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Deciphering DNA variant-associated aberrant splicing with the aid of RNA sequencing (vol 55, pg 732, 2023)

NATURE GENETICS 2023年第7期55卷 1251-1251页

作者： Zhang, Bin Gao, Xin Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology (KAUST) Thuwal Saudi Arabia KAUST Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia

Aberrant RNA splicing events resulting from DNA variations are common causes of genetic disorders. Two studies published in Nature Genetics independently describe methods to decipher DNA-variant-associated aberrant sp... 详细信息

关键词： Data mining High-throughput screening

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Offsets Reconstruction Method for Clock Skew Measurement Over High-Jitter Communication

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SN computer science 2025年第5期6卷 1-14页

作者： Sastra, Nyoman Putra Saputra, Komang Oka Teng, Wei-Chung Study Program of Electrical Engineering Faculty of Engineering Udayana University Jalan Raya Kampus Bukit Jimbaran Bali Badung 80361 Indonesia Department of Computer Science and Information Engineering National Taiwan University of Science and Technology No. 43 Section 4 Keelung Rd Taipei 106 China

Measuring clock skew of devices over a network fully relies on the offsets, the differences between sending and receiving times. Offsets that shape a thick line are the most ideal one as their slope is directly the clock skew sought. When some outliers separate from the thick line due to higher delay jitter, current advanced approaches use the lower bound or the majority of offsets to derive accurate clock skew. However, outliers in offsets that shape parallel dotted lines, reduce the availability of offsets in the lower region, and scatter widely the offsets from their majority zone. These conditions drive the current skew estimation approaches to lose their accuracy. This paper then developed a new method, which reconstructs back the outliers into their origin positions, in order to provide ideal offsets for clock skew measurement. The experimental evaluations have demonstrated that the clock skew accuracy of dotted-lines offsets tampered by outliers was improved from 2.1 to 0.9 ppm by the proposed reconstruction method. For a broader purpose, the reconstruction method has been adjusted to be implemented also on non-dotted-lines offsets. The robustness of the proposed method for this case has also been exhibited by the very ideal reconstructed offsets that shape like a thick line. © The Author(s) 2025.

关键词： Clock skew Delay jitter Dotted lines Hough transform

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Neurocognitive assessment under various human-robot teaming environments 46

Neurocognitive assessment under various human-robot teaming ...

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46th Annual International Conference of the IEEE engineering in Medicine and Biology Society, EMBC 2024

作者： Packy, Anna L. Jayahankar, Jayesh Teymourlouei, Arya Stone, Joshua Oh, Hyuk Katz, Garrett E. Reggia, James A. Gentili, Rodolphe J. University of Maryland Neuroscience and Cognitive Science Program College Park United States University of Maryland Department of Computer Science College Park United States University of Maryland Department of Electrical & Computer Engineering College Park United States University of Maryland Department of Kinesiology College Park United States Syracuse University Department of Electrical Engineering & Computer Science Syracuse United States

ISBN: (纸本)9798350371499

Human-robot teaming has become increasingly important with the advent of intelligent machines. Prior efforts suggest that performance, mental workload, and trust are critical elements of human-robot dynamics that can be altered by the robot's behavior. Most prior human-robot teaming studies used behavioral analyses, but a limited number used neural markers, without the use of physical robots and complex tasks. Here we combine behavioral and EEG cortical dynamics to examine cognitive-motor processes when individuals complete a complex task under various team environments with a robot. The results revealed that altering the robot quality affected both behavioral and EEG dynamics. Task completion with an experienced robot led to greater team performance and human trust along with lower mental workload compared to an inexperienced teammate or when individuals performed alone. EEG changes suggest that different attentional processes were engaged when humans worked with the robot and performed alone, and that visual processing was more prominent when teaming with an inexperienced teammate. This work can inform human cognitive-motor processes and the design of robotic controllers in human-robot teams. © 2024 IEEE.

关键词： Man machine systems

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Implementation and Performance Evaluation of Collective Communications Using CIRCUS on Multiple FPGAs

Implementation and Performance Evaluation of Collective Comm...

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2023 International Conference on High Performance Computing in Asia-Pacific Region Workshops, HPC Asia 2023

作者： Kikuchi, Kohei Fujita, Norihisa Kobayashi, Ryohei Boku, Taisuke Master's Program in Computer Science Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Japan Center for Computational Sciences University of Tsukuba Tsukuba Japan

ISBN: (纸本)9781450399890

In the high-performance computing domain, Field programmable Gate Array (FPGA) is a novel accelerator that exhibits high flexibility and performance characteristics distinct from other accelerators such as the Graphics Processing Unit (GPU). Recent advanced high-end FPGA is equipped with multiple channels of high speed optical link up to 100Gbps performance for each. This is a crucial feature when we construct PC clusters with FPGAs as accelerators, however it is not easy to utilize from user kernels because this feature is implemented in low level and simple direct communication between neighboring FPGAs. In order to provide the communication feature between FPGAs for accelerated PC clusters, we developed a communication system named CIRCUS which implies a user-friendly API from OpenCL and is equipped with routing function over multi-hop communication on multi-dimensional torus network of FPGAs. However, current CIRCUS only provides a point-to-point communication between source and destination FPGAs. In ordinary parallel processing environment such as MPI, the user program the message passing with various collective communication functions for parallel algorithm, for instance Allreduce, Allgather, etc. In this paper, we implement the collective communication function over CIRCUS for user-friendly programming of ordinary parallel algorithms on FPGAs. As the first target, we implement Allreduce function which is the most essential and important function. The paper describes the CIRCUS system briefly followed by the design, implementation and preliminary performance evaluation on Intel Stratix10 FPGAs. © 2023 ACM.

关键词： Field programmable gate arrays (FPGA)

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Prior-Guided Parallel Residual Bi-Fusion Network in USV Obstacle Detection

Prior-Guided Parallel Residual Bi-Fusion Network in USV Obst...

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2023 International Conference on Consumer Electronics - Taiwan, ICCE-Taiwan 2023

作者： Hsu, Chih-Chung Yang, Sophia Hou, Xiu-Yu Jhang, Yu-An Institute of Data Science National Cheng Kung University Taiwan National Tsing Hua University Interdisciplinary Program of Electrical Engineering and Computer Science Taiwan

ISBN: (纸本)9798350324174

In this paper, we propose a novel Prior-Guided Parallel Residual Bi-Fusion Feature Pyramid Network (PPRB-FPN) for accurate obstacle detection in unmanned surface vehicle (USV) sailing. Our method tackles the challenge of detecting small objects, which are prone to information vanishing. To the end, we leverage the PRB-FPN for small object detection and YOLOv7 as a single-stage object detector to effectively identify obstacles. Our experimental results on the Obstacle Detection Challenge dataset at the 1st Workshop on Maritime computer Vision (MaCVi) demonstrate that our method outperforms both Mask R-CNN (mrcnn) and YOLOv7, achieving an F-avg score of 0.514. © 2023 IEEE.

关键词： Unmanned surface vehicles

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Seafloor Imaging Maps by Incorporating Side Scan Sonar Technology on Hybrid Autonomous Underwater Glider 6

Seafloor Imaging Maps by Incorporating Side Scan Sonar Techn...

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6th International Seminar on Research of Information Technology and Intelligent Systems, ISRITI 2023

作者： Atmaja, Ardian Budi Kusuma Hidayat, Egi Muhammad Idris Riyanto Trilaksono, Bambang Siregar, Simon Habibullah, Natsir School of Electrical Engineering and Informatics Institut Teknologi Bandung Bandung Indonesia Institut Teknologi Bandung Telkom University Doctoral Program of Electrical Engineering Department Computer Engineering Faculty of Applied Science Indonesia

ISBN: (纸本)9798350358346

This research aims to construct a two-dimensional image to represent an underwater geometry map with a Side Scan Sonar (SSS) mounted on a Hybrid Autonomous Underwater Glider (HAUG). Building the underwater map has two stages of the process. The first stage is preprocessing which includes Time-varying gains (TVG), slant range correction, and ground range correction. The second is HAUG navigation, the movement of HAUG orientation to the angle and distance of SSS readings and plotting the geometry of the grid map. With these two stages, a two-dimensional grid map will be formed. Meanwhile, the 3D plot utilizes slant range and ground range correction to obtain the surface height of the bottom of the pool. From the experiments conducted to conduct mapping in the pool, two-dimensional and three-dimensional visual forms of the pool floor and pool walls were produced. The results of the estimated measurement of the width of the pool obtained 14.05 meters and the height of the pool 3.199 meters with an SSS beam angle of 58 degrees. © 2023 IEEE.

关键词： Geometry

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Link Connectivity based Reliability with Security in Autonomous Mobile Network

Link Connectivity based Reliability with Security in Autonom...

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2023 International Conference on Sustainable Computing and Smart Systems, ICSCSS 2023

作者： Sivasankar, C. Kumanan, T. Sekhar, Ch Chandra Srinivasan, T.R. Saveetha Institute of Medical and Technical Sciences Saveetha School of Engineering Department of Computer Science and Engineering Tamil Nadu Chennai India Dr Mgr Educational and Research Institute Department of Computer Science and Engineering Tamil Nadu Chennai India Ap Residential Degree College Department of Computer Science and Engineering Andhra Pradesh Guntur India Jimma Institute of Technology Jimma University Faculty of Electrical and Computer Engineering Department of Computer Engineering Jimma Ethiopia

ISBN: (纸本)9798350333602

Autonomous Mobile Network (AMN) contains mobile nodes which can predict the surrounding and forward the data to the receiver in undesirable conditions. AMN can observe, activate, calculate, and interconnect with others by applying point-to-point multi-hop transactions. Achieving such a fundamental agreement in a resource-constrained environment is a challenging problem since security methods always need additional energy and computational storage burdens. This paper proposes Link Connectivity based Reliability with Security (LCRS) in AMN to overcome this problem. This paper aims to detect abnormal nodes and improve link connectivity. The Link Connectivity Threshold (LCT) parameter estimates the link availability among the present sender and the subsequent forwarder node on the route to the destination. It selects the forwarder node by energy, link connectivity, and distance parameters. Furthermore, it isolates abnormal nodes using the lightweight Extended Kalman Filter (EKF) algorithm. This technique isolates the abnormal nodes and provides an effective route. The experimental outcomes demonstrate that the LCRS scheme diminishes the packet loss rate and delay. Furthermore, it raises the abnormal node detection ratio. © 2023 IEEE.

关键词： Energy efficiency

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Improved IP lookup technology for trie-based data structures

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Journal of computer and System sciences 2023年 133卷 41-55页

作者： Lin, Yen-Heng Hsieh, Sun-Yuan Master Degree Program on Artificial Intelligence National Cheng Kung University Tainan701 Taiwan Department of Computer Science and Information Engineering Institute of Manufacturing Information Systems Institute of Medical Informatics National Cheng Kung University Tainan701 Taiwan Department of Computer Science and Information Engineering National Chi Nan University Nantou Puli Township54561 Taiwan

Many Internet protocol (IP) lookup algorithms have been formulated to improve network performance. This study reviewed and experimentally evaluated technologies for trie-based methods that reduce memory access, memory consumption and IP lookup time. Experiments involving binary tries (for simplicity) were conducted on four real-world data sets, two of which were on IPv4 router tables (855,997 and 876,489 active prefixes) and two of which were on IPv6 router tables (155,310 and 157,579 active prefixes). Technologies designed to reduce time taken (at the expense of memory consumption) worked well for IPv4, and those designed to reduce memory consumption worked well for IPv6. Various combinations of these technologies were applied together in the experiments. © 2022 Elsevier Inc.

关键词： Table lookup

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Spectral Learning of Shared Dynamics Between Generalized-Linear Processes 38

Spectral Learning of Shared Dynamics Between Generalized-Lin...

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38th Conference on Neural Information Processing Systems, NeurIPS 2024

作者： Oganesian, Lucine L. Sani, Omid G. Shanechi, Maryam M. Ming Hsieh Department of Electrical and Computer Engineering University of Southern California Los AngelesCA United States Ming Hsieh Department of Electrical and Computer Engineering Thomas Lord Department of Computer Science Alfred E. Mann Department of Biomedical Engineering Neuroscience Graduate Program University of Southern California Los AngelesCA United States

Generalized-linear dynamical models (GLDMs) remain a widely-used framework within neuroscience for modeling time-series data, such as neural spiking activity or categorical decision outcomes. Whereas the standard usage of GLDMs is to model a single data source, certain applications require jointly modeling two generalized-linear time-series sources while also dissociating their shared and private dynamics. Most existing GLDM variants and their associated learning algorithms do not support this capability. Here we address this challenge by developing a multi-step analytical subspace identification algorithm for learning a GLDM that explicitly models shared vs. private dynamics within two generalized-linear time-series. In simulations, we demonstrate our algorithm's ability to dissociate and model the dynamics within two time-series sources while being agnostic to their respective observation distributions. In neural data, we consider two specific applications of our algorithm for modeling discrete population spiking activity with respect to a secondary time-series. In both synthetic and real data, GLDMs learned with our algorithm more accurately decoded one time-series from the other using lower-dimensional latent states, as compared to models identified using existing GLDM learning algorithms. © 2024 Neural information processing systems foundation. All rights reserved.

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Comments on a Computation-Transferable Authenticated Key Agreement Protocol for Smart Healthcare

Comments on a Computation-Transferable Authenticated Key Agr...

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9th International Conference on Applied System Innovation, ICASI 2023

作者： Chang, Ya-Fen Tsai, Chung-Yi Tai, Wei-Liang National Taichung University of Science and Technology Department of Computer Science and Information Engineering Taichung Taiwan National Taichung University of Science and Technology Bachelor Degree Program of Artificial Intelligence Taichung Taiwan

ISBN: (纸本)9798350398380

Recently, Wang et al. proposed a computationally transferable authenticated key agreement protocol for smart healthcare by adopting the certificateless public-key cryptography. They claimed that their protocol could ensure privacy, resist various attacks, and possess superior properties. After analyzing their protocol, we find that it suffers from some flaws. Firstly, user privacy is not ensured as claimed. Secondly, some statements are inaccurate or missing. Thirdly, it cannot resist DoS attack. In this paper, the details of how these flaws threaten Wang et al.'s protocol are shown. © 2023 IEEE.

关键词： Denial-of-service attack

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