Soha Hassoun

100 papers A* 14A 8C 1Misc 1Journal 52Unranked 23
YearRankTypeTitle / Venue / Authors
2025 J jnl
Evaluating Large Language Models in Scientific Discovery.
CoRR
Zhangde Song, Jieyu Lu, Yuanqi Du, Botao Yu, Thomas M. Pruyn, Yue Huang, Kehan Guo, Xiuzhe Luo, Yuanhao Qu, Yi Qu, Yinkai Wang, Haorui Wang, Jeff Guo, Jingru Gan, Parshin Shojaee, Di Luo, Andres M. Bran, Gen Li, Qiyuan Zhao, Shao-Xiong Lennon Luo, Yuxuan Zhang, Xiang Zou, Wanru Zhao, Yifan F. Zhang, Wucheng Zhang, Shunan Zheng, Saiyang Zhang, Sartaaj Takrim Khan, Mahyar Rajabi Kochi, Samantha Paradi-Maropakis, Tony Baltoiu, Fengyu Xie, Tianyang Chen, Kexin Huang, Weiliang Luo, Meijing Fang, Xin Yang, Lixue Cheng, Jiajun He, Soha Hassoun, Xiangliang Zhang, Wei Wang, Chandan K. Reddy, Chao Zhang, Zhiling Zheng, Mengdi Wang, Le Cong, Carla P. Gomes, Chang-Yu Hsieh, Aditya Nandy, Philippe Schwaller, Heather J. Kulik, Haojun Jia, Huan Sun, Seyed Mohamad Moosavi, Chenru Duan
2025 J jnl
General Intelligence-based Fragmentation (GIF): A framework for peak-labeled spectra simulation.
CoRR
Margaret R. Martin, Soha Hassoun
2025 A* conf
Graph Generative Pre-trained Transformer.
ICML
Xiaohui Chen, Yinkai Wang, Jiaxing He, Yuanqi Du, Soha Hassoun, Xiaolin Xu, Liping Liu
2025 J jnl
Graph Generative Pre-trained Transformer.
CoRR
Xiaohui Chen, Yinkai Wang, Jiaxing He, Yuanqi Du, Soha Hassoun, Xiaolin Xu, Li-Ping Liu
2025 J jnl
JESTR: Joint Embedding Space Technique for Ranking candidate molecules for the annotation of untargeted metabolomics data.
Bioinform.
Apurva Kalia, Yan Zhou Chen, Dilip Krishnan, Soha Hassoun
2025 J jnl
Large Language Model is Secretly a Protein Sequence Optimizer.
CoRR
Yinkai Wang, Jiaxing He, Yuanqi Du, Xiaohui Chen, Jianan Canal Li, Liping Liu, Xiaolin Xu, Soha Hassoun
2025 A* conf
MADGEN: Mass-Spec attends to De Novo Molecular generation.
ICLR
Yinkai Wang, Xiaohui Chen, Liping Liu, Soha Hassoun
2025 J jnl
MADGEN: Mass-Spec attends to De Novo Molecular generation.
CoRR
Yinkai Wang, Xiaohui Chen, Liping Liu, Soha Hassoun
2025 J jnl
MetaboT: AI-based agent for natural language-based interaction with metabolomics knowledge graphs.
CoRR
Madina Bekbergenova, Lucas Pradi, Benjamin Navet, Emma Tysinger, Franck Michel, Matthieu Feraud, Yousouf Taghzouti, Yan Zhou Chen, Olivier Kirchhoffer, Florence Mehl, Martin Legrand, Tao Jiang, Marco Pagni, Soha Hassoun, Jean-Luc Wolfender, Wout Bittremieux, Fabien Gandon, Louis-Félix Nothias
2025 J jnl
Protein-ligand co-design: a case for improving binding affinity between type II NADH:quinone oxidoreductase and quinones.
J. Comput. Aided Mol. Des.
Vladimir Porokhin, Anne M. Brown, Soha Hassoun
2024 J jnl
An Ensemble Spectral Prediction (ESP) model for metabolite annotation.
Bioinform.
Xinmeng Li, Yan Zhou Chen, Apurva Kalia, Hao Zhu, Liping Liu, Soha Hassoun
2024 J jnl
Computational Metabolomics: Towards Molecules, Models, and their Meaning (Dagstuhl Seminar 24181).
Dagstuhl Reports
Timothy M. D. Ebbels, Soha Hassoun, Ewy A. Mathé, Justin J. J. van der Hooft, Haley Chatelaine
2024 J jnl
JESTR: Joint Embedding Space Technique for Ranking Candidate Molecules for the Annotation of Untargeted Metabolomics Data.
CoRR
Apurva Kalia, Dilip Krishnan, Soha Hassoun
2024 A* conf
MassSpecGym: A benchmark for the discovery and identification of molecules.
NeurIPS
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Liping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2024 J jnl
MassSpecGym: A benchmark for the discovery and identification of molecules.
CoRR
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge, Adamo Young, Fleming Kretschmer, Raman Samusevich, Janne Heirman, Fei Wang, Luke Zhang, Kai Dührkop, Marcus Ludwig, Nils A. Haupt, Apurva Kalia, Corinna Brungs, Robin Schmid, Russell Greiner, Bo Wang, David S. Wishart, Li-Ping Liu, Juho Rousu, Wout Bittremieux, Hannes Rost, Tytus D. Mak, Soha Hassoun, Florian Huber, Justin J. J. van der Hooft, Michael A. Stravs, Sebastian Böcker, Josef Sivic, Tomás Pluskal
2023 J jnl
CSI: Contrastive data Stratification for Interaction prediction and its application to compound-protein interaction prediction.
Bioinform.
Apurva Kalia, Dilip Krishnan, Soha Hassoun
2023 A* conf
On Separate Normalization in Self-supervised Transformers.
NeurIPS
Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Liping Liu
2023 J jnl
On Separate Normalization in Self-supervised Transformers.
CoRR
Xiaohui Chen, Yinkai Wang, Yuanqi Du, Soha Hassoun, Li-Ping Liu
2023 J jnl
Using graph neural networks for site-of-metabolism prediction and its applications to ranking promiscuous enzymatic products.
Bioinform.
Vladimir Porokhin, Li-Ping Liu, Soha Hassoun
2022 J jnl
Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction.
Bioinform.
Xinmeng Li, Li-Ping Liu, Soha Hassoun
2022 J jnl
Ensemble Spectral Prediction (ESP) Model for Metabolite Annotation.
CoRR
Xinmeng Li, Hao Zhu, Li-Ping Liu, Soha Hassoun
2022 C conf
Few-Shot Link Prediction with Domain-Agnostic Graph Embedding.
ICMLA
Hao Zhu, Mahashweta Das, Mangesh Bendre, Fei Wang, Hao Yang, Soha Hassoun
2021 J jnl
Boost-RS: Boosted Embeddings for Recommender Systems and its Application to Enzyme-Substrate Interaction Prediction.
CoRR
Xinmeng Li, Li-Ping Liu, Soha Hassoun
2021 J jnl
Contrastive Multiview Coding for Enzyme-Substrate Interaction Prediction.
CoRR
Apurva Kalia, Dilip Krishnan, Soha Hassoun
2021 J jnl
Enzyme promiscuity prediction using hierarchy-informed multi-label classification.
Bioinform.
Gian Marco Visani, Michael C. Hughes, Soha Hassoun
2021 J jnl
Learning graph representations of biochemical networks and its application to enzymatic link prediction.
Bioinform.
Julie Jiang, Li-Ping Liu, Soha Hassoun
2021 A* conf
Stochastic Iterative Graph Matching.
ICML
Linfeng Liu, Michael C. Hughes, Soha Hassoun, Liping Liu
2021 J jnl
Stochastic Iterative Graph Matching.
CoRR
Linfeng Liu, Michael C. Hughes, Soha Hassoun, Li-Ping Liu
2020 J jnl
ASAP-SML: An Antibody Sequence Analysis Pipeline Using Statistical Testing and Machine Learning.
CoRR
Xinmeng Li, James Van Deventer, Soha Hassoun
2020 J jnl
ASAP-SML: An antibody sequence analysis pipeline using statistical testing and machine learning.
PLoS Comput. Biol.
Xinmeng Li, James Van Deventer, Soha Hassoun
2020 J jnl
Hierarchical Classification of Enzyme Promiscuity Using Positive, Unlabeled, and Hard Negative Examples.
CoRR
Gian Marco Visani, Michael C. Hughes, Soha Hassoun
2020 J jnl
Towards scaling elementary flux mode computation.
Briefings Bioinform.
Ehsan Ullah, Mona Yosafshahi, Soha Hassoun
2020 J jnl
Using Graph Neural Networks for Mass Spectrometry Prediction.
CoRR
Hao Zhu, Li-Ping Liu, Soha Hassoun
2019 J jnl
Pathway Activity Analysis and Metabolite Annotation for Untargeted Metabolomics using Probabilistic Modeling.
CoRR
Ramtin Hosseini, Neda Hassanpour, Li-Ping Liu, Soha Hassoun
2019 — conf
Workshop on Microbiomics, Metagenomics, and Metabolomics.
BCB
Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen
2017 — conf
A Tool for Predicting the Dark Side of Enzymes.
BCB
Linfeng Liu, Soha Hassoun
2017 — conf
A Workshop on Microbiomics, Metagenomics, and Metabolomics.
BCB
Soha Hassoun, Curtis Huttenhower
2017 — conf
An Advanced Workflow for Metabolite Annotation.
BCB
Neda Hassanpour, Nicholas Alden, Kyongbum Lee, Soha Hassoun
2017 — conf
Pathway Enrichment Analysis for Untargeted Metabolomics.
BCB
Vladimir Porokhin, Xinmeng Li, Soha Hassoun
2017 — conf
ProSol DB: A Protein Solubility Database.
BCB
Sara A. Amin, Venkatesh Endalur Gopinarayanan, Nikhil U. Nair, Soha Hassoun
2017 — conf
Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences.
BCB
Xinmeng Li, James Van Deventer, Soha Hassoun
2016 J jnl
Steven P. Levitan (1950-2016).
IEEE Des. Test
Mary Jane Irwin, Soha Hassoun
2016 J jnl
gEFM: An Algorithm for Computing Elementary Flux Modes Using Graph Traversal.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ehsan Ullah, Shuchin Aeron, Soha Hassoun
2015 J jnl
Discovery of substrate cycles in large scale metabolic networks using hierarchical modularity.
BMC Syst. Biol.
Gautham Vivek Sridharan, Ehsan Ullah, Soha Hassoun, Kyongbum Lee
2015 J jnl
PROXIMAL: a method for Prediction of Xenobiotic Metabolism.
BMC Syst. Biol.
Mona Yousofshahi, Sara Manteiga, Charmian Wu, Kyongbum Lee, Soha Hassoun
2015 J jnl
PreProPath: An Uncertainty-Aware Algorithm for Identifying Predictable Profitable Pathways in Biochemical Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Ehsan Ullah, Mark Walker, Kyongbum Lee, Soha Hassoun
2015 J jnl
Simulation Methodology and Evaluation of Through Silicon Via (TSV)-FinFET Noise Coupling in 3-D Integrated Circuits.
IEEE Trans. Very Large Scale Integr. Syst.
Brad D. Gaynor, Soha Hassoun
2014 J jnl
Guest Editors' Introduction: Highlights of the 50th DAC.
IEEE Des. Test
Yervant Zorian, Soha Hassoun
2013 — conf
Abstraction of Kinetic Models For Biochemical Networks.
BCB
Calvin Hopkins, Soha Hassoun
2013 — conf
Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal.
BCB
Ehsan Ullah, Calvin Hopkins, Shuchin Aeron, Soha Hassoun
2013 — book
Designing TSVs for 3D Integrated Circuits
Nauman H. Khan, Soha Hassoun
2013 A* conf
Gene modification identification under flux capacity uncertainty.
DAC
Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun
2013 J jnl
MC
BMC Syst. Biol.
Mona Yousofshahi, Ehsan Ullah, Russell Stern, Soha Hassoun
2013 Misc conf
New topic session 2B: Why (Re-)Designing Biology is ∗Slightly∗ more challenging than designing electronics.
VTS
Bozena Kaminska, Bernard Courtois, Soha Hassoun
2013 J jnl
Probabilistic strain optimization under constraint uncertainty.
BMC Syst. Biol.
Mona Yousofshahi, Michael Orshansky, Kyongbum Lee, Soha Hassoun
2012 J jnl
Design Automation for Synthetic Biological Systems.
IEEE Des. Test Comput.
Douglas Densmore, Soha Hassoun
2012 A conf
Genetic/bio design automation for (re-)engineering biological systems.
DATE
Soha Hassoun
2012 J jnl
Guest Editors' Introduction: Synthetic Biology.
IEEE Des. Test Comput.
Douglas Densmore, Soha Hassoun
2012 J jnl
Metabolic Flux-Based Modularity using Shortest Retroactive distances.
BMC Syst. Biol.
Gautham Vivek Sridharan, Michael Yi, Soha Hassoun, Kyongbum Lee
2012 A* ed.
The 49th Annual Design Automation Conference 2012, DAC '12, San Francisco, CA, USA, June 3-7, 2012
DAC
Patrick Groeneveld, Donatella Sciuto, Soha Hassoun
2012 — conf
The feasibility of Carbon Nanotubes for power delivery in 3-D Integrated Circuits.
ASP-DAC
Nauman H. Khan, Soha Hassoun
2011 J jnl
Identification of Biochemical Network Modules Based on Shortest Retroactive Distances.
PLoS Comput. Biol.
Gautham Vivek Sridharan, Soha Hassoun, Kyongbum Lee
2011 — conf
Mitigating TSV-induced substrate noise in 3-D ICs using GND plugs.
ISQED
Nauman H. Khan, Syed M. Alam, Soha Hassoun
2011 J jnl
Power Delivery Design for 3-D ICs Using Different Through-Silicon Via (TSV) Technologies.
IEEE Trans. Very Large Scale Integr. Syst.
Nauman H. Khan, Syed M. Alam, Soha Hassoun
2011 A* ed.
Proceedings of the 48th Design Automation Conference, DAC 2011, San Diego, California, USA, June 5-10, 2011
DAC
Leon Stok, Nikil D. Dutt, Soha Hassoun
2010 — conf
Early estimation of TSV area for power delivery in 3-D integrated circuits.
3DIC
Nauman H. Khan, Sherief Reda, Soha Hassoun
2010 — conf
Fast, accurate a priori routing delay estimation.
SLIP
Jinhai Qiu, Sherief Reda, Soha Hassoun
2010 A* conf
Joint DAC/IWBDA special session engineering biology: fundamentals and applications.
DAC
Marc D. Riedel, Soha Hassoun, Ron Weiss, Pamela Silver, J. Christopher Anderson, Richard M. Murray
2009 A conf
An algorithm for identifying dominant-edge metabolic pathways.
ICCAD
Ehsan Ullah, Kyongbum Lee, Soha Hassoun
2009 — conf
Evolving soft robotic locomotion in PhysX.
GECCO (Companion)
John Rieffel, Frank Saunders, Shilpa Nadimpalli, Harvey Zhou, Soha Hassoun, Jason H. Rife, Barry Trimmer
2009 — conf
System-level comparison of power delivery design for 2D and 3D ICs.
3DIC
Nauman H. Khan, Syed M. Alam, Soha Hassoun
2009 — conf
Through-Silicon Via (TSV)-induced noise characterization and noise mitigation using coaxial TSVs.
3DIC
Nauman H. Khan, Syed M. Alam, Soha Hassoun
2008 J jnl
Electro-Thermal Analysis of Multi-Fin Devices.
IEEE Trans. Very Large Scale Integr. Syst.
Brian Swahn, Soha Hassoun
2006 A ed.
2006 International Conference on Computer-Aided Design, ICCAD 2006, San Jose, CA, USA, November 5-9, 2006
ICCAD
Soha Hassoun
2006 A* conf
Gate sizing: finFETs vs 32nm bulk MOSFETs.
DAC
Brian Swahn, Soha Hassoun
2006 — conf
METS: A Metric for Electro-Thermal Sensitivity, and Its Application To FinFETs.
ISQED
Brian Swahn, Soha Hassoun
2005 J jnl
A transaction-based unified architecture for simulation and emulation.
IEEE Trans. Very Large Scale Integr. Syst.
Soha Hassoun, Murali Kudlugi, Duaine Pryor, Charles Selvidge
2003 J jnl
First CADathlon Programming Contest held at 2002 ICCAD.
IEEE Des. Test Comput.
Soha Hassoun, Geert Janssen
2003 J jnl
Guest Editorial.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Soha Hassoun, Steven M. Nowick, Leon Stok
2003 J jnl
Guest Editors' Introduction: Clockless VLSI Systems.
IEEE Des. Test Comput.
Soha Hassoun, Yong-Bin Kim, Fabrizio Lombardi
2003 J jnl
Guest Editors' Introduction: On-Chip Power Distribution Networks.
IEEE Des. Test Comput.
Sani R. Nassif, Soha Hassoun
2003 A conf
Hardware Scheduling for Dynamic Adaptability using External Profiling and Hardware Threading.
ICCAD
Brian Swahn, Soha Hassoun
2003 J jnl
Optimal path routing in single- and multiple-clock domain systems.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Soha Hassoun, Charles J. Alpert
2003 — conf
Optimal use of 2-phase transparent latches in buffered maze routing.
ISCAS (4)
Soha Hassoun
2003 J jnl
Static timing analysis for level-clocked circuits in the presence of crosstalk.
IEEE Trans. Comput. Aided Des. Integr. Circuits Syst.
Soha Hassoun, Christopher Cromer, Eduardo H. Calvillo Gámez
2002 A conf
Optimal buffered routing path constructions for single and multiple clock domain systems.
ICCAD
Soha Hassoun, Charles J. Alpert, Meera Thiagarajan
2002 — conf
Robust SAT-Based Search Algorithm for Leakage Power Reduction.
PATMOS
Fadi A. Aloul, Soha Hassoun, Karem A. Sakallah, David T. Blaauw
2002 A conf
Verifying Clock Schedules in the Presence of Cross Talk.
DATE
Soha Hassoun, Eduardo H. Calvillo Gámez, Christopher Cromer
2001 A* conf
A Transaction-Based Unified Simulation/Emulation Architecture for Functional Verification.
DAC
Murali Kudlugi, Soha Hassoun, Charles Selvidge, Duaine Pryor
2001 — conf
Practices for Recruiting and Retaining Graduate Women Students in Computer Science and Engineering.
MSE
Soha Hassoun, Soheila Bana
2000 A* conf
Critical path analysis using a dynamically bounded delay model.
DAC
Soha Hassoun
1999 A conf
Regularity extraction via clan-based structural circuit decomposition.
ICCAD
Soha Hassoun, Carolyn McCreary
1998 — conf
Architecture of a Message-Driven Processor.
25 Years ISCA: Retrospectives and Reprints
William J. Dally, Linda Chao, Andrew A. Chien, Soha Hassoun, Waldemar Horwat, Jon Kaplan, Paul Song, Brian Totty, D. Scott Wills
1998 — conf
Fine Grain Incremental Rescheduling Via Architectural Retiming.
ISSS
Soha Hassoun
1998 A conf
Using precomputation in architecture and logic resynthesis.
ICCAD
Soha Hassoun, Carl Ebeling
1996 A* conf
Architectural Retiming: Pipelining Latency-Constrained Circuts.
DAC
Soha Hassoun, Carl Ebeling
1993 — conf
The chaos router chip: design and implementation of an adaptive router.
VLSI
Kevin Bolding, Sen-Ching S. Cheung, Sung-Eun Choi, Carl Ebeling, Soha Hassoun, Ton Anh Ngo, Robert Wille
1992 J jnl
A 200-MHz 64-b dual-issue CMOS microprocessor.
IEEE J. Solid State Circuits
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
1992 J jnl
A 200-MHz 64-bit Dual-Issue CMOS Microprocessor.
Digit. Tech. J.
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
1987 A* conf
Architecture of a Message-Driven Processor.
ISCA
William J. Dally, Linda Chao, Andrew A. Chien, Soha Hassoun, Waldemar Horwat, Jon Kaplan, Paul Song, Brian Totty, D. Scott Wills