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林俊淵 副教授

http://csie.cgu.edu.tw/ezfiles/50/1050/img/41/11.jpg

姓名:林俊淵
職稱:教授
分機:3581
信箱:cyulin@mail.cgu.edu.tw
最高學歷:逢甲大學資訊工程博士
專長領域:平行與分散式處理 (MPI, OpenMP, CUDA)、生物資訊(基因體學、蛋白質體學、系統生物學、Solexa)、平行與分散是演算法、資料探勘與機器學習
實驗室:  平行處理與計算生物實驗室

經歷:
2007/10~2013/7
長庚大學資訊工程學系助理教授

2006/5~2007/10 清華大學資訊工程學系博士後研究員

2003/10~2006/4 清華大學分子與細胞生物研究所博士後研究員

教授課程:
計算機圖學、平行與分散式系統、計算生物學

研究計畫:

  1. 可同時用於單機、自建雲、公有雲的生物資訊分析平台技術開發及其應用(106-2221-E182-068-),科技部,共同主持人,2017/08/01-2018/07/31
  2. 果蠅頭部影像分析系統之研發 (106-2221-E-182070-),科技部,主持人,2017/08/01-2018/07/31
  3. 建置基於NVIDIATK1叢集架構的生物資訊分析平台(105-2221-E182-067-),科技部,主持人,2016/08/01-2017/07/31
  4. 發展基於多核心加速器的樣式比對分析平台(1042221-E-182-050-),科技部,主持人,2015/08/01-2016/07/31
  5. 發展基於圖形處理器之化合物比對及分群技術 (104-2221-E-182051-),科技部,主持人,2015/08/01-2016/07/31
  6. 發展樣式比對分析平台於巨量資料的總體基因體及轉錄體之研究 (103-2221-E-182027-),科技部,主持人,2014/08/01-2015/07/31
  7. 磁振影像雲:一個具雲端儲存與雲端運算服務之磁振造影資料平台(103-2221-E182-002-),科技部,共同主持人,2014/08/01-2015/09/30
  8. 建置新一代高通量定序分析平台:從定序、功能、到基因網路-發展樣式比對技術於 次世代RNA定序之應用(100-2221E-182-057-MY3) ,科技部,主持人,2011/08/01-2014/07/31
  9. 線上遊戲客服系統及資料分析平台,幫趣網,計畫主持人,2014/10/01-2015/09/30
  10. 新版CUDA教育訓練設計及材料製作計畫案,Nvidia,計畫主持人,2015/01/01-2015/06/30
  11. 多應用領域函式庫及程式套件庫於ARM/GPU混合處理器NVIDIA Jetson TK1平台 之評估報告,斯博科公司,計畫主持人,2015/04/01-2015/11/30
  12. NVIDIATK1平台導入,捷揚光電股份有限公司,計畫主持人,2016/02/22-2016/06/22
  13. 高效能平行計算演算法研究,科盛科技股份有限公司,主持人,2017/03/01-2018/02/08
  14. 凌華科技伺服器效能測試計畫,邁仕安防企業社,主持人,2017/06/19-2017/10/30
  15. 利用深度學習進行儀錶分類及數值讀取,台塑網股份有限公司,計畫主持人,2017/12/01-2018/11/30

論文發表

(A) 期刊論文

1. Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan and Chuan Yi Tang (2017, Sep). MGUPGMA: A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL. Evolutionary Bioinformatics, 13: 1–7.

2. Jyh-Da Wei, Hui-Jun Cheng, Chun-Yuan Lin, Jin Ye and Kuan-Yu Yeh (2017, Aug). Embedded-Based Graphics Processing Unit Cluster Platform for Multiple Sequence Alignments. Evolutionary Bioinformatics, 13: 1-10. MOST 105-2221E-182-067. 本人為通訊作者.

3. Shih-Yen Chen, Chi-Neu Tsai, Yun-Shien Lee, Chun-Yuan Lin, Kuan-Yeh Huang, Hsun-Ching Chao, Ming-Wei Lai & Cheng-Hsun Chiu (2017, Apr). Intestinal microbiome in children with severe and complicated acute viral Gastroenteritis. Scientific Reports, 7:46130.

4. Chun-Yuan Lin, Huang Ting Yen, Che-Lun Hung* (2016, Jul). Compressing Three-Dimensional Sparse Arrays using Inter- and Intra-task Parallelization Strategies on Intel Xeon and Xeon Phi. The Journal of Supercomputing. (SCI, 23/51, Subject categories: Computer Science, Hardware & Architecture). MOST 104-2221-E-182-050. 本人為第一作者.

5. Che-Lun Hung, Chun-Yuan Lin*, Po-Chang Wu (2016, Apr). An Efficient GPUBased Multiple Pattern Matching Algorithm for Packet Filtering. The Journal of Signal Processing Systems. (SCI, 212/255, Subject categories: Engineering, Electrical & Electronic). 本人為通訊作者.

6. Che Lun Hung, Chun-Yuan Lin* (2016, Jan). Efficient parallelized Search Engine based on Virtual Cluster. International Journal of Computational Science and Engineering, vol. 12, issue 1, January 2016, pp.53-7. (EI). 本人為通訊作者.

7. Che-Lun Hung, Chun-Yuan Lin*, Chia-Shin Ou, Ceng-Yuan Hong, Ship-Peng Li, Po-Yen Hung (2015, Dec). Efficient Bit-Parallel Subcircuit Extraction Approach Based on CUDA. Concurrency and Computation: Practice and Experience. (SCI, 59/105, Subject categories: Computer Science Theory & Methods)). MOST 103-2221-E-126-013. 本人為通訊作者.

8. Min Su, Jianjun Tan*, Chun-Yuan Lin* (2015, Nov). Development of HIV-1 Integrase Inhibitors: recent molecular modeling perspectives. Drug Discovery Today, vol. 20, issue 11, 2015, pp. 1337-1348. (SCI, 13/253, Subject categories: Pharmacology & Pharmacy). MOST 104-2221-E-182-051. 本人為通訊作者.

9. Chun-Yuan Lin, Jin Ye, Che-Lun Hung*, Chung-Hung Wang, Min Su, Jianjun Tan (2015, Oct). Constructing a Bioinformatics Platform with Web and Mobile Services based on NVIDIA Jetson TK1. International Journal of Grid and High Performance Computing, vol. 7, issue 4, pp. 57-73. (EI). MOST 104-2221-E182-050. 本人為第一作者.

10. Chuan Yi Tang, Che-Lun Hung, Huiru Zheng, Chun-Yuan Lin, and Hai Jiang (2015, Sep). Novel Computational Technologies for Next-Generation Sequencing Data Analysis and Their Applications. International Journal of Genomics, vol. 2015, Article ID 254685. (SCI, 97/161, Subject categories: Biotechnology & Applied Microbiology).

11. Chun-Yuan Lin, Chung-Hung Wang, Che-Lun Hung*, Yu-Shiang Lin (2015, Sep). Accelerating Multiple Compound Comparison Using LINGO-based LoadBalancing Strategies on Multi-GPUs. International Journal of Genomics , vol. 2015, Article ID 950905. (SCI, 97/161, Subject categories: Biotechnology & Applied Microbiology). MOST 104-2221-E-182-050. 本人為第一作者.

12. Zhi-ting Yu, Quan Qian, Chun-Yuan Lin, Che-Lun Hung (2015, Sep). Datafly Based Anonymity Algorithm and Its L-Diversity. International Journal of Grid and High Performance Computing, vol. 7, no. 3, pp. 85-100. (EI).

13. Yu Liu, Yang Hong, Chun-Yuan Lin, Che-Lun Hung* (2015, Aug). Accelerating Smith-Waterman Alignment for Protein Database Search Using Frequency Distance Filtration Scheme Based on CPU-GPU Collaborative System. International Journal of Genomics, vol. 2015, Article ID 761063. (SCI, 97/161, Subject categories: Biotechnology & Applied Microbiology). MOST 104-2221E-182-050.

14. Che-Lun Hung, Yu-Shiang Lin, Chun-Yuan Lin*, Yeh-Ching Chung, Yi-Fang Chung (2015, May). CUDA ClustalW: an efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs. Computational Biology and Chemistry, vol. 58, October 2015, pp. 62-68. (SCI, 59/86, Subject categories: Biology). MOST 100-2221-E-182-057-MY3. 本人為通訊作者.

15. Shih-Yen Chen, Ye Feng, Hsun-Chin Chao, Ming-Wei Lai, Wen-Ling Huang, Chun-Yuan Lin, Chi-Neu Tsai, Chyi-Liang Chen, Cheng-Hsun Chiu (2015, May). Emergence in Taiwan of Novel Norovirus GII.4 Variants Causing Acute Gastroenteritis and Intestinal Hemorrhage in Children. Journal of Medical Microbiology, vol. 64, May 2015, pp. 544-550. (SCI, 72/123, Subject categories: Microbiology).

16. Chuan Yi Tang*, Che-Lun Hung, Ching-Hsien (Robert) Hsu, Huiru Zheng, and Chun-Yuan Lin (2014, Dec). Novel Computing Technologies for Bioinformatics and Cheminformatics. BioMed Research International, vol.2014, Article ID 392150. (SCI, 81/161, Subject categories: Biotechnology & Applied Microbiology).

17. Yu-Shiang Lin, Chun-Yuan Lin, Che Lun Hung*, Yeh-Ching Chung, Kual-Zheng Lee (2014, Aug). GPU-UPGMA: high-performance computing for UPGMA algorithm based on Graphics Processing Units. Concurrency and Computation: Practice and Experience. (SCI, 59/105, Subject categories: Computer Science Theory & Methods). MOST 100-2221-E-126-007-MY3.

18. Che-Lun Hung, Chun-Yuan Lin*, Hsiao-hsi Wang (2014, May). An Efficient Parallel-Network Packet Pattern-Matching Approach Using GPUs. Journal of Systems Architecture, 60(5): 431-439. (SCI, 34/51, Subject categories: Computer Science, Hardware & Architecture). 本人為通訊作者.

19. Chun-Yuan Lin* and Yen-Ling Wang (2014, Apr). Novel Design Strategy for Checkpoint Kinase 2 Inhibitors Using Pharmacophore Modeling, Combinatorial Fusion and Virtual Screening. BioMed Research International, 2014: 359494. (SCI, 81/161, Subject categories: Biotechnology & Applied Microbiology). MOST 100-2221-E-182-057-MY3. 本人為第一作者、通訊作者.

20. Chun-Yuan Lin, Hsiao-Chieh Chi, Kuei-Chung Shih*, Jiayi Zhou, Nai-Wan Hsiao, and Chuan-Yi Tang (2014, Mar). Development of 3D-QSAR Combination Approach for Discovering and Analyzing Neuraminidase Inhibitors in Silico. International Journal of Data Mining and Bioinformatics, 9(3): 305320. (SCI, 54/56, Subject categories: Mathematical and Computational Biology). NSC 97-2221-E-182-033-MY3. 本人為第一作者.

21. Chi-Neu Tsai, Chun-Yuan Lin, Che-Wei Lin, Kuei-Chung Shih, Cheng-Hsun Chiu*, Shih-Yen Chen (2014, Feb). Clinical relevance and genotypes of circulating noroviruses in northern Taiwan, 2006-2011. Journal of Medical Virology, 86(2):335-346. (SCI, 23/33, Subject categories: Virology). 本人為第一作者.

22. Chun-Yuan Lin*, and Yu-Shiang Lin (2014, Jan). Efficient Parallel Algorithm for Multiple Sequence Alignments with Regular Expression Constrains on Graphics Processing Units. International Journal of Computational Science and Engineering, 9(1/2):11-20. (EI). NSC 100-2221-E-182-033-MY3. 本人為第一作者、通訊作者.

23. Chun-Yuan Lin, Sheng-Ta Li, and Che Lun Hung* (2014, Jan). Frequency-based RE-Sequencing tool for short reads onGraphics Processing Units. International Journal of Computational Science and Engineering, 9(1/2):3-10. (EI). 本人為第一作者.

24. Yen-Ling Wang, Chun-Yuan Lin* (co-first author), Kuei-Chung Shih, Jui-Wen Huang, Chuan-Yi Tang (2013, Dec). Design Checkpoint Kinase 2 Inhibitors by Pharmacophore Modeling and Virtual Screening Techniques. Bioorganic & Medicinal Chemistry Letters, vol.23, no. 23, 2013, pp. 6286-6291. (SCI, 23/59, Subject categories: Chemistry, Organic). NSC 100-2221-E-182-057-MY3. 本人為第一作者、通訊作者.

25. Ching-Hsien Hsu*, Chun-Yuan Lin, Ming Ouyang, and Yi Ke Guo (2013, Sep). Biocloud: Cloud Computing for Biological, Genomics, and Drug Design. BioMed Research International , 2013: 909470. (SCI, 81/161, Subject categories: Biotechnology & Applied Microbiology).

26. Chuan-Ching Huang, Chun-Yuan Lin, Cheng-Wen Chang and Chuan Yi Tang (2013, Jul). Enzyme reaction annotation using cloud techniques. BioMed Research International, vol. 2013, Article ID 140237, 11 pages. (SCI, 81/161, Subject categories: Biotechnology & Applied Microbiology). NSC 100-2221-E182-057-MY3.

27. Chunhung Richard Lin, Chun-Hao Wen, Ying-Chih Lin, Kuang-Yuan Tung, Rung-Wei Lin and Chun-Yuan Lin (2013, Apr). A P2P Framework for Developing Bioinformatics Applications in Dynamic Cloud Environments. International Journal of Genomics , vol. 2013, Article ID 361327, 9 pages. (SCI, 97/161, Subject categories: Biotechnology & Applied Microbiology). NSC 1002221-E-182-057-MY3.

28. Yen-Ling Wang, Chun-Yuan Lin, Kuei-Chung Shih, Hsiao-Chieh Chi and Chuan-Yi Tang (2013, Apr). 3D-QSAR Study for Checkpoint Kinase 2 Inhibitors through Pharmacophore Hypotheses. International Journal of Chemical Engineering and Applications, 4(2):62-65. (Google Scholar). 本人為通訊作者.

29. Sheng-Ta Lee (co-first author), Chun-Yuan Lin (co-first author), and Che-Lun Hung* (2013, Mar). GPU-Based Cloud Service for Smith-Waterman algorithm Using Frequency Distance Filtration Scheme. BioMed Research International, vol.2013, Article ID 721738, 8 pages. (SCI, 81/161, Subject categories: Biotechnology & Applied Microbiology). NSC 100-2221-E-182-057-MY3. 本人 為第一作者.

30. Che-Lun Hung and Chun-Yuan Lin* (2013, Feb). Open Reading Frame Phylogenetic Analysis on the Cloud. International Journal of Genomics, vol.2013, Article ID 614923, 9 pages. (SCI, 97/161, Subject categories: Biotechnology & Applied Microbiology). NSC 100-2221-e-182-057-MY3. 本人為通訊作者.

31. Chun-Yuan Lin, Che-Lun Hung, and Yu-Chen Hu (2013, Jan). A Re-sequencing Tool for High-throughput Long Reads Based on UNImarker with Non Overlapping iNterval Indexing Strategy. Information-An International Interdisciplinary Journal (INFORMATION-TOKYO), vol. 16, no. 1(B), pp. 827832. (EI). NSC 100-2221-E-182-057-MY3. 本人為第一作者.

32. Yu-Shiang Lin, Chun-Yuan Lin*, Hsiao-Chieh Chi, Yeh-Ching Chung (2013). Multiple Sequence Alignments with Regular Expression Constraints on a Cloud Service System. International Journal of Grid and High Performance Computing, vol. 5, issue 3, 10 pages. (EI). 本人為通訊作者.

33. Chun-Yuan Lin*, Wei Sheng Lee, and Chuan Yi Tang (2012, Sep). Parallel Shellsort Algorithm for Many-core GPUs with CUDA. International Journal of Grid and High Performance Computing, vol. 4, no.2, pp. 1-16. (EI). 本人為第一作者、通訊作者.

34. Kuei-Chung Shih, Chun-Yuan Lin (co-first author), Hsiao-Chieh Chi, ChrongShiong Hwang, Ting-Shou Chen, Chuan-Yi Tang*, and Nai-Wan Hsiao* (2012, Jan). Design of Novel FLT-3 Inhibitors Based on Dual-layer 3D-QSAR Model and Fragment-Based Compounds in Silico. Journal of Chemical Information and Modeling, vol. 52, pp. 146-155. (SCI, 6/143, Subject categories: Computer Science, Information Systems). NSC 100-2221-E-182-057-MY3. 本人為第一作者.

(B)研討會論文

1. Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, and Yu-Wei Chan (2016, Dec). Efficient Parallel UPGMA algorithm based on Multiple GPUs. he third International Workshop on High Performance Computing on Bioinformatics (HPCB 2016), 中國大陸深圳. MOST 105-2221-E-182-067.

2. Hui-Jun Cheng, Jin Ye, Jyh-Da Wei, Chun-Yuan Lin* (2016, Dec). Patch-based Sobel Operator Method to detect Seam-Carved Images by Extreme Learning Machines. The International Conference on Extreme Learning Machines (ELM2016), 新加坡. MOST 105-2221-E-182-067. 本人為通訊作者.

3. Kuan-Yu Yeh, Hui-Jun Cheng, Jin Ye, Jyh-Da Wei, and Chun-Yuan Lin (2016, Dec). Constructing a GPU Cluster Platform based on Multiple NVIDIA Jetson TK1. The third International Workshop on High Performance Computing on Bioinformatics (HPCB 2016), 中國大陸深圳. MOST 105-2221-E-182-067. 本人為通訊作者.

4. Chun-Chien Mao, Hui-Jun Cheng, Jyh-Da Wei, Chun-Yuan Lin*, Yu-Ru Liu, Hsin-Hsin Peng (2016, Nov). Accelerating Particle-Cell Distance Calculations for Biological Image Identification Based on CPU-GPU Collaborative System. The 6th International Workshop on Embedded Multi-core Computing and Applications (EMCA 2016), France. 本人為通訊作者.

5. Che-Lun Hung, Chun-Yuan Lin and Yuan-Huai Wu (2015). Efficient Brain MRI Segmentation Algorithm on TK1. The International Workshop on Innovative Computational Technologies and Its Applications.

6. Che-Lun Hung, Po-Chang Wu, Chun-Yuan Lin and Hsiao-Hsi Wang (2015). Efficient Parallel Muti-pattern Matching Using GPGPU Acceleration for Packet Filtering. 5rd International Workshop on Embedded Multi-core Computing and Applications.

7. Chun-Yuan Lin, Huang Ting Yen and Che-Lun Hung* (2015). Efficient Strategies of Compressing Three-Dimensional Sparse Arrays based on Intel XEON and Intel XEON Phi Environments. The International Workshop on Innovative Computational Technologies and Its Applications. 本人為第一作者.

8. Min Su, Jianjun Tan, Chun-Yuan Lin, Jin Ye, Chung-Hung Wang, Che-Lun Hung* (2015). Constructing a Mobility and Acceleration Computing Platform with NVIDIA Jetson TK1. 5rd International Workshop on Embedded Multi-core Computing and Applications .

9. Yu Liu, Yang Hong, Chung-Hung Wang, ShengTa Lee, Chun-Yuan Lin, and CheLun Hung* (2015). Innovative Approach for Porting Existing CPU Program to Its CUDA Program. The second International Workshop on High Performance Computing on Bioinformatics .

10. Chun-Yuan Lin, Chung-Hung Wang, Che-Lun Hung, and Yu-Shiang Lin (2014, Nov). Efficient Parallel Algorithm for Compound Comparisons on Multi-GPUs. the first International Workshop on High Performance Computing on Bioinformatics (HPCB 2014). MOST 103-2221-E-182-027. 本人為第一作者.

11. Che-Lun Hung, Chun-Yuan Lin, Hsiao-Hsi Wang, Jieh-Shan Yeh, Yu-Chen Hu and Yaw-Ling Lin (2013). Preference Utility Algorithm Using GPGPU Architecture. IEEE/ACIS International Conference on Computer and Information Science .

12. Chun-Yuan Lin, Che-Lun Hung, Jen-Cheng Huang (2013). Efficient GPU-Based Algorithm for Aligning Huge Sequence Database. 3rd International Workshop on Embedded Multi-core Computing and Applications in conjuction with IEEE HPCC 2013. 本人為第一作者.

13. Kuan-Ju Lin, Yi-Hsuan Huang, and Chun-Yuan Lin* (2013). Efficient Parallel Knuth-Morris-Pratt Algorithm for Multi-GPUs with CUDA. Advances in Intelligent Systems and Applications - Volume 2: Smart Innovation, Systems and Technologies. 本人為通訊作者.

14. Wei-Shu Hsu, Che Lun Hung, Chun-Yuan Lin*, Kual-Zheng Lee (2013). Efficient Strategy for Compressing Sparse Matrices on Graphics Processing Units. 2013 High Speed Intelligent Communication Forum (HSIC-2013) in conjuction with 4th International Conference on Computational Problem-solving, ICCP 2013. 本人為通訊作者.

15. Yen-Ling Wang, Chun-Yuan Lin, Kuei-Chung Shih, Hsiao-Chieh Chi and Chuan-Yi Tang (2013). 3D-QSAR Study for Checkpoint Kinase 2 Inhibitors through Pharmacophore Hypotheses. 2013 3rd International Conference on Chemistry and Chemical Process. 本人為通訊作者.

16. Yu-Shiang Lin, Chun-Yuan Lin, Jon-Yu Lee (2013). A New Non-Blocking Approach on GPU Dynamical Memory Management. 2013 International Workshop on Computational Science and Engineering.

17. Che-Lun Hung and Chun-Yuan Lin* (2012). Cloud Service of Analyzing Virus Data: A Case Study for Norovirus. The 2012 International Workshop on Cloud Computing for Bioinformatics and Its Applications. 本人為通訊作者.

18. Che-Lun Hung, Chun-Yuan Lin, Hsiao-hsi Wang, Chin-Yuan Chang (2012). Efficient Packet Pattern Matching for Gigabit Network Intrusion Detection using GPUs. The 2nd International Workshop on Embedded Multi-Core computing and Applications in conjuction with IEEE ICESS 2012.

19. Chuan-Ching Huang, Chun-Yuan Lin, Cheng-Wen Chang, Chuan Yi Tang (2012). Automatic Prediction of Enzyme Functions from Domain Compositions Using Enzyme Reaction Prediction Scheme. The 2012 International Conference on Biomedical Engineering and Biotechnology.

20. Chun Yuan Lin*, Jen-Cheng Huang, and Sheng-Ta Li (2012). Accelerating Smith-Waterman Algorithm Using Frequency Distance Filtration on Graphics Processing Units. The 17th Mobile Computing Workshop. 本人為第一作者、通訊作者.

21. Sheng-Ta Lee, Chun-Yuan Lin*, Che Lun Hung, Hsuan Ying Huang (2012). Using Frequency Distance Filteration for Reducing Database Search Workload on GPU-Based Cloud Service. The 2012 International Workshop on Cloud Computing for Bioinformatics and Its Applications in conjuction with IEEE CloudCom 2012. 本人為通訊作者.

22. Yu-Rong Chen, Che Lun Hung, Yu-Shiang Lin, Chun-Yuan Lin*, Tien-Lin Lee, Kual-Zheng Lee (2012). Parallel UPGMA Algorithm on Graphics Processing Units Using CUDA. The third International Workshop on Forntier of GPU Computing in conjuction with IEEE HPCC 2012. 本人為通訊作者.

23. Yu-Shiang Lin, Chun-Yuan Lin*, and Der-Chyuan Lou (2012). Efficient Parallel RSA Decryption Algorithm for Many-core GPUs with CUDA. 2012 International Conference on Telecommunication Systems Management. 本人為通訊作者.

24. Yu-Shiang Lin, Chun-Yuan Lin*, and Yeh-Ching Chung (2012). GPU-Based Cloud Service for Multiple Sequence Alignments with Regular Expression Constrains. The 2012 International Workshop on Cloud Computing for Bioinformatics and Its Applications in conjuction wiith IEEE CloudCom 2012. 本人為通訊作者.

 

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