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We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high…

Genomics · Quantitative Biology 2017-07-05 Byunghan Lee , Taesup Moon , Sungroh Yoon , Tsachy Weissman

Brain-computer interfaces (BCIs) promise to enable vital functions, such as speech and prosthetic control, for individuals with neuromotor impairments. Central to their success are neural decoders, models that map neural activity to…

Machine Learning · Computer Science 2025-10-24 Georgios Mentzelopoulos , Ioannis Asmanis , Konrad P. Kording , Eva L. Dyer , Kostas Daniilidis , Flavia Vitale

Retrieval-augmented generation (RAG) systems trained using reinforcement learning (RL) with reasoning are hampered by inefficient context management, where long, noisy retrieved documents increase costs and degrade performance. We introduce…

Computation and Language · Computer Science 2025-10-14 Zhichao Xu , Minheng Wang , Yawei Wang , Wenqian Ye , Yuntao Du , Yunpu Ma , Yijun Tian

The cost of DNA sequencing has dropped exponentially over the past decade, making genomic data accessible to a growing number of scientists. In bioinformatics, localization of short DNA sequences (reads) within large genomic sequences is…

Genomics · Quantitative Biology 2021-06-16 Robin Kobus , André Müller , Daniel Jünger , Christian Hundt , Bertil Schmidt

General Purpose computing on Graphical Processing Units (GPGPU) has resulted in unprecedented levels of speedup over its CPU counterparts, allowing programmers to harness the computational power of GPU shader cores to accelerate other…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-03-20 Vani Nagarajan , Milind Kulkarni

Ribonucleic acid (RNA) plays fundamental roles in biological systems, from carrying genetic information to performing enzymatic function. Understanding and designing RNA can enable novel therapeutic application and biotechnological…

Biomolecules · Quantitative Biology 2025-12-01 Dana Rubin , Allan dos Santos Costa , Manvitha Ponnapati , Joseph Jacobson

Electroencephalography (EEG) foundation models hold significant promise for universal Brain-Computer Interfaces (BCIs). However, existing approaches often rely on end-to-end fine-tuning and exhibit limited efficacy under frozen-probing…

Machine Learning · Computer Science 2026-03-20 Jiquan Wang , Sha Zhao , Yangxuan Zhou , Yiming Kang , Shijian Li , Gang Pan

In existing systems, to perform any bulk data movement operation (copy or initialization), the data has to first be read into the on-chip processor, all the way into the L1 cache, and the result of the operation must be written back to main…

This paper introduces a groundbreaking digital neuromorphic architecture that innovatively integrates Brain Code Unit (BCU) and Fundamental Code Unit (FCU) using mixedsignal design methodologies. Leveraging open-source datasets and the…

Hardware Architecture · Computer Science 2024-03-19 Murat Isik , Sols Miziev , Wiktoria Pawlak , Newton Howard

In this paper, we propose Suppression-Enhancing Mask based attention and Interactive Channel transformatiON (SEMICON) to learn binary hash codes for dealing with large-scale fine-grained image retrieval tasks. In SEMICON, we first develop a…

Computer Vision and Pattern Recognition · Computer Science 2022-09-29 Yang Shen , Xuhao Sun , Xiu-Shen Wei , Qing-Yuan Jiang , Jian Yang

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts,…

Neural Architecture Search (NAS) is an automated technique to design optimal neural network architectures for a specific workload. Conventionally, evaluating candidate networks in NAS involves extensive training, which requires significant…

Machine Learning · Computer Science 2025-06-05 Tomomasa Yamasaki , Zhehui Wang , Tao Luo , Niangjun Chen , Bo Wang

Imitation learning enables robots to learn new tasks from human examples. One fundamental limitation while learning from humans is causal confusion. Causal confusion occurs when the robot's observations include both task-relevant and…

Robotics · Computer Science 2025-03-04 Robert Ramirez Sanchez , Heramb Nemlekar , Shahabedin Sagheb , Cara M. Nunez , Dylan P. Losey

Deep learning-based image retrieval techniques for the loop closure detection demonstrate satisfactory performance. However, it is still challenging to achieve high-level performance based on previously trained models in different…

Computer Vision and Pattern Recognition · Computer Science 2022-01-11 M. Usman Maqbool Bhutta , Yuxiang Sun , Darwin Lau , Ming Liu

Programmers often reuse code from source code repositories to reduce the development effort. Code clones are candidates for reuse in exploratory or rapid development, as they represent often repeated functionality in software systems. To…

Software Engineering · Computer Science 2020-12-08 Muhammad Hammad , Önder Babur , Hamid Abdul Basit , Mark van den Brand

Nanopore sequencing technology has the potential to render other sequencing technologies obsolete with its ability to generate long reads and provide portability. However, high error rates of the technology pose a challenge while generating…

Genomics · Quantitative Biology 2019-12-20 Damla Senol Cali , Jeremie S. Kim , Saugata Ghose , Can Alkan , Onur Mutlu

Recall initiator identification and assessment are the preliminary steps to prevent medical device recall. Conventional analysis tools are inappropriate for processing massive and multi-formatted data comprehensively and completely to meet…

Computation and Language · Computer Science 2024-06-18 Yang Hu

Conventional medical image registration approaches directly optimize over the parameters of a transformation model. These approaches have been highly successful and are used generically for registrations of different anatomical regions.…

Computer Vision and Pattern Recognition · Computer Science 2024-03-12 Lin Tian , Hastings Greer , Roland Kwitt , Francois-Xavier Vialard , Raul San Jose Estepar , Sylvain Bouix , Richard Rushmore , Marc Niethammer

We propose a novel molecular computing approach based on reservoir computing. In reservoir computing, a dynamical core, called a reservoir, is perturbed with an external input signal while a readout layer maps the reservoir dynamics to a…

Neural and Evolutionary Computing · Computer Science 2019-11-12 Alireza Goudarzi , Matthew R. Lakin , Darko Stefanovic

Neurosymbolic programs combine deep learning with symbolic reasoning to achieve better data efficiency, interpretability, and generalizability compared to standalone deep learning approaches. However, existing neurosymbolic learning…

Programming Languages · Computer Science 2025-10-01 Paul Biberstein , Ziyang Li , Joseph Devietti , Mayur Naik