Curriculum Vitae  
Michal Sofka, PhD


Michal is a Principal Scientist at 4Catalyzer.

Between 2013 and 2015, Michal worked at Cisco Systems in the Security Business Group.

Previously, Michal worked at Siemens Corporation, Corporate Research in the Image Analytics and Informatics group headed by Dr. Dorin Comaniciu.

Michal did his doctoral work with professor Chuck Stewart in the Computer Vision Group in the Department of Computer Science at RPI.

Passion: Innovating to transform ideas into solutions.

  • Over 15 years of experience in image analysis and computer vision; over 7 years of industrial experience from top R&D labs.
  • Senior Scientist and Technical Leader on research and development projects; coordinated multi-cultural international team of scientists, developers, and interns; led strategic planning of core technology directions.
  • Conducted cutting edge research in the area of computer vision for industrial applications; expertise in machine learning, object detection and segmentation, feature-based registration, uncertainty modeling, and curvilinear structure extraction. Pioneered data analysis research in the area of network security; focus on threat detection and classification, machine learning, clustering, weakly-supervised techniques, and behavioral analytics.
  • Outstanding publication record in leading international journals (TMI, MedIA, PAMI) and conferences (CVPR, IPMI, MICCAI); strong patenting activity; published 7+ journal articles, 22+ conference articles, 18+ patents.
  • Excellent software development and prototyping skills (C/C++, Matlab, Java); integration with software libraries and large systems; individual contributor and team leader; mentoring and coaching of team members; exceptional communication and interpersonal skills.
Rensselaer Polytechnic Institute Troy, NY
Doctor of Philosophy, Computer Science August 2008
Master of Science, Computer Science May 2006
Union College Schenectady, NY
Master of Science, Electrical Engineering June 2001
Czech Technical University Prague, Czech Republic
Electrical Engineering (Undergraduate Student) 1996 - 1998, 1999 - 2000
Union College Schenectady, NY
Electrical Engineering (Exchange Student) 1998 - 1999
Industrial and Academic Experience

Team Leader 2016 -        
Cisco Systems
Security Business Group

Sr. Technical Leader 2015 - 2016
Spearheaded the innovation in the analysis of encrypted network traffic. Designed novel algorithms for the representation of network traffic. Evaluated inventions through internal committee memberships to expand technological portfolio.
Technical Leader 2013 - 2015
Grew an R&D team in the area of large scale machine learning for threat analytics. Defined R&D goals and targets. Devised strategic roadmap for generating impactful intellectual property. Maintained and expanded university relationships. Built new data-driven classification algorithms for cybersecurity. Developed new machine learning techniques constrained by scarce or expensive labeling.
Siemens Corporation, Corporate Research
Imaging and Computer Vision

Princeton, NJ
R&D Project Manager 2011 - 2013
Managed research and development projects for various Siemens business units and external customers. Lead multi-cultural international teams. Prepared proposals for project acquisition. Monitored targets, carried out software deliveries, and maintained customer relations. Contributed to the strategic decisions by defining research, development, and product goals. Group leader: Dorin Comaniciu.
Research Scientist 2008 - 2011
Developed innovative industrial strength systems for image analysis (automatic detection of ultrasound anatomies and organ segmentation in CT and MR). Designed a learning-based algorithm leveraging expert knowledge embedded in a large annotated databases of medical images. Built architecture and lead development of machine learning library for object detection and segmentation (150K+ lines of C++ code in July 2012). Supervised interns. Group leader: Dorin Comaniciu.
Temporary Technical Employee Jan. 2004 - Aug. 2004
Designed, analyzed, validated, and maintained algorithms for automatic composing of Magnetic Resonance Images and Angiograms (two patents granted). Supervised an undergraduate intern.
Rensselaer Polytechnic Institute
Department of Computer Science

Troy, NY
Research Assistant 2003 - 2008
Implemented innovative and robust solutions to research problems in the areas of retinal vessel extraction, uncertainty in point and image registration, multimodal and illumination invariant keypoint descriptors, and location registration and recognition for mapping regions in CT scans. Published 8 papers and wrote 70K+ lines of C++ code. Supervised undergraduate research students.
Teaching Assistant 2001 - 2005 (4 semesters)
Led labs of 60 students in 2 groups; graded and designed homework assignments, projects, and exams; held office hours; supervised exams; and provided help outside the class. Served as a master TA the last semester.
Union College
Department of Electrical Engineering

Schenectady, NY
Union College, Department of Electrical Engineering 2000 - 2001
Tutored students; provided guidance on assignments; held review sessions; and helped students to master the coursework material. Computer assistant in the Curricular Support group.
Technical Expertise and Interests

Machine Learning: Leveraging large annotated databases; discriminative learning; effective sampling techniques; applications in image analysis and network security.

Image Segmentation: Machine learning-based estimation of boundaries of structures and curve-linear segments; efficient centerline tracing; statistical shape models; interactive segmentation editing.

Object Detection: Multi-object detection; hierarchical detection networks.

Registration: Robust and automatic feature-based registration in the presence of physical and illumination changes, noise, outliers, occlusions and missing structure; uncertainty modeling for correspondence estimation; statistical models in image registration; alignment verification.

Point Matching: Initialization of registration algorithms; keypoint detectors, descriptors and matching; feature extraction and scale space.

Medical imaging: Whole body image analysis; computer-assisted diagnosis and treatment planning; automatic measurements and quantification.

Data: Experience with range data (LIDAR), visible spectrum and infra red (IR) imagery, computed tomography (CT), Ultrasound (US), magnetic resonance (MR) images and angiograms (MRA).

Network Data: Netflows and proxy log records.

Software Development Skills
  • Expert in C/C++ (multi-platform and compiler independent development) with strong debugging, optimization, and integration skills; proficient in Matlab; versed in Java.
  • Practical experience in software engineering and collaborative product development of large projects, version control systems, regression testing, continuous integration, and nightly builds.
  • Familiar with scripting languages Bash, Python, Lua.
  • Exposure to MapReduce, HBase, Mahout, Scala.
Mentor and Supervisor

Daguang Xu (Johns Hopkins University, Baltimore, MD, USA), 2013

Adam Harrison (University of Alberta, Canada), 2012

Enrico Kuhn (Karlsruhe Institute of Technology, Germany), 2011

Vimal Singh (University of Texas, Austin, TX, USA), 2011

Jens Wetzl (University of Erlangen, Germany), 2010

Neil Birkbeck (University of Alberta, Canada), 2010

Kristof Ralovich (Technical University Munich, Germany), 2009

Professional Activities
Referee and Reviewer
IEEE Transactions on Medical Imaging (TMI)
Medical Image Analysis (MedIA)
IEEE Pattern Analysis and Machine Intelligence (PAMI)
Computer Vision and Image Understanding (CVIU)
IEEE Transactions on Image Processing (TIP)
IEEE Transactions on Biomedical Engineering (TBE)
IEEE Computer Vision and Pattern Recognition (CVPR)
IEEE International Conference on Computer Vision (ICCV)
European Conference on Computer Vision (ECCV)
International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI)
Publications and Research
Please see a separate page dedicated to publications and research projects.


Copyright 2017 Michal Sofka