NSF CAREER: High Performance Spatial Queries and Analytics for Spatial Big Data

Last updated: December 31, 2021

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Project Title: High Performance Spatial Queries and Analytics for Spatial Big Data

NSF IIS #1350885

The goal of this CAREER project is to address the research challenges for delivering a high performance software system for spatial queries and analytics of spatial big data on MapReduce and CPU-GPU hybrid platforms, promote the use of the created open source software to support problem solving in multiple disciplines, and educate the next generation workforce in big data.

People

Principle Investigator: Fusheng Wang

Students:

Kayley Abell-Hart, Ph.D.student, Stony Brook University
Hongyi Duanmu, Ph.D. student, Stony Brook University
Mousumi Roy, Ph.D. student, Stony Brook University
Lu Chen, Ph.D. student, Stony Brook University

Past members:

Dejun Teng, Ph.D., Stony Brook University. First employement: Alibaba
Furqan Baig, Ph.D., Stony Brook University. First employement: PostDoc at UIUC
Hoang Vo, Ph.D., Stony Brook University. First employement: Pitney Bowes.
Xin Chen, Ph.D., Stony Brook University. First employement: Cambia Health Solutions
Yanhui Liang, Ph.D., Stony Brook University. First employment: Google Research
Ablimit Aji, Stony Brook University. First employment: HP Labs

Publications

Fiona Murphy, Kayley Abell-Hart and Fusheng Wang: A Fine-grain Geospatial and Demographic Analysis of Breast Cancer Patterns in New York State. IEEE BigData 2021 REU Symposium. December 15, 2021.
Dejun, Yanhui Liang, Hoang Vo, Jun Kong and Fusheng Wang: Efficient 3D Spatial Queries for Complex Objects. In Press. ACM Transactions on Spatial Algorithms and Systems (TSAS).
Dejun Teng, Akshay Nehe, Prajeeth Emanuel, Furqan Baig, Jun Kong and Fusheng Wang: GPU-based Real-time Contact Tracing at Scale. In Proceedings of the 29th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM SIGSPATIAL 2021), November 2-5, 2021, Beijing, China.
Hongyi Duanmu, Shristi Bhattarai, Hongxiao Li, Chia Cheng Cheng, Fusheng Wang, George Teodoro, Emiel A.M. Janssen, Keerthi Gogineni, Preeti Subhedar, Ritu Aneja, Jun Kong: Spatial Attention-based Deep Learning System for Breast Cancer Pathological Complete Response Prediction with Serial Histopathology Images in Multiple Stains. The 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). September 27, November 1, 2021. Strasbourg, France.
Hongyi Duanmu, Fusheng Wang, George Teodoro and Jun Kong: Foveal Blur-Boosted Segmentation of Nuclei in Histopathology Images with Shape Prior Knowledge and Probability Map Constraints. Bioinformatics. Volume 37, Issue 21, 1 November 2021.
Anthony Xiang, Wei Hou, Sina Rashidian, Richard N Rosenthal, Kayley Abell-Hart, Xia Zhao and Fusheng Wang: Association of Opioid Use Disorder With 2016 Presidential Voting Patterns: A Cross-Sectional Study in New York State at Census Tract Level. JMIR Public Health Surveill 2021;7(4):e23426
Xin Chen, Wei Hou, Sina Rashidian, Yu Wang, Xia Zhao, George Stuart Leibowitz, Richard N Rosenthal, Mary Saltz, Joel H Saltz, Elinor Randi Schoenfeld and Fusheng Wang: A Large-Scale Retrospective Study of Opioid Poisoning in New York State with Implications for Targeted Interventions. Scientific Reports 11, 5152 (2021).
Furqan Baig, Dejun Teng, Jun Kong and Fusheng Wang: SPEAR: Dynamic Spatio-Temporal Query Processing over High Velocity Data Streams. In Proceedings of the 37th IEEE International Conference on Data Engineering, Apr 19-22, 2021, Chania, Greece.
Mousumi Roy, Jun Kong, Satyananda Kashyap, Vito Paolo Pastore, Fusheng Wang, Ken C. L. Wong and Vandana Mukherjee:Convolutional Autoencoder Based Model HistoCAE for Segmentation of Viable Tumor Regions in Liver Whole-Slide Images. Scientific Reports. Sci Rep 11, 139 (2021).
Mousumi Roy, Fusheng Wang*, Hoang Vo, Dejun Teng, George Teodoro, Alton Farris III, Eduardo Castillo-Leon, Miriam Vos and Jun Kong*: Deep Learning Based Accurate Hepatic Steatosis Quantification for Histological Assessment of Liver Biopsies. Laboratory Investigation. 100, 1367–1383 (2020). (*: Corresponding authors.)
Hongyi Duanmu, Pauline Boning Huang, Srinidhi Brahmavar, Stephanie Lin, Thomas Ren, Jun Kong, Fusheng Wang* and Tim Duong*: Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy Using Deep Learning with Integrative Imaging, Molecular and Demographic Data. To Appear in Proceedings of Medical Image Computing and Computer Assisted Interventions 2020 (MICCAI 2020), October 4 - 8, 2020, Lima, Peru. (*: Corresponding authors.)
Furqan Baig, Chao Gao, Dejun Teng, Jun Kong and Fusheng Wang: Accelerating Spatial Cross-Matching on CPU-GPU Hybrid Platform with CUDA and OpenACC. Frontiers in Big Data. May 8, 2020.
Hongyi Duanmu, Jinkoo Kim, Praitayini Kanakaraj, Andrew Wang, John Joshua, Jun Kong and Fusheng Wang: Automatic Brain Organ Segmentation with 3D Fully Convolutional Neural Network for Radiation Therapy Treatment Planning. In Proceedings of 2020 IEEE 17th International Symposium on Biomedical Imaging (ISBI). Apr 2-7, 2020, Iowa City, Iowa, USA.
Elinor Schoenfeld, George Leibowitz, Yu Wang, Xin Chen, Wei Hou, Sina Rashidian, Mary M Saltz, Joel H Saltz, and Fusheng Wang: Geographic, temporal and sociodemographic differences in opioid poisoning. American Journal of Preventive Medicine. Volume 57, Issue 2, Pages 153–164. 2019.
Pengyue Zhang, Fusheng Wang, George Teodoro, Yanhui Liang, Mousumi Roy, Daniel Brat and Jun Kong: Effective nuclei segmentation with sparse shape prior and dynamic occlusion constraint for glioblastoma pathology images. Journal of Medical Imaging. 6(1), 017502 (2019).
Chao Gao, Furqan Baig, Hoang Vo, Yangyang Zhu and Fusheng Wang: Accelerating Cross-Matching Operations of Geospatial Datasets using a CPU/GPU Hybrid Platform. In Proceedings of the 3rd International Workshop on Big Spatial Data (in conjunction with IEEE Big Data 2018). December 10-13, 2018, Seattle, Washington, USA. (Best paper award.)
Daniel Kim, Fusheng Wang and Chrisa Arcan: Geographic Association Between Income Inequality and Obesity Among Adults in New York State. Preventing Chronic Disease. Vol 15:180217, 2018.
Xiaoyuan Guo, Fusheng Wang, George Teodoro, Alton Farris and Jun Kong: Liver Steatosis Segmentation with Deep Learning Methods. In Proceedings of IEEE International Symposium on Biomedical Imaging (ISBI) , pp. 24-27Venice, Italy, April 8 - 11, 2019.
Sina Rashidian, Xinyu Dong, Shubham Kumar Jain and Fusheng Wang: EaserGeocoder: Integrative Geocoding with Machine Learning. Demo Paper. In Proceedings of ACM SIGSPATIAL 2018, November 6 - 9, 2018. Seattle, Washington, USA.
Hoang Vo, Jun Kong, Dejun Teng, Yanhui Liang, Ablimit Aji, George Teodoro and Fusheng Wang: MaReIA: A Cloud MapReduce Based High Performance Whole Slide Image Analysis Framework. Distributed and Parallel Databases. Special Issue on Data Management and Analytics for Healthcare. 37 (2), 2019.
Dejun Teng, Jun Kong and Fusheng Wang: Scalable and Flexible Management of Medical Image Big Data. Distributed and Parallel Databases. 37 (2), 2019.
Xin Chen, Hoang Vo, Yu Wang and Fusheng Wang: A Framework for Annotating OpenStreetMap Objects Using Geo-tagged Tweets. Geoinformatica. Volume 22, Issue 3, pp 589–613, 2018.
Pengyue Zhang, Fusheng Wang Wei Xu, and Yulee Li: Multi-channel Generative Adversarial Network for Parallel Magnetic Resonance Image Reconstruction in K-space. To Appear in Proceedings of the 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018). September 16th to 20th, 2018, Granada, Spain.
Pengyue Zhang, Fusheng Wang, Yefeng Zheng: Deep Reinforcement Learning for Vessel Centerline Tracing in Multi-modality 3D Volumes. To Appear in Proceedings of the 21st International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2018). September 16th to 20th, 2018, Granada, Spain.
Yanhui Liang, Hoang Vo, Jun Kong and Fusheng Wang: iSPEED: an Scalable and Distributed In-Memory Based Spatial Query System for Large and Structurally Complex 3D Data. Demo Paper. To Appear in Proceedings of the 44th International Conference on Very Large Data Bases (VLDB 2018), August 27-31, 2018, Rio de Janeiro, Brazil.
Mousumi Roy, Fusheng Wang, George Teodoro, Vos Miriam, Alton Farris and Jun Kong: Segmentation of Overlapped Steatosis in Whole-Slide Liver Histopathology Microscopy Images. To Appear in Proceedings of 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Honolulu, HI, USA, July 17-21, 2018.
Mousumi Roy, Fusheng Wang, George Teodoro, José E. Velázquez Vega, Daniel Brat and Jun Kong: Analysis of Cellular Feature Differences of Astrocytomas with Distinct Mutational Profiles Using Digitized Histopathology Images. To Appear in Proceedings of 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Honolulu, HI, USA, July 17-21, 2018.
Yu Wang, Wei Hou and Fusheng Wang: Mining Co-occurrence and Sequence Patterns from Cancer Diagnoses in New York State. PLOS One. 13(4):e0194407.
Xiaobo Sun, Jingjing Gao, Peng Jin, Fusheng Wang*, Zhaohui Qin*: Optimized Distributed Systems Achieve Significant Performance Improvement on Sorted Merging of Massive VCF Files. GigaScience. (* these authors contributed equally)
Furqan Baig, Hoang Vo, Tahsin Kurc, Joel Saltz and Fusheng Wang: SparkGIS: Resource Aware Efficient In-Memory Spatial Query Processing. In Proceedings of SIGSPATIAL 2017. November 7 - 10, 2017, Redondo Beach, California, USA.
Sina Rashidian, Xinyu Dong, Amogh Avadhani, Prachi Poddar and Fusheng Wang: Effective Scalable and Integrative Geocoding for Massive Address Datasets in Public Health Studies . In Proceedings of SIGSPATIAL 2017. November 7 - 10, 2017, Redondo Beach, California, USA.

Yanhui Liang, Hoang Vo, Jun Kong and Fusheng Wang: iSPEED: an Efficient In-Memory Based Spatial Query System for Large-Scale 3D Data with Complex Structures. In Proceedings of SIGSPATIAL 2017. November 7 - 10, 2017, Redondo Beach, California, USA.
S. K. Prasad, D. Aghajarian, Mi. McDermott, D. Shah, M. Mokbel, S. Puri, S. J. Rey, S. Shekhar, Y. Xe, R. R. Vatsavai, F. Wang, Y. Liang, H. Vo and S. Wang: Parallel Processing over Spatial-Temporal Datasets from Geo, Bio, Climate and Social Science Communities: A Research Roadmap. In Proceedings of IEEE BigData Congress. June 25 - June 30, 2017, Honolulu, Hawaii, USA.
Xiaobo Sun, Fusheng Wang and Zhaohui Qin: Comparative Studies on Merging Massive Data from Genome-Wide Association Studies using Big Data Platforms. In Proceedings of the Third VLDB Workshop on Data Management and Analytics on Healthcare and Medicine (DMAH 2017), September 1, 2017, Munich, Germany.
Xin Chen, Yu Wang, Xiaxia Yu and Fusheng Wang: Large Scale Analysis of Opioid Poisoning Related Hospital Visits in New York State. In AMIA Annual Symposium, November 4-8, 2017, Wasington DC, USA.
X. Sun, W. Pittard, T. Xu, Tianlei, M. Zwick, X. Jiang, F. Wang, and Z. Qin: OmicSeq: A web-based search engine for exploring omics datasets. Nucleic Acids Research, Volume 45, Issue W1, April 2017.
Pengyue Zhang, Fusheng Wang, George Teodoro, Yanhui Liang, Daniel Brat and Jun Kong: Automated Level Set Segmentation of Histopathologic Cells with Sparse Shape Prior Support and Dynamic Occlusion Constraint. In Proc. of 2017 IEEE International Symposium on Biomedical Imaging, April 18 - 21, 2017, Melbourne, Australia.
Pengyue Zhang, Fusheng Wang and Yefeng Zheng: Self supervised deep representation learning for fine-grained body part recognition. In Proc. of 2017 IEEE International Symposium on Biomedical Imaging, April 18 - 21, 2017, Melbourne, Australia.
Blair Rossetti, Fusheng Wang, Pengyue Zhang, George Teodoro, Daniel Brat and Jun Kong: Dynamic Registration for Gigapixel Serial Whole Slide Images. In Proc. of 2017 IEEE International Symposium on Biomedical Imaging, April 18 - 21, 2017, Melbourne, Australia.
Xin Chen, Yu Wang, Elinor Schoenfeld, Mary Saltz, Joel Saltz and Fusheng Wang: Spatio-temporal Analysis for New York State SPARCS Data. In Proc. of 2017 AMIA Joint Summits on Translational Science, March 27 - 30, 2017, San Francisco,CA, USA.
Yanhui Liang, Fusheng Wang, Pengyue Zhang, Daniel J. Brat, Joel Saltz, Jun Kong: Development of a Framework for Large Scale Three-Dimensional Pathology and Biomarker Imaging and Spatial Analytics. In Proc. of 2017 AMIA Joint Summits on Translational Science, March 27 - 30, 2017, San Francisco,CA, USA.
Yanhui Liang, Hoang Vo, Ablimit Aji, Jun Kong and Fusheng Wang: Scalable 3D Spatial Queries for Analytical Pathology Imaging with MapReduce. In Proc. of the 24nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM SIGSPATIAL 2016), October 31 to November 3, 2016, San Francisco Bay Area, California, USA.
Xin Chen, Hoang Vo, and Fusheng Wang: Annotating Geographical Objects in OpenStreetMap with Geo-tagged Social Media. In Proc. of the 9th ACM SIGSPATIAL International Workshop on Location-Based Social Networks (LBSN 2016), October 31, 2016, San Francisco Bay Area, California, USA.
Hoang Vo, Jun Kong, Dejun Teng, Yanhui Liang, Ablimit Aji, George Teodoro and Fusheng Wang: Cloud-Based Whole Slide Image Analysis Using MapReduce. In Proceedings of the Second International Workshop on Data Management and Analytics for Medicine and Healthcare (DMAH 2016). New Delhi, September 9, 2016.
Cong Xie, Wen Zhong, Jun Kong, Wei Xu, Klaus Mueller and Fusheng Wang: IEVQ: An Iterative Example-based Visual Query for Pathology Database. In Proceedings of the Second International Workshop on Data Management and Analytics for Medicine and Healthcare (DMAH 2016). New Delhi, September 9, 2016.
Jun Kong, Pengyue Zhang, Yanhui Liang, George Teodorou, Daniel J. Brat and Fusheng Wang: Robust Cell Segmentation for Histological Images of Glioblastoma. In Proceedings of International Symposium on Biomedical Imaging (ISBI 2016), April 13-16, 2016, Prague, Czech.
Xin Chen and Fusheng Wang: Integrative Spatial Data Analytics for Public Health Studies of New York State. To Appear in Proceedings of AMIA 2016 Annual Symposium. Chicago, IL, Nov 12-16, 2016.
Hoang Vo, Jun Kong, Dejun Teng, Yanhui Liang, Ablimit Aji, George Teodoro and Fusheng Wang: A MapReduce Based High Performance Whole Slide Image Analysis Framework in the Cloud. To Appear in Proceedings of the Second International Workshop on Data Management and Analytics for Medicine and Healthcare (DMAH 2016). New Delhi, September 9, 2016.
Cong Xie, Wen Zhong, Jun Kong, Wei Xu, Klaus Mueller and Fusheng Wang: IEVQ: An Iterative Example-based Visual Query for Pathology Database. To Appear in Proceedings of the Second International Workshop on Data Management and Analytics for Medicine and Healthcare (DMAH 2016). New Delhi, September 9, 2016.
Yanhui Liang, Jun Kong, Yangyang Zhu and Fusheng Wang: Three-Dimensional Data Analytics for Pathology Imaging. In Proceedings of the First International Workshop on Data Management and Analytics for Medicine and Healthcare. Waikoloa, Hawaii, September 4, 2015.
Ablimit Aji and Fusheng Wang: Challenges and Approaches in Spatial Big Data Management. "Big Data: Storage, Sharing, and Security (3S)". By Auerbach Publications, 2016.
Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, George Teodoro, Yangyang Zhu and Jun Kong: Whole-Slide Histological Image Analysis for 3D Primary Vessel Reconstruction. In Proc. of the 18th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2015). Munich, Germany, October 5-9, 2015.
Xin Chen, Yu Wang, Eugene Agichtein and Fusheng Wang: A comparative study of demographic inference in Twitter. In Proc. of the 9th International AAAI Conference on Web and Social Media (ICWSM 2015). Oxford, UK, May 26-29, 2015.
Fusheng Wang, Ablimit Aji and George Teodoro: High Performance Spatial Queries for Spatial Big Data: from Medical Imaging to GIS. ACM SIGSPATIAL Special, Vol 6(3), November, 2014.
Hoang Vo and Fusheng Wang: Effective Temporal Modeling for Scalable Spatio-Temporal Queries. In Proc. of the International Workshop on Spatiotemporal Computing (IWSC'2015). Fairfax, Virginia, July 13-15th, 2015.
Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, George Teodoro, Yangyang Zhu and Jun Kong: Liver Whole Slide Image Analysis for 3D Vessel Reconstruction. In Proc. of the 12th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2015). Brooklyn, New York, USA, April 16-19, 2015.
Jun Kong, Fusheng Wang, George Teodoro, Yanhui Liang, Yangyang Zhu, Carol Tucker-Burden, Daniel Brat: Automated Cell Segmentation with 3D Fluorescence Microscopy Images. In Proc. of the 12th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2015). Brooklyn, New York, USA, April 16-19, 2015.
Chunjie Zhou, Pengfei Dai, Fusheng Wang and Renpu Li: Mining Spatial and Temporal Movement Patterns of Passengers on Bus Networks. In Proc. of the Seventh International Conference on Advanced Geographic Information Systems, Applications, and Services (GEOProcessing 2015). February 22 - 27, 2015 - Lisbon, Portugal.
Fusheng Wang, Ablimit Aji, and George Teodoro: Medical Image Dataset Processing over Cloud/MapReduce with Heterogeneous Architectures. Encyclopedia of GIS. Springer. Forthcoming.
Yanhui Liang, Fusheng Wang, Darren Treanor, Derek Magee, George Teodoro, Yangyang Zhu, Jun Kong: A Framework for 3D Vessel Analysis with Whole Slide Images of Serial Liver Sections. In Proc. of International Conference on Intelligent Biology and Medicine (ICIBM 2014), December 4-6, 2014, San Antonio, TX, USA.
Xin Chen, Hoang Vo, Ablimit Aji and Fusheng Wang: High Performance Integrated Spatial Big Data Analytics. In Proc. of the Third ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data (BigSpatial-2014), Nov 4, 2014, Dallas, TX, USA.
Ablimit Aji, George Teodoro and Fusheng Wang: Haggis: Turbo Charge A MapReduce based Spatial Data Warehousing System with GPU Engine. In Proc. of the Third ACM SIGSPATIAL International Workshop on Analytics for Big Geospatial Data (BigSpatial-2014), Nov 4, 2014, Dallas, TX, USA.
Ablimit Aji, George Teodoro and Fusheng Wang: SATO: A Spatial Data Partitioning Framework for Scalable Query Processing. In Proc. of the 22nd ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM SIGSPATIAL 2014), Dallas, Texas in November 4-7, 2014, Dallas, TX, USA.

Software

Patent

Y. Liang, F. Wang and H. Vo: System and method associated with progressive spatial analysis of prodigious 3d data including complex structures. United States Patent No. 11,188,738. November 30, 2021.