Soha Hassoun

Publication Activity (10 Years)

Years Active: 1987-2023
Publications (10 Years): 27

Top Topics

Graph Representations

Biochemical Networks

Probabilistic Modeling

Sequence Analysis

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Li-Ping Liu
On Separate Normalization in Self-supervised Transformers. CoRR (2023)
Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Liping Liu
On Separate Normalization in Self-supervised Transformers. NeurIPS (2023)
Vladimir Porokhin, Li-Ping Liu, Soha Hassoun
Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products. Bioinform. 39 (3) (2023)
Apurva Kalia, Dilip Krishnan, Soha Hassoun
CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction. Bioinform. 39 (8) (2023)
Hao Zhu, Mahashweta Das, Mangesh Bendre, Fei Wang, Hao Yang, Soha Hassoun
Few-Shot Link Prediction with Domain-Agnostic Graph Embedding. ICMLA (2022)
Xinmeng Li, Li-Ping Liu, Soha Hassoun
Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction. Bioinform. 38 (10) (2022)
Xinmeng Li, Hao Zhu, Li-Ping Liu, Soha Hassoun
Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation. CoRR (2022)
Apurva Kalia, Dilip Krishnan, Soha Hassoun
Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction. CoRR (2021)
Xinmeng Li, Li-Ping Liu, Soha Hassoun
Boost-RS: Boosted Embeddings for Recommender Systems and its Application to Enzyme-Substrate Interaction Prediction. CoRR (2021)
Julie Jiang, Li-Ping Liu, Soha Hassoun
Learning graph representations of biochemical networks and its application to enzymatic link prediction. Bioinform. 37 (6) (2021)
Linfeng Liu, Michael C. Hughes, Soha Hassoun, Liping Liu
Stochastic Iterative Graph Matching. ICML (2021)
Linfeng Liu, Michael C. Hughes, Soha Hassoun, Li-Ping Liu
Stochastic Iterative Graph Matching. CoRR (2021)
Xinmeng Li, James Van Deventer, Soha Hassoun
ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning. PLoS Comput. Biol. 16 (4) (2020)
Xinmeng Li, James Van Deventer, Soha Hassoun
ASAP-SML: An Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning. CoRR (2020)
Ehsan Ullah, Mona Yosafshahi, Soha Hassoun
Towards scaling elementary flux mode computation. Briefings Bioinform. 21 (6) (2020)
Gian Marco Visani, Michael C. Hughes, Soha Hassoun
Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples. CoRR (2020)
Hao Zhu, Li-Ping Liu, Soha Hassoun
Using Graph Neural Networks for Mass Spectrometry Prediction. CoRR (2020)
Ramtin Hosseini, Neda Hassanpour, Li-Ping Liu, Soha Hassoun
Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling. CoRR (2019)
Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen
Workshop on Microbiomics, Metagenomics, and Metabolomics. BCB (2019)
Xinmeng Li, James Van Deventer, Soha Hassoun
Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences. BCB (2017)
Neda Hassanpour, Nicholas Alden, Kyongbum Lee, Soha Hassoun
An Advanced Workflow for Metabolite Annotation. BCB (2017)
Linfeng Liu, Soha Hassoun
A Tool for Predicting the Dark Side of Enzymes. BCB (2017)
Soha Hassoun, Curtis Huttenhower
A Workshop on Microbiomics, Metagenomics, and Metabolomics. BCB (2017)
Vladimir Porokhin, Xinmeng Li, Soha Hassoun
Pathway Enrichment Analysis for Untargeted Metabolomics. BCB (2017)
Sara A. Amin, Venkatesh Endalur Gopinarayanan, Nikhil U. Nair, Soha Hassoun
ProSol DB: A Protein Solubility Database. BCB (2017)
Ehsan Ullah, Shuchin Aeron, Soha Hassoun
gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal. IEEE ACM Trans. Comput. Biol. Bioinform. 13 (1) (2016)
Mary Jane Irwin, Soha Hassoun
Steven P. Levitan (1950-2016). IEEE Des. Test 33 (3) (2016)
Gautham Vivek Sridharan, Ehsan Ullah, Soha Hassoun, Kyongbum Lee
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity. BMC Syst. Biol. 9 (2015)
Brad D. Gaynor, Soha Hassoun
Simulation Methodology and Evaluation of Through Silicon Via (TSV)-FinFET Noise Coupling in 3-D Integrated Circuits. IEEE Trans. Very Large Scale Integr. Syst. 23 (8) (2015)
Ehsan Ullah, Mark Walker, Kyongbum Lee, Soha Hassoun
PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 12 (6) (2015)
Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee, Soha Hassoun
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. BMC Syst. Biol. 9 (2015)
Yervant Zorian, Soha Hassoun
Guest Editors' Introduction: Highlights of the 50th DAC. IEEE Des. Test 31 (2) (2014)
Calvin Hopkins, Soha Hassoun
Abstraction of Kinetic Models For Biochemical Networks. BCB (2013)
Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun
Probabilistic strain optimization under constraint uncertainty. BMC Syst. Biol. 7 (2013)
Ehsan Ullah, Calvin Hopkins, Shuchin Aeron, Soha Hassoun
Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal. BCB (2013)
Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun
: a steady-state model and constraint consistency checker for biochemical networks. BMC Syst. Biol. 7 (2013)
Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun
Gene modification identification under flux capacity uncertainty. DAC (2013)
Bozena Kaminska, Bernard Courtois, Soha Hassoun
New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics. VTS (2013)
Nauman H. Khan, Soha Hassoun
The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits. ASP-DAC (2012)
Douglas Densmore, Soha Hassoun
Design Automation for Synthetic Biological Systems. IEEE Des. Test Comput. 29 (3) (2012)
Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee
Metabolic Flux-Based Modularity using Shortest Retroactive distances. BMC Syst. Biol. 6 (2012)
Douglas Densmore, Soha Hassoun
Guest Editors' Introduction: Synthetic Biology. IEEE Des. Test Comput. 29 (3) (2012)
Soha Hassoun
Genetic/bio design automation for (re-)engineering biological systems. DATE (2012)
Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee
Identification of Biochemical Network Modules Based on Shortest Retroactive Distances. PLoS Comput. Biol. 7 (11) (2011)
Nauman H. Khan, Syed M. Alam, Soha Hassoun
Power Delivery Design for 3-D ICs Using Different Through-Silicon Via (TSV) Technologies. IEEE Trans. Very Large Scale Integr. Syst. 19 (4) (2011)
Nauman H. Khan, Syed M. Alam, Soha Hassoun
Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs. ISQED (2011)
Marc Riedel, Soha Hassoun, Ron Weiss, Pamela Silver, J. Christopher Anderson, Richard M. Murray
Joint DAC/IWBDA special session engineering biology: fundamentals and applications. DAC (2010)
Jinhai Qiu, Sherief Reda, Soha Hassoun
Fast, accurate a priori routing delay estimation. SLIP (2010)
Nauman H. Khan, Sherief Reda, Soha Hassoun
Early estimation of TSV area for power delivery in 3-D integrated circuits. 3DIC (2010)
Nauman H. Khan, Syed M. Alam, Soha Hassoun
Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs. 3DIC (2009)
Ehsan Ullah, Kyongbum Lee, Soha Hassoun
An algorithm for identifying dominant-edge metabolic pathways. ICCAD (2009)
Nauman H. Khan, Syed M. Alam, Soha Hassoun
System-level comparison of power delivery design for 2D and 3D ICs. 3DIC (2009)
John Rieffel, Frank Saunders, Shilpa Nadimpalli, Harvey Zhou, Soha Hassoun, Jason H. Rife, Barry Trimmer
Evolving soft robotic locomotion in PhysX. GECCO (Companion) (2009)
Brian Swahn, Soha Hassoun
Electro-Thermal Analysis of Multi-Fin Devices. IEEE Trans. Very Large Scale Integr. Syst. 16 (7) (2008)
Brian Swahn, Soha Hassoun
Gate sizing: finFETs vs 32nm bulk MOSFETs. DAC (2006)
Brian Swahn, Soha Hassoun
METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs. ISQED (2006)
Soha Hassoun, Murali Kudlugi, Duaine Pryor, Charles Selvidge
A transaction-based unified architecture for simulation and emulation. IEEE Trans. Very Large Scale Integr. Syst. 13 (2) (2005)
Soha Hassoun, Christopher Cromer, Eduardo H. Calvillo Gámez
Static timing analysis for level-clocked circuits in the presence of crosstalk. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22 (9) (2003)
Sani R. Nassif, Soha Hassoun
Guest Editors' Introduction: On-Chip Power Distribution Networks. IEEE Des. Test Comput. 20 (3) (2003)
Brian Swahn, Soha Hassoun
Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading. ICCAD (2003)
Soha Hassoun, Charles J. Alpert
Optimal path routing in single- and multiple-clock domain systems. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22 (11) (2003)
Soha Hassoun, Geert Janssen
First CADathlon Programming Contest held at 2002 ICCAD. IEEE Des. Test Comput. 20 (3) (2003)
Soha Hassoun, Steven M. Nowick, Leon Stok
Guest Editorial. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22 (6) (2003)
Soha Hassoun
Optimal use of 2-phase transparent latches in buffered maze routing. ISCAS (4) (2003)
Soha Hassoun, Yong-Bin Kim, Fabrizio Lombardi
Guest Editors' Introduction: Clockless VLSI Systems. IEEE Des. Test Comput. 20 (6) (2003)
Soha Hassoun, Charles J. Alpert, Meera Thiagarajan
Optimal buffered routing path constructions for single and multiple clock domain systems. ICCAD (2002)
Soha Hassoun, Eduardo H. Calvillo Gámez, Christopher Cromer
Verifying Clock Schedules in the Presence of Cross Talk. DATE (2002)
Fadi A. Aloul, Soha Hassoun, Karem A. Sakallah, David T. Blaauw
Robust SAT-Based Search Algorithm for Leakage Power Reduction. PATMOS (2002)
Murali Kudlugi, Soha Hassoun, Charles Selvidge, Duaine Pryor
A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification. DAC (2001)
Soha Hassoun, Soheila Bana
Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering. MSE (2001)
Soha Hassoun
Critical path analysis using a dynamically bounded delay model. DAC (2000)
Soha Hassoun, Carolyn McCreary
Regularity extraction via clan-based structural circuit decomposition. ICCAD (1999)
William J. Dally, Linda Chao, Andrew A. Chien, Soha Hassoun, Waldemar Horwat, Jon Kaplan, Paul Song, Brian Totty, D. Scott Wills
Architecture of a Message-Driven Processor. 25 Years ISCA: Retrospectives and Reprints (1998)
Soha Hassoun, Carl Ebeling
Using precomputation in architecture and logic resynthesis. ICCAD (1998)
Soha Hassoun
Fine Grain Incremental Rescheduling Via Architectural Retiming. ISSS (1998)
Soha Hassoun, Carl Ebeling
Architectural Retiming: Pipelining Latency-Constrained Circuts. DAC (1996)
Kevin Bolding, Sen-Ching S. Cheung, Sung-Eun Choi, Carl Ebeling, Soha Hassoun, Ton Anh Ngo, Robert Wille
The chaos router chip: design and implementation of an adaptive router. VLSI (1993)
Daniel W. Dobberpuhl, Richard T. Witek, Randy L. Allmon, Robert Anglin, David Bertucci, Sharon M. Britton, Linda Chao, Robert A. Conrad, Daniel E. Dever, Bruce Gieseke, Soha Hassoun, Gregory W. Hoeppner, Kathryn Kuchler, Maureen Ladd, Burton M. Leary, Liam Madden, Edward J. McLellan, Derrick Meyer, James Montanaro, Donald A. Priore, Vidya Rajagopalan, Sridhar Samudrala, Sribalan Santhanam
A 200-MHz 64-bit Dual-Issue CMOS Microprocessor. Digit. Tech. J. 4 (4) (1992)
William J. Dally, Linda Chao, Andrew A. Chien, Soha Hassoun, Waldemar Horwat, Jon Kaplan, Paul Song, Brian Totty, D. Scott Wills
Architecture of a Message-Driven Processor. ISCA (1987)