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Soha Hassoun
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- affiliation: Tufts University, Medford, MA, USA
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2020 – today
- 2024
- [i10]Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, Haley Chatelaine:
Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181). Dagstuhl Reports 14(4): 124-141 (2024) - 2023
- [j29]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) - [j28]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) - [c41]Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Liping Liu:
On Separate Normalization in Self-supervised Transformers. NeurIPS 2023 - [i9]Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Li-Ping Liu:
On Separate Normalization in Self-supervised Transformers. CoRR abs/2309.12931 (2023) - 2022
- [j27]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): 2832-2838 (2022) - [c40]Hao Zhu, Mahashweta Das, Mangesh Bendre, Fei Wang, Hao Yang, Soha Hassoun:
Few-Shot Link Prediction with Domain-Agnostic Graph Embedding. ICMLA 2022: 659-664 - [i8]Xinmeng Li, Hao Zhu, Li-Ping Liu, Soha Hassoun:
Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation. CoRR abs/2203.13783 (2022) - 2021
- [j26]Julie Jiang
Learning graph representations of biochemical networks and its application to enzymatic link prediction. Bioinform. 37(6): 793-799 (2021) - [c39]Linfeng Liu, Michael C. Hughes, Soha Hassoun, Liping Liu:
Stochastic Iterative Graph Matching. ICML 2021: 6815-6825 - [i7]Linfeng Liu, Michael C. Hughes, Soha Hassoun, Li-Ping Liu:
Stochastic Iterative Graph Matching. CoRR abs/2106.02206 (2021) - [i6]Xinmeng Li, Li-Ping Liu, Soha Hassoun:
Boost-RS: Boosted Embeddings for Recommender Systems and its Application to Enzyme-Substrate Interaction Prediction. CoRR abs/2109.14766 (2021) - [i5]Apurva Kalia, Dilip Krishnan, Soha Hassoun:
Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction. CoRR abs/2111.09467 (2021) - 2020
- [j25]Ehsan Ullah, Mona Yosafshahi, Soha Hassoun:
Towards scaling elementary flux mode computation. Briefings Bioinform. 21(6): 1875-1885 (2020) - [j24]Xinmeng Li
ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning. PLoS Comput. Biol. 16(4) (2020) - [i4]Gian Marco Visani, Michael C. Hughes, Soha Hassoun:
Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples. CoRR abs/2002.07327 (2020) - [i3]Xinmeng Li, James Van Deventer, Soha Hassoun:
ASAP-SML: An Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning. CoRR abs/2003.03811 (2020) - [i2]Hao Zhu, Li-Ping Liu, Soha Hassoun:
Using Graph Neural Networks for Mass Spectrometry Prediction. CoRR abs/2010.04661 (2020)
2010 – 2019
- 2019
- [c38]Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen:
Workshop on Microbiomics, Metagenomics, and Metabolomics. BCB 2019: 618 - [i1]Ramtin Hosseini, Neda Hassanpour, Li-Ping Liu, Soha Hassoun:
Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling. CoRR abs/1912.05753 (2019) - 2017
- [c37]Neda Hassanpour, Nicholas Alden, Kyongbum Lee, Soha Hassoun:
An Advanced Workflow for Metabolite Annotation. BCB 2017: 582 - [c36]Linfeng Liu, Soha Hassoun:
A Tool for Predicting the Dark Side of Enzymes. BCB 2017: 622 - [c35]Vladimir Porokhin, Xinmeng Li, Soha Hassoun:
Pathway Enrichment Analysis for Untargeted Metabolomics. BCB 2017: 623 - [c34]Xinmeng Li, James Van Deventer, Soha Hassoun:
Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences. BCB 2017: 624 - [c33]Sara A. Amin, Venkatesh Endalur Gopinarayanan, Nikhil U. Nair, Soha Hassoun:
ProSol DB: A Protein Solubility Database. BCB 2017: 625 - [c32]Soha Hassoun, Curtis Huttenhower:
A Workshop on Microbiomics, Metagenomics, and Metabolomics. BCB 2017: 776 - 2016
- [j23]Mary Jane Irwin, Soha Hassoun:
Steven P. Levitan (1950-2016). IEEE Des. Test 33(3): 142-143 (2016) - [j22]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): 122-134 (2016) - 2015
- [j21]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: 5 (2015) - [j20]Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. BMC Syst. Biol. 9: 94 (2015) - [j19]Ehsan Ullah, Mark Walker
PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 12(6): 1405-1415 (2015) - [j18]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): 1499-1507 (2015) - 2014
- [j17]Yervant Zorian, Soha Hassoun:
Guest Editors' Introduction: Highlights of the 50th DAC. IEEE Des. Test 31(2): 6-8 (2014) - 2013
- [b1]Nauman H. Khan, Soha Hassoun:
Designing TSVs for 3D Integrated Circuits. Springer Briefs in Electrical and Computer Engineering, Springer 2013, ISBN 978-1-4614-5507-3, pp. i-x, 1-76 - [j16]Mona Yousofshahi, Michael Orshansky, Kyongbum Lee
Probabilistic strain optimization under constraint uncertainty. BMC Syst. Biol. 7: 29 (2013) - [j15]Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun:
MC3: a steady-state model and constraint consistency checker for biochemical networks. BMC Syst. Biol. 7: 129 (2013) - [c31]Ehsan Ullah, Calvin Hopkins, Shuchin Aeron, Soha Hassoun:
Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal. BCB 2013: 211 - [c30]Calvin Hopkins, Soha Hassoun:
Abstraction of Kinetic Models For Biochemical Networks. BCB 2013: 720 - [c29]Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun:
Gene modification identification under flux capacity uncertainty. DAC 2013: 45:1-45:5 - [c28]Bozena Kaminska, Bernard Courtois, Soha Hassoun:
New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics. VTS 2013: 1 - 2012
- [j14]Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee
Metabolic Flux-Based Modularity using Shortest Retroactive distances. BMC Syst. Biol. 6: 155 (2012) - [j13]Douglas Densmore, Soha Hassoun:
Guest Editors' Introduction: Synthetic Biology. IEEE Des. Test Comput. 29(3): 5-6 (2012) - [j12]Douglas Densmore, Soha Hassoun:
Design Automation for Synthetic Biological Systems. IEEE Des. Test Comput. 29(3): 7-20 (2012) - [c27]Nauman H. Khan, Soha Hassoun:
The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits. ASP-DAC 2012: 53-58 - [c26]Soha Hassoun:
Genetic/bio design automation for (re-)engineering biological systems. DATE 2012: 242-247 - [e3]Patrick Groeneveld, Donatella Sciuto, Soha Hassoun:
The 49th Annual Design Automation Conference 2012, DAC '12, San Francisco, CA, USA, June 3-7, 2012. ACM 2012, ISBN 978-1-4503-1199-1 [contents] - 2011
- [j11]Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee
Identification of Biochemical Network Modules Based on Shortest Retroactive Distances. PLoS Comput. Biol. 7(11) (2011) - [j10]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): 647-658 (2011) - [c25]Nauman H. Khan, Syed M. Alam, Soha Hassoun:
Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs. ISQED 2011: 751-756 - [e2]Leon Stok, Nikil D. Dutt, Soha Hassoun:
Proceedings of the 48th Design Automation Conference, DAC 2011, San Diego, California, USA, June 5-10, 2011. ACM 2011, ISBN 978-1-4503-0636-2 [contents] - 2010
- [c24]Nauman H. Khan, Sherief Reda, Soha Hassoun:
Early estimation of TSV area for power delivery in 3-D integrated circuits. 3DIC 2010: 1-6 - [c23]Marc D. Riedel
Joint DAC/IWBDA special session engineering biology: fundamentals and applications. DAC 2010: 220-221 - [c22]Jinhai Qiu, Sherief Reda, Soha Hassoun:
Fast, accurate a priori routing delay estimation. SLIP 2010: 77-82
2000 – 2009
- 2009
- [c21]Nauman H. Khan, Syed M. Alam, Soha Hassoun:
Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs. 3DIC 2009: 1-7 - [c20]Nauman H. Khan, Syed M. Alam, Soha Hassoun:
System-level comparison of power delivery design for 2D and 3D ICs. 3DIC 2009: 1-7 - [c19]John Rieffel, Frank Saunders, Shilpa Nadimpalli
Evolving soft robotic locomotion in PhysX. GECCO (Companion) 2009: 2499-2504 - [c18]Ehsan Ullah, Kyongbum Lee, Soha Hassoun:
An algorithm for identifying dominant-edge metabolic pathways. ICCAD 2009: 144-150 - 2008
- [j9]Brian Swahn, Soha Hassoun:
Electro-Thermal Analysis of Multi-Fin Devices. IEEE Trans. Very Large Scale Integr. Syst. 16(7): 816-829 (2008) - 2006
- [c17]Brian Swahn, Soha Hassoun:
Gate sizing: finFETs vs 32nm bulk MOSFETs. DAC 2006: 528-531 - [c16]Brian Swahn, Soha Hassoun:
METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs. ISQED 2006: 121-126 - [e1]Soha Hassoun:
2006 International Conference on Computer-Aided Design, ICCAD 2006, San Jose, CA, USA, November 5-9, 2006. ACM 2006, ISBN 1-59593-389-1 [contents] - 2005
- [j8]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): 278-287 (2005) - 2003
- [j7]Sani R. Nassif, Soha Hassoun:
Guest Editors' Introduction: On-Chip Power Distribution Networks. IEEE Des. Test Comput. 20(3): 5-6 (2003) - [j6]Soha Hassoun, Geert Janssen:
First CADathlon Programming Contest held at 2002 ICCAD. IEEE Des. Test Comput. 20(3): 104-107 (2003) - [j5]Soha Hassoun, Yong-Bin Kim, Fabrizio Lombardi:
Guest Editors' Introduction: Clockless VLSI Systems. IEEE Des. Test Comput. 20(6): 5-8 (2003) - [j4]Soha Hassoun, Steven M. Nowick, Leon Stok:
Guest Editorial. IEEE Trans. Comput. Aided Des. Integr. Circuits Syst. 22(6): 662-664 (2003) - [j3]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): 1270-1277 (2003) - [j2]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): 1580-1588 (2003) - [c15]Brian Swahn, Soha Hassoun:
Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading. ICCAD 2003: 58-65 - [c14]Soha Hassoun:
Optimal use of 2-phase transparent latches in buffered maze routing. ISCAS (4) 2003: 688-691 - 2002
- [c13]Soha Hassoun, Eduardo H. Calvillo Gámez, Christopher Cromer:
Verifying Clock Schedules in the Presence of Cross Talk. DATE 2002: 346-350 - [c12]Soha Hassoun, Charles J. Alpert, Meera Thiagarajan:
Optimal buffered routing path constructions for single and multiple clock domain systems. ICCAD 2002: 247-253 - [c11]Fadi A. Aloul, Soha Hassoun, Karem A. Sakallah, David T. Blaauw:
Robust SAT-Based Search Algorithm for Leakage Power Reduction. PATMOS 2002: 167-177 - 2001
- [c10]Murali Kudlugi, Soha Hassoun, Charles Selvidge, Duaine Pryor:
A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification. DAC 2001: 623-628 - [c9]Soha Hassoun, Soheila Bana:
Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering. MSE 2001: 106- - 2000
- [c8]Soha Hassoun:
Critical path analysis using a dynamically bounded delay model. DAC 2000: 260-265
1990 – 1999
- 1999
- [c7]Soha Hassoun, Carolyn McCreary:
Regularity extraction via clan-based structural circuit decomposition. ICCAD 1999: 414-419 - 1998
- [c6]Soha Hassoun, Carl Ebeling:
Using precomputation in architecture and logic resynthesis. ICCAD 1998: 316-323 - [c5]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: 337-344 - [c4]Soha Hassoun:
Fine Grain Incremental Rescheduling Via Architectural Retiming. ISSS 1998: 158-163 - 1996
- [c3]Soha Hassoun, Carl Ebeling:
Architectural Retiming: Pipelining Latency-Constrained Circuts. DAC 1996: 708-713 - 1993
- [c2]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: 311-320 - 1992
- [j1]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)
1980 – 1989
- 1987
- [c1]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: 189-196
Coauthor Index
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