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Faculty of Informatics
Technical University of Munich

Technical University of Munich

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Biomedicine

Contact: Vladimir Golkov

The following is a list of publications where we partially or entirely focus on biomedicine. Also many of our other methods can be applied to biomedical data.

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2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2018
Conference and Workshop Papers
q-Space Novelty Detection with Variational Autoencoders (A. Vasilev, V. Golkov, I. Lipp, E. Sgarlata, V. Tomassini, D. K. Jones, D. Cremers), In ArXiv preprint, 2018.(arXiv:1806.02997) [bib] [pdf]
Precursor microRNA Identification Using Deep Convolutional Neural Networks (B. T. Do, V. Golkov, G. E. Gürel, D. Cremers), In bioRxiv preprint, 2018.(bioRxiv:414656) [bib] [pdf]
q-Space Deep Learning for Alzheimer's Disease Diagnosis: Global Prediction and Weakly-Supervised Localization (V. Golkov, P. Swazinna, M. M. Schmitt, Q. A. Khan, C. M. W. Tax, M. Serahlazau, F. Pasa, F. Pfeiffer, G. J. Biessels, A. Leemans, D. Cremers), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018. [bib] [pdf]
q-Space Novelty Detection in Short Diffusion MRI Scans of Multiple Sclerosis (V. Golkov, A. Vasilev, F. Pasa, I. Lipp, W. Boubaker, E. Sgarlata, F. Pfeiffer, V. Tomassini, D. K. Jones, D. Cremers), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2017
Journal Articles
Tau Like Proteins Reduce Torque Generation in Microtubule Bundles (Michael Krieg, Jan Stühmer, Juan G Cueva, Richard Fetter, Kerri Spilker, Daniel Cremers, Kang Shen, Alex R Dunn, Miriam B Goodman), In Biophysical Journal, Elsevier, volume 112, 2017. [bib]
Genetic defects in ß-spectrin and tau sensitize C. elegans axons to movement-induced damage via torque-tension coupling (Michael Krieg, Jan Stühmer, Juan G Cueva, Richard Fetter, Kerri Spilker, Daniel Cremers, Kang Shen, Alexander R Dunn, Miriam B Goodman), In eLife, eLife Sciences Publications Limited, volume 6, 2017. [bib]
Conference and Workshop Papers
3D Deep Learning for Biological Function Prediction from Physical Fields (V. Golkov, M. J. Skwark, A. Mirchev, G. Dikov, A. R. Geanes, J. Mendenhall, J. Meiler, D. Cremers), In ArXiv preprint, 2017.(arXiv:1704.04039) [bib] [pdf]
Establishment of an interdisciplinary workflow of machine learning-based Radiomics in sarcoma patients (J.C. Peeken, C. Knie, V. Golkov, K. Kessel, F. Pasa, Q. Khan, M. Seroglazov, J. Kukačka, T. Goldberg, L. Richter, J. Reeb, B. Rost, F. Pfeiffer, D. Cremers, F. Nüsslin, S.E. Combs), In 23. Jahrestagung der Deutschen Gesellschaft für Radioonkologie (DEGRO), 2017. [bib]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2016
Journal Articles
q-Space Deep Learning: Twelve-Fold Shorter and Model-Free Diffusion MRI Scans (V. Golkov, A. Dosovitskiy, J. I. Sperl, M. I. Menzel, M. Czisch, P. Sämann, T. Brox, D. Cremers), In IEEE Transactions on Medical Imaging, volume 35, 2016. [bib] [pdf]Special Issue on Deep Learning
Conference and Workshop Papers
Protein Contact Prediction from Amino Acid Co-Evolution Using Convolutional Networks for Graph-Valued Images (V. Golkov, M. J. Skwark, A. Golkov, A. Dosovitskiy, T. Brox, J. Meiler, D. Cremers), In Annual Conference on Neural Information Processing Systems (NIPS), 2016.([video]) [bib] [pdf]Oral Presentation (acceptance rate: under 2%)
Model-Free Novelty-Based Diffusion MRI (V. Golkov, T. Sprenger, J. I. Sperl, M. I. Menzel, M. Czisch, P. Sämann, D. Cremers), In IEEE International Symposium on Biomedical Imaging (ISBI), 2016. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2015
Book Chapters
Holistic Image Reconstruction for Diffusion MRI (V. Golkov, J. M. Portegies, A. Golkov, R. Duits, D. Cremers), Chapter in Computational Diffusion MRI, Springer, 2015. [bib] [pdf]Book Chapter, and Oral Presentation at MICCAI 2015 Workshop on Computational Diffusion MRI
Journal Articles
Field phenotyping of grapevine growth using dense stereo reconstruction (M. Klodt, K. Herzog, R. Töpfer, D. Cremers), In BMC Bioinformatics, volume 16, 2015. [bib]
Conference and Workshop Papers
q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans (V. Golkov, A. Dosovitskiy, P. Sämann, J. I. Sperl, T. Sprenger, M. Czisch, M. I. Menzel, P. A. Gómez, A. Haase, T. Brox, D. Cremers), In Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015. [bib] [pdf]
Free-Breathing, Self-Navigated RUFIS Lung Imaging with Motion Compensated Image Reconstruction (A. Menini, V. Golkov, F. Wiesinger), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015. [bib]
Robustness of Phase Sensitive Reconstruction in Diffusion Spectrum Imaging (M.I. Menzel, T. Sprenger, E.T. Tan, V. Golkov, C.J. Hardy, L. Marinelli, J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015. [bib]
Using Diffusion and Structural MRI for the Automated Segmentation of Multiple Sclerosis Lesions (P.A. Gómez, T. Sprenger, A.A. López, J.I. Sperl, B. Fernandez, M. Molina-Romero, X. Liu, V. Golkov, M. Czisch, P. Saemann, M.I. Menzel, B.H. Menze), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015. [bib]
A Fast Projection Method for Connectivity Constraints in Image Segmentation (J. Stühmer, D. Cremers), In Energy Minimization Methods in Computer Vision and Pattern Recognition (EMMCVPR) (X.-C. Tai, E. Bae, T. F. Chan, M. Lysaker, eds.), 2015. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2014
Book Chapters
Joint Super-Resolution Using Only One Anisotropic Low-Resolution Image per q-Space Coordinate (V. Golkov, J.I. Sperl, M.I. Menzel, T. Sprenger, E.T. Tan, L. Marinelli, C.J. Hardy, A. Haase, D. Cremers), Chapter in Computational Diffusion MRI, Springer, 2014. [bib] [pdf]Book Chapter, and Oral Presentation at MICCAI 2014 Workshop on Computational Diffusion MRI
Conference and Workshop Papers
Improved Diffusion Kurtosis Imaging and Direct Propagator Estimation Using 6-D Compressed Sensing (V. Golkov, M.I. Menzel, T. Sprenger, M. Souiai, A. Haase, D. Cremers, J.I. Sperl), In Organization for Human Brain Mapping (OHBM) Annual Meeting, 2014. [bib]
Semi-Joint Reconstruction for Diffusion MRI Denoising Imposing Similarity of Edges in Similar Diffusion-Weighted Images (V. Golkov, M.I. Menzel, T. Sprenger, A. Haase, D. Cremers, J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014. [bib]
Direct Reconstruction of the Average Diffusion Propagator with Simultaneous Compressed-Sensing-Accelerated Diffusion Spectrum Imaging and Image Denoising by Means of Total Generalized Variation Regularization (V. Golkov, M.I. Menzel, T. Sprenger, M. Souiai, A. Haase, D. Cremers, J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014. [bib]
Total Variation-Regularized Compressed Sensing Reconstruction for Multi-Shell Diffusion Kurtosis Imaging (J.I. Sperl, T. Sprenger, E.T. Tan, V. Golkov, M.I. Menzel, C.J. Hardy, L. Marinelli), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014. [bib]
Novel Acquisition Scheme for Diffusion Kurtosis Imaging Based on Compressed-Sensing Accelerated DSI Yielding Superior Image Quality (T. Sprenger, J.I. Sperl, B. Fernandez, V. Golkov, E.T. Tan, C.J. Hardy, L. Marinelli, M. Czisch, P. Sämann, A. Haase, M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014. [bib]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2013
Book Chapters
Moment Constraints in Convex Optimization for Segmentation and Tracking (M. Klodt, F. Steinbruecker, D. Cremers), Chapter in Advanced Topics in Computer Vision, Springer, 2013. [bib] [pdf]
Journal Articles
Spatially Varying Color Distributions for Interactive Multi-Label Segmentation (C. Nieuwenhuis, D. Cremers), In IEEE Transactions on Pattern Analysis and Machine Intelligence, volume 35, 2013.(Code available) [bib] [pdf]
Conference and Workshop Papers
Tree Shape Priors with Connectivity Constraints using Convex Relaxation on General Graphs (J. Stühmer, P. Schröder, D. Cremers), In IEEE International Conference on Computer Vision (ICCV), 2013. [bib] [pdf]Oral Presentation
Noise Reduction in Accelerated Diffusion Spectrum Imaging through Integration of SENSE Reconstruction into Joint Reconstruction in Combination with q-Space Compressed Sensing (V. Golkov, T. Sprenger, M.I. Menzel, E.T. Tan, K.F. King, C.J. Hardy, L. Marinelli, D. Cremers, J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013. [bib]
Phase Sensitive Reconstruction in Diffusion Spectrum Imaging Enabling Velocity Encoding and Unbiased Noise Distribution (J.I. Sperl, E.T. Tan, T. Sprenger, V. Golkov, K.F. King, C.J. Hardy, L. Marinelli, M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013. [bib]
SNR-dependent Quality Assessment of Compressed-Sensing-Accelerated Diffusion Spectrum Imaging Using a Fiber Crossing Phantom (T. Sprenger, B. Fernandez, J.I. Sperl, V. Golkov, M. Bach, E.T. Tan, K.F. King, C.J. Hardy, L. Marinelli, M. Czisch, P. Sämann, A. Haase, M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013. [bib]
Corrected Joint SENSE Reconstruction, Low-Rank Constraints, and Compressed-Sensing-Accelerated Diffusion Spectrum Imaging in Denoising and Kurtosis Tensor Estimation (V. Golkov, M.I. Menzel, T. Sprenger, A. Menini, D. Cremers, J.I. Sperl), In ISMRM Workshop on Diffusion as a Probe of Neural Tissue Microstructure, 2013. [bib]
Reconstruction, Regularization, and Quality in Diffusion MRI Using the Example of Accelerated Diffusion Spectrum Imaging (V. Golkov, M.I. Menzel, T. Sprenger, A. Menini, D. Cremers, J.I. Sperl), In 16th Annual Meeting of the German Chapter of the ISMRM, 2013. [bib]Oral Presentation
Line-Process-Based Joint SENSE Reconstruction of Diffusion Images with Intensity Inhomogeneity Correction and Noise Non-Stationarity Correction (V. Golkov, T. Sprenger, M.I. Menzel, D. Cremers, J.I. Sperl), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013. [bib]Certificate of Merit Award
Effects of Low-Rank Constraints, Line-Process Denoising, and q-Space Compressed Sensing on Diffusion MR Image Reconstruction and Kurtosis Tensor Estimation (V. Golkov, T. Sprenger, A. Menini, M.I. Menzel, D. Cremers, J.I. Sperl), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013. [bib]Oral Presentation
Other Publications
Label Configuration Priors for Continuous Multi-Label Optimization (M. Souiai, E. Strekalovskiy, C. Nieuwenhuis, D. Cremers), 2013. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2012
Journal Articles
An image classification approach to analyze the suppression of plant immunity by the human pathogen Salmonella Typhimurium (M. Schikora, B. Neupane, S. Madhogaria, W. Koch, D. Cremers, H. Hirt, K.-H. Kogel, A. Schikora), In BMC Bioinformatics, volume 13, 2012. [bib] [pdf]
Image segmentation with one shape prior - A template-based formulation (S. Chen, D. Cremers, R. J. Radke), In Image and Vision Computing, volume 30, 2012. [bib] [pdf]
Conference and Workshop Papers
Comparison of Diffusion Kurtosis Tensor Estimation Methods in an Advanced Quality Assessment Framework (V. Golkov, J.I. Sperl, T. Sprenger, H.-J. Bungartz, M. Sedlacek, E.T. Tan, L. Marinelli, C.J. Hardy, K.F. King, M.I. Menzel), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012. [bib]
Evaluation of DSI Imaging with Compressed Sensing under the Presence of Different Noise Levels on a Diffusion Phantom (T. Sprenger, B. Fernandez, M. Bach, J.I. Sperl, V. Golkov, E.T. Tan, L. Marinelli, K.F. King, C.J. Hardy, Q. Zhu, M. Czisch, P. Sämann, A. Haase, M.I. Menzel), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012. [bib]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2011
Journal Articles
A Variational Approach to Vesicle Membrane Reconstruction from Fluorescence Imaging (K. Kolev, N. Kirchgessner, S. Houben, A. Csiszar, W. Rubner, C. Palm, B. Eiben, R. Merkel, D. Cremers), In Pattern Recognition, volume 44, 2011. [bib] [pdf]
Conference and Workshop Papers
Pixel-based Classification Method for Detecting Unhealthy Regions in Leaf Images (S. Madhogaria, M. Schikora, W. Koch, D. Cremers), In 6th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2011. [bib] [pdf]
A Convex Framework for Image Segmentation with Moment Constraints (M. Klodt, D. Cremers), In IEEE International Conference on Computer Vision (ICCV), 2011. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2010
Conference and Workshop Papers
Probabilistic Classification of Disease Symptoms caused by Salmonella on Arabidopsis Plants (M. Schikora, A. Schikora, K.-H. Kogel, W. Koch, D. Cremers), In 5th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2010. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2009
Conference and Workshop Papers
A Convex Relaxation Approach for Computing Minimal Partitions (T. Pock, A. Chambolle, H. Bischof, D. Cremers), In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2009. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2008
Conference and Workshop Papers
Fast and Exact Solution of Total Variation Models on the GPU (T. Pock, M. Unger, D. Cremers, H. Bischof), In CVPR Workshop on Visual Computer Vision on GPU's, 2008. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2007
Book Chapters
Efficient kernel density estimation of shape and intensity priors for level set segmentation (D. Cremers, M. Rousson), Chapter in Parametric and Geometric Deformable Models: An application in Biomaterials and Medical Imagery (J. S. Suri, A. Farag, eds.), Springer, 2007. [bib] [pdf]
Journal Articles
A review of statistical approaches to level set segmentation: integrating color, texture, motion and shape (D. Cremers, M. Rousson, R. Deriche), In International Journal of Computer Vision, volume 72, 2007. [bib] [pdf]
Conference and Workshop Papers
A probabilistic level set formulation for interactive organ segmentation (D. Cremers, O. Fluck, M. Rousson, S. Aharon), In Proc. of the SPIE Medical Imaging, 2007. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2006
Journal Articles
Kernel density estimation and intrinsic alignment for shape priors in level set segmentation (D. Cremers, S. J. Osher, S. Soatto), In International Journal of Computer Vision, volume 69, 2006. [bib] [pdf]
Conference and Workshop Papers
4D shape priors for level set segmentation of the left myocardium in SPECT sequences (T. Kohlberger, D. Cremers, M. Rousson, R. Ramaraj), In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 4190, 2006. [bib] [pdf]
Nonparametric priors on the space of joint intensity distributions for non-rigid multi-modal image registration (D. Cremers, C. Guetter, C. Xu), In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), volume 2, 2006. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2005
Conference and Workshop Papers
Efficient kernel density estimation of shape and intensity priors for level set segmentation (M. Rousson, D. Cremers), In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 1, 2005. [bib] [pdf]
2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2002
Journal Articles
Travelling waves of exitation in neural field models: Equivalence of rate descriptions and integrate-and-fire dynamics (D. Cremers, A. V. M. Herz), In Neural Computation, volume 14, 2002. [bib] [pdf]
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