ANL2022

Contact

E-mail:
Email
Phone:
+1.630.252.3910 (Office)
Mailing Address:
9700 S. Cass Ave.
Bldg. 240, Rm: 5143
Lemont, IL 60439, US

I'm a computer scientist at Data Science and Learning (DSL) division at Argonne National Laboratory. I also hold joint appointments in X-ray Science division (XSD) at Advanced Photon Source (APS) and Consortium for Advanced Science and Engineering (CASE) at the University of Chicago.
Currently, I'm working on large-scale high-performance systems that deal with compute- and data-intensive synchrotron radiation imaging problems.

Research Interests

  • Large-Scale Parallel and Distributed Systems
  • High-End Computing Systems
  • High-Performance Computing
  • Software System Architectures

Education

  • PhD., Computer Science & Engineering, Ohio State University, 2010-2014
  • MSc., Computer Science & Engineering, Ohio State University, 2008-2010
  • BEng., Computer Engineering, Izmir Institute of Technology, 2001-2006

Throughout my career, I have been fortunate to hold the following positions:

  • Argonne National Laboratory (ANL), Computer Scientist at Data Science and Learning Division, Lemont, IL, USA (2018-Present)
  • Argonne National Laboratory (ANL), Computer Scientist at X-ray Science Division, Lemont, IL, USA (2018-Present)
  • University of Chicago (UChicago), Senior Scientist at Consortium for Advanced Science and Engineering, Chicago, IL, USA (Aug. 2020-Present)
  • Argonne National Laboratory (ANL), Assistant Computer Scientist at Mathematics and Computer Science Division, Lemont, IL, USA (Sept. 2016-2018)
  • Argonne National Laboratory (ANL), Postdoctoral Researcher at Mathematics and Computer Science Division, Lemont, IL, USA (June 2014-Sept. 2016)
  • Pacific Northwest National Laboratory (PNNL), PhD Intern in Data Intensive Scientific Computing Group, Richland, WA, USA (Fall 2012)
  • IBM T.J. Watson Research Center (IBM), Research Intern in Distributed Streaming Systems Group, Yorktown Heights, NY, USA (Summer 2012)
  • Pacific Northwest National Laboratory (PNNL), PhD Intern in Data Intensive Scientific Computing Group, Richland, WA, USA (Summer 2011)
  • Ohio State University (OSU), Graduate Research or Teaching Associate in CSE Department, Columbus, OH, USA (2010-2014)

Some of the awards, honors, and recognitions that I have received over the years include the following:

  • Best Paper Runner-Up at High Performance Computing for Imaging (HPCI), Electronic Imaging Symposium (Jan. 2023)
  • Best Paper Award at Supercomputing, 2020 (out of 378 submisions)
  • (Two times) Impact Argonne Award for notable achievement in Innovation, DSL/ANL (June 2022, May 2020)
  • SIGHPC Certificate of Appreciation, ACM Student Cluster Competition at Supercomputing, 2020
  • Top Recognition for an Exemplary blend of Network, Computing, and Storage, SCinet Technology Challenge at Supercomputing, 2019
  • Pacesetter Award for excellence in achievement and performance, DSL/ANL (Jan. 2019)
  • Best Paper Nomination at CCGrid, 2014 (283 submitted, 3 selected)
  • Travel Grants: CCGrid'14, IPDPS'13, IPDPS'10
  • Senior Member of IEEE and ACM

I try to serve in committees and give back to our community as much as possible. The following are some of the venues I have served:

Track Chair

  • Algorithms for Data Science, IEEE International Parallel and Distributed Processing Symposium (IPDPS 2023)

Associate Editor

  • Frontiers in High Performance Big Data Systems (2023 Aug. - Present, Chief Editor: Geoffrey Fox)

Program Committee Member

  • High Performance Computing for Imaging, Electronic Imaging, Society for Imaging Science and Technology (HPCI 2024, 2023)
  • IEEE/ACM International Conference for High Performance Computing, Networking, Storage and Analysis (SC 2022)
  • IEEE International Parallel and Distributed Processing symposium (IPDPS 2021, 2018)
  • IEEE International Conference on Distributed Computing Systems (ICDCS 2021)
  • IEEE Annual Workshop on Extreme-scale Experiment-in-the-Loop Computing in conjuction with IEEE/ACM SC (XLOOP 2023, 2022, 2021, 2020)
  • IEEE International Conference on High Performance Computing (HiPC 2019, 2018, 2017, 2015)
  • Workshop on Autonomous Infrastructure for Science in conjuction with ACM HPDC (AI-Science 2019, 2018)
  • IEEE International Conference on Future Internet of Things and Cloud (FiCloud 2018, 2017)
  • IEEE International Conference on Green and Human Information Technology (ICGHIT 2018)
  • IEEE International Conference on Advances in Computing, Communications and Informatics (ICACCI 2018, 2017)
  • International Symposium on Cloud Computing and Services for High Performance Computing Systems (InterCloud-HPC 2018, 2017, 2016, 2015)
  • The International Conference on Advanced Communications and Computation (INFOCOMP 2022, 2019, 2018)
  • International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2015)

Referee for Journals

  • Future Generation Computer Sytstems (2023, 2020, 2016, 2015)
  • Neural Computing and Applications, Springer (2023, 2021-2019)
  • Computers in Biology and Medicine (2023)
  • Tomography of Materials and Structures (2023)
  • Computer Physics Communications, Elsevier (2023, 2022)
  • Transactions on Architecture and Code Optimization (2022)
  • Software: Practive and Experience, Wiley (2022)
  • Scientific Reports, Nature (2019)
  • Journal of Parallel and Distributed Computing (2019, 2018, 2017, 2016)
  • Transactions on Services Computing (2019, 2018, 2017, 2015, 2014)
  • The Computer Journal (2022-2014)
  • Transactions on Cloud Computing (2022, 2021, 2019, 2016, 2015, 2014)
  • IEEE Access (2017)
  • Big Data Research (2017)
  • Transactions on Parallel and Distributed Systems (2016, 2015)
  • Journal of Systems and Software (2013)

Referee for Conferences

  • International Conference on High Performance Computing and Communications (HPCC 2016)
  • International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2013, 2012)
  • Big Data Conference (2014)

The following list might not be up-to-date. If you are interested in learning more about my relatively recent works, you can check my google scholar page.

Journals

  • A. V Babu, T. Zhou, S. Kandel, T. Bicer, Z. Liu , W. Judge, D. Ching, Y. Jiang, S. Veseli, S. Henke, R. Chard, Y. Yao, E. Sirazitdinova, G. Gupta, M. Holt, I. Foster, A. Miceli, M. J. Cherukara, "Deep learning at the edge enables real-time streaming ptychographic imaging", Nature Communications, 2023
  • R. Vescovi, R. Chard, N. D. Saint, B. Blaiszik, J. Pruyne, T. Bicer, A. Lavens, Z. Liu, M. E. Papka, S. Narayanan, N. Schwarz, K. Chard and I. T. Foster, "Linking scientific instruments and computation: Patterns, technologies, and experiences", Patterns, Cell Press, 2022
  • C. Benmore, T. Bicer, M. Chan, Z. Di, D. Gürsoy, I. Hwang, N. Kuklev, D. Lin, Z. Liu, I. Lobach, Z. Qiao, L. Rebuffi, H. Sharma, X. Shi, C. Sun, Y. Yao, T. Zhou, A. Sandy, A. Miceli, Y. Sun, N. Schwarz and M. J Cherukara, "Advancing AI/ML at the Advanced Photon Source", Synchrotron Radiation News, 2022
  • *X. Yu, V. Nikitin, D. Ching, S. Aslan, D. Gursoy and T. Bicer, "Scalable and accurate multi-GPU-based image reconstruction of large-scale ptychography data", Scientific Reports, 2022
  • *M. Hidayetoglu, T. Bicer, S. G. de Gonzalo, B. Ren, D. Gursoy, R. Kettimuthu, I. T. Foster and W. W. Hwu, "MemXCT: Design, Optimization, Scaling, and Reproducibility", IEEE Transactions on Parallel and Distributed Systems, 2021
  • S. Aslan, Z. Liu, V. Nikitin, T. Bicer, S. Leyffer and D. Gursoy, "Joint Ptycho-Tomography with Deep Generative Priors", Machine Learning: Science and Technology, IOPScience, 2021
  • Z. Liu, T. Bicer, R. Kettimuthu, D. Gursoy, F. De Carlo, I. T. Foster, "TomoGAN: Low-Dose Synchrotron X-Ray Tomography with Generative Adversarial Networks", Journal of the Optical Society of America A, 2020
  • V. Nikitin, S. Aslan, Y. Yao, T. Bicer, S. Leyffer, R. Mokso and D. Gursoy, "Photon-limited ptychography of 3D objects via Bayesian reconstruction", OSA Continuum 2(10), 2019
  • S. Aslan, V. Nikitin, D. J. Ching, T. Bicer, S. Leyffer and D. Gursoy, "Joint ptycho-tomography reconstruction through alternating direction method of multipliers", Optics Express, 2019
  • D. J. Ching, M. Hidayetoglu, T. Bicer and D. Gursoy, "Rotation-as-fast-axis scanning-probe x-ray tomography: the importance of angular diversity for fly-scan modes", Applied Optics, 2018
  • T. Bicer, D. Gursoy , V. De Andrade, R. Kettimuthu, W. Scullin, F. De Carlo, I. T. Foster, "Trace: A High-Throughput Tomographic Reconstruction Engine for Large-Scale Datasets", Special Issue on High-Throughput X-Ray Imaging and Algorithms, Advanced Structural and Chemical Imaging, 2017 [News] Advanced Structural and Chemical Imaging
  • T. Bicer, D. Gursoy , R. Kettimuthu, F. De Carlo, I. T. Foster, "Optimization of tomographic reconstruction workflows on geographically distributed resources", Journal of Synchrotron Radiation, 2016 Journal of Synchrotron Radiation
  • D. Gursoy, T. Bicer, A. Lanzirotti, M.G. Newville, F. De Carlo, "Hyperspectral Image Reconstruction for X-ray Fluorescence Tomography", Optics Express, 2015 [News] Optics Express
  • D. Gursoy, T. Bicer, J.D. Almer, R. Kettimuthu, S. R. Stock, F. De Carlo, "Maximum a Posteriori Estimation of Crystallographic Phases in X-ray Diffraction Tomography", Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 2015 Philosophical Transactions A
  • D. J. Duke, N. Sovis, A. B. Swantek, F. Z. Tilocco, A. L. Kastengren, D. Gursoy and T. Bicer, "Time-Resolved X-ray Tomography of Gasoline Direct Injection Sprays," SAE Paper No. 2015-01-1873, JSAE International Journal of Automotive Engineering, 2015 JSAE/SAE JSAE/SAE

Conferences

  • J. Chung, A. Wisniewski, W. Zacherek, Z. Liu, T. Bicer, R. Kettimuthu and I. T. Foster, "SciStream: Architecture and Toolkit for Data Streaming between Federated Science Instruments", in Proceedings of the 31st International ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC'22), June 2022.
  • T. Bicer, *X. Yu, D. Ching, R. Chard, M. Cherukara, B. Nicolae, R. Kettimuthu and I. T. Foster, "High-Performance Ptychographic Reconstruction with Federated Facilities", in Proceedings of the Smoky Mountains Computational Sciences and Engineering Conference (SMC'21), Oct. 2021.
  • *X. Yu, T. Bicer, R. Kettimuthu and I. T. Foster, "Topology-aware Optimizations for Multi-GPU Ptychographic Image Reconstruction", in Proceedings of the International Conference on Supercomputing (ICS'21), June 2021.
  • A. Tekawade, Z. Liu, P. Kenesei, T. Bicer, F. De Carlo, R. Kettimuthu and I. T. Foster, "Autoencoders for Feature Extraction in X-ray Tomography", in Proceedings of the IEEE International Conference on Image Processing (ICIP'21), Sept. 2021.
  • *M. Hidayetoglu, T. Bicer, S. G. de Gonzalo, B. Ren, Vincent De Andrade, D. Gursoy, R. Kettimuthu, I. T. Foster and W. W. Hwu, "Petascale XCT: 3D Image Reconstruction with Hierarchical Communications on Multi-GPU Nodes", in Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'20), Nov. 2020 [Best Paper Award] sc20
  • *X. Yu, F. Wei, X. Ou, M. Becchi, T. Bicer, D. Yao, "GPU-Based Static Data-Flow Analysis for Fast and Scalable Android App Vetting", in Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS'20), New Orleans, LA, May 2020
  • *M. Hidayetoglu, T. Bicer, S. G. de Gonzalo, B. Ren, D. Gursoy, R. Kettimuthu, I. T. Foster and W. W. Hwu, "MemXCT: Memory-Centric X-ray CT Reconstruction with Massive Parallelization", in Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'19), Denver, Colorado, Nov. 2019 [ACM SIGHPC Certificate of Appreciation, Student Cluster Reproducibility Challenge 2020] [News] sc19
  • Z. Peng, A. Powell, B. Wu, T. Bicer and B. Ren, "GraphPhi: efficient parallel graph processing on emerging throughput-oriented architectures", in Proceedings of the 27th International Conference on Parallel Architectures and Compilation Techniques (PACT'18), Limassol, Cyprus, Nov. 2018
  • T. Bicer, D. Gursoy, R. Kettimuthu, I. T. Foster, B. Ren, V. De Andrede and F. De Carlo, "Real-Time Data Analysis and Autonomous Steering of Synchrotron Light Source Experiments", in Proceedings of the International eScience Conference (eScience'17), Auckland, New Zealand, Oct. 2017 [News] escience17
  • Y. Wang, G. Agrawal, T. Bicer and W. Jiang "Smart: A MapReduce-Like Framework for In-Situ Scientific Analytics", in Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC'15), Austin, Texas, Nov. 2015 sc15
  • T. Bicer, D. Gursoy, R. Kettimuthu, F. De Carlo, G. Agrawal and I. Foster "Rapid Tomographic Image Reconstruction via Large-Scale Parallelization", in Proceedings of the International European Conference on Parallel and Distributed Computing (EuroPar'15), Vienna, Austria, Aug. 2015 [News] europar2015 europar2015
  • D. J. Duke, N. Sovis, A. B. Swantek, F. Z. Tilocco, A. L. Kastengren, D. Gursoy and T. Bicer, "Time-resolved X-ray Tomography of Gasoline Direct Injection Sprays", in JSAE/SAE International Powertrains, Fuels and Lubricants Meeting, Kyoto Japan, Sept. 2015
  • T. Bicer, J. Yin and G. Agrawal, "Improving I/O Throughput of Scientific Applications using Transparent Parallel Compression", in Proceedings of the International Symposium on Cluster, Cloud and Grid Computing (CCGrid'14), Chicago IL, May 2014 (283 submitted, 54 accepted, 19.1% acceptance rate) [Best Paper Nomination] ccgrid2014 ccgrid2014
  • T. Bicer, J. Yin, D. Chiu, G. Agrawal and K. Schuchardt, "Integrating Online Compression to Accelerate Large-Scale Data Analytics Applications", in Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS'13), Boston MA, May 2013 (494 submitted, 106 accepted, 21.5% acceptance rate) ipdps2013 ipdps2013
  • T. Bicer, D. Chiu, and G. Agrawal, "Time and Cost Sensitive Data-Intensive Computing on Hybrid Clouds", in Proceedings of the International Symposium on Cluster, Cloud and Grid Computing (CCGrid'12), Ottowa Canada, May 2012 (302 submitted, 83 accepted, 27.5% acceptance rate) ccgrid2012 ccgrid2012
  • T. Bicer, D. Chiu, and G. Agrawal, "A Framework for Data-Intensive Computing with Cloud Bursting", in Proceedings of the International Conference on Cluster Computing (Cluster'11), Austin TX, Sept. 2011 (140 submitted, 39 accepted, 27.8% acceptance rate) cluster2011 cluster2011
  • T. Bicer, W. Jiang, and G. Agrawal, "Supporting Fault Tolerance in a Data-Intensive Computing Middleware", in Proceedings of the International Parallel and Distributed Processing Symposium (IPDPS'10), Atlanta GA, Apr. 2010. (527 submitted, 127 accepted, 24.1% acceptance rate) ipdps2010 ipdps2010

Refereed Workshops

  • A. V. Babu, T. Bicer, S. Kandel, T. Zhou, D. J. Ching, S. Henke, S. Veseli, R. Chard, A. Miceli, and M. Cherukara, "AI-assisted Automated Workflow for Real-time X-ray Ptychography Data Analysis via Federated Resources", in High Performance Computing for Imaging, Electronic Imaging Symposium, IS&T, Jan. 2023. [Best Paper Runner-Up]
  • H. Jamil, J. Chung, T. Bicer, T. Kosar, and R. Kettimuthu, "Throughput Optimization with a NUMA-Aware Runtime System for Efficient Scientific Data Streaming", in 10th Annual International Workshop on Innovating the Network for Data-Intensive Science, Nov. 2023.
  • J. Liu, B. Nicolae, D. Li, J. M. Wozniak, T. Bicer, Z. Liu and I. Foster, "Large Scale Caching and Streaming of Training Data for Online Deep Learning" in Proceedings of the 12th Workshop on AI and Scientific Computing at Scale using Flexible Computing Infrastructures (Flex'22), July 2022.
  • T. Bicer, Viktor Nikitin, Selin Aslan, Doga Gursoy, Rajkumar Kettimuthu and Ian T. Foster, "Tomographic Reconstruction of Dynamic Features with Streaming Sliding Subsets", in Extreme-Scale Experiment-in-the-Loop-Computing Workshop, in conjunction with The International Conference for High Performance Computing, Networking, Storage and Analysis (SC'20), Nov. 2020 [Accepted] xloop20
  • *Ziling Wu, T. Bicer, Zhengchun Liu, Vincent De Andrade, Yunhui Zhu and I. T. Foster, "Deep Learning-based Low-dose Tomography Reconstruction with Hybrid-dose Measurements", in Artificial Intelligence and Machine Learning for Scientific Applications Workshop, in conjunction with The International Conference for High Performance Computing, Networking, Storage and Analysis (SC'20), Nov. 2020 [Accepted] ai4s20
  • Z. Liu, **T. Bicer, R. Kettimuthu, I. T. Foster, "Deep Learning Accelerated Light Source Experiments", in Deep Learning on Supercomputers Workshop, in conjunction with The International Conference for High Performance Computing, Networking, Storage and Analysis (SC'19), Denver, Colorado, Nov. 2019 [Accepted]
  • T. Bicer, D. Chiu, and G. Agrawal, "MATE-EC2: A Middleware for Processing Data with AWS", in Proceedings of the 4th Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS'11), in conjunction with Supercomputing (SC), Seattle WA, Nov. 2011 [Invited Paper] mtags2011
  • A. Raveendran, T. Bicer, and G. Agrawal, "A Framework for Elastic Execution of Existing MPI Programs", in Proceedings of the High-Performance Grid and Cloud Computing (HPGC'11), in conjunction with the International Parallel and Distributed Processing Symposium (IPDPS), Anchorage AK, May. 2011 ipdps2011
  • T. Bicer, and G. Agrawal, "Supporting Dynamic Load Balancing in a Parallel Data Mining Middleware", in Proceedings of the Parallel Data-Mining Workshop (PDM'11), in conjunction with the Society of Industrial and Applied Mathematics (SIAM) International Conference on Data Mining, Mesa AZ, Apr. 2011 pdf2011

Refereed Short Papers/Abstracts/Posters

  • T. Bicer, and G. Agrawal, "A Compression Framework for Multidimensional Scientific Datasets", in Proceedings of the TCPP PhD Forum 2013, in conjunction with International Parallel and Distributed Processing Symposium (IPDPS'13), Boston MA, May 2013 (Short Paper) phdforum2013 phdforum2013
  • T. Bicer, D. Chiu, and G. Agrawal, "A Framework for Data-Intensive Computing with Cloud Bursting", 24th International Conference for Supercomputing (SC'11), Seattle WA, Nov. 2011 gri2011 gri2011
  • A. Raveendran, T. Bicer, and G. Agrawal, "An Autonomic Framework for Time and Cost Driven Execution of MPI Programs on Cloud Environments", 12th IEEE/ACM International Conference on Grid Computing (Grid'11), Lyon, France, Sep. 2011 gri2011

* Supervised postdoc/interns
** Equal contribution with the first author