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Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…

Genomics · Quantitative Biology 2017-03-03 Sebastin Deorowicz , Agnieszka Debudaj-Grabysz , Adam Gudys

Neural Architecture Search (NAS) has enabled automatic discovery of more efficient neural network architectures, especially for mobile and embedded vision applications. Although recent research has proposed ways of quickly estimating…

Machine Learning · Computer Science 2022-04-28 Saeejith Nair , Saad Abbasi , Alexander Wong , Mohammad Javad Shafiee

Recent innovations in Transformer-based large language models have significantly advanced the field of general-purpose neural language understanding and generation. With billions of trainable parameters, deployment of these large models…

Hardware Architecture · Computer Science 2024-10-11 Haocheng Xu , Faraz Tahmasebi , Ye Qiao , Hongzheng Tian , Hyoukjun Kwon , Sitao Huang

Modern deep neural networks must demonstrate state-of-the-art accuracy while exhibiting low latency and energy consumption. As such, neural architecture search (NAS) algorithms take these two constraints into account when generating a new…

Machine Learning · Computer Science 2022-05-26 Saad Abbasi , Alexander Wong , Mohammad Javad Shafiee

Deep neural networks (DNN) are increasingly being accelerated on application-specific hardware such as the Google TPU designed especially for deep learning. Timing speculation is a promising approach to further increase the energy…

Machine Learning · Computer Science 2018-07-03 Jeff Zhang , Siddharth Garg

Recent years have witnessed tremendously improved efficiency of Automated Machine Learning (AutoML), especially Automated Deep Learning (AutoDL) systems, but recent work focuses on tabular, image, or NLP tasks. So far, little attention has…

Machine Learning · Computer Science 2022-07-25 Difan Deng , Florian Karl , Frank Hutter , Bernd Bischl , Marius Lindauer

Recent advance in sparse attention mechanisms has demonstrated strong potential for reducing the computational cost of long-context training and inference in large language models (LLMs). Native Sparse Attention (NSA), one state-of-the-art…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-10-14 Ran Yan , Youhe Jiang , Zhuoming Chen , Haohui Mai , Beidi Chen , Binhang Yuan

Data analytics systems commonly utilize in-memory query processing techniques to achieve better throughput and lower latency. Modern computers increasingly rely on Non-Uniform Memory Access (NUMA) architectures in order to achieve…

Databases · Computer Science 2020-01-28 Puya Memarzia , Suprio Ray , Virendra C Bhavsar

A key advantage of Recurrent Neural Networks (RNNs) over Transformers is their linear computational and space complexity enables faster training and inference for long sequences. However, RNNs are fundamentally unable to randomly access…

Computation and Language · Computer Science 2025-11-04 Xiang Hu , Jiaqi Leng , Jun Zhao , Kewei Tu , Wei Wu

The use of low numerical precision is a fundamental optimization included in modern accelerators for Deep Neural Networks (DNNs). The number of bits of the numerical representation is set to the minimum precision that is able to retain…

Signal Processing · Electrical Eng. & Systems 2019-11-12 Franyell Silfa , Jose-Maria Arnau , Antonio Gonzàlez

We develop a new efficient sequential approximate leverage score algorithm, SALSA, using methods from randomized numerical linear algebra (RandNLA) for large matrices. We demonstrate that, with high probability, the accuracy of SALSA's…

Machine Learning · Statistics 2024-01-02 Ali Eshragh , Luke Yerbury , Asef Nazari , Fred Roosta , Michael W. Mahoney

In neural network topologies, algorithms are running on batches of data tensors. The batches of data are typically scheduled onto the computing cores which execute in parallel. For the algorithms running on batches of data, an optimal batch…

Performance · Computer Science 2020-02-18 Phani Kumar Nyshadham , Mohit Sinha , Biswajit Mishra , H S Vijay

Similarity search is a key to a variety of applications including content-based search for images and video, recommendation systems, data deduplication, natural language processing, computer vision, databases, computational biology, and…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-07-11 Vincent T. Lee , Amrita Mazumdar , Carlo C. del Mundo , Armin Alaghi , Luis Ceze , Mark Oskin

Near-memory Computing (NMC) promises improved performance for the applications that can exploit the features of emerging memory technologies such as 3D-stacked memory. However, it is not trivial to find such applications and specialized…

Performance · Computer Science 2019-06-26 Stefano Corda , Gagandeep Singh , Ahsan Javed Awan , Roel Jordans , Henk Corporaal

Traditional digital implementations of neural accelerators are limited by high power and area overheads, while analog and non-CMOS implementations suffer from noise, device mismatch, and reliability issues. This paper introduces a CMOS…

The matrix profile is an effective data mining tool that provides similarity join functionality for time series data. Users of the matrix profile can either join a time series with itself using intra-similarity join (i.e., self-join) or…

Databases · Computer Science 2023-11-07 Chin-Chia Michael Yeh , Yan Zheng , Junpeng Wang , Huiyuan Chen , Zhongfang Zhuang , Wei Zhang , Eamonn Keogh

Data movement is becoming the dominant contributor to the time and energy costs of computation across a wide range of application domains. However, time complexity is inadequate to analyze data movement. This work expands upon Data Movement…

Data Structures and Algorithms · Computer Science 2022-03-08 Wesley Smith , Aidan Goldfarb , Chen Ding

The inherent diversity of computation types within the deep neural network (DNN) models often requires a variety of specialized units in hardware processors, which limits computational efficiency, increasing both inference latency and power…

Machine Learning · Computer Science 2024-08-21 Ruiqi Sun , Siwei Ye , Jie Zhao , Xin He , Jianzhe Lin , Yiran Li , An Zou

The GEneral Matrix Multiplication (GEMM) is one of the essential algorithms in scientific computing. Single-thread GEMM implementations are well-optimised with techniques like blocking and autotuning. However, due to the complexity of…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-01-15 Yufan Xia , Marco De La Pierre , Amanda S. Barnard , Giuseppe Maria Junior Barca

Optimizing resource utilization in target platforms is key to achieving high performance during DNN inference. While optimizations have been proposed for inference latency, memory footprint, and energy consumption, prior hardware-aware…

Machine Learning · Computer Science 2022-03-24 Ahmet Caner Yüzügüler , Nikolaos Dimitriadis , Pascal Frossard