The Embodied AI Circuits, Architectures, and Systems Lab

Mohamed Ibrahim

Research Faculty Member

Contact Info:

Publications

Books

  1. Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms, Mohamed Ibrahim and Krishnendu Chakrabarty, CRC Press, 2020.
  2. Secure and Trustworthy Cyberphysical Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Springer, 2020.

Book Chapters

  1. Digital Microfluidic Biochip Security, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri — in Mark Tehranipoor, Domenic Forte, Garrett Rose, and Swarup Bhunia, ed., Security Opportunities by Nano Devices and Emerging Technologies, CRC Press, December 2017.
  2. Advances in Design Automation Techniques for Digital-Microfluidic Biochips, Mohamed Ibrahim, Zipeng Li, and Krishnendu Chakrabarty — in Rolf Drechsler and Ulrich Kühne, ed., Formal Modeling and Verification of Cyber Physical Systems, pp. 190-223, Springer Fachmedien Wiesbaden, September 2015.
  3. Pin-Count and Wire Length Optimization for Electrowetting-on-Dielectric Chips: A Metaheuristics-Based Routing Algorithm, Mohamed Ibrahim, Cherif Salama, Mohamed Watheq El-Kharashi, and Ayman Wahba — in Mourad Fakhfakh, Esteban Tlelo-Cuautle and Patrick Siarry, ed., Computational Intelligence in Digital and Network Designs and Applications, pp. 271-294, Springer International Publishing, 2015.

Journals

  1. Towards Efficient Neuro-Symbolic AI: From Workload Characterization to Hardware Architecture, Zishen Wan, Che-Kai Liu, Hanchen Yang, Ritik Raj, Chaojian Li, Haoran You, Yonggan Fu, Cheng Wan, Sixu Li, Youbin Kim, Ananda Samajdar, Yingyan (Celine) Lin, Mohamed Ibrahim, Jan M. Rabaey, Tushar Krishna, and Arijit Raychowdhury, IEEE Transactions on Circuits and Systems for Artificial Intelligence (TCASAI), 2024. [ Press: Fotune ]
  2. Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA Biochips, Mohamed Ibrahim, Zhanwei Zhong, Bhargab B. Bhattacharya, and Krishnendu Chakrabarty, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2021.
  3. Molecular Barcoding as a Defense against Benchtop Biochemical Attacks on DNA Fingerprinting and Information Forensics, Mohamed Ibrahim, Tung-Che Liang, Kristin Scott, Ramesh Karri, and Krishnendu Chakrabarty, IEEE Transactions on Information Forensics & Security (TIFS), 2020. [ Press: Pratt School of Engineering – WRAL TechWire – Phys.org ]
  4. Bio-chemical Assay Locking to Thwart Bio-IP Theft, Sukanta Bhattacharjee, Jack Tang, Sudip Poddar, Mohamed Ibrahim, Ramesh Karri, and Krishnendu Chakrabarty, ACM Transactions on Design Automation of Electronic Systems (TODAES), 2019.
  5. Synterface: Efficient Chip-to-World Interfacing for Flow-Based Microfluidic Biochips Using Control-Pin Minimization, Aditya Sridhar, Mohamed Ibrahim, and Krishnendu Chakrabarty, ACM Transactions on Embedded Computing Systems (TECS), 2019.
  6. Analysis and Design of Tamper-Mitigating Microfluidic Routing Fabrics, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2019.
  7. An Efficient Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis, Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
  8. Synthesis of Tamper-Resistant Pin-Constrained Digital Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
  9. Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening, Mohamed Ibrahim, Aditya Sridhar, Krishnendu Chakrabarty, and Ulf Schlichtmann, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018. [ Technical Report ]
  10. Towards Secure and Trustworthy Cyberphysical Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018. [ Keynote Paper ]
  11. Randomized Checkpoints: A Practical Defense for Cyberphysical Microfluidic Systems, Jack Tang, Mohamed Ibrahim, and Krishnendu Chakrabarty, IEEE Design & Test (D&T), 2018.
  12. Synthesis of a Cyberphysical Hybrid Microfluidic Platform for Single-Cell Analysis, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018. [ Technical Report ]
  13. Randomized Checkpoints: A Practical Defense for Cyberphysical Microfluidic Systems, Jack Tang, Mohamed Ibrahim, and Krishnendu Chakrabarty, IEEE Design & Test (D&T), 2018.
  14. From EDA to IoT eHealth: Promises, Challenges, and Solutions, Farshad Firouzi, Bahar Farahani, Mohamed Ibrahim, and Krishnendu Chakrabarty, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018. [ Keynote Paper ]
  15. Cyber-physical Digital-Microfluidic Biochips: Bridging the Gap between Microfluidics and Microbiology, Mohamed Ibrahim and Krishnendu Chakrabarty, Proceedings of the IEEE, 2018. [ 2016 Impact Factor = 9.237 ]
  16. Secure Randomized Checkpointing for Digital Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2017.
  17. BioCyBig: A Cyberphysical System for Microfluidics-Driven Analysis of Integrative Genomic Association Studies, Mohamed Ibrahim, Krishnendu Chakrabarty, and Jun Zeng, IEEE Transactions on Big Data (TBD), 2017.
  18. Synthesis of Cyberphysical Digital-Microfluidic Biochips for Real-Time Quantitative Analysis, Mohamed Ibrahim, Krishnendu Chakrabarty, and Kristin Scott, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2016.
  19. Supply-Chain Security of Digital-Microfluidic Biochips, Sk Subidh Ali, Mohamed Ibrahim, Jeyavijayan Rajendran, Ozgur Sinanoglu, and Krishnendu Chakrabarty, IEEE Computer, 2016. [ “Cover Feature” in the August 2016 issue of IEEE Computer ]
  20. Security Assessment of Cyberphysical Digital-Microfluidic Biochips, Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 2015.
  21. Efficient Error Recovery in Cyberphysical Digital-Microfluidic Biochips, Mohamed Ibrahim and Krishnendu Chakrabarty, IEEE Transactions on Multiscale Computing Systems (TMSCS), 2015.

Conference Papers

  1. ReCA: Integrated Acceleration for Real-Time and Efficient Cooperative Embodied Autonomous Agents, Zishen Wan, Yuhang Du, Mohamed Ibrahim, Jiayi Qian, Jason Jabbour, Yang (Katie) Zhao, Vijay Janapa Reddi, Tushar Krishna, and Arijit Raychowdhury, Proceedings of ACM International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS), 2025.
  2. Thinking and Moving: An Efficient Computing Approach for Integrated Task and Motion Planning in Cooperative Embodied AI Systems, Zishen Wan, Yuhang Du, Mohamed Ibrahim, Yang (Katie) Zhao, Tushar Krishna, Arijit Raychowdhury, Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 2024.
  3. Neuro-Symbolic Architecture Meets Large Language Models: A Memory-Centric Perspective, Mohamed Ibrahim, Zishen Wan, Haitong Li, Priyadarshini Panda, Tushar Krishna, Pentti Kanerva, Yiran Chen, and Arijit Raychowdhury, Proceedings of IEEE/ACM International Conference on Hardware/Software Codesign and System Synthesis (CODES+ISSS), 2024.
  4. H3DFact: Heterogeneous 3D Integrated CIM for Factorization with Holographic Perceptual Representations, Zishen Wan, Che-Kai Liu, Mohamed Ibrahim, Hanchen Yang, Samuel Spetalnick, Tushar Krishna, and Arijit Raychowdhury, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2024.
  5. Efficient Design of a Hyperdimensional Processing Unit for Multi-Layer Cognition, Mohamed Ibrahim, Youbin Kim, and Jan M. Rabaey, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2024.
  6. A Brain-Inspired Hierarchical Reasoning Framework for Cognition-Augmented Prosthetic Grasping, Laura I. Galindez Olascoaga, Alisha Menon, Mohamed Ibrahim, and Jan M. Rabaey, International Workshop on Combining Learning and Reasoning: Programming Languages, Formalisms, and Representations (CLeaR), 2022.
  7. AdaPool: Multi-Armed Bandits for Adaptive Virology Screening on Cyber-Physical Digital-Microfluidic Biochips, Mohamed Ibrahim, Proceedings of the ACM/IEEE Workshop on Machine Learning for CAD (MLCAD), 2020.
  8. Internet of Microfluidic Things: Perspectives on System Architecture and Design Challenges, Mohamed Ibrahim, Maria Gorlatova, and Krishnendu Chakrabarty, Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 2019.
  9. BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips, Mohamed Ibrahim, Bhargab Bhattacharya, and Krishnendu Chakrabarty, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2019.
  10. Tamper-Resistant Pin-Constrained Digital Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE/ACM Design Automation Conference (DAC), 2018.
  11. Locking of Biochemical Assays for Digital Microfluidic Biochips, Sukanta Bhattacharjee, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE European Test Symposium (ETS), 2018.
  12. Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis, Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2018.
  13. Exact Synthesis of Biomolecular Protocols for Multiple Sample Pathways on Digital Microfluidic Biochips, Oliver Keszocze, Mohamed Ibrahim, Robert Wille, Krishnendu Chakrabarty, and Rolf Drechsler, Proceedings of the IEEE International Conference on VLSI Design (VLSID), pp. 121-126, 2018.
  14. Security Trade-offs in Microfluidic Routing Fabrics, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE International Conference on Computer Design (ICCD), 2017.
  15. Security Implications of Cyberphysical Flow-Based Microfluidic Biochips, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE Asian Test Symposium (ATS), 2017.
  16. Sortex: Efficient Timing-Driven Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening, Mohamed Ibrahim, Aditya Sridhar, Krishnendu Chakrabarty, and Ulf Schlichtmann, Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 2017.
  17. Digital-Microfluidic Biochips for Quantitative Analysis: Bridging the Gap between Microfluidics and Microbiology, Mohamed Ibrahim and Krishnendu Chakrabarty, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2017.
  18. CoSyn: Efficient Single-Cell Analysis Using a Hybrid Microfluidic Platform, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2017. [ Received Best Paper Award! ][ Extended Technical Report ]
  19. Cyberphysical Adaptation in Digital-Microfluidic Biochips, Mohamed Ibrahim and Krishnendu Chakrabarty, Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), 2016.
  20. Microfluidic Encryption of On-Chip Biochemical Assays, Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), 2016.
  21. Securing Digital-Microfluidic Biochips by Randomizing Checkpoints, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE International Test Conference (ITC), 2016.
  22. A Real-Time Digital-Microfluidic Platform for Epigenetics, Mohamed Ibrahim, Craig Boswell, Krishnendu Chakrabarty, Kristin Scott, and Miroslav Pajic, Proceedings of the IEEE/ACM International Conference on Compilers, Architectures and Synthesis For Embedded Systems (CASES), 2016.
  23. Integrated and Real-Time Quantitative Analysis Using Cyberphysical Digital-Microfluidic Biochips, Mohamed Ibrahim, Krishnendu Chakrabarty, and Kristin Scott, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2016.
  24. Security Implications of Cyber-Physical Digital-Microfluidic Biochips, Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri, Proceedings of the IEEE International Conference on Computer Design (ICCD), 2015.
  25. Experimental Demonstration of Error Recovery in an Integrated Cyberphysical Digital-Microfluidic Platform, Kai Hu, Mohamed Ibrahim, Liji Chen, Zipeng Li, Krishnendu Chakrabarty, and Richard Fair, Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), 2015.
  26. Error Recovery in Digital Microfluidics for Personalized Medicine, Mohamed Ibrahim and Krishnendu Chakrabarty, Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2015.

Posters & Talks

Cyberphysical Integration for Digital Microfluidic Biochips, Poster at the NSF CPS PI Meeting, Arlington, Virginia, USA, November 2014.

Biologically Inspired Neuro-Symbolic Computing for Human-Centered AI, Talk at UT Dallas, Dallas, Texas, January 2025.

Efficient Design of a Hyperdimensional Processing Unit for Multi-Layer Cognition, Talk and Poster at the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), Valencia, Spain, March 2024.

The Hyperdimensional Processing Unit, Poster at IBM IEEE CAS/EDS AI Compute Symposium, Yorktown Heights, New York, USA, October 2022. [ Presented by Youbin Kim ]

AdaPool: Multi-Armed Bandits for Adaptive Virology Screening on Cyber-Physical Digital-Microfluidic Biochips, Talk at the ACM/IEEE Workshop on Machine Learning for CAD (MLCAD), Virtual, November 2020.

Internet of Microfluidic Things: Perspectives on System Architecture and Design Challenges, Talk at the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), Colorado, USA, November 2019.

BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips, Talk at the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), Florence, Italy, March 2019.

Sortex: Efficient Timing-Driven Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening, Talk at the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), Irvine, California, USA, November 2017.

Design and Optimization of Microfluidic Platforms for Scalable Biomolecular Quantitative Analysis, Poster at the SIGDA PhD Forum, IEEE/ACM Design Automation Conference (DAC), Austin, Texas, USA, June 2017.

Hacking Digital Microfluidic High-Level Synthesis, Poster at Hack@DAC contest, IEEE/ACM Design Automation Conference (DAC), Austin, Texas, USA, June 2017. [Presented by Jack Tang ]

CoSyn: Efficient Single-Cell Analysis Using a Hybrid Microfluidic Platform, Invited Talk at the Technical University of Munich, Munich, Germany, April 2017.

CoSyn: Efficient Single-Cell Analysis Using a Hybrid Microfluidic Platform, Talk at the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), Lausanne, Switzerland, March 2017.

Cyberphysical Integration for Digital Microfluidic Biochips, Poster at the NSF CPS PI Meeting, Arlington, Virginia, USA, November 2016.

A Real-Time Digital-Microfluidic Platform for Epigenetics, Talk and poster at the Embedded Systems Week (ESWeek), Pittsburgh, Pennsylvania, USA, October 2016.

A Real-Time Digital-Microfluidic Platform for Epigenetics, Talk at Duke ECE Graduate Student Workshop, Durham, North Carolina, USA, September 2016.

Design and Automated Control of Cyberphysical Digital-Microfluidic Biochips: From Error Recovery Towards Quantitative Analysis, Invited Talk at the University of Bremen, Bremen, Germany, May 2016.

Integrated and Real-Time Quantitative Analysis Using Cyberphysical Digital-Microfluidic Biochips, Talk at the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), Dresden, Germany, March 2016.

Integrated and Real-Time Quantitative Analysis Using Cyberphysical Digital-Microfluidic Biochips, Poster at Duke ECE Graduate Student Workshop, Durham, North Carolina, USA, September 2015.

Experimental Demonstration of Error Recovery in an Integrated Cyberphysical Digital-Microfluidic Platform, Talk at IEEE Biomedical Circuits & Systems Conference (BioCAS), Atlanta, Georgia, USA, October 2015.

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