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The Ribonucleic Acid (RNA) inverse folding problem, designing nucleotide sequences that fold into specific tertiary structures, is a fundamental computational biology problem with important applications in synthetic biology and…

Biomolecules · Quantitative Biology 2025-12-01 Mehyar Mlaweh , Tristan Cazenave , Ines Alaya

DNA strings and their properties are widely studied since last 20 years due to its applications in DNA computing. In this area, one designs a set of DNA strings (called DNA code) which satisfies certain thermodynamic and combinatorial…

Information Theory · Computer Science 2025-10-03 Krishna Gopal Benerjee , Manish K Gupta

This paper presents a novel approach to enhance the Binary-Addition-Tree algorithm (BAT) by integrating incremental learning techniques. BAT, known for its simplicity in development, implementation, and application, is a powerful implicit…

Machine Learning · Computer Science 2024-09-25 Wei-Chang Yeh

In recent years, deep neural networks have had great success in machine learning and pattern recognition. Architecture size for a neural network contributes significantly to the success of any neural network. In this study, we optimize the…

Machine Learning · Computer Science 2021-01-19 Yigit Alparslan , Ethan Jacob Moyer , Isamu Mclean Isozaki , Daniel Schwartz , Adam Dunlop , Shesh Dave , Edward Kim

Recent Deep Neural Networks (DNNs) managed to deliver superhuman accuracy levels on many AI tasks. Several applications rely more and more on DNNs to deliver sophisticated services and DNN accelerators are becoming integral components of…

Hardware Architecture · Computer Science 2022-03-17 Ourania Spantidi , Georgios Zervakis , Iraklis Anagnostopoulos , Hussam Amrouch , Jörg Henkel

Various networks are broadly and deeply applied in real-life applications. Reliability is the most important index for measuring the performance of all network types. Among the various algorithms, only implicit enumeration algorithms, such…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-09-21 Wei-Chang Yeh

Several technological limitations of traditional silicon based computing are leading towards the paradigm shift, from silicon to carbon, in computational world. Among the unconventional modes of computing evolved in past several decades,…

Biomolecules · Quantitative Biology 2020-10-02 Mandrita Mondal , Kumar S. Ray

In this paper we propose a novel network adaption method called Differentiable Network Adaption (DNA), which can adapt an existing network to a specific computation budget by adjusting the width and depth in a differentiable manner. The…

Computer Vision and Pattern Recognition · Computer Science 2021-03-31 Shaopeng Guo , Yujie Wang , Kun Yuan , Quanquan Li

Innovation in the physical layer of communication systems has traditionally been achieved by breaking down the transceivers into sets of processing blocks, each optimized independently based on mathematical models. Conversely, deep learning…

Information Theory · Computer Science 2022-05-04 Mathieu Goutay

We design new continuous phase modulation (CPM) formats which are based on the combination of a proper precoder with binary input and a ternary CPM. The proposed precoder constrains the signal phase evolution in order to increase the…

Information Theory · Computer Science 2016-11-17 Malek Messai , Amina Piemontese , Giulio Colavolpe , Karine Amis , Frederic Guilloud

Weak multivalent interactions govern a large variety of biological processes like cell-cell adhesion and virus-host interactions. These systems distinguish sharply between surfaces based on receptor density, known as superselectivity.…

Biological Physics · Physics 2023-06-30 Christine Linne , Eva Heemskerk , Jos Zwanikken , Daniela J. Kraft , Liedewij Laan

Ternary weight quantization (e.g., BitNet b1.58) offers a promising path to mitigate the memory bandwidth bottleneck in Large Language Model (LLM) inference. However, conventional compute platforms lack native support for ternary-weight…

Hardware Architecture · Computer Science 2026-04-29 Robin Geens , Joran Heldens , Joren Dumoulin , Marian Verhelst

Accommodating all the weights on-chip for large-scale NNs remains a great challenge for SRAM based computing-in-memory (SRAM-CIM) with limited on-chip capacity. Previous non-volatile SRAM-CIM (nvSRAM-CIM) addresses this issue by integrating…

Hardware Architecture · Computer Science 2024-01-12 Dengfeng Wang , Liukai Xu , Songyuan Liu , Zhi Li , Yiming Chen , Weifeng He , Xueqing Li , Yanan Sun

Quantization is widely applied in machine learning to reduce computational and storage costs for both data and models. Considering that classification tasks are fundamental to the field, it is crucial to investigate how quantization impacts…

Machine Learning · Computer Science 2025-07-14 Weizhi Lu , Mingrui Chen , Weiyu Li

Multilinear transformations are key in high-performance computing (HPC) and artificial intelligence (AI) workloads, where data is represented as tensors. However, their high computational and memory demands, which grow with dimensionality,…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-07-01 Stanislav Sedukhin , Yoichi Tomioka , Kazuya Matsumoto , Yuichi Okuyama

In [1], the authors proposed a new model of DNA storage system that integrates all three steps of retrieval and introduced the concept of DNA-correcting codes, which guarantees that the output of the storage system can be decoded to the…

Information Theory · Computer Science 2023-11-17 Huawei Wu

Binary embedding of high-dimensional data requires long codes to preserve the discriminative power of the input space. Traditional binary coding methods often suffer from very high computation and storage costs in such a scenario. To…

Machine Learning · Statistics 2014-05-14 Felix X. Yu , Sanjiv Kumar , Yunchao Gong , Shih-Fu Chang

Binary neural networks (BNNs), where both weights and activations are binarized into 1 bit, have been widely studied in recent years due to its great benefit of highly accelerated computation and substantially reduced memory footprint that…

Computer Vision and Pattern Recognition · Computer Science 2021-01-01 Zhuo Su , Linpu Fang , Deke Guo , Dewen Hu , Matti Pietikäinen , Li Liu

We introduce a novel scheme to train binary convolutional neural networks (CNNs) -- CNNs with weights and activations constrained to {-1,+1} at run-time. It has been known that using binary weights and activations drastically reduce memory…

Machine Learning · Computer Science 2017-12-01 Xiaofan Lin , Cong Zhao , Wei Pan

Harnessing the intrinsic dynamics of physical systems for information processing opens new avenues for computation embodied in matter. Using simulations of a model system, we show that assemblies of DNA tiles capable of self-organizing into…

Soft Condensed Matter · Physics 2025-10-23 Tim E. Veenstra , René van Roij , Marjolein Dijkstra