Soha Hassoun

Orcid: 0000-0001-9477-2199

According to our database1, Soha Hassoun authored at least 75 papers between 1992 and 2023.

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Bibliography

2023
CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction.
Bioinform., August, 2023

Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.
Bioinform., March, 2023

On Separate Normalization in Self-supervised Transformers.
Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2022
Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation.
CoRR, 2022

Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction.
Bioinform., 2022

Few-Shot Link Prediction with Domain-Agnostic Graph Embedding.
Proceedings of the 21st IEEE International Conference on Machine Learning and Applications, 2022

2021
Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction.
CoRR, 2021

Learning graph representations of biochemical networks and its application to enzymatic link prediction.
Bioinform., 2021

Stochastic Iterative Graph Matching.
Proceedings of the 38th International Conference on Machine Learning, 2021

2020
ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.
PLoS Comput. Biol., 2020

Using Graph Neural Networks for Mass Spectrometry Prediction.
CoRR, 2020

Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples.
CoRR, 2020

Towards scaling elementary flux mode computation.
Briefings Bioinform., 2020

2019
Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling.
CoRR, 2019

Workshop on Microbiomics, Metagenomics, and Metabolomics.
Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2017
Pathway Enrichment Analysis for Untargeted Metabolomics.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

A Tool for Predicting the Dark Side of Enzymes.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

A Workshop on Microbiomics, Metagenomics, and Metabolomics.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

An Advanced Workflow for Metabolite Annotation.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

ProSol DB: A Protein Solubility Database.
Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016
gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Steven P. Levitan (1950-2016).
IEEE Des. Test, 2016

2015
Simulation Methodology and Evaluation of Through Silicon Via (TSV)-FinFET Noise Coupling in 3-D Integrated Circuits.
IEEE Trans. Very Large Scale Integr. Syst., 2015

PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2015

PROXIMAL: a method for Prediction of Xenobiotic Metabolism.
BMC Syst. Biol., 2015

Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity.
BMC Syst. Biol., 2015

2014
Guest Editors' Introduction: Highlights of the 50th DAC.
IEEE Des. Test, 2014

2013
Designing TSVs for 3D Integrated Circuits
Springer Briefs in Electrical and Computer Engineering, Springer, ISBN: 978-1-4614-5508-0, 2013

MC<sup>3</sup>: a steady-state model and constraint consistency checker for biochemical networks.
BMC Syst. Biol., 2013

Probabilistic strain optimization under constraint uncertainty.
BMC Syst. Biol., 2013

New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics.
Proceedings of the 31st IEEE VLSI Test Symposium, 2013

Gene modification identification under flux capacity uncertainty.
Proceedings of the 50th Annual Design Automation Conference 2013, 2013

Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal.
Proceedings of the ACM Conference on Bioinformatics, 2013

Abstraction of Kinetic Models For Biochemical Networks.
Proceedings of the ACM Conference on Bioinformatics, 2013

2012
Design Automation for Synthetic Biological Systems.
IEEE Des. Test Comput., 2012

Guest Editors' Introduction: Synthetic Biology.
IEEE Des. Test Comput., 2012

Metabolic Flux-Based Modularity using Shortest Retroactive distances.
BMC Syst. Biol., 2012

Genetic/bio design automation for (re-)engineering biological systems.
Proceedings of the 2012 Design, Automation & Test in Europe Conference & Exhibition, 2012

The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits.
Proceedings of the 17th Asia and South Pacific Design Automation Conference, 2012

2011
Power Delivery Design for 3-D ICs Using Different Through-Silicon Via (TSV) Technologies.
IEEE Trans. Very Large Scale Integr. Syst., 2011

Identification of Biochemical Network Modules Based on Shortest Retroactive Distances.
PLoS Comput. Biol., 2011

Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs.
Proceedings of the 12th International Symposium on Quality Electronic Design, 2011

2010
Fast, accurate a priori routing delay estimation.
Proceedings of the International Workshop on System Level Interconnect Prediction Workshop, 2010

Joint DAC/IWBDA special session engineering biology: fundamentals and applications.
Proceedings of the 47th Design Automation Conference, 2010

Early estimation of TSV area for power delivery in 3-D integrated circuits.
Proceedings of the IEEE International Conference on 3D System Integration, 2010

2009
An algorithm for identifying dominant-edge metabolic pathways.
Proceedings of the 2009 International Conference on Computer-Aided Design, 2009

Evolving soft robotic locomotion in PhysX.
Proceedings of the Genetic and Evolutionary Computation Conference, 2009

System-level comparison of power delivery design for 2D and 3D ICs.
Proceedings of the IEEE International Conference on 3D System Integration, 2009

Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs.
Proceedings of the IEEE International Conference on 3D System Integration, 2009

2008
Electro-Thermal Analysis of Multi-Fin Devices.
IEEE Trans. Very Large Scale Integr. Syst., 2008

2006
METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs.
Proceedings of the 7th International Symposium on Quality of Electronic Design (ISQED 2006), 2006

Gate sizing: finFETs vs 32nm bulk MOSFETs.
Proceedings of the 43rd Design Automation Conference, 2006

2005
A transaction-based unified architecture for simulation and emulation.
IEEE Trans. Very Large Scale Integr. Syst., 2005

2003
Guest Editorial.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Static timing analysis for level-clocked circuits in the presence of crosstalk.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Optimal path routing in single- and multiple-clock domain systems.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst., 2003

Guest Editors' Introduction: On-Chip Power Distribution Networks.
IEEE Des. Test Comput., 2003

Guest Editors' Introduction: Clockless VLSI Systems.
IEEE Des. Test Comput., 2003

First CADathlon Programming Contest held at 2002 ICCAD.
IEEE Des. Test Comput., 2003

Optimal use of 2-phase transparent latches in buffered maze routing.
Proceedings of the 2003 International Symposium on Circuits and Systems, 2003

Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading.
Proceedings of the 2003 International Conference on Computer-Aided Design, 2003

2002
Robust SAT-Based Search Algorithm for Leakage Power Reduction.
Proceedings of the Integrated Circuit Design. Power and Timing Modeling, 2002

Optimal buffered routing path constructions for single and multiple clock domain systems.
Proceedings of the 2002 IEEE/ACM International Conference on Computer-aided Design, 2002

Verifying Clock Schedules in the Presence of Cross Talk.
Proceedings of the 2002 Design, 2002

2001
Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering.
Proceedings of the 2001 International Conference on Microelectronics Systems Education, 2001

A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification.
Proceedings of the 38th Design Automation Conference, 2001

2000
Critical path analysis using a dynamically bounded delay model.
Proceedings of the 37th Conference on Design Automation, 2000

1999
Regularity extraction via clan-based structural circuit decomposition.
Proceedings of the 1999 IEEE/ACM International Conference on Computer-Aided Design, 1999

1998
Fine Grain Incremental Rescheduling Via Architectural Retiming.
Proceedings of the 11th International Symposium on System Synthesis, 1998

Architecture of a Message-Driven Processor.
Proceedings of the 25 Years of the International Symposia on Computer Architecture (Selected Papers)., 1998

Using precomputation in architecture and logic resynthesis.
Proceedings of the 1998 IEEE/ACM International Conference on Computer-Aided Design, 1998

1996
Architectural Retiming: Pipelining Latency-Constrained Circuts.
Proceedings of the 33st Conference on Design Automation, 1996

1993
The chaos router chip: design and implementation of an adaptive router.
Proceedings of the VLSI 93, 1993

1992
A 200-MHz 64-bit Dual-Issue CMOS Microprocessor.
Digit. Tech. J., 1992


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