About
Welcome! I am Mohamed Ibrahim, a Senior Research Staff at Georgia Institute of Technology (COCOSYS), advised by Prof. Arijit Raychowdhury. Before joining Georgia Tech, I was a Postdoctoral Researcher at the University of California, Berkeley, advised by Prof. Jan M. Rabaey. My research focuses on developing robust, trustworthy, and explainable cognitive computing frameworks to improve the efficiency of collaborative human-AI systems. I am particularly interested in applying these frameworks to improve sensory-motor healthcare technologies and collaborative robotic systems. My expertise includes computer architecture, CMOS VLSI design, algorithm-hardware co-design, and electronic design automation (EDA).
I received my Ph.D. and M.Sc. degrees in 2018 and 2017, respectively, both in Electrical and Computer Engineering from Duke University. Following my PhD studies, I worked for three years in the semiconductor industry, where I gained extensive experience in hardware-software co-design for a variety of SoC designs, ranging from the data center to the edge. I have also been on the technical program committees for multiple conferences, including IEEE/ACM ICCAD, IEEE/ACM DATE, and IEEE ISVLSI. Additionally, I serve as an expert reviewer for a large number of conferences and journals.
My research has resulted in two co-authored books and over 40 papers published in premier journals and refereed conference proceedings. It has also been recognized with several prestigious awards, including the Council of Graduate Schools/ProQuest Distinguished Dissertation Award in Mathematics, Physical Sciences, and Engineering, and an Outstanding Dissertation award from the department of Electrical and Computer Engineering at Duke University. My hardware-software co-design for point-of-care analysis also received a Best Paper Award at the 2017 IEEE/ACM DATE Conference.
Press
Dr. Ibrahim Received 2018 Council of Graduate Schools(CGS)/ProQuest Distinguished Dissertation Award [Duke Graduate School] [Council of Graduate Schools]
Areas of Expertise
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Computer Architecture: Domain-Specific Architectures; Hardware-Software Co-Design; Hyperdimensional Computing.
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VLSI Circuits: Low-Power Optimization; Static Timing Analysis (STA); Design-for-Test (DfT).
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Cyber-Physical Embedded Systems: Sensory-Motor Microfluidic Platforms; Real-Time Synthesis.
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EDA and Optimization: Machine Learning; Linear Programming; Graph Search; Dynamic Programming; Complexity Analysis.
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Wet Lab & Cyberbiosecurity: Quantitative PCR; Gene Expression Analysis; Molecular (DNA) Barcoding.
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Education
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2018
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Ph.D. of Electrical and Computer Engineering
Duke University.
[ Dissertation: "Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms" ]
Awards:
* 2018 Council of Graduate Schools/ProQuest Distinguished Dissertation Award in Mathematics, Physical Sciences, and Engineering.
* 2019 Outstanding Dissertation Award from the department of Electrical and Computer Engineering, Duke University.
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2017
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M.Sc. of Electrical and Computer Engineering
Duke University.
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2013
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M.Sc. of Electrical Engineering
Ain Shams University, Cairo, Egypt.
[ Thesis: "Pin-Count and Wire Length Optimization for Electrowetting-on-Dielectric Chips: A Metaheuristics-Based Routing Algorithm" ]
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2010
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B.Sc. of Electrical Engineering
Ain Shams University, Cairo, Egypt.
[ Distinction with Honors | Ranking: 3rd out of 136 ]
[ Thesis: "An Efficient Hardware Accelerator for Floating-Point Matrix Operations: Design and Applications" ]
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Honors and Awards
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2019
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Recipient of the 2019 Departmental Outstanding Dissertation Award
Department of Electrical and Computer Engineering, Duke University.
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2017
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DATE 2017 Best Paper Award
Lausanne, Switzerland.
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2017
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ACM-SIGDA 2017 DAC PhD Forum Travel Award
To present my PhD work in 2017 DAC PhD Forum.
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2017
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TUM Postdoc Mobility Award
Awarded to only 49 young scientists (including senior postdocs) from all over the world every year. Acceptance rate is 18%. Fully funded visit to TUM campus to explore research facilities and opportunities.
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2016
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ACM-SIGBD 2016 ESWeek Travel Award
To present our paper in 2016 IEEE/ACM CASES.
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2015
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Spotlight Paper
IEEE Transactions on Multi-scale Computing Systems (TMSCS).
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2013
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Duke Graduate School Fellowship
Awarded tuition and stipend for my Ph.D.
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2010
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Full Tuition Scholarship for Postgraduate Studies
Ain Shams University, Cairo, Egypt.
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2010
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Distinction Award, Graduation with Honors
Department of Computer and Systems Engineering, Ain Shams University, Cairo, Egypt.
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2009
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Engineering Robotics CORD'9 Gladiator Competition First Place
Award in the fighting-robot competition, Ain Shams University, Cairo, Egypt.
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2005
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Egyptian Government Award for Excellence in Undergraduate Studies
2005-2010, Ain Shams University, Cairo, Egypt.
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Collaboration
Dr. Mohamed Ibrahim has collaborated with many research groups, working on design methodologies and security of bio-systems. Here is the list of collaborators:
- Duke Molecular Genetics and Microbiology (Professor Kristin Scott): Study, implementation, and modeling of benchtop biomolecular analysis
- Duke Microfluidics Lab (Professor Richard Fair): Design and test of cyber-physical digital microfluidic platforms that enable resilient control of biochemical reactions
- NYU Center for Cybersecurity (Professor Ramesh Karri): Security and trust of microfluidic devices and forensic DNA-analysis flows
- UBremen Computer Architecture Group (Professor Rolf Drechsler): Developing efficient synthesis techniques (using formal methods, e.g., satisfiability modulo theories "SMT") for digital microfluidic biochips to support biomolecular quantitative-analysis applications
- TUM Chair of Electronic Design Automation (Professor Ulf Schlichtmann): Optimizing flow-based microfluidic systems to enable integrated biomolecular analysis
- Duke Cyber-Physical Systems Lab (Professor Miroslav Pajic): Introducing cyber-physical system and real-time system theories into lab-on-chip designs to support dynamic execution of quantitative analysis
- Duke's Internet of Things Group (Professor Maria Gorlatova), HP Labs (Dr. Jun Zeng), and MSG Group, Germany (Dr. Farshad Firouzi): Defining the Internet of Microfluidic Things.
Research Projects
[Click on the images to read more details!]
1. Hardware-Software Codesign for Real-Time Error Recovery in Cyber-Physical Digital Microfluidic Biochips [Completed]
Digital microfluidics is a reconfigurable lab-on-chip technology that has achieved remarkable success in miniaturizing point-of-care (POC) quantitative-analysis testing. However, a major stumbling block in the monitoring and controlling of diseases via such POC systems is the lack of reliable diagnostic tests that can recover from unexpected errors. In addition, diagnostic tests, similar to all other quantitative-analysis procedures, are inherently stochastic systems that exhibit complex interactions among their constituent biochemical components. Such characteristics signify the need for real-time error-recovery methods that verify the correctness of on-chip fluidic interactions on-the-fly during bioassay execution.
To add resilience to digital-microfluidic control, Mohamed first introduced an efficient design method for digital microfluidic platforms to support error detection and recovery. The proposed design is based on cyber-physical system integration and it enables real-time monitoring of biochemical reactors (droplets) using capacitive sensors. Mohamed and his colleagues from Duke Microfluidics Lab designed and tested an all-hardware implementation of a cyber-physical microfluidic platform, thus enabling a portable POC setting that is resilient against faults.
Related Publications: [J1][C1][C2]
2. Hardwre-Software Codesign of Hybrid Microfluidic Biochips for Biomolecular Quantitative Analysis: System Modeling, Synthesis, and Optimization Methodologies
Considerable effort has been devoted in recent years to the design and implementation of microfluidic platforms for biomolecular quantitative analysis. However, today's platforms suffer from the drawback that they were optimized for sample limited analyses, thus they are inadequate for practical quantitative analysis and the processing of multiple samples through independent pathways. Design optimization techniques for microfluidics have been studied in recent years, but they overlook the myriad complexities of biomolecular protocols and are yet to make an impact in microbiology research. The realization of microfluidic platforms for real-life quantitative analysis requires a new optimization flow that is based on the realistic modeling of biomolecular protocols.
Motivated by the above needs, this project is focused on an optimized and trustworthy transfer of benchtop biomolecular analysis, particularly epigenetic studies, to programmable and cyber-physical microfluidic biochips. In collaboration with Duke Molecular Genetics and Microbiology, Mohamed has transferred gene-expression analysis and epigenetic protocols, e.g., chromatin immunoprecipitation, from bench-scale settings and has streamlined a generic optimization flow for various classes of biomolecular analysis protocols. Adopted optimization methods were based on cyber-physical system integration, real-time systems, CFD simulations, formal methods, modeling of stochastic processes, regression analysis, and more.
Related Publications: [J4][J7][J9][J12][J16][C4][C5][C8][C9][C10][C11][C14][C15][C18]
3. Improving Trust in Emerging Microfluidic Biochips-based DNA Forensics
Microfluidics-driven biomolecular analysis can offer remarkable benefits, especially for mission-critical applications such as forensic DNA analysis. Several microfluidic commercial developers, including U.S.-based IntegenX, ANDE, and Lockheed Martin, have already started to roll out prototypes aiming to replace traditional benchtop procedures for DNA forensics, and it is anticipated that design automation and cyber-physical integration will play a significant role in advancing this technology. However, the pressure to drive down costs besides the proliferation of IoT-based connectedness will lead to cheap untrusted microfluidic devices and a multitude of unanticipated privacy violations if preventative measures are not taken. Trustworthy DNA forensic science are particularly relevant to defense applications and broader security needs.
Sensitive information in a microfluidic device can include data collected after processing of the fluids and personally identifying metadata. Irresponsible handling of patient data has led to the breakup of companies in the past, and current device makers would do well to learn from those mistakes. Other issues include trust in the sensor readings themselves; the rise and fall of Theranos, and the invalidation of two years worth of test results set a poor precedent for microuidics diagnostics. The nascent nature of microfluidics in biomolecular quantitative analysis presents an opportunity to incorporate security and trust in such critical applications before it becomes too late to rescue this rising industry from security threats.
Motivated by the above needs, this project is focused on creating the science of secure DNA forensics with the help of microfluidics technology. In collaboration with NYU Center for Cybersecurity (Professor Ramesh Karri's group) and Duke Molecular Genetics and Microbiology, Mohamed has worked on the assessment of the security implications of emerging forensic flows and has also provided appropriate countermeasures to secure such flows.
Related Publications: [J2][J3][J6][J10][J11][J13][J15][J17][J18][C3][C6][C7][C12][C16][C17]
4. The Internet of Microfluidic Things: An Integrative Cyber-Physical System for Large-Scale Microfluidics-Driven Diagnostics
The integration of microfluidics and biosensor technology is transforming microbiology research by providing new capabilities for clinical diagnostics, cancer research, and pharmacology studies. This integration enables new approaches for biochemistry automation and cyber-physical adaptation. Similarly, recent years have witnessed the rapid growth of the Internet of Things (IoT) paradigm, where different types of real-world elements such as wearable sensors are connected and allowed to autonomously interact with each other. Combining the advances of both cyber-physical microfluidics and IoT domains can generate new opportunities for knowledge fusion by transforming distributed local microfluidic elements into a global network of coordinated microfluidic systems.
This research aims to streamline this transformation and it presents a research vision for enabling the Internet of Microfluidic Things (IoMT). To leverage advances in connected Microfluidic Things, the research introduces new perspectives on system architecture, and describe technical challenges related to design automation, temporal flexibility, security, and service assignment. This vision can play a critical role in advancing the responses of clinical healthcare to global pandemics such as COVID-19. It can also be used to support complex cancer research and pharmacology studies.
Related Publications: [J5][J8][C19]
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Books
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B2
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Optimization of Trustworthy Biomolecular Quantitative Analysis Using Cyber-Physical Microfluidic Platforms
By Mohamed Ibrahim and Krishnendu Chakrabarty.
[ In Preparation ][ In Print by June/July 2020 ]
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B1
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Secure and Trustworthy Cyberphysical Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Springer, 2020.
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Book Chapters
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BC3
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Digital Microfluidic Biochip Security
By 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.
[ Online version ]
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BC2
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Advances in Design Automation Techniques for Digital-Microfluidic Biochips
By 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.
[ Online version ]
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BC1
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Pin-Count and Wire Length Optimization for Electrowetting-on-Dielectric Chips: A Metaheuristics-Based Routing Algorithm
By 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.
[ Online version ]
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Journals
Accepted for Publication OR Published:
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J19
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Efficient Regulation of Synthetic Biocircuits Using Droplet-Aliquot Operations on MEDA Biochips
By Mohamed Ibrahim, Zhanwei Zhong, Bhargab B. Bhattacharya, and Krishnendu Chakrabarty.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2021.
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J18
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Molecular Barcoding as a Defense against Benchtop Biochemical Attacks on DNA Fingerprinting and Information Forensics
By 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.
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J17
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Bio-chemical Assay Locking to Thwart Bio-IP Theft
By Sukanta Bhattacharjee, Jack Tang, Sudip Poddar, Mohamed Ibrahim, Ramesh Karri, and Krishnendu Chakrabarty.
ACM Transactions on Design Automation of Electronic Systems (TODAES), 2019.
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J16
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Synterface: Efficient Chip-to-World Interfacing for Flow-Based Microfluidic Biochips Using Control-Pin Minimization
By Aditya Sridhar, Mohamed Ibrahim, and Krishnendu Chakrabarty.
ACM Transactions on Embedded Computing Systems (TECS), 2019.
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J15
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Analysis and Design of Tamper-Mitigating Microfluidic Routing Fabrics
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2019.
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J14
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An Efficient Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis
By Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
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J13
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Synthesis of Tamper-Resistant Pin-Constrained Digital Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
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J12
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Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening
By Mohamed Ibrahim, Aditya Sridhar, Krishnendu Chakrabarty, and Ulf Schlichtmann.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
[ Technical Report ]
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J11
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Towards Secure and Trustworthy Cyberphysical Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
[ Keynote Paper ]
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J10
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Randomized Checkpoints: A Practical Defense for Cyberphysical Microfluidic Systems
By Jack Tang, Mohamed Ibrahim, and Krishnendu Chakrabarty.
IEEE Design & Test (D&T), 2018.
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J9
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Synthesis of a Cyberphysical Hybrid Microfluidic Platform for Single-Cell Analysis
By Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
[ Technical Report ][ PDF ]
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J8
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From EDA to IoT eHealth: Promises, Challenges, and Solutions
By Farshad Firouzi, Bahar Farahani, Mohamed Ibrahim, and Krishnendu Chakrabarty.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), 2018.
[ Keynote Paper ][ PDF ]
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J7
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Cyber-physical Digital-Microfluidic Biochips: Bridging the Gap between Microfluidics and Microbiology
By Mohamed Ibrahim and Krishnendu Chakrabarty.
Proceedings of the IEEE, vol. 106, no. 9, pp. 1717-1743, 2018.
[ 2016 Impact Factor = 9.237 ][ PDF ]
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J6
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Secure Randomized Checkpointing for Digital Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), vol. 37, no. 6, pp. 1119-1132, 2017.
[ PDF ]
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J5
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BioCyBig: A Cyberphysical System for Microfluidics-Driven Analysis of Integrative Genomic Association Studies
By Mohamed Ibrahim, Krishnendu Chakrabarty, and Jun Zeng.
IEEE Transactions on Big Data (TBD), 2017.
[ PDF ]
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J4
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Synthesis of Cyberphysical Digital-Microfluidic Biochips for Real-Time Quantitative Analysis
By Mohamed Ibrahim, Krishnendu Chakrabarty, and Kristin Scott.
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), vol. 36, no. 5, pp. 733-746, 2016.
[ PDF ]
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J3
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Supply-Chain Security of Digital-Microfluidic Biochips
By Sk Subidh Ali, Mohamed Ibrahim, Jeyavijayan Rajendran, Ozgur Sinanoglu, and Krishnendu Chakrabarty.
IEEE Computer, vol. 49, no. 8, pp. 36-43, 2016.
[ "Cover Feature" in the August 2016 issue of IEEE Computer ][ PDF ]
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J2
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Security Assessment of Cyberphysical Digital-Microfluidic Biochips
By Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 13, no. 3, pp. 445-458, 2015.
[ PDF ]
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J1
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Efficient Error Recovery in Cyberphysical Digital-Microfluidic Biochips
By Mohamed Ibrahim and Krishnendu Chakrabarty.
IEEE Transactions on Multiscale Computing Systems (TMSCS), vol. 1, no. 1, pp. 46-58, 2015.
[ Showcased in the June 2016 issue of IEEE Computer as "Spotlight on the Transactions" ][ PDF ]
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Peer-Reviewed Conference Papers
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C23
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H3DFact: Heterogeneous 3D Integrated CIM for Factorization with Holographic Perceptual Representations
By 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.
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C22
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Efficient Design of a Hyperdimensional Processing Unit for Multi-Layer Cognition
By Mohamed Ibrahim, Youbin Kim, and Jan M. Rabaey.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2024.
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C21
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A Brain-Inspired Hierarchical Reasoning Framework for Cognition-Augmented Prosthetic Grasping
By 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.
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C20
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AdaPool: Multi-Armed Bandits for Adaptive Virology Screening on Cyber-Physical Digital-Microfluidic Biochips
By Mohamed Ibrahim.
Proceedings of the ACM/IEEE Workshop on Machine Learning for CAD (MLCAD), 2020.
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C19
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Internet of Microfluidic Things: Perspectives on System Architecture and Design Challenges
By Mohamed Ibrahim, Maria Gorlatova, and Krishnendu Chakrabarty.
Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), 2019.
[ Invited Paper ]
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C18
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BioScan: Parameter-Space Exploration of Synthetic Biocircuits Using MEDA Biochips
By Mohamed Ibrahim, Bhargab Bhattacharya, and Krishnendu Chakrabarty.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2019.
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C17
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Tamper-Resistant Pin-Constrained Digital Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE/ACM Design Automation Conference (DAC), 2018.
[ PDF ]
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C16
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Locking of Biochemical Assays for Digital Microfluidic Biochips
By Sukanta Bhattacharjee, Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE European Test Symposium (ETS), 2018.
[ PDF ]
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C15
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Fault-Tolerant Valve-Based Microfluidic Routing Fabric for Droplet Barcoding in Single-Cell Analysis
By Yasamin Moradi, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), 2018.
[ PDF ]
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C14
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Exact Synthesis of Biomolecular Protocols for Multiple Sample Pathways on Digital Microfluidic Biochips
By 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.
[ PDF ]
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C13
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Security Trade-offs in Microfluidic Routing Fabrics
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE International Conference on Computer Design (ICCD), pp. 25-32, 2017.
[ PDF ]
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C12
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Security Implications of Cyberphysical Flow-Based Microfluidic Biochips
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE Asian Test Symposium (ATS), 2017.
[ Invited Paper ][ PDF ]
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C11
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Sortex: Efficient Timing-Driven Synthesis of Reconfigurable Flow-Based Biochips for Scalable Single-Cell Screening
By Mohamed Ibrahim, Aditya Sridhar, Krishnendu Chakrabarty, and Ulf Schlichtmann.
Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), pp. 623-630, 2017.
[ PDF ]
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C10
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Digital-Microfluidic Biochips for Quantitative Analysis: Bridging the Gap between Microfluidics and Microbiology
By Mohamed Ibrahim and Krishnendu Chakrabarty.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), pp. 1787-1792, 2017.
[ PDF ]
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C9
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CoSyn: Efficient Single-Cell Analysis Using a Hybrid Microfluidic Platform
By Mohamed Ibrahim, Krishnendu Chakrabarty, and Ulf Schlichtmann.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), pp. 1673-1678, 2017.
[ PDF ][ Received Best Paper Award! ][ Extended Technical Report ]
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C8
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Cyberphysical Adaptation in Digital-Microfluidic Biochips
By Mohamed Ibrahim and Krishnendu Chakrabarty.
Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), pp. 444-447, 2016.
[ PDF ]
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C7
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Microfluidic Encryption of On-Chip Biochemical Assays
By Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), pp. 152-155, 2016.
[ PDF ]
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C6
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Securing Digital-Microfluidic Biochips by Randomizing Checkpoints
By Jack Tang, Mohamed Ibrahim, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE International Test Conference (ITC), pp. 1-10, 2016.
[ PDF ]
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C5
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A Real-Time Digital-Microfluidic Platform for Epigenetics
By 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), pp. 10:1-10, 2016.
[ PDF ]
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C4
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Integrated and Real-Time Quantitative Analysis Using Cyberphysical Digital-Microfluidic Biochips
By Mohamed Ibrahim, Krishnendu Chakrabarty, and Kristin Scott.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), pp. 630-635, 2016.
[ PDF ]
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C3
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Security Implications of Cyber-Physical Digital-Microfluidic Biochips
By Sk Subidh Ali, Mohamed Ibrahim, Ozgur Sinanoglu, Krishnendu Chakrabarty, and Ramesh Karri.
Proceedings of the IEEE International Conference on Computer Design (ICCD), pp. 483-486, 2015.
[ PDF ]
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C2
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Experimental Demonstration of Error Recovery in an Integrated Cyberphysical Digital-Microfluidic Platform
By Kai Hu, Mohamed Ibrahim, Liji Chen, Zipeng Li, Krishnendu Chakrabarty, and Richard Fair.
Proceedings of the IEEE Biomedical Circuits & Systems Conference (BioCAS), pp. 22-24, 2015.
[ PDF ]
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C1
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Error Recovery in Digital Microfluidics for Personalized Medicine
By Mohamed Ibrahim and Krishnendu Chakrabarty.
Proceedings of the IEEE/ACM Design, Automation and Test in Europe Conference (DATE), pp. 247-252, 2015.
[ PDF ]
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Posters & Talks
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PT17
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The Hyperdimensional Processing Unit
Poster at IBM IEEE CAS/EDS AI Compute Symposium, Yorktown Heights, New York, USA, October 2022 (Presented by Youbin Kim).
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PT16
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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.
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PT15
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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.
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PT14
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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.
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PT13
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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.
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PT12
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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.
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PT11
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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, NYU].
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PT10
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CoSyn: Efficient Single-Cell Analysis Using a Hybrid Microfluidic Platform
Invited Talk at the Technical University of Munich, Munich, Germany, April 2017.
[ Hosted by Professor Ulf Schlichtmann ]
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PT9
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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.
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PT8
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Cyberphysical Integration for Digital Microfluidic Biochips
Poster at the NSF CPS PI Meeting, Arlington, Virginia, USA, November 2016.
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PT7
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A Real-Time Digital-Microfluidic Platform for Epigenetics
Talk and poster at the Embedded Systems Week (ESWeek), Pittsburgh, Pennsylvania, USA, October 2016.
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PT6
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A Real-Time Digital-Microfluidic Platform for Epigenetics
Talk at Duke ECE Graduate Student Workshop, Durham, North Carolina, USA, September 2016.
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PT5
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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.
[ Hosted by Professor Rolf Drechsler ]
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PT4
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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.
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PT3
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Integrated and Real-Time Quantitative Analysis Using Cyberphysical Digital-Microfluidic Biochips
Poster at Duke ECE Graduate Student Workshop, Durham, North Carolina, USA, September 2015.
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PT2
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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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PT1
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Cyberphysical Integration for Digital Microfluidic Biochips
Poster at the NSF CPS PI Meeting, Arlington, Virginia, USA, November 2014.
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Online Education
2020 |
Fundamentals of Reinforcement Learning
Sample-based Learning Methods
Prediction and Control with Function Approximation
A Complete Reinforcement Learning System (Capstone)
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2019 |
Neural Networks and Deep Learning
Improving Deep Neural Networks: Hyperparameter tuning, Regularization and Optimization
Structuring Machine Learning Projects
Convolutional Neural Networks
Sequence Models
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Teaching at UC Berkeley
2021 |
Guest Lecturer
Computing with High-Dimensional Vectors (Neuroscience 299)
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Teaching at Duke University
2018 |
Graduate Teaching Assistant
VLSI System Testing (ECE-538)
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2016 |
Guest Lecturer
CMOS VLSI Design Methodologies (ECE-539)
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2015 |
Graduate Teaching Assistant
Programming, Data Structure, and Algorithms in C++ (ECE-551)
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2014 |
Graduate Teaching Assistant
Computer Architecture (ECE-250)
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Teaching at Ain Shams University
2013 |
Graduate Teaching Assistant
Computer Organization I (CSE-211)
Computer Organization II (CSE-311)
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2012 |
Graduate Teaching Assistant
Computer Organization I (CSE-211)
Computer Organization II (CSE-311)
System Dynamics and Control Components (CSE-271)
System Modeling and Simulation (CSE-467)
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2011 |
Graduate Teaching Assistant
Computer Organization I (CSE-211)
System Dynamics and Control Components (CSE-271)
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Grant Proposal Writing
During my Ph.D. studies, I worked with my advisor, Professor Chakrabarty, on four grant proposals. I made major contributions to the following funded grants:
2017 |
National Science Foundation "CCF-1702596"
"Microbiology on a Programmable Biochip: An Integrated Hardware/Software Digital Microfluidics Platform"
Start Date:07/15/2017; Award Amount:$900,000.00
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2017 |
U.S. Department of Defense, Army Research Office (ARO) "W911NF-17-1-0320"
"Improving Trust in Emerging Digital Microfluidic Biochips-based DNA Forensics"
In collaboration with Professor Ramesh Karri (NYU)
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Visiting Scholar
2017 |
Technical University of Munich, Germany
Institute of Electronic Design Automation
Generously hosted by Professor Ulf Schlichtmann
Visit funded by TUM
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2016 |
University of Bremen, Germany
Computer Architecture Group
Generously hosted by Professor Rolf Drechsler
Visit funded by the Alexander von Humboldt Foundation
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Academic Services
CR |
Conference Reviewer:
IEEE/ACM Design, Automation and Test in Europe Conference (DATE)
IEEE/ACM Design Automation Conference (DAC)
IEEE/ACM International Conference on Computer-Aided Design (ICCAD)
IEEE International Symposium on Circuits and Systems (ISCAS)
IEEE European Test Symposium (ETS)
ACM International Conference on Nanoscale Computing and Communication (NanoCom)
IEEE International Conference on Artificial Intelligence Circuits and Systems (AICAS)
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JR |
Journal Reviewer:
IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD)
IEEE Transactions on Very Large Scale Integration Systems (TVLSI)
IEEE Transactions on Biomedical Circuits and Systems (TBioCAS)
ACM Transactions on Design Automation of Electronic Systems (ACM TODAES)
ACM Journal on Emerging Technologies in Computing Systems (ACM JETC)
Integration, the VLSI Journal (Elsevier)
Microelectronics Journal
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TPC |
Technical Program Committee Member:
IEEE/ACM Design, Automation and Test in Europe Conference (DATE) 2019-
IEEE International Conference on VLSI Design (VLSID) 2019
IEEE Computer Society Annual Symposium on VLSI (ISVLSI) 2019-2022
ACM International Conference on Nanoscale Computing and Communication (NanoCom) 2019, 2021
IFIP/IEEE International Conference on Very Large Scale Integration (VLSI-SoC) 2019
IEEE/ACM International Conference on Computer-Aided Design (ICCAD) 2021-
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Ment |
Mentoring:
Craig Boswell (Duke | 2015-2016): Pratt Undergraduate Fellow. Co-author of C5
Aditya Sridhar (Duke | 2016-2018): Undergraduate. Co-author of C11, J12, and J16
Yasamin Moradi (TUM | 2016-2017): Ph.D. student. Co-author of C15 and J15
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Mem |
Membership:
The Institute of Electrical and Electronics Engineers (IEEE)
IEEE Council on Electronic Design Automation (IEEE-CEDA)
IEEE Circuits and Systems Society (IEEE-CAS)
The Association for Computing Machinery (ACM)
ACM Special Interest Group on Embedded Systems (ACM-SIGBED)
ACM Special Interest Group on Design Automation (ACM-SIGDA)
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Industry
2018 |
SoC Design Engineer (Full Time)
Intel Santa Clara, CA, June 2018-Present
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2017 |
DFT Engineer (Internship)
Intel Santa Clara, CA, May 2017-November 2017
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2016 |
SoC DFX Design Engineer (Internship)
Intel Austin, TX, May 2016-August 2016
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2015 |
SoC DFX Design Engineer (Internship)
Intel Austin, TX, May 2015-August 2015
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2011 |
VLSI Design and Verification Engineer (Part Time)
Newport Media Inc., Cairo, Egypt, July 2011-June 2013
[ NMI acquired by Atmel in August 2014 ]
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2010 |
VLSI Design Engineer (Full Time)
Mentor Graphics, Cairo, Egypt, August 2010-January 2011
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2009 |
Embedded Systems Engineer (Internship)
Mentor Graphics, Cairo, Egypt, May 2009-August 2009
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