Sharif

Sharif University of Technology

Department of Computer Engineering

 

US Patents

 

 Book Chapter

S. Koohi, S. Hessabi, “Scalable Architecture for All-Optical Wavelength-Routed Networks-on-Chip,” in Routing Algorithms in Networks on-Chip, Springer New York, pp 339-375, 2014.

 

Selected Journal Papers

  1. S. Akbari Rokn-Abadi, A. Mohammadi, S. Koohi, "PC-mer: An Ultra-fast memory-efficient tool for metagenomics profiling and classification , " in PLOS One, Vol. 19, No. 8, 2024.

  2. M. Kalemati, M. Zamani, S. Koohi, " DCGAN-DTA: Predicting Drug-Target Binding Affinity with Deep Convolutional Generative Adversarial Networks", BMC Genomics, Vol. 11, No. 1, 2024.

  3. S. Akbari Rokn-Abadi, S. F. Tabatabaei, S. Koohi, "KDeep: a new memory-efficient data extraction method for accurately predicting DNA/RNA transcription factor binding sites, " Journal of Translational Medicine, Vol. 11, No. 1, 2023.

  4. S. Akbari Rokn-Abadi, A. Mohammadi, S. Koohi, "A new profiling approach for DNA sequences based on the nucleotides' physicochemical features for accurate analysis of SARS-COV-2 genomes, " BMC Genomics, 24: 266, 2023.

  5. S. Akbari Rokn-Abadi, P. Laghaee, S. Koohi, “An optimized graph-based structure for single-cell RNA-seq cell-type classification based on non-linear dimension reduction”, BMC Genomics, 24: 227, 2023.

  6. M. Kalemati, S. Darvishi, S. Koohi, “CapsNet-MHC predicts peptide-MHC class I binding based on capsule neural networks”, Nature Communication Biology, Vol. 6, 2023.

  7. M. Kalemati, M. Zamani, S. Koohi, "BiComp-DTA: Drug-target binding affinity prediction through complementary biological related and compression-based featurization approach", PLOS Computational Biology, Vol. 19, No. 3, 2023.

  8. S. Akbari Rokn-Abadi, A. Mohammadi, S. Koohi, "An automated ultra-fast, memory-efficient, and accurate method for viral genome classification", Journal of Biomedical Informatics, 139, p.104316, 2023.

  9. N. Rezaei, S. Koohi, "Flat Ball: Dynamic topology for energy management of optical interconnection networks in data centers ", Optical Switching and Networking, 17, p. 100730, 2023.

  10. E. Maleki, S. Akbari Rokn-Abadi, S. Koohi, “HELIOS: high-speed sequence alignment in optics”, PLOS Computational Biology, Vol. 18, No. 11, 2022.

  11. H. Sadeghzadeh, S. Koohi, “Translation-invariant optical neural network for image classification”, Vol. 12, October, Nature Scientific Reports, 2022.

  12. S. Akbari Rokn Abadi, A. Abdosalehi, F. Pouyamehr, S. Koohi, "An Accurate Alignment-free Protein Sequence Comparator Based on Physicochemical Properties of Amino Acids", Vol. 12, July, Nature Scientific Reports, 2022.

  13. H. Sadeghzadeh, S. Koohi,  "High-speed Multi-layer Convolutional Neural Network Based on Free-space Optics ", IEEE Photonics Journal, Vol.  14, No. 4, 2022.

  14. A. Ebrahimi Dehghanpour , S. Koohi, "All-Optical Recurrent Neural Network with Reconfigurable Activation Function  ", in IEEE Journal of Selected Topics in Quantum Electronics , Vol. 29, No. 2, 2022.

  15. S. Akbari Rokn-Abadi, A. Mohammadi, S. Koohi, "WalkIm: compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs  ", PLOS One, Vol. 17, No. 1, 2022.

  16. E. Khani, S. Hessabi, S. Koohi, F. Yan, N. Calabretta, "HFOSL: hyper scale fast optical switch-based data center network with L-level sub-network", accepted to be appeard in Telecommunication Systems, 2022.

  17. H. Sadeghzadeh, S. Koohi, A. Fele Paranj, "Free-space Optical Neural Network Based on Optical Nonlinearity and Pooling Operations," IEEE Access, Vol. 9, pp.146533-146549, 2021.

  18. S. Akbari Rokn-Abadi, N. Hashemi, S. Koohi, "Optical Pattern Generator for Efficient Bio-data Encoding in a Photonic Sequence Comparison Architecture ", PLOS One, Vol. 16, No. 1 , 2021.

  19. E. Maleki, S. Koohi, Z. Kavehvash, A. Mashaghi, " OptCAM: an ultra-fast all-optical architecture for DNA variant discovery,”  Journal of Biophotonics, Vol. 13, No. 1, 2020.

  20. R. Karimi, M. Tinati, S. Koohi, S. Hessabi, " A thermally-resilient all-optical network-on-chip ", Journal of Microelectronics Reliability,  Vol. 99,  pp. 74-86, 2019.

  21.  S. Akbari Rokn-Abadi, S. Koohi, "Exploitation of Wavelength, Hardware, and Path Redundancies in Fault-tolerant All-optical DCNs", Journal of Optical Fiber Technology, Vol. 51,  pp. 77-89, 2019.

  22.  M. Tinati, S. Koohi, S. Hessabi, "Low-Overhead Thermally Resilient Optical Network-on-Chip Architecture",  Journal of Nano Communication Networks, Vol. 70,  pp. 31-47, 2019.

  23. A. Nezhadi, S. Koohi, “OMUX: Optical Multicast and Unicast-Capable Interconnection Network for Data Centers”, Journal of Optical Switching and Networking, Vol. 33,  pp. 1-12, 2019.

  24. H. Babashah, Z. Kavehvash, A. Khavasi, S. Koohi, "Temporal Analog Optical Computing using an On-Chip Fully Reconfigurable Photonic Signal Processor", Journal of Optics & Laser Technology, Vol. 111, pp. 66-74, 2019.

  25. E. Maleki, H. Babashah, S. Koohi, Z. Kavehvash, "All-optical DNA variant discovery utilizing extended DV-curve-based wavelength modulation", Journal of the Optical Society of America A, Vol. 35, Issue 11, pp. 1-12, 2018.

  26. F. Mozafari, H. Babashah, S. Koohi, Z. Kavehvash, “Speeding up DNA sequence alignment by optical Correlator”, Journal of Optics & Laser Technology, Vol. 118, pp. 124-135, 2018.

  27. H. Babashah, Z. Kavehvash, S. Koohi, A. Khavasi, "Integration in analog optical computing using metasurfaces revisited: toward ideal optical integration ", Journal of the Optical Society of America B , Vol. 34, Issue 6, pp. 1070-1318, 2017.

  28. E. Maleki, H. Babashah, S. Koohi, Z. Kavehvash , "High-speed all-optical DNA local sequence alignment based on a three-dimensional artificial neural network ", Journal of the Optical Society of America A,  Vol. 34,  Issue 7,  pp. 1173-1186, 2017.

  29. M. Tinati, R. Karimi, S. Koohi, S. Hessabi, "Topology exploration of a thermally resilient wavelength-based ONoC", Journal of Parallel and Distributed Computing (JPDC), Vol. 100, pp. 140-156, 2017.

  30. H. Falahati, S. Koohi, and S. Hessabi, “Application-Based Dynamic Reconfiguration in Optical Network-on-Chip ,” Elsevier Journal of Computer and Electrical Engineering, Vol. 45, Pages 417–429 , July 2015.

  31. S. Koohi, Y. Yin, S. Hessabi, and S. J. Ben Yoo, “Towards a Scalable, Low-Power All-optical Architecture for Networks-on-Chip,” ACM Transactions on Embedded Computing Systems, vol. 13, no. 3, pp. 101:1-101:30, March 2014.

  32. S. Koohi, S. Hessabi, “All-Optical Wavelength-Routed Architecture for a Power-Efficient Network on Chip,” IEEE Transactions on Computer, vol. 63, no. 6, pp. 777-792 , March 2014.

  33.  S. Koohi, S. Hessabi, “Scalable architecture for a contention-free optical network on-chip,” Elsevier Journal of Parallel and Distributed Computing (JPDC), vol. 72, no. 11, pp 1493-1506, Nov 2012.

  34. S. Koohi, S. Hessabi, “Hierarchical Opto-Electrical on-Chip Network for Future Multiprocessor Architectures,” Elsevier Journal of Systems Architecture (JSA), vol. 57, no. 1, pp 4-23, Jan 2011.

  35. M. Kamal, S. Koohi, S. Hessabi, “GPH: A Group-based Partitioning Scheme for Reducing Total Power Consumption of Parallel Bus,” Elsevier Journal of Microprocessors and Microsystems, vol. 35, no. 1, pp. 68-80, 2011.

 

Selected Conference Papers

  1. S. Akbari Rokn Abadi, S. Koohi,  "OTF: Optical Torus-based Fault-tolerant DCN,” 14th International Conference on the Design of Reliable Communication Networks (DRCN), 2018.

  2. S. Akbari Rokn Abadi, S. Koohi,  "O-TF and O-FTF, Optical Fault-Tolerant DCNs,” 26th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP), 2018.

  3. M. Tinati, S. Koohi, S. Hessabi, "Impact of On-chip Power Distribution on Temperature-Induced Faults in Optical NoCs", in pp. 161-168, IEEE 10th International Symposium on Embedded Multicore/Many-core Systems-on-Chip (MCSoC), 2016.

  4. S. Koohi,  Y. Yin, S. Hessabi, and S. J. Ben Yoo, “Energy Efficient All-Optical Arbitration in Optical Network-on-Chip,” in OSA Optical Fiber Communication (OFC), March 2012.

  5. S. Koohi, S. Hessabi, “Power Efficient Nanophotonic on-Chip Network for Future Large Scale Multiprocessor Architectures,” in ACM/IEEE International Symposium on Nanoscale Architecture (NanoArch), pp. 114-121, June 2011.

  6. S. Koohi, M. Abdollahi, S. Hessabi, “All-optical wavelength-routed NoC based on a novel hierarchical topology,” in ACM/IEEE International Symposium on Networks-on-Chip (NOCS), pp. 97-104, May 2011.

  7. S. Koohi, A. Shafaei, S. Hessabi, “An Optical Wavelength Switching Architecture for a High-Performance Low-Power Photonic NoC,” in International Symposium on Frontiers of Information Systems and Network Applications (FINA), pp. 1-6, March 2011.

  8. S. Koohi, A. Shafaei, S. Hessabi, “Scalable Architecture for Wavelength-Switched Optical NoC with Multicasting Capability,” in Euromicro Conference on Digital System Design Architectures, Methods, and Tools (DSD), pp. 398-403, Sep. 2010.

  9. S. Koohi, S. Hessabi, “Hierarchical on-Chip Routing of Optical Packets in Large Scale MPSoCs,” in Euromicro International Conference on Parallel, Distributed and Network-Based Computing (PDP), pp. 515-524, Feb 2010.

  10. S. Koohi, S. Hessabi, “Contention-Free on-Chip Routing of Optical Packets,” in ACM/IEEE International Symposium on Networks-on-Chip (NOCS), pp. 134-143, May 2009.

  11. M. Abdollahi, M. Khavari Tavana, S. Koohi, S. Hessabi, “All-Optical NoC based on Cube-Connected Cycles with Quasi-DOR Algorithm,” accepted to be presented at Euromicro Conference on Digital System Design Architectures, Methods, and Tools (DSD, 2012.

  12. H. Aghaei Khouzani, S. Koohi, S. Hessabi, “Fully Contention-Free Optical NoC Based on Wavelength Routing,” in International Symposium on Computer Architectures and Digital Systems (CADS), 2012.

  13. S. Koohi, M. M. Aghatabar, S. Hessabi, “Evaluation of Traffic Pattern Effect on      Power Consumption in Mesh and Torus-based Network-on-Chips,” in International Symposium on Integrated Circuits (ISIC), pp. 512-515, Sept. 2007.

  14. M. Mirza-Aghatabar, S.Koohi, S. Hessabi, M. Pedram, “An Empirical Investigation of Mesh and Torus NoC Topologies under Different Routing Algorithms and Traffic Models,” in 10th EuroMicro Conference on Digital System Design Architectures, Methods and Tools (DSD), pp. 19-26, Aug. 2007.

  15. S. Koohi, M. Babagoli, T. Lotfi, S. Kasaei, “Video Cut Detection in E-Learning Applications,” in IEEE International Symposium on Signal Processing and its Applications (ISSPA), pp. 1-4, Feb. 2007.

  16. M. Kamal, S. Koohi, S. Hessabi, ”Empirical Analysis of the Dependence of Test Power, Delay, Energy and Fault Coverage on the Architecture of LFSR-Based TPGs,” in 22nd IEEE International Symposium on Defect and Fault Tolerance in VLSI Systems (DFT'07), pp. 179-187, Sept. 2007.

  17. S. Koohi, M. M. Aghatabar, S. Hessabi, “High-Level Modeling Approach for Analyzing the Effects of Traffic Models on Power and Throughput in Mesh-based NoCs,” in 21st International Conference on VLSI Design, pp. 415-420, Jan. 2008.

  18. M. Kamal, S. Koohi, S. Hessabi, ”Analyzing Capability of LFSR Architecture as a TPG to Reduce Power, Energy and Test Delay,” in 5th IEEE East-West Design & Test International Symposium, pp. 509-512, Sept. 2007.

  19. M. Mirza-Aghatabar, S.Koohi, S. Hessabi, “An Adaptive Approach to Manage the Number of Virtual Channels,” in 22nd International Conference on Advanced Information Networking and Applications, pp. 353-358, March 2008.

  20. M. Kamal, S. Koohi, S. Hessabi, “A Novel Partitioned Encoding Scheme for Reducing Total Power Consumption of Parallel Bus,” in 13th International CSI Computer Science, pp. 90-97, March. 2007.

 Invited Talks

  1. KEIO - UC Davis Workshop, "Scalable Wavelength-Switched Architecture for Optical Networks on Chip", Davis, CA, Feb. 2011.

  2. Danish-Californian Workshop on Photonics Technologies for Access and Bio-Photonics, “An Optical Wavelength Switching Architecture for a High-Performance Low-Power Photonic Network on Chip”, University of Stanford, CA, Jan. 2011.

 

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Last Updated: April   2024