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Accelerating Group Fusion for Ligand-Based Virtual Screening on Multi-core and Many-core Platforms

  • Mohd-Hilmi, Mohd-Norhadri;Al-Laila, Marwah Haitham;Hassain Malim, Nurul Hashimah Ahamed
    • Journal of Information Processing Systems
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    • v.12 no.4
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    • pp.724-740
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    • 2016
  • The performance issues of screening large database compounds and multiple query compounds in virtual screening highlight a common concern in Chemoinformatics applications. This study investigates these problems by choosing group fusion as a pilot model and presents efficient parallel solutions in parallel platforms, specifically, the multi-core architecture of CPU and many-core architecture of graphical processing unit (GPU). A study of sequential group fusion and a proposed design of parallel CUDA group fusion are presented in this paper. The design involves solving two important stages of group fusion, namely, similarity search and fusion (MAX rule), while addressing embarrassingly parallel and parallel reduction models. The sequential, optimized sequential and parallel OpenMP of group fusion were implemented and evaluated. The outcome of the analysis from these three different design approaches influenced the design of parallel CUDA version in order to optimize and achieve high computation intensity. The proposed parallel CUDA performed better than sequential and parallel OpenMP in terms of both execution time and speedup. The parallel CUDA was 5-10x faster than sequential and parallel OpenMP as both similarity search and fusion MAX stages had been CUDA-optimized.

Implementation of High Speed LDPC Decode for Multi-Giga bps Cable Communication Service (Multi-Giga bps 케이블 통신 서비스를 위한 고속 LDPC 복호기 구현)

  • Jung, Joon-Young;Choi, Dong-Joon;Hur, Namho
    • Proceedings of the Korean Society of Broadcast Engineers Conference
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    • 2015.07a
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    • pp.301-302
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    • 2015
  • 케이블 방송망에서 멀티-Gbps(Giga bit per second) 초고속 인터넷 서비스 제공을 위해 최근 북미에서 DOCSIS 3.1(Data over Cable Service Interface Specifications Version 3.1) 표준을 발표하였다. DOCSIS 3.1 은 최대 10Gbps 하향 데이터 전송과 최대 2Gbps 의 상향 데이터 전송을 목표로 한다. DOCSIS 3.1 이 이전 DOCSIS 표준들과 다른 점은 전송 효율을 높이기 위해 물리계층 전송 방식에 큰 변화를 주었다는 점이다. 기존 6MHz 대역폭의 단일 반송파 전송 방식에서 최대 192MHz 광역 채널의 다중 반송파 전송 방식으로 변경하였다. 또한 채널 오류정정 방식으로 BCH(Bose, Chaudhuri, and Hocquenghem)와 LDPC(Low Density Parity Check) 연접부호를 적용하여, 이로 인한 SNR 성능 이득 통해 4096-QAM 의 고차 변조를 지원한다. 본 논문에서는 최대 192MHz 의 광역 채널로 전송되는 약 2Gbps 의 전송 데이터에 대한 채널 오류 정정을 위해 고속의 LDPC 복호기 구현 방법을 제시한다.

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A Practical Off-line Electronic Cash System on Smart Cards Achieving Untraceability, Divisibility, and Transferability

  • Chung, Ho-Suk;Lee, Pil-Joong-
    • Proceedings of the Korea Institutes of Information Security and Cryptology Conference
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    • 1994.11a
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    • pp.51-66
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    • 1994
  • A divisible off-line electronic cash system based on cut-and-choose has first been proposed by [OO91] and recently more efficient single term divisible cash system was presented in [EO94] which is based on Brand's scheme [Bra93]. In this paper, we present a different type of single term divisible electronic cash system which is more efficient than previously proposed systems such as [OO91], [YLR93], and [EO94] in the standpoint of the amount of communication, the number of modular multiplications required in the payment transactions, and the storage requirement in the withdrawal protocol. Our scheme is a modified version of [LL93], where the major improvement has been made in its withdrawal transaction to introduce untraceability and multi-spendability. We have borrowed the idea of the withdrawal protocol of our scheme from [EO94] with minor modifications. Transferability in our scheme allows only a finite number of transfer. Our scheme satisfies an the desirable properties of an electronic cash system such as untraceability, divisibility and transferability. In addition, we present a n-spendable cash. The basic idea of extension to multi-spendability has been borrowed from [Bra93] with minor modifications.

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A Buck-Boost Converter-Based Bipolar Pulse Generator

  • Elserougi, Ahmed A.;Massoud, Ahmed M.;Ahmed, Shehab
    • Journal of Power Electronics
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    • v.17 no.6
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    • pp.1422-1432
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    • 2017
  • This paper presents a buck-boost converter-based bipolar pulse generator, which is able to generate bipolar exponential pulses across a resistive load. The concept of the proposed approach depends on operating the involved buck-boost converters in discontinuous current conduction mode with high-voltage gain and enhanced efficiency. A full design of the pulse generator and its passive components is presented to ensure generating the pulses with the desired specifications (rise time, pulse width, and pulse magnitude) for a given load resistance and input dc voltage. In case of moderate pulsed output voltages (i.e. few of kV), one module of the presented bipolar generator can be employed. While in case of high-voltage pulsed output, multi-module version can be employed, where each module is fed from an isolated dc source and their outputs are connected in series. Simulation models for the proposed approach are built to elucidate their performance in case of one-module as well as multi-module based generator. Finally, a scaled-down prototype for one-module of buck-boost converter-based bipolar pulse generator is implemented to validate the proposed concept.

A Multi-task Self-attention Model Using Pre-trained Language Models on Universal Dependency Annotations

  • Kim, Euhee
    • Journal of the Korea Society of Computer and Information
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    • v.27 no.11
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    • pp.39-46
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    • 2022
  • In this paper, we propose a multi-task model that can simultaneously predict general-purpose tasks such as part-of-speech tagging, lemmatization, and dependency parsing using the UD Korean Kaist v2.3 corpus. The proposed model thus applies the self-attention technique of the BERT model and the graph-based Biaffine attention technique by fine-tuning the multilingual BERT and the two Korean-specific BERTs such as KR-BERT and KoBERT. The performances of the proposed model are compared and analyzed using the multilingual version of BERT and the two Korean-specific BERT language models.

A Standardization Study of the Korean Version of Eating Attitudes Test-26 I : Reliability and Factor Analysis (한국판 식사태도검사-26(The Korean Version of Eating Attitudes Test-26 : KEAT-26) 표준화 연구 I : 신뢰도 및 요인분석)

  • Rhee, Min-Kyu;Lee, Young-Ho;Park, Se-Hyun;Sohn, Chang-Ho;Chung, Young-Cho;Hong, Sung-Kook;Lee, Byung-Kwan;Chang, Phi-Lip;Yoon, A-Rhee
    • Korean Journal of Psychosomatic Medicine
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    • v.6 no.2
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    • pp.155-175
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    • 1998
  • The purpose of this study was to test a reliability and validity of the Korean version of Eating Attitudes Test-26(KEAT-26). Using multi-stage sampling, we finally got 3,496 subjects(1422 males and 2074 females) who were available for analysis from target 4,400 Korean adults over 18 in the nationwide areas of9 kus, 10 middle or small cities, and 17 kuns. We tried to make T score norm of the KEAT-26 as a cutoff score and STEN score norm as a index of severity for disordered eating behaviors. For the male group, Cronhach's internal consistency was .83 and Spearman-Brown split half correlation coefficiency was .75. For the female group, each of them was .81 and .75, and .81, .75 for the grand total group respectively. Validity test was performed by construct validation analysis. By a iterated principal axis factoring, 4 factors were extracted. There were some differences in the factors of the KEAT-26 by sex. In the male group, factor I was 'self-control of eating and bulimic symptom', factor II was 'food preoccupation and dieting', factor III was 'preoccupation with being thinner', factor N was 'avoidance of sweet foods'. In contrast with the male group, factor I was 'self-control of eating and bulimic symptom', factor II was 'preoccupation with being thinner', factor III was 'food preoccupation' and factor N was 'dieting' in the female group. We used T score 65 as a cutoff score. T score 65 corresponded to raw score 19 in the male group, 22 in the female group and 21 in the grand total group. Severity of disordered eating behaviors was measured by a STEN score. In the male group, each of the score range of 0-10, 11-14, 15-18, 19-22 and over 23 represented the degree of none, subclinical, manifest, moderate and severe severity respectively. Each of the score range of 0-13, 14-17, 18-21, 22-26 and over 27 in the female group, and the score range of 0-12, 13-16, 17-20, 21-25 and over 26 in the grand total group also represented the same degree of severity as like in the male group. These results support that KEAT-26 is a reliable and valid scale for evaluating disordered eating behaviors and eating problems.

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Design and Implementation of a Linux-based Message Processor to Minimize the Response-time Delay of Non-real-time Messages in Multi-core Environments (멀티코어 환경에서 비실시간 메시지의 응답시간 지연을 최소화하는 리눅스 기반 메시지 처리기의 설계 및 구현)

  • Wang, Sangho;Park, Younghun;Park, Sungyong;Kim, Seungchun;Kim, Cheolhoe;Kim, Sangjun;Jin, Cheol
    • Journal of KIISE
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    • v.44 no.2
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    • pp.115-123
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    • 2017
  • A message processor is server software that receives non-realtime messages as well as realtime messages from clients that need to be processed within a deadline. With the recent advances of micro-processor technologies and Linux, the message processor is often implemented in Linux-based multi-core servers and it is important to use cores efficiently to maximize the performance of system in multi-core environments. Numerous research efforts on a real-time scheduler for the efficient utilization of the multi-core environments have been conducted. Typically, though, they have been conducted theoretically or via simulation, making a subsequent real-system application difficult. Moreover, many Linux-based real-time schedulers can only be used in a specific Linux version, or the Linux source code needs to be modified. This paper presents the design of a Linux-based message processor for multi-core environments that maps the threads to the cores at user level. The message processor is implemented through a modification of the traditional RM algorithm that consolidates the real-time messages into certain cores using a first-fit-based bin-packing algorithm; this minimizes the response-time delay of the non-real-time messages, while guaranteeing the violation rate of the real-time messages. To compare the performances, the message processor was implemented using the two multi-core-scheduling algorithms GSN-EDF and P-FP, which are provided by the LITMUS framework. The benchmarking results show that the response-time delay of non-real-time messages in the proposed system was improved up to a maximum of 17% to 18%.

A Modified Decision-Directed LMS Algorithm (수정된 DD LMS 알고리즘)

  • Oh, Kil Nam
    • Journal of the Institute of Electronics and Information Engineers
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    • v.53 no.7
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    • pp.3-8
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    • 2016
  • We propose a modified form of the decision-directed least mean square (DD LMS) algorithm that is widely used in the optimization of self-adaptive equalizers, and show the modified version greatly improves the initial convergence properties of the conventional algorithm. Existing DD LMS regards the difference between a equalizer output and a quantization value for it as an error, and achieves an optimization of the equalizer based on minimizing the mean squared error cost function for the equalizer coefficients. This error generating method is useful for binary signal or a single-level signals, however, in the case of multi-level signals, it is not effective in the initialization of the equalizer. The modified DD LMS solves this problem by modifying the error generation. We verified the usefulness and performance of the modified DD LMS through experiments with multi-level signals under distortions due to intersymbol interference and additive noise.

Multi-channel QoS scheduling algorithm in IEEE 802.15.4e (IEEE 802.15.4e 멀티 채널 QoS 스케줄링 알고리즘)

  • Wu, Hyuk;Kim, Hak-Kyu;Lee, Dong-Jun;Kang, Ho-Yong
    • Journal of Advanced Navigation Technology
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    • v.15 no.5
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    • pp.764-773
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    • 2011
  • IEEE 802.15.4 is a standard for LWPAN based on TDMA. IEEE 802.15.4 has not been used widely because of restrictions on the QoS, scalability, and reliability. IEEE 802.15.4 utilizes GTS for one-hop QoS transmission. However GTS is not an effective method to satisfy QoS in multi-hop environments. Currently IEEE 802.15.4e, an extended version of IEEE 802.15.4 MAC sub-layer, is being developed to satisfy more diverse performance requirements than IEEE 802.15.4. IEEE 802.15.4e provides muti-hop QoS transmission functionality and uses multiple frequency channels. In this paper, a multi-channel TDMA scheduling scheme is proposed to satisfy end-to-end transmission delay in IEEE 802.15.4e. The performance of the proposed scheme is evaluated using simulation.

An Analysis for the Characteristics of Digital TVs in CES in the View of Technology Growth and Substitution Curves (기술 성장 및 대체 곡선 관점에서의 CES 출품 Digital TV의 특성 분석)

  • Kim, Do-Goan;Shin, Seong-Yoon;Jin, Chan-Yong
    • Proceedings of the Korean Institute of Information and Commucation Sciences Conference
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    • 2013.05a
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    • pp.96-98
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    • 2013
  • Through reviewing the characteristics of digital TVs, which have emerged in CES since 2005, in the view of technology growth and substitution curves, this paper is to provide a prediction on the next generation's multi-media on smart environment. As a result, digital TV has been developed on the flow of its technology growth curve from the early version in 2005 to smart digital TV in 2013, which emphasizes the key word "connected", and it has already come to the market puberty. Also, as it has the characteristics such as supporting multi functional and multi media environments and introducing curved or flexible display, the digital TV in CES 2013 has reached in introductory stage on the technology substitution curve.

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