these operations are primary drivers of area, power, and delay in modern datapath…

Hardware Architecture · Computer Science 2026-02-24 Md Rownak Hossain Chowdhury , Mostafizur Rahman

Nonnegative Tucker decomposition (NTD) is a powerful tool for the extraction of nonnegative parts-based and physically meaningful latent components from high-dimensional tensor data while preserving the natural multilinear structure of…

Machine Learning · Computer Science 2015-09-17 Guoxu Zhou , Andrzej Cichocki , Qibin Zhao , Shengli Xie

Neural Architecture Search (NAS) is increasingly popular to automatically explore the accuracy versus computational complexity trade-off of Deep Learning (DL) architectures. When targeting tiny edge devices, the main challenge for DL…

Machine Learning · Computer Science 2023-01-26 Matteo Risso , Alessio Burrello , Luca Benini , Enrico Macii , Massimo Poncino , Daniele Jahier Pagliari

Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…

Information Theory · Computer Science 2024-05-28 Omer Sabary , Inbal Preuss , Ryan Gabrys , Zohar Yakhini , Leon Anavy , Eitan Yaakobi

The state-of-art DNN structures involve intensive computation and high memory storage. To mitigate the challenges, the memristor crossbar array has emerged as an intrinsically suitable matrix computation and low-power acceleration framework…

Signal Processing · Electrical Eng. & Systems 2019-09-04 Xiaolong Ma , Geng Yuan , Sheng Lin , Caiwen Ding , Fuxun Yu , Tao Liu , Wujie Wen , Xiang Chen , Yanzhi Wang

It looks very attractive to coordinate racetrack-memory (RM) and stochastic-computing (SC) jointly to build an ultra-low power neuron-architecture.However, the above combination has always been questioned in a fatal weakness that the heavy…

Distributed, Parallel, and Cluster Computing · Computer Science 2024-10-23 Jihe Wang , Zhiying Zhang , Xingwu Dong , Danghui Wang

Being able to learn from complex data with phase information is imperative for many signal processing applications. Today' s real-valued deep neural networks (DNNs) have shown efficiency in latent information analysis but fall short when…

Machine Learning · Computer Science 2021-08-11 Hongwu Peng , Shanglin Zhou , Scott Weitze , Jiaxin Li , Sahidul Islam , Tong Geng , Ang Li , Wei Zhang , Minghu Song , Mimi Xie , Hang Liu , Caiwen Ding

1 bit deep neural networks (DNNs), of which both the activations and weights are binarized , are attracting more and more attention due to their high computational efficiency and low memory requirement . However, the drawback of large…

Computer Vision and Pattern Recognition · Computer Science 2019-07-12 Biao Qian , Yang Wang

Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…

Data Structures and Algorithms · Computer Science 2026-04-28 Tianshuo Zhou , David H. Mathews , Liang Huang

The binary neural network, largely saving the storage and computation, serves as a promising technique for deploying deep models on resource-limited devices. However, the binarization inevitably causes severe information loss, and even…

Neural and Evolutionary Computing · Computer Science 2020-04-08 Haotong Qin , Ruihao Gong , Xianglong Liu , Xiao Bai , Jingkuan Song , Nicu Sebe

Neural network binarization accelerates deep models by quantizing their weights and activations into 1-bit. However, there is still a huge performance gap between Binary Neural Networks (BNNs) and their full-precision (FP) counterparts. As…

Computer Vision and Pattern Recognition · Computer Science 2022-07-19 Yuzhang Shang , Dan Xu , Ziliang Zong , Liqiang Nie , Yan Yan

Many network applications are based on binary-state networks, where each component has one of two states: success or failure. Efficient algorithms to evaluate binary-state network reliability are continually being developed. Reliability…

Networking and Internet Architecture · Computer Science 2020-12-01 Wei-Chang Yeh

We live in a period where bio-informatics is rapidly expanding, a significant quantity of genomic data has been produced as a result of the advancement of high-throughput genome sequencing technology, raising concerns about the costs…

Quantitative Methods · Quantitative Biology 2023-03-10 Mehedi Hasan Sarkar , Adnan Ferdous Ashrafi

Ternary content addressable memory (TCAM) has been a critical component in caches, routers, etc., in which density, speed, power efficiency, and reliability are the major design targets. There have been the conventional low-write-power but…

Emerging Technologies · Computer Science 2021-01-26 Hongtao Zhong , Shengjie Cao , Huazhong Yang , Xueqing Li

The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…

Soft Condensed Matter · Physics 2015-06-02 William M. Jacobs , Aleks Reinhardt , Daan Frenkel

DNA sequences encode critical genetic information, yet their variable length and discrete nature impede direct utilization in deep learning models. Existing DNA representation schemes convert sequences into numerical vectors but fail to…

Genomics · Quantitative Biology 2025-12-16 Zhiyuan Peng , Naifan Zhang , Yuanbo Tang , Yang Li

This paper proposes ReBNet, an end-to-end framework for training reconfigurable binary neural networks on software and developing efficient accelerators for execution on FPGA. Binary neural networks offer an intriguing opportunity for…

Machine Learning · Computer Science 2018-03-29 Mohammad Ghasemzadeh , Mohammad Samragh , Farinaz Koushanfar
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