Publications

• Journal
• Book Chapters
• Conference
• Patents

All publications in one bibtex file.

Journal

Automatic Detection and Measurement of Structures in Fetal Head Ultrasound Volumes Using Sequential Estimation and Integrated Detection Network (IDN)
Michal Sofka and Jingdan Zhang and Sara Good and S. Kevin Zhou and Dorin Comaniciu
IEEE Transactions on Medical Imaging (TMI), vol. 33, no. 5, pp. 1054-1070, May 2014.
[pdf] [bibtex] [website] [publisher]

Retinal Vascular Tree Reconstruction With Anatomical Realism
Kai-Shun Lin, Chia-Ling Tsai, Chih-Hsiangng Tsai, Michal Sofka, Shih-Jen Chen, and Wei-Yang Lin
IEEE Transactions on Biomedical Engineering (TBE), vol. 59, no. 12, pp. 3337-3347, Dec. 2012.
[pdf] [bibtex] [publisher]

Progressive Data Transmission for Anatomical Landmark Detection in a Cloud
Michal Sofka, Kristof Ralovich, Jingdan Zhang, S. Kevin Zhou, and Dorin Comaniciu
Methods of Information in Medicine, Invited Paper, vol. 51, no. 3, pp. 268-278, Jun. 2012.
[pdf] [bibtex] [website] [publisher]

Location Registration and Recognition (LRR) for Serial Analysis of Nodules in Lung CT Scans
Michal Sofka and Charles V. Stewart
In Medical Image Analysis, vol. 14, no. 3, pp. 407-428, Jun. 2010.
[pdf] [bibtex] [website] [code] [publisher]

Automated Retinal Image Analysis over the Internet
Chia-Ling Tsai, Benjamin Madore, Matthew Leotta, Michal Sofka, Gehua Yang, Anna Majerovics, Howard L. Tanenbaum, Charles V. Stewart, and Badrinath Roysam
IEEE Transactions on Information Technology in Biomedicine, vol. 12, no. 4, pp. 480-487, July 2008.
[pdf] [bibtex] [publisher]

Registration of challenging image pairs: initialization, estimation, and decision
Gehua Yang, Charles V. Stewart, Michal Sofka, and Chia-Ling Tsai
IEEE Pattern Analysis and Machine Intelligence (PAMI), vol. 29, no. 11, pp. 1973-1989, Nov. 2007.
[pdf] [bibtex] [website] [publisher]

Retinal Vessel Centerline Extraction Using Multiscale Matched Filters, Confidence and Edge Measures
Michal Sofka and Charles V. Stewart
IEEE Transactions on Medical Imaging (TMI), vol. 25, no. 12, pp. 1531-1546, Dec. 2006.
[pdf with erratum] [bibtex] [website] [binaries] [publisher and erratum]

Invited Book Chapters

Integrated Detection Network for Multiple Object Recognition
Michal Sofka
In S. Kevin Zhou, editor, Medical Image Recognition, Segmentation and Parsing. Elsevier, 2015.
[pdf] [bibtex] [publisher]

Robust segmentation of challenging lungs in CT using multi-stage learning and level set optimization
Neil Birkbeck, Michal Sofka, Timo Kohlberger, Jingdan Zhang, Jens Wetzl, Jens Kaftan, and S. Kevin Zhou
In Suzuki Kenji, editor, Computational Intelligence in Biomedical Imaging. Springer New York, 2014. pp 185-208.
[pdf] [bibtex] [publisher]

Unpublished

Learning detectors of malicious web requests for intrusion detection in network traffic
Lukas Machlica, Karel Bartos, and Michal Sofka arXiv:1702.02530 [stat.ML] 2017.
[pdf] [bibtex] [arXiv]

Conference

Fully convolutional regression network for accurate detection of measurement points
Michal Sofka, Fausto Milletari, Jimmy Jia, and Alex Rothberg
Deep Learning in Medical Image Analysis and Multimodal Learning for Clinical Decision Support (DLMIA), Quebec City, Quebec, Candada, 14 Sep. 2017. Oral presentation (19% acceptance).
[pdf] [bibtex]

Integrating statistical prior knowledge into convolutional neural networks
Fausto Milletari, Alex Rothberg, Jimmy Jia, Michal Sofka
Proceedings of the 20th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI 2017), Quebec City, Quebec, Candada, 11 - 13 Sep. 2017.
[pdf] [bibtex]

Learning Invariant Representation for Malicious Network Traffic Detection
Vojtech Franc, Michal Sofka, and Karel Bartos
In Proceedings of the European Conference on Artificial Intelligence, Hague, Holland, 29 Aug - 2 Sep. 2016.
[pdf] [bibtex] [slides]

Optimized Invariant Representation of Network Traffic for Detecting Unseen Malware Variants
Vojtech Franc, Michal Sofka, and Karel Bartos
USENIX Security Symposium, Austin, TX, 10-12 Aug. 2016. 15.6% acceptatnce rate.
[pdf] [bibtex]

Learning detector of malicious network traffic from weak labels
Vojtech Franc, Michal Sofka, and Karel Bartos
In Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD), Porto, Portugal, 7-11 Sep. 2015.
[pdf] [bibtex] [website] [publisher]

Robust representation of network traffic for detecting malware variations
Karel Bartos and Michal Sofka
In Proceedings of the European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML PKDD), Porto, Portugal, 7-11 Sep. 2015.
[pdf] [bibtex] [website] [publisher]

Segmentation of Multiple Knee Bones from CT for Orthopedic Knee Surgery Planning
Dijia Wu, Michal Sofka, Neil Birkbeck, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Boston, MA, USA, 14-18 Sep. 2014.
[pdf] [bibtex] [publisher]

Lung Segmentation from CT with Severe Pathologies Using Anatomical Constraints
Neil Birkbeck, Timo Kohlberger, Jingdan Zhang, Michal Sofka, Jens Kaftan, Dorin Comaniciu, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Boston, MA, USA, 14-18 Sep. 2014.
[pdf] [bibtex] [publisher]

IntellEditS: Intelligent Learning-Based Editor of Segmentations
Adam P. Harrison, Neil Birkbeck, and Michal Sofka
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, 22-26 Sep. 2013.
[pdf] [bibtex] [publisher]

Automatic Nuchal Translucency Measurement from Ultrasonography
JinHyeong Park, Michal Sofka, SunMi Lee, DaeYoung Kim, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, 22-26 Sep. 2013.
[pdf] [bibtex] [website] [publisher]

Hierarchical Discriminative Framework for Detecting Tubular Structures in 3D Images
Dirk Breitenreicher, Michal Sofka, Stefan Britzen, and S. Kevin Zhou
Proceedings of the 23rd International Conference on Information Processing in Medical Imaging (IPMI 2013), Asilomar, CA, USA, 29 Jun-3 Jul 2013.
[pdf] [bibtex] [publisher]

A Splice-Guided Data Driven Interactive Editing
Noha El-Zehiry, Marie-Pierre Jolly, and Michal Sofka
Proceedings of the International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2013), San Francisco, CA, USA, 7-11 Apr, 2013.
[pdf] [bibtex] [publisher]

Multi-stage Learning for Robust Lung Segmentation in Challenging CT Volumes
Michal Sofka, Jens Wetzl, Neil Birkbeck, Jingdan Zhang, Timo Kohlberger, Jens Kaftan, Jérôme Declerck, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, 18-22 Sep. 2011.
[pdf] [bibtex] [publisher] [website]

Automatic Contrast Phase Estimation in CT Volumes
Michal Sofka, Dijia Wu, Michael Suehling, David Liu, Christian Tietjen, Grzegorz Soza, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, 18-22 Sep. 2011.
[pdf] [bibtex] [publisher] [website]

Automatic Multi-Organ Segmentation Using Learning-based Segmentation and Level Set Optimization
Timo Kohlberger, Michal Sofka, Jingdan Zhang, Neil Birkbeck, Jens Wetzl, Jens Kaftan, Jérôme Declerck, and S. Kevin Zhou
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), Toronto, Canada, 18-22 Sep. 2011.
[pdf] [bibtex] [publisher] [website]

Neil Birkbeck, Michal Sofka, and S. Kevin Zhou
Proceedings of the 7th IEEE Workshop on Embedded Computer Vision (in conjunction with IEEE CVPR) Colorado Springs, CO, USA, 20 Jun 2011.
[pdf] [bibtex] [publisher] [website]

Integrated Detection Network (IDN) for Pose and Boundary Estimation in Medical Images
Michal Sofka, Kristof Ralovich, Neil Birkbeck, Jingdan Zhang, and S. Kevin Zhou
Proceedings of the 8th International Symposium on Biomedical Imaging (ISBI 2011), Chicago, IL, USA, 30 Mar-2 Apr 2011.
[pdf] [bibtex] [publisher] [website]

Progressive Data Transmission for Hierarchical Detection in a Cloud
Michal Sofka, Kristof Ralovich, Jingdan Zhang, S. Kevin Zhou, and Dorin Comaniciu
Proceedings of the 2nd International Workshop on High-Performance Medical Image Computing for Image-Assisted Clinical Intervention and Decision-Making (HP-MICCAI 2010), Bejing, China, 22 Sep 2010. Best Paper Award.
[pdf] [bibtex] [website]

Multiple Object Detection by Sequential Monte Carlo and Hierarchical Detection Network
Michal Sofka, Jingdan Zhang, S. Kevin Zhou, and Dorin Comaniciu
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), San Francisco, CA, 13-18 June 2010.
[pdf] [bibtex] [publisher] [website]

Location Registration and Recognition (LRR) for Longitudinal Evaluation of Corresponding Regions in CT Volumes
Michal Sofka and Charles V. Stewart
In Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), vol. 2, pp. 989-997, New York, NY, 6-10 Sep. 2008.
[pdf] [bibtex] [publisher] [website] [code]

Keypoint Descriptors for Matching Across Multiple Image Modalities and Non-linear Intensity Variations
Avi Kelman, Michal Sofka, and Charles V. Stewart
Proceedings of the IEEE Computer Society Workshop on Image Registration and Fusion (in conjunction with IEEE CVPR), Minneapolis, MN, 23 June 2007.
[pdf] [bibtex] [website] [publisher]

Simultaneous Covariance Driven Correspondence (CDC) and Transformation Estimation in the Expectation Maximization Framework
Michal Sofka, Gehua Yang, and Charles V. Stewart
Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Minneapolis, MN, 18-23 June 2007.
[pdf] [bibtex] [website] [publisher]

A Correspondence-Based Software Toolkit for Image Registration
Chia-Ling Tsai, Charles V. Stewart, Amitha Perera, Ying-Lin Lee, Gehua Yang, and Michal Sofka
Proceedings of the IEEE International Conference on Systems, Man, and Cybernetics, pp. 3972-3977, 2006.
[pdf] [bibtex] [publisher]

Automatic robust image registration system: Initialization, estimation, and decision
Gehua Yang, Charles V. Stewart, Michal Sofka, and Chia-Ling Tsai
Proceedings of the IEEE International conference on Computer Vision Systems (ICVS), pp. 23-31, 2006.
[pdf] [bibtex] [website] [publisher]

Archeological mosaic image indexing by color-based segmentation and skeleton extraction
Michal Sofka, Rachid Benslimane, Ludovic Macaire, Michael Rudko and Jack-Gérard Postaire
Proceedings of the second IEEE International Symposium on Signal Processing and Information Technology, pp 327-331, Marrakesh (Marocco), 2002.
[pdf] [bibtex]

Patents Granted
USPTO Granted

Semi-Automated Preoperative Resection Planning
Noha Youssry El-Zehiry, Leo Grady, Michal Sofka, Christian Tietjen, and Shaohua Kevin Zhou
Patent number: US9129391. Issued: Sep. 8, 2015.
[pdf] [bibtex] [Google] [USPTO]

Method and System for Multi-Organ Segmentation Using Learning-Based Segmentation and Level Set Optimization
Timo Kohlberger, Michal Sofka, Jens Wetzl, Jingdan Zhang, S. Kevin Zhou, Neil Birkbeck, Jens Kaftan. and Jérôme Declerck
Patent number: US9042620. Issued: May. 26, 2015.
[pdf] [bibtex] [Google] [USPTO]

Method and System for Evaluation Using Probabilistic Boosting Trees
Neil Birkbeck, Michal Sofka, and S. Kevin Zhou
Patent number: US8860715. Issued: Oct. 14, 2014.
[pdf] [bibtex] [Google] [USPTO]

Data Transmission in Remote Computer Assisted Detection
Michal Sofka, Kristof Ralovich, Jingdan Zhang, Shaohua Kevin Zhou, Gianluca Paladini, and Dorin Comaniciu
Patent number: US8811697. Issued: Aug. 19, 2014.
[pdf] [bibtex] [Google] [USPTO]

Method and System for Multiple Object Detection by Sequential Monte Carlo and Hierarchical Detection Network
Michal Sofka, Jingdan Zhang, S. Kevin Zhou, and Dorin Comaniciu
Patent number: US8605969. Issued: Dec. 10, 2013.
[pdf] [bibtex] [Google] [USPTO]

Feature-Based Composing for 3D MR Angiography Images
Li Zhang, Michal Sofka, and Ulf Schaefer
Patent number: US8265354. Issued Sep. 12, 2012.
[pdf] [bibtex] [Google] [USPTO]

Validation Scheme For Composing Magnetic Resonance Images (MRI)
Michal Sofka, Li Zhang, and Ulf Schaefer
Patent number: US7711161. Issued May 4, 2010.
[pdf] [bibtex] [Google] [USPTO]

Patents Pending
USPTO Applications

Method and System for Automatic Pelvis Unfolding from 3D Computed Tomography Images
Neil Birkbeck, Dijia Wu, Michal Sofka, Meizhu Liu, Grzegorz Soza ,and S. Kevin Zhou
Application number: 14/178,583. Publication number: US20150228070 A1. Filed: Aug. 13, 2015.
[bibtex] [Google] [USPTO]

Identifying threats based on hierarchical classification
Karel Bartos and Michal Sofka
Application number: 14/519,444. Filed: 21 October, 2014.
[USPTO]

Method and System for Bone Segmentation and Landmark Detection for Joint Replacement Surgery
Michal Sofka, Meizhu Liu, Dijia Wu, and S. Kevin Zhou
Application number: 14/041,029. Publication number: US20140093153 A1. Filed: Apr. 3, 2014.
[pdf] [bibtex] [Google] [USPTO]

Multi-Bone Segmentation for 3D Computed Tomography
Dijia Wu, Neil Birkbeck, Michal Sofka, Meizhu Liu, and S. Kevin Zhou
Application number: 13/953,825, Publication number: US20140086465 A1. Filed: Mar. 27, 2014.
[pdf] [bibtex] [Google] [USPTO]

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