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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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2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2019
Journal Articles
[]A Non-invasive 3D Body Scanner and Software Tool towards Analysis of Scoliosis (S. Roy, A.T.D. Gruenwald, A. Alves-Pinto, R. Maier, D. Cremers, D. Pfeiffer and R. Lampe), In BioMed Research International (BMRI), 2019. ([pdf]) [bibtex]
[] Efficient Deep Network Architectures for Fast Chest X-Ray Tuberculosis Screening and Visualization (F. Pasa, V. Golkov, F. Pfeiffer, D. Cremers and D. Pfeiffer), In Scientific Reports, volume 9, 2019.  [bibtex] [pdf] [doi]
Conference and Workshop Papers
[]Negative-Unlabeled Learning for Diffusion MRI (P. Swazinna, V. Golkov, I. Lipp, E. Sgarlata, V. Tomassini, D. K. Jones and D. Cremers), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2019.  [bibtex] [pdf]
2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2002 
2018
Preprints
[]q-Space Novelty Detection with Variational Autoencoders (A. Vasilev, V. Golkov, I. Lipp, E. Sgarlata, V. Tomassini, D. K. Jones and D. Cremers), In arXiv preprint arXiv:1806.02997, 2018.  [bibtex] [arXiv:1806.02997] [pdf]
Conference and Workshop Papers
[]Precursor microRNA Identification Using Deep Convolutional Neural Networks (B. T. Do, V. Golkov, G. E. Gürel and D. Cremers), In bioRxiv preprint, 2018. (bioRxiv:414656) [bibtex] [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 and D. Cremers), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018.  [bibtex] [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 and D. Cremers), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018.  [bibtex] [pdf]
2019 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 (Krieg, Michael, Stühmer, Jan, Cueva, Juan G, Fetter, Richard, Spilker, Kerri, Cremers, Daniel, Shen, Kang, Dunn, Alex R and Goodman, Miriam B), In Biophysical Journal, Elsevier, volume 112, 2017.  [bibtex]
[]Genetic defects in ß-spectrin and tau sensitize C. elegans axons to movement-induced damage via torque-tension coupling (Krieg, Michael, Stühmer, Jan, Cueva, Juan G, Fetter, Richard, Spilker, Kerri, Cremers, Daniel, Shen, Kang, Dunn, Alexander R and Goodman, Miriam B), In eLife, eLife Sciences Publications Limited, volume 6, 2017.  [bibtex]
Preprints
[]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 and D. Cremers), In arXiv preprint arXiv:1704.04039, 2017.  [bibtex] [arXiv:1704.04039] [pdf]
Conference and Workshop Papers
[]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 and S.E. Combs), In 23. Jahrestagung der Deutschen Gesellschaft für Radioonkologie (DEGRO), 2017.  [bibtex]
2019 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 and D. Cremers), In IEEE Transactions on Medical Imaging, volume 35, 2016. Special Issue on Deep Learning [bibtex] [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 and D. Cremers), In Annual Conference on Neural Information Processing Systems (NIPS), 2016. ([video]) [bibtex] [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 and D. Cremers), In IEEE International Symposium on Biomedical Imaging (ISBI), 2016.  [bibtex] [pdf]
2019 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 and D. Cremers), Chapter in Computational Diffusion MRI, Springer, 2015.  [bibtex] [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 and D. Cremers), In BMC Bioinformatics, volume 16, 2015.  [bibtex]
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 and D. Cremers), In Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.  [bibtex] [pdf]
[]Free-Breathing, Self-Navigated RUFIS Lung Imaging with Motion Compensated Image Reconstruction (A. Menini, V. Golkov and F. Wiesinger), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.  [bibtex]
[]Robustness of Phase Sensitive Reconstruction in Diffusion Spectrum Imaging (M.I. Menzel, T. Sprenger, E.T. Tan, V. Golkov, C.J. Hardy, L. Marinelli and J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.  [bibtex]
[]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 and B.H. Menze), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.  [bibtex]
[]A Fast Projection Method for Connectivity Constraints in Image Segmentation (J. Stühmer and 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.  [bibtex] [pdf]
2019 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 and D. Cremers), Chapter in Computational Diffusion MRI, Springer, 2014.  [bibtex] [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 and J.I. Sperl), In Organization for Human Brain Mapping (OHBM) Annual Meeting, 2014.  [bibtex]
[]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 and J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.  [bibtex]
[]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 and J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.  [bibtex]
[]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 and L. Marinelli), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.  [bibtex]
[]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 and M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.  [bibtex]
2019 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 and D. Cremers), Chapter in Advanced Topics in Computer Vision, Springer, 2013.  [bibtex] [pdf]
Journal Articles
[]Spatially Varying Color Distributions for Interactive Multi-Label Segmentation (C. Nieuwenhuis and D. Cremers), In IEEE Transactions on Pattern Analysis and Machine Intelligence, volume 35, 2013. (Code available) [bibtex] [pdf]
Conference and Workshop Papers
[]Tree Shape Priors with Connectivity Constraints using Convex Relaxation on General Graphs (J. Stühmer, P. Schröder and D. Cremers), In IEEE International Conference on Computer Vision (ICCV), 2013.  [bibtex] [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 and J.I. Sperl), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.  [bibtex]
[]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 and M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.  [bibtex]
[]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 and M.I. Menzel), In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.  [bibtex]
[]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 and J.I. Sperl), In ISMRM Workshop on Diffusion as a Probe of Neural Tissue Microstructure, 2013.  [bibtex]
[]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 and J.I. Sperl), In 16th Annual Meeting of the German Chapter of the ISMRM, 2013.  [bibtex]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 and J.I. Sperl), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013.  [bibtex]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 and J.I. Sperl), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013.  [bibtex]Oral Presentation
Technical Reports
[]Label Configuration Priors for Continuous Multi-Label Optimization (M. Souiai, E. Strekalovskiy, C. Nieuwenhuis and D. Cremers), Technical report, , 2013.  [bibtex] [pdf]
2019 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 and A. Schikora), In BMC Bioinformatics, volume 13, 2012.  [bibtex] [pdf]
[]Image segmentation with one shape prior - A template-based formulation (S. Chen, D. Cremers and R. J. Radke), In Image and Vision Computing, volume 30, 2012.  [bibtex] [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 and M.I. Menzel), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012.  [bibtex]
[]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 and M.I. Menzel), In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012.  [bibtex]
2019 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 and D. Cremers), In Pattern Recognition, volume 44, 2011.  [bibtex] [pdf]
Conference and Workshop Papers
[]Pixel-based Classification Method for Detecting Unhealthy Regions in Leaf Images (S. Madhogaria, M. Schikora, W. Koch and D. Cremers), In 6th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2011.  [bibtex] [pdf]
[]A Convex Framework for Image Segmentation with Moment Constraints (M. Klodt and D. Cremers), In IEEE International Conference on Computer Vision (ICCV), 2011.  [bibtex] [pdf]
2019 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 and D. Cremers), In 5th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2010.  [bibtex] [pdf]
2019 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 and D. Cremers), In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2009.  [bibtex] [pdf]
2019 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 and H. Bischof), In CVPR Workshop on Visual Computer Vision on GPU's, 2008.  [bibtex] [pdf]
2019 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 and M. Rousson), Chapter in Parametric and Geometric Deformable Models: An application in Biomaterials and Medical Imagery (J. S. Suri, A. Farag, eds.), Springer, 2007.  [bibtex] [pdf]
Journal Articles
[]A review of statistical approaches to level set segmentation: integrating color, texture, motion and shape (D. Cremers, M. Rousson and R. Deriche), In International Journal of Computer Vision, volume 72, 2007.  [bibtex] [pdf]
Conference and Workshop Papers
[]A probabilistic level set formulation for interactive organ segmentation (D. Cremers, O. Fluck, M. Rousson and S. Aharon), In Proc. of the SPIE Medical Imaging, 2007.  [bibtex] [pdf]
2019 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 and S. Soatto), In International Journal of Computer Vision, volume 69, 2006.  [bibtex] [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 and R. Ramaraj), In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 4190, 2006.  [bibtex] [pdf]
[]Nonparametric priors on the space of joint intensity distributions for non-rigid multi-modal image registration (D. Cremers, C. Guetter and C. Xu), In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), volume 2, 2006.  [bibtex] [pdf]
2019 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 and D. Cremers), In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 1, 2005.  [bibtex] [pdf]
2019 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 and A. V. M. Herz), In Neural Computation, volume 14, 2002.  [bibtex] [pdf]
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