This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
ImplantBench: Characterizing and Projecting Representative Benchmarks for Emerging Bioimplantable Computing
July/August 2008 (vol. 28 no. 4)
pp. 71-91
Zhanpeng Jin, University of Pittsburgh
Allen C. Cheng, University of Pittsburgh
Healthcare will advance dramatically when micro- and nanoscale computing chips, implanted in the human body, can assist digitally in clinical diagnosis and therapy. To design and engineer the necessary processor and accelerator architectures, computer architects must first understand the current and potential workloads. ImplantBench, the first attempt at a representative workload taxonomy, includes realistic, full-blown workloads spanning security, reliability, bioinformatics, genomics, physiology, and heart activity.

1. Y. Zheng, J. Pieprzyk, and J. Seberry, "HAVAL—A One-Way Hashing Algorithm with Variable Length of Output," Proc. Int'l Conf. Cryptology: Advances in Cryptology, LNCS 718, Springer-Verlag, 1993, pp. 83-104.
2. P. Barreto and V. Rijmen, "The Khazad Legacy-Level Block Cipher," 1st Open NESSIE Workshop, 2000, pp. 13-14, https://www.cosic.esat.kuleuven.be/nessie workshop.
3. H. Gilbert and H. Handschuh, "Security Analysis of SHA-256 and Sisters," Selected Areas in Cryptography, LNCS 3006, Springer-Verlag, 2003, pp. 175-193.
4. R.N. Williams, A Painless Guide to CRC Error Detection Algorithms, Rocksoft Party, 1993.
5. H.P. Luhn, Computer for Verifying Numbers, US patent 2,950,048, Patent and Trademark Office, 1960.
6. D.J.C. MacKay, Information Theory, Inference and Learning Algorithms, Cambridge University Press, 2003.
7. S. Lin and D.J. Costello, Error Control Coding: Fundamentals and Applications, 2nd ed., Prentice Hall, 2005.
8. P. Deutsch, A. Enterprises, and J.-L Gailly, ZLIB Compressed Data Format Specification, RFC 1950, Internet Engineering Task Force, May 1996, ftp://ftp.rfc-editor.org/in-notesrfc1950.pdf .
9. R. Dawkins, The Blind Watchmaker: Why the Evidence of Evolution Reveals a Universe Without Design, W.W. Norton &Co., 1996.
10. P. Clote and R. Backofen, Computational Biology: An Introduction, John Wiley &Sons, 2000.
11. H.C. Romeburg, Cluster Analysis for Researchers, Lifetime Learning Publications, 1984.
12. C.M. Dobson, "Protein Folding and Misfolding," Nature, vol. 426, no. 6968, 18 Dec. 2003, pp. 884-890.
13. L.R. Rabiner, "A Tutorial on Hidden Markov Models and Selected Applications in Speech Recognition," Proc. IEEE, vol. 77, no. 2, Feb. 1989, pp. 257-286.
14. T.M. Przytycka, "Hidden Markov Models," Nature Encyclopedia of the Human Genome, D. Cooper ed. Nature Publishing Group, 2003.
15. B. Fuglede, and F. Topsoe, "Jensen-Shannon Divergence and Hilbert Space Embedding," Proc. Int'l Symp. Information Theory (ISIT 04), IEEE Press, 2004, pp. 31-36.
16. R. Nussinov and A.B. Jacobson, "Fast Algorithm for Predicting the Secondary structure of Single Standard RNA," Proc. National Academy of Sciences, vol. 77, no. 11, Nov. 1980, pp. 6309-6313.
17. T.F. Smith and M.S. Waterman, "Identification of Common Molecular Subsequences," J. Molecular Biology, vol. 147, 1981, pp. 195-197.
18. S. Needleman and C. Wunsch, "A General Method Applicable to the Research for Similarities in the Amino Acid Sequence of Two Proteins," J. Molecular Biology, vol. 48, 1970, pp. 443-453.
19. J. Lian, D. Mussig, and V. Lang, "Computer Modeling of Ventricular Rhythm During Atrial Fibrillation and Ventricular Pacing," IEEE Trans. Biomedical Engineering, vol. 53, no. 8, Aug. 2006, pp. 1512-1520.
20. F. Jager, A. Smrdel, and R.G. Mark, "An Open-Source Tool to Evaluate Performance of Transient ST Segment Episode Detection Algorithms," Computers in Cardiology, IEEE Press, 2004, pp. 585-588.
21. P.E. McSharry et al., "A Dynamical Model for Generating Synthetic Electrocardiogram Signals, ," IEEE Trans. Biomedical Engineering, vol. 50, no. 3, Mar. 2003, pp. 289-294.
22. G.D. Clifford, F. Azuaje, and P.E. McSharry, Advanced Methods and Tools for ECG Analysis, Artech House Publishing, 2006.
23. G.B. Moody, "ECG-Based Indices of Physical Activity," Computers in Cardiology, IEEE Press, 1992, pp. 403-406.
24. A.L. Goldberger et al., "PhysioBank, Physio Toolkit, and PhysioNet Components of a New Research Resource for Complex Physiologic Signals," Circulation, vol. 101, no. 23, 13 June 2000, pp. e215-e220.
25. J.E. Mietus et al., "The pNNx Files: Re-examining a Widely Used Heart Rate Variability Measure," J. Heart, vol. 88, no. 4, Oct. 2002, pp. 378-380.
26. J.X. Sun et al., "Estimating Cardiac Output from Arterial Blood Pressure Waveforms: A Critical Evaluation Using the MIMIC II Database," Computers in Cardiology, IEEE Press, 2005, pp. 295-298.
1. J.J. Yi and D.J. Lijia, "Simulation of Computer Architectures: Simulators, Benchmarks, Methodologies, and Recommendations," IEEE Trans. Computers, vol. 55, no. 3, Mar. 2006, pp. 268-280.
2. J. Henning, "SPEC CPU 2000: Measuring CPU Performance in the New Millennium," Computer, vol. 33, no. 7, July 2000, pp. 28-35.
3. H. Vandierendonck and K. De Bosschere, "Eccentric and Fragile Benchmarks," Proc. Int'l Symp. Performance Analysis of Systems and Software (ISPASS 04), IEEE CS Press, 2004, pp. 2-11.
4. M.R. Guthaus et al., "MiBench, A Free, Commercially Representative Embedded Benchmark Suite," Proc. IEEE Int'l Workshop Workload Characterization (WWC 01), IEEE CS Press, 2001, pp. 3-14.
5. A. Weiss, "The Standardization of Embedded Benchmarking: Pitfalls and Opportunities," Proc. Int'l Conf. Computer Design (ICCD 99), IEEE CS Press, 1999, pp. 492-498.
6. T. Wolf and M. Franklin, "Commbench—A Telecommunications Benchmark for Network Processors," Proc. Int'l Symp. Performance Analysis of Systems and Software (ISPASS 00), IEEE CS Press, 2000, pp. 154-162.
7. G. Memik, W. Mangione-Smith, and W. Hu, "NetBench: A Benchmarking Suite for Network Processors," Proc. Int'l Conf. Computer-Aided Design (ICCAD 01), IEEE CS Press, 2001, pp. 39-42.
8. B. Lee and L. Kurian John, "NpBench: A Benchmark Suite for Control Plane and Data Plane Applications for Network Processors," Proc. Int'l Conf. Computer Design (ICCD 03), IEEE CS Press, 2003, pp. 226-233.
9. C. Lee, M. Potkonjak, and W.H. Mangione-Smith, "MediaBench: A Tool for Evaluating and Synthesizing Multimedia and Communications Systems," Proc. 30th Ann. Int'l Symp. Microarchitecture (MICRO 97), IEEE CS Press, 1997, pp. 330-335.
10. L. Nazhandali, M. Minuth, and T. Austin, "SenseBench: Toward an Accurate Evaluation of Sensor Network Processors," Proc. Int'l Symp. Workload Characterization (WWC 05), IEEE CS Press, 2005, pp. 197-203.
11. A.J. KleinOsowski and D.J. Lijia, "MinneSPEC: A New SPEC Benchmark Workload for Simulation-Based Computer Architecture Research," IEEE Computer Architecture Letters, vol. 1, no. 1, Jan. 2002, pp. 7-10.
12. DMark05 Whitepaper, Futuremark, 2006; http://www.futuremark.com/products3dmark05 .
13. R. Ramaswamy and T. Wolf, "PacketBench: A Tool for Workload Characterization of Network Processing," Proc. Int'l Workshop Workload Characterization (WWC 03), IEEE CS Press, 2003, pp. 42-50.
14. G. Chen et al., "PennBench: A Benchmark Suite for Embedded Java," Proc. Int'l Workshop Workload Characterization (WWC 02), IEEE CS Press, 2002, pp. 71-80.
15. K. Albayraktaroglu et al., "BioBench: A Benchmark Suite of Bioinformatics Applications," Proc. Int'l Symp. Performance Analysis of Systems and Software (ISPASS 05), IEEE CS Press, 2005, pp. 2-9.
16. D.A. Bader et al., "BioPerf: A Benchmark Suite to Evaluate High-Performance Computer Architecture on Bioinformatics Applications," Proc. Int'l Symp. Workload Characterization (WWC 05), IEEE CS Press, 2005, pp. 163-173.

Index Terms:
biomedical benchmarking, workload characterization, bioimplantable systems, benchmarking
Citation:
Zhanpeng Jin, Allen C. Cheng, "ImplantBench: Characterizing and Projecting Representative Benchmarks for Emerging Bioimplantable Computing," IEEE Micro, vol. 28, no. 4, pp. 71-91, July-Aug. 2008, doi:10.1109/MM.2008.55
Usage of this product signifies your acceptance of the Terms of Use.