Linda R. Petzold

144 papers A* 3A 1B 3Journal 110Unranked 24

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Adaptive Finite State Projection with Quantile-Based Pruning for Solving the Chemical Master Equation. CoRR Aditya Dendukuri, Linda R. Petzold
2025	J	`jnl`	Flux-Preserving Adaptive Finite State Projection for Multiscale Stochastic Reaction Networks. CoRR Aditya Dendukuri, Shivkumar Chandrasekaran, Linda R. Petzold
2025	J	`jnl`	The Vanishing Gradient Problem for Stiff Neural Differential Equations. CoRR Colby Fronk, Linda R. Petzold
2024	—	`conf`	A Survey on Detection of LLMs-Generated Content. EMNLP (Findings) Xianjun Yang, Liangming Pan, Xuandong Zhao, Haifeng Chen, Linda R. Petzold, William Yang Wang, Wei Cheng
2024	J	`jnl`	A Survey on Large Language Models for Critical Societal Domains: Finance, Healthcare, and Law. CoRR Zhiyu Zoey Chen, Jing Ma, Xinlu Zhang, Nan Hao, An Yan, Armineh Nourbakhsh, Xianjun Yang, Julian J. McAuley, Linda R. Petzold, William Yang Wang
2024	J	`jnl`	An empirical study on the robustness of the segment anything model (SAM). Pattern Recognit. Yuqing Wang, Yun Zhao, Linda R. Petzold
2024	J	`jnl`	Bayesian polynomial neural networks and polynomial neural ordinary differential equations. PLoS Comput. Biol. Colby Fronk, Jaewoong Yun, Prashant Singh, Linda R. Petzold
2024	J	`jnl`	Performance Evaluation of Single-step Explicit Exponential Integration Methods on Stiff Ordinary Differential Equations. CoRR Colby Fronk, Linda R. Petzold
2024	J	`jnl`	Quokka: An Open-source Large Language Model ChatBot for Material Science. CoRR Xianjun Yang, Stephen D. Wilson, Linda R. Petzold
2024	J	`jnl`	Training Stiff Neural Ordinary Differential Equations with Explicit Exponential Integration Methods. CoRR Colby Fronk, Linda R. Petzold
2024	J	`jnl`	Training Stiff Neural Ordinary Differential Equations with Implicit Single-Step Methods. CoRR Colby Fronk, Linda R. Petzold
2023	J	`jnl`	A Survey on Detection of LLMs-Generated Content. CoRR Xianjun Yang, Liangming Pan, Xuandong Zhao, Haifeng Chen, Linda R. Petzold, William Yang Wang, Wei Cheng
2023	J	`jnl`	An Empirical Study on the Robustness of the Segment Anything Model (SAM). CoRR Yuqing Wang, Yun Zhao, Linda R. Petzold
2023	—	`conf`	Are Large Language Models Ready for Healthcare? A Comparative Study on Clinical Language Understanding. MLHC Yuqing Wang, Yun Zhao, Linda R. Petzold
2023	J	`jnl`	Are Large Language Models Ready for Healthcare? A Comparative Study on Clinical Language Understanding. CoRR Yuqing Wang, Yun Zhao, Linda R. Petzold
2023	J	`jnl`	Bayesian polynomial neural networks and polynomial neural ordinary differential equations. CoRR Colby Fronk, Jaewoong Yun, Prashant Singh, Linda R. Petzold
2023	J	`jnl`	DNA-GPT: Divergent N-Gram Analysis for Training-Free Detection of GPT-Generated Text. CoRR Xianjun Yang, Wei Cheng, Linda R. Petzold, William Yang Wang, Haifeng Chen
2023	J	`jnl`	Dynamic Prompting: A Unified Framework for Prompt Tuning. CoRR Xianjun Yang, Wei Cheng, Xujiang Zhao, Linda R. Petzold, Haifeng Chen
2023	—	`conf`	Few-Shot Document-Level Event Argument Extraction. ACL (1) Xianjun Yang, Yujie Lu, Linda R. Petzold
2023	J	`jnl`	MatKB: Semantic Search for Polycrystalline Materials Synthesis Procedures. CoRR Xianjun Yang, Stephen D. Wilson, Linda R. Petzold
2023	—	`conf`	OASum: Large-Scale Open Domain Aspect-based Summarization. ACL (Findings) Xianjun Yang, Kaiqiang Song, Sangwoo Cho, Xiaoyang Wang, Xiaoman Pan, Linda R. Petzold, Dong Yu
2023	J	`jnl`	Shadow Alignment: The Ease of Subverting Safely-Aligned Language Models. CoRR Xianjun Yang, Xiao Wang, Qi Zhang, Linda R. Petzold, William Yang Wang, Xun Zhao, Dahua Lin
2023	J	`jnl`	Zero-Shot Detection of Machine-Generated Codes. CoRR Xianjun Yang, Kexun Zhang, Haifeng Chen, Linda R. Petzold, William Yang Wang, Wei Cheng
2022	J	`jnl`	BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022	J	`jnl`	BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr
2022	J	`jnl`	Enhancing Transformer Efficiency for Multivariate Time Series Classification. CoRR Yuqing Wang, Yun Zhao, Linda R. Petzold
2022	J	`jnl`	Few-Shot Document-Level Event Argument Extraction. CoRR Xianjun Yang, Yujie Lu, Linda R. Petzold
2022	J	`jnl`	Identification of dynamic mass-action biochemical reaction networks using sparse Bayesian methods. PLoS Comput. Biol. Richard M. Jiang, Prashant Singh, Fredrik Wrede, Andreas Hellander, Linda R. Petzold
2022	J	`jnl`	Improving Medical Predictions by Irregular Multimodal Electronic Health Records Modeling. CoRR Xinlu Zhang, Shiyang Li, Zhiyu Chen, Xifeng Yan, Linda R. Petzold
2022	J	`jnl`	Integrating Physiological Time Series and Clinical Notes with Transformer for Early Prediction of Sepsis. CoRR Yuqing Wang, Yun Zhao, Rachael Callcut, Linda R. Petzold
2022	J	`jnl`	Interpretable Polynomial Neural Ordinary Differential Equations. CoRR Colby Fronk, Linda R. Petzold
2022	J	`jnl`	OASum: Large-Scale Open Domain Aspect-based Summarization. CoRR Xianjun Yang, Kaiqiang Song, Sangwoo Cho, Xiaoyang Wang, Xiaoman Pan, Linda R. Petzold, Dong Yu
2022	—	`conf`	PcMSP: A Dataset for Scientific Action Graphs Extraction from Polycrystalline Materials Synthesis Procedure Text. EMNLP (Findings) Xianjun Yang, Ya Zhuo, Julia Zuo, Xinlu Zhang, Stephen D. Wilson, Linda R. Petzold
2022	J	`jnl`	PcMSP: A Dataset for Scientific Action Graphs Extraction from Polycrystalline Materials Synthesis Procedure Text. CoRR Xianjun Yang, Ya Zhuo, Julia Zuo, Xinlu Zhang, Stephen D. Wilson, Linda R. Petzold
2022	J	`jnl`	Predicting the Need for Blood Transfusion in Intensive Care Units with Reinforcement Learning. CoRR Yuqing Wang, Yun Zhao, Linda R. Petzold
2022	—	`conf`	Predicting the need for blood transfusion in intensive care units with reinforcement learning. BCB Yuqing Wang, Yun Zhao, Linda R. Petzold
2022	B	`conf`	Robust and integrative Bayesian neural networks for likelihood-free parameter inference. IJCNN Fredrik Wrede, Robin Eriksson, Richard M. Jiang, Linda R. Petzold, Stefan Engblom, Andreas Hellander, Prashant Singh
2022	—	`conf`	VREN: Volleyball Rally Dataset with Expression Notation Language. ICKG Haotian Xia, Rhys Tracy, Yun Zhao, Erwan Fraisse, Yuan-Fang Wang, Linda R. Petzold
2022	J	`jnl`	VREN: Volleyball Rally Dataset with Expression Notation Language. CoRR Haotian Xia, Rhys Tracy, Yun Zhao, Erwan Fraisse, Yuan-Fang Wang, Linda R. Petzold
2021	J	`jnl`	Accelerated regression-based summary statistics for discrete stochastic systems via approximate simulators. BMC Bioinform. Richard M. Jiang, Fredrik Wrede, Prashant Singh, Andreas Hellander, Linda R. Petzold
2021	—	`conf`	An Analysis of Relation Extraction within Sentences from Wet Lab Protocols. IEEE BigData Xianjun Yang, Xinlu Zhang, Julia Zuo, Stephen D. Wilson, Linda R. Petzold
2021	J	`jnl`	Associations of longitudinal D-Dimer and Factor II on early trauma survival risk. BMC Bioinform. Richard M. Jiang, Arya A. Pourzanjani, Mitchell J. Cohen, Linda R. Petzold
2021	J	`jnl`	BERTSurv: BERT-Based Survival Models for Predicting Outcomes of Trauma Patients. CoRR Yun Zhao, Qinghang Hong, Xinlu Zhang, Yu Deng, Yuqing Wang, Linda R. Petzold
2021	J	`jnl`	Coordinating cell polarization and morphogenesis through mechanical feedback. PLoS Comput. Biol. Samhita P. Banavar, Michael Trogdon, Brian Drawert, Tau-Mu Yi, Linda R. Petzold, Otger Campàs
2021	—	`conf`	Domain Adaptation for Trauma Mortality Prediction in EHRs with Feature Disparity. BIBM Xinlu Zhang, Shiyang Liy, Zhuowei Cheng, Rachael Callcut, Linda R. Petzold
2021	J	`jnl`	Empirical Analysis of Machine Learning Configurations for Prediction of Multiple Organ Failure in Trauma Patients. CoRR Yuqing Wang, Yun Zhao, Rachael Callcut, Linda R. Petzold
2021	—	`conf`	Empirical Quantitative Analysis of COVID-19 Forecasting Models. ICDM (Workshops) Yun Zhao, Yuqing Wang, Junfeng Liu, Haotian Xia, Zhenni Xu, Qinghang Hong, Zhiyang Zhou, Linda R. Petzold
2021	J	`jnl`	Empirical Quantitative Analysis of COVID-19 Forecasting Models. CoRR Yun Zhao, Yuqing Wang, Junfeng Liu, Haotian Xia, Zhenni Xu, Qinghang Hong, Zhiyang Zhou, Linda R. Petzold
2021	J	`jnl`	Epidemiological modeling in StochSS Live! Bioinform. Richard M. Jiang, Bruno Jacob, Matthew Geiger, Sean Matthew, Bryan Rumsey, Prashant Singh, Fredrik Wrede, Tau-Mu Yi, Brian Drawert, Andreas Hellander, Linda R. Petzold
2021	J	`jnl`	Multiple Organ Failure Prediction with Classifier-Guided Generative Adversarial Imputation Networks. CoRR Xinlu Zhang, Yun Zhao, Rachael Callcut, Linda R. Petzold
2021	J	`jnl`	Robust and integrative Bayesian neural networks for likelihood-free parameter inference. CoRR Fredrik Wrede, Robin Eriksson, Richard M. Jiang, Linda R. Petzold, Stefan Engblom, Andreas Hellander, Prashant Singh
2020	J	`jnl`	Advances in Deep Space Exploration via Simulators & Deep Learning. CoRR James Bird, Linda R. Petzold, Philip Lubin, Dulia Deacon
2020	—	`conf`	How Much Does It Hurt: A Deep Learning Framework for Chronic Pain Score Assessment. ICDM (Workshops) Yun Zhao, Franklin Ly, Qinghang Hong, Zhuowei Cheng, Tyler Santander, Henry T. Yang, Paul K. Hansma, Linda R. Petzold
2020	J	`jnl`	How Much Does It Hurt: A Deep Learning Framework for Chronic Pain Score Assessment. CoRR Yun Zhao, Franklin Ly, Qinghang Hong, Zhuowei Cheng, Tyler Santander, Henry T. Yang, Paul K. Hansma, Linda R. Petzold
2020	J	`jnl`	Model Optimization for Deep Space Exploration via Simulators and Deep Learning. CoRR James Bird, Kellan Colburn, Linda R. Petzold, Philip Lubin
2020	J	`jnl`	Regulation of CSF and Brain Tissue Sodium Levels by the Blood-CSF and Blood-Brain Barriers During Migraine. Frontiers Comput. Neurosci. Hamed O. Ghaffari, Samuel C. Grant, Linda R. Petzold, Michael G. Harrington
2020	J	`jnl`	Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings. CoRR Yun Zhao, Richard M. Jiang, Zhenni Xu, Elmer Guzman, Paul K. Hansma, Linda R. Petzold
2019	—	`conf`	A Deep Learning Framework for Classification of in vitro Multi-Electrode Array Recordings. ICDM (Posters) Yun Zhao, Elmer Guzman, Morgane Audouard, Zhuowei Cheng, Paul K. Hansma, Kenneth S. Kosik, Linda R. Petzold
2019	J	`jnl`	A Deep Learning Framework for Classification of in vitro Multi-Electrode Array Recordings. CoRR Yun Zhao, Elmer Guzman, Morgane Audouard, Zhuowei Cheng, Paul K. Hansma, Kenneth S. Kosik, Linda R. Petzold
2019	J	`jnl`	A Minimum Free Energy Model of Motor Learning. Neural Comput. Brian A. Mitchell, Nina Lauharatanahirun, Javier O. Garcia, Nicholas F. Wymbs, Scott T. Grafton, Jean M. Vettel, Linda R. Petzold
2019	J	`jnl`	A hybrid smoothed dissipative particle dynamics (SDPD) spatial stochastic simulation algorithm (sSSA) for advection-diffusion-reaction problems. J. Comput. Phys. Brian Drawert, Bruno Jacob, Zhen Li, Tau-Mu Yi, Linda R. Petzold
2019	J	`jnl`	Integrating machine learning and multiscale modeling - perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences. npj Digit. Medicine Mark S. Alber, Adrian Buganza Tepole, William R. Cannon, Suvranu De, Salvador Dura-Bernal, Krishna C. Garikipati, George E. Karniadakis, William W. Lytton, Paris Perdikaris, Linda R. Petzold, Ellen Kuhl
2018	J	`jnl`	Graph-based semi-supervised learning with genomic data integration using condition-responsive genes applied to phenotype classification. J. Am. Medical Informatics Assoc. Abolfazl Doostparast Torshizi, Linda R. Petzold
2018	—	`conf`	Identification of Disease States for Trauma Patients using Commonly Available Hospital Data. ICCABS Mahnaz Koupaee, Yuanyang Zhang, Tie Bo Wu, Mitchell J. Cohen, Linda R. Petzold
2018	J	`jnl`	Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis. PLoS Comput. Biol. Samhita P. Banavar, Carlos Gomez, Michael Trogdon, Linda R. Petzold, Tau-Mu Yi, Otger Campàs
2018	J	`jnl`	Sparse Pathway-Induced Dynamic Network Biomarker Discovery for Early Warning Signal Detection in Complex Diseases. IEEE ACM Trans. Comput. Biol. Bioinform. Abolfazl Doostparast Torshizi, Linda R. Petzold
2018	J	`jnl`	The effect of cell geometry on polarization in budding yeast. PLoS Comput. Biol. Michael Trogdon, Brian Drawert, Carlos Gomez, Samhita P. Banavar, Tau-Mu Yi, Otger Campàs, Linda R. Petzold
2017	J	`jnl`	Multivariate soft repulsive system identification for constructing rule-based classification systems: Application to trauma clinical data. Neurocomputing Abolfazl Doostparast Torshizi, Linda R. Petzold, Mitchell J. Cohen
2017	A*	`conf`	Survival Topic Models for Predicting Outcomes for Trauma Patients. ICDE Yuanyang Zhang, Richard M. Jiang, Linda R. Petzold
2017	—	`conf`	Understanding Coagulopathy using Multi-view Data in the Presence of Sub-Cohorts: A Hierarchical Subspace Approach. MLHC Arya A. Pourzanjani, Tie Bo Wu, Richard M. Jiang, Mitchell J. Cohen, Linda R. Petzold
2016	—	`conf`	Bitsliced High-Performance AES-ECB on GPUs. The New Codebreakers Rone Kwei Lim, Linda R. Petzold, Çetin Kaya Koç
2016	J	`jnl`	High-performance simulation of fracture in idealized 'brick and mortar' composites using adaptive Monte Carlo minimization on the GPU. Int. J. High Perform. Comput. Appl. Rone Kwei Lim, J. William Pro, Matthew R. Begley, Marcel Utz, Linda R. Petzold
2016	J	`jnl`	Identification of disease states associated with coagulopathy in trauma. BMC Medical Informatics Decis. Mak. Yuanyang Zhang, Tie Bo Wu, Bernie J. Daigle Jr., Mitchell J. Cohen, Linda R. Petzold
2016	J	`jnl`	MOLNs: A Cloud Platform for Interactive, Reproducible, and Scalable Spatial Stochastic Computational Experiments in Systems Biology Using PyURDME. SIAM J. Sci. Comput. Brian Drawert, Michael Trogdon, Salman Zubair Toor, Linda R. Petzold, Andreas Hellander
2016	J	`jnl`	Macromolecular Crowding Regulates the Gene Expression Profile by Limiting Diffusion. PLoS Comput. Biol. Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R. Petzold
2016	J	`jnl`	Multi-View Treelet Transform. CoRR Brian A. Mitchell, Linda R. Petzold
2016	J	`jnl`	Research and Education in Computational Science and Engineering. CoRR Ulrich Rüde, Karen Willcox, Lois Curfman McInnes, Hans De Sterck, George Biros, Hans-Joachim Bungartz, James Corones, Evin Cramer, James Crowley, Omar Ghattas, Max D. Gunzburger, Michael Hanke, Robert J. Harrison, Michael A. Heroux, Jan S. Hesthaven, Peter K. Jimack, Chris Johnson, Kirk E. Jordan, David E. Keyes, Rolf H. Krause, Vipin Kumar, Stefan Mayer, Juan Meza, Knut Martin Mørken, J. Tinsley Oden, Linda R. Petzold, Padma Raghavan, Suzanne M. Shontz, Anne E. Trefethen, Peter R. Turner, Vladimir V. Voevodin, Barbara I. Wohlmuth, Carol S. Woodward
2016	J	`jnl`	Stochastic Simulation Service: Bridging the Gap between the Computational Expert and the Biologist. PLoS Comput. Biol. Brian Drawert, Andreas Hellander, Benjamin B. Bales, Debjani Banerjee, Giovanni Bellesia, Bernie J. Daigle Jr., Geoffrey Douglas, Mengyuan Gu, Anand Gupta, Stefan Hellander, Christopher B. Horuk, Dibyendu Nath, Aviral Takkar, Sheng Wu, Per Lötstedt, Chandra Krintz, Linda R. Petzold
2016	—	`conf`	What Drives Consumer Choices? Mining Aspects and Opinions on Large Scale Review Data Using Distributed Representation of Words. ICDM Workshops Kasturi Bhattacharjee, Linda R. Petzold
2015	A*	`conf`	A Cure Time Model for Joint Prediction of Outcome and Time-to-Outcome. ICDM Yuanyang Zhang, Bernie J. Daigle Jr., Mitchell J. Cohen, Linda R. Petzold
2015	—	`conf`	Detecting Opinions in a Temporally Evolving Conversation on Twitter. SocInfo Kasturi Bhattacharjee, Linda R. Petzold
2015	—	`conf`	Direct higher order fuzzy rule-based classification system: Application in mortality prediction. BIBM Abolfazl Doostparast Torshizi, Linda R. Petzold, Mitchell J. Cohen
2015	J	`jnl`	Inferring single-cell gene expression mechanisms using stochastic simulation. Bioinform. Bernie J. Daigle Jr., Mohammad Soltani, Linda R. Petzold, Abhyudai Singh
2015	J	`jnl`	MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME. CoRR Brian Drawert, Michael Trogdon, Salman Zubair Toor, Linda R. Petzold, Andreas Hellander
2014	J	`jnl`	An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice. J. Comput. Phys. Andri Bezzola, Benjamin B. Bales, Richard C. Alkire, Linda R. Petzold
2014	—	`conf`	Automatic and portable cloud deployment for scientific simulations. HPCS Christopher B. Horuk, Geoffrey Douglas, Anand Gupta, Chandra Krintz, Benjamin B. Bales, Giovanni Bellesia, Brian Drawert, Rich Wolski, Linda R. Petzold, Andreas Hellander
2014	J	`jnl`	BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum. PLoS Comput. Biol. Marc Griesemer, Carissa Young, Anne S. Robinson, Linda R. Petzold
2014	J	`jnl`	Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting. J. Comput. Phys. Andreas Hellander, Michael J. Lawson, Brian Drawert, Linda R. Petzold
2014	—	`conf`	Probabilistic User-Level Opinion Detection on Online Social Networks. SocInfo Kasturi Bhattacharjee, Linda R. Petzold
2014	J	`jnl`	The time dependent propensity function for acceleration of spatial stochastic simulation of reaction-diffusion systems. J. Comput. Phys. Jin Fu, Sheng Wu, Hong Li, Linda R. Petzold
2013	J	`jnl`	Core modular blood and brain biomarkers in social defeat mouse model for post traumatic stress disorder. BMC Syst. Biol. Ruoting Yang, Bernie J. Daigle Jr., Seid Y. Muhie, Rasha Hammamieh, Marti Jett, Linda R. Petzold, Francis J. Doyle III
2013	B	`conf`	I act, therefore I judge: network sentiment dynamics based on user activity change. ASONAM Kathy Macropol, Petko Bogdanov, Ambuj K. Singh, Linda R. Petzold, Xifeng Yan
2013	J	`jnl`	Local error estimates for adaptive simulation of the Reaction-Diffusion Master Equation via operator splitting CoRR Andreas Hellander, Michael J. Lawson, Brian Drawert, Linda R. Petzold
2013	J	`jnl`	Spatial Stochastic Dynamics Enable Robust Cell Polarization. PLoS Comput. Biol. Michael J. Lawson, Brian Drawert, Mustafa Khammash, Linda R. Petzold, Tau-Mu Yi
2013	J	`jnl`	Time dependent solution for acceleration of tau-leaping. J. Comput. Phys. Jin Fu, Sheng Wu, Linda R. Petzold
2012	—	`conf`	Abstractions for Scaling eScience Applications to Distributed Computing Environments - A StratUm Integration Case Study in Molecular Systems Biology. BIOINFORMATICS Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda R. Petzold
2012	J	`jnl`	Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinform. Bernie J. Daigle Jr., Min K. Roh, Linda R. Petzold, Jarad Niemi
2012	J	`jnl`	Core module biomarker identification with network exploration for breast cancer metastasis. BMC Bioinform. Ruoting Yang, Bernie J. Daigle Jr., Linda R. Petzold, Francis J. Doyle III
2012	J	`jnl`	Language and Runtime Support for Automatic Configuration and Deployment of Scientific Computing Software over Cloud Fabrics. J. Grid Comput. Chris Bunch, Brian Drawert, Navraj Chohan, Chandra Krintz, Linda R. Petzold, Khawaja S. Shams
2012	B	`conf`	Reducing Complexity in Management of eScience Computations. CCGRID Per-Olov Östberg, Andreas Hellander, Brian Drawert, Erik Elmroth, Sverker Holmgren, Linda R. Petzold
2012	—	`conf`	Stochastic Simulation Service: Towards an Integrated Development Environment for Modeling and Simulation of Stochastic Biochemical Systems. SC Companion Linda R. Petzold, Chandra Krintz
2011	J	`jnl`	StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinform. Kevin R. Sanft, Sheng Wu, Min K. Roh, Jin Fu, Rone Kwei Lim, Linda R. Petzold
2011	J	`jnl`	Undergraduate Computational Science and Engineering Education. SIAM Rev. Peter R. Turner, Linda R. Petzold, Angela B. Shiflet, Ignatios Vakalis, Kirk E. Jordan, Samuel St. John
2010	J	`jnl`	An algorithm for simulation of electrochemical systems with surface-bulk coupling strategies. J. Comput. Phys. Matthew Buoni, Linda R. Petzold
2010	J	`jnl`	Confidence from uncertainty - A multi-target drug screening method from robust control theory. BMC Syst. Biol. Camilla Luni, Jason E. Shoemaker, Kevin R. Sanft, Linda R. Petzold, Francis J. Doyle III
2010	J	`jnl`	Efficient Parallelization of the Stochastic Simulation Algorithm for Chemically Reacting Systems On the Graphics Processing Unit. Int. J. High Perform. Comput. Appl. Hong Li, Linda R. Petzold
2009	J	`jnl`	Effect of excluded volume on 2D discrete stochastic chemical kinetics. J. Comput. Phys. Sotiria Lampoudi, Daniel T. Gillespie, Linda R. Petzold
2009	J	`jnl`	Parallel simulation for a fish schooling model on a general-purpose graphics processing unit. Concurr. Comput. Pract. Exp. Hong Li, Allison Kolpas, Linda R. Petzold, Jeff Moehlis
2008	J	`jnl`	A hybrid multiscale kinetic Monte Carlo method for simulation of copper electrodeposition. J. Comput. Phys. Zheming Zheng, Ryan M. Stephens, Richard D. Braatz, Richard C. Alkire, Linda R. Petzold
2008	J	`jnl`	A stabilized explicit Lagrange multiplier based domain decomposition method for parabolic problems. J. Comput. Phys. Zheming Zheng, Bernd Simeon, Linda R. Petzold
2008	J	`jnl`	Differential-algebraic equations. Scholarpedia Stephen L. Campbell, Vu Hoang Linh, Linda R. Petzold
2008	J	`jnl`	Sensitivity Measures for Oscillating Systems: Application to Mammalian Circadian Gene Network. IEEE Trans. Autom. Control. Stephanie R. Taylor, Rudiyanto Gunawan, Linda R. Petzold, Francis J. Doyle III
2007	J	`jnl`	An efficient, scalable numerical algorithm for the simulation of electrochemical systems on irregular domains. J. Comput. Phys. Matthew Buoni, Linda R. Petzold
2007	J	`jnl`	Error Estimation for Reduced-Order Models of Dynamical Systems. SIAM Rev. Chris Homescu, Linda R. Petzold, Radu Serban
2007	J	`jnl`	The Effect of Problem Perturbations on Nonlinear Dynamical Systems and their Reduced-Order Models. SIAM J. Sci. Comput. Radu Serban, Chris Homescu, Linda R. Petzold
2006	J	`jnl`	Accuracy limitations and the measurement of errors in the stochastic simulation of chemically reacting systems. J. Comput. Phys. Yang Cao, Linda R. Petzold
2006	J	`jnl`	Runge-Kutta-Chebyshev projection method. J. Comput. Phys. Zheming Zheng, Linda R. Petzold
2006	J	`jnl`	Sensitivity analysis of differential-algebraic equations and partial differential equations. Comput. Chem. Eng. Linda R. Petzold, Shengtai Li, Yang Cao, Radu Serban
2005	J	`jnl`	Consistency and Stability of Tau-Leaping Schemes for Chemical Reaction Systems. Multiscale Model. Simul. Muruhan Rathinam, Linda R. Petzold, Yang Cao, Daniel T. Gillespie
2005	J	`jnl`	Error Estimation for Reduced-Order Models of Dynamical Systems. SIAM J. Numer. Anal. Chris Homescu, Linda R. Petzold, Radu Serban
2004	J	`jnl`	A Posteriori Error Estimation and Global Error Control for Ordinary Differential Equations by the Adjoint Method. SIAM J. Sci. Comput. Yang Cao, Linda R. Petzold
2004	A	`conf`	Parallel Simulation of Fluid Slip in a Microchannel. IPDPS Jingyu Zhou, Luoding Zhu, Linda R. Petzold, Tao Yang
2003	J	`jnl`	A New Look at Proper Orthogonal Decomposition. SIAM J. Numer. Anal. Muruhan Rathinam, Linda R. Petzold
2003	J	`jnl`	A Subspace Error Estimate for Linear Systems. SIAM J. Matrix Anal. Appl. Yang Cao, Linda R. Petzold
2003	—	`conf`	A multiscale measure for mixing and its applications. CDC George Mathew, Igor Mezic, Linda R. Petzold
2003	J	`jnl`	Adjoint Sensitivity Analysis for Differential-Algebraic Equations: The Adjoint DAE System and Its Numerical Solution. SIAM J. Sci. Comput. Yang Cao, Shengtai Li, Linda R. Petzold, Radu Serban
2003	A*	`conf`	Deriving User Interface Requirements from Densely Interleaved Scientific Computing Applications. ASE Andrew Strelzoff, Linda R. Petzold
2002	J	`jnl`	Dynamic Iteration Using Reduced Order Models: A Method for Simulation of Large Scale Modular Systems. SIAM J. Numer. Anal. Muruhan Rathinam, Linda R. Petzold
2002	J	`jnl`	Efficient Computation of Sensitivities for Ordinary Differential Equation Boundary Value Problems. SIAM J. Numer. Anal. Radu Serban, Linda R. Petzold
2002	J	`jnl`	Halo orbit mission correction maneuvers using optimal control. Autom. Radu Serban, Wang Sang Koon, Martin W. Lo, Jerrold E. Marsden, Linda R. Petzold, Shane D. Ross, Roby S. Wilson
2001	J	`jnl`	Constraint Partitioning for Stability in Path-Constrained Dynamic Optimization Problems. SIAM J. Sci. Comput. Soumyendu Raha, Linda R. Petzold
2000	—	`conf`	An iterative method for simulation of large scale modular systems using reduced order models. CDC Muruhan Rathinam, Linda R. Petzold
1999	J	`jnl`	Parallel sensitivity analysis for DAEs with many parameters. Concurr. Pract. Exp. Wenjie Zhu, Linda R. Petzold
1998	J	`jnl`	An Efficient Newton-Type Iteration for the Numerical Solution of Highly Oscillatory Constrained Multibody Dynamic Systems. SIAM J. Sci. Comput. Jeng Yen, Linda R. Petzold
1998	—	`book`	Computer methods for ordinary differential equations and differential-algebraic equations. Uri M. Ascher, Linda R. Petzold
1998	J	`jnl`	Consistent Initial Condition Calculation for Differential-Algebraic Systems. SIAM J. Sci. Comput. Peter N. Brown, Alan C. Hindmarsh, Linda R. Petzold
1998	J	`jnl`	Stability of Moving Mesh Systems of Partial Differential Equations. SIAM J. Sci. Comput. Shengtai Li, Linda R. Petzold, Yuhe Ren
1997	J	`jnl`	Regularization of Higher-Index Differential-Algebraic Equations with Rank-Deficient Constraints. SIAM J. Sci. Comput. Linda R. Petzold, Yuhe Ren, Timothy Maly
1996	—	`book`	Numerical solution of initial-value problems in differential-algebraic equations. Kathryn E. Brenan, Stephen L. Campbell, Linda R. Petzold
1995	J	`jnl`	Parallel solution of large-scale differential-algebraic systems. Concurr. Pract. Exp. Robert S. Maier, W. Rath, Linda R. Petzold
1994	J	`jnl`	Using Krylov Methods in the Solution of Large-Scale Differential-Algebraic Systems. SIAM J. Sci. Comput. Peter N. Brown, Alan C. Hindmarsh, Linda R. Petzold
1993	—	`ed.`	Proceedings of the Sixth SIAM Conference on Parallel Processing for Scientific Computing, PP 1993, Norfolk, Virginia, USA, March 22-24, 1993 PP Richard F. Sincovec, David E. Keyes, Michael R. Leuze, Linda R. Petzold, Daniel A. Reed
1993	J	`jnl`	Stability of Computational Methods for Constrained Dynamics Systems. SIAM J. Sci. Comput. Uri M. Ascher, Linda R. Petzold
1992	J	`jnl`	Special Issue on Iterative Methods in Numerical Linear Algebra. SIAM J. Sci. Comput. Thomas A. Manteuffel, Linda R. Petzold