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Biomedicine
Below, you can find 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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2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2024
Conference and Workshop Papers
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The Pulseq-CEST Library: Definition of Preparations and Simulations, Example Data, and Example Evaluations , In 10th International Workshop on Chemical Exchange Saturation Transfer (CEST 2024), 2024.
Oral Presentation [] 
Joint sequence optimization beats pure neural network approaches for super-resolution TSE , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2024.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2023
Preprints
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Joint MR sequence optimization beats pure neural network approaches for spin-echo MRI super-resolution (12-page version) , In arXiv preprint arXiv:2305.07524, 2023.
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Scale-Equivariant Deep Learning for 3D Data , In arXiv preprint, 2023.
Conference and Workshop Papers
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GPT4MR: Exploring GPT-4 as an MR Sequence and Reconstruction Programming Assistant , In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2023.
Oral Presentation 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2022
Conference and Workshop Papers
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A data-driven variability assessment of brain diffusion MRI preprocessing pipelines , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2022.
Oral Presentation 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2021
Preprints
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Rotation-Equivariant Deep Learning for Diffusion MRI , In arXiv preprint, 2021.
Conference and Workshop Papers
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Rotation-Equivariant Deep Learning for Diffusion MRI (short version) , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2021.
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Faster and better HARDI using FSE and holistic reconstruction , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2021.
PhD Thesis
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Deep learning and variational analysis for high-dimensional and geometric biomedical data , PhD thesis, Department of Informatics, Technical University of Munich, Germany, 2021.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2020
Journal Articles
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Accelerating in vivo fast spin echo high angular resolution diffusion imaging with an isotropic resolution in mice through compressed sensing , In Magnetic Resonance in Medicine, volume 85, 2020.
Preprints
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Deep Learning for Virtual Screening: Five Reasons to Use ROC Cost Functions , In arXiv preprint arXiv:2007.07029, 2020.
Conference and Workshop Papers
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3D Deep Learning for Biological Function Prediction from Physical Fields , In International Conference on 3D Vision (3DV), 2020.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2019
Journal Articles
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Efficient Deep Network Architectures for Fast Chest X-Ray Tuberculosis Screening and Visualization , In Scientific Reports, volume 9, 2019.
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A Non-invasive 3D Body Scanner and Software Tool towards Analysis of Scoliosis , In BioMed Research International (BMRI), 2019. ([pdf])
Conference and Workshop Papers
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Negative-Unlabeled Learning for Diffusion MRI , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2019.
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q-Space Novelty Detection with Variational Autoencoders , In MICCAI 2019 International Workshop on Computational Diffusion MRI, 2019.
Oral Presentation 2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2018
Preprints
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Precursor microRNA Identification Using Deep Convolutional Neural Networks , In bioRxiv preprint 414656, 2018. (bioRxiv:414656)
Conference and Workshop Papers
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q-Space Deep Learning for Alzheimer's Disease Diagnosis: Global Prediction and Weakly-Supervised Localization , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018.
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q-Space Novelty Detection in Short Diffusion MRI Scans of Multiple Sclerosis , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2018.
2024 | 2023 | 2022 | 2021 | 2020 | 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 , In Biophysical Journal, Elsevier, volume 112, 2017.
[] Genetic defects in ß-spectrin and tau sensitize C. elegans axons to movement-induced damage via torque-tension coupling , In eLife, eLife Sciences Publications Limited, volume 6, 2017.
Conference and Workshop Papers
[] Establishment of an interdisciplinary workflow of machine learning-based Radiomics in sarcoma patients , In 23. Jahrestagung der Deutschen Gesellschaft für Radioonkologie (DEGRO), 2017.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2016
Journal Articles
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q-Space Deep Learning: Twelve-Fold Shorter and Model-Free Diffusion MRI Scans , In IEEE Transactions on Medical Imaging, volume 35, 2016. Special Issue on Deep Learning
Special Issue on Deep Learning
Conference and Workshop Papers
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Protein Contact Prediction from Amino Acid Co-Evolution Using Convolutional Networks for Graph-Valued Images , In Annual Conference on Neural Information Processing Systems (NIPS), 2016. ([video])
Oral Presentation (acceptance rate: under 2%) [] 
Model-Free Novelty-Based Diffusion MRI , In IEEE International Symposium on Biomedical Imaging (ISBI), 2016.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2015
Book Chapters
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Holistic Image Reconstruction for Diffusion MRI , Chapter in Computational Diffusion MRI, Springer, 2015.
Book Chapter, and Oral Presentation at MICCAI 2015 Workshop on Computational Diffusion MRI
Journal Articles
[] Field phenotyping of grapevine growth using dense stereo reconstruction , In BMC Bioinformatics, volume 16, 2015.
Conference and Workshop Papers
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q-Space Deep Learning for Twelve-Fold Shorter and Model-Free Diffusion MRI Scans , In Medical Image Computing and Computer Assisted Intervention (MICCAI), 2015.
[] Free-Breathing, Self-Navigated RUFIS Lung Imaging with Motion Compensated Image Reconstruction , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.
[] Robustness of Phase Sensitive Reconstruction in Diffusion Spectrum Imaging , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.
[] Using Diffusion and Structural MRI for the Automated Segmentation of Multiple Sclerosis Lesions , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2015.
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A Fast Projection Method for Connectivity Constraints in Image Segmentation , In Energy Minimization Methods in Computer Vision and Pattern Recognition (EMMCVPR) (X.-C. Tai, E. Bae, T. F. Chan, M. Lysaker, eds.), 2015.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2014
Book Chapters
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Joint Super-Resolution Using Only One Anisotropic Low-Resolution Image per q-Space Coordinate , Chapter in Computational Diffusion MRI, Springer, 2014.
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 , In Organization for Human Brain Mapping (OHBM) Annual Meeting, 2014.
[] Semi-Joint Reconstruction for Diffusion MRI Denoising Imposing Similarity of Edges in Similar Diffusion-Weighted Images , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.
[] 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 , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.
[] Total Variation-Regularized Compressed Sensing Reconstruction for Multi-Shell Diffusion Kurtosis Imaging , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.
[] Novel Acquisition Scheme for Diffusion Kurtosis Imaging Based on Compressed-Sensing Accelerated DSI Yielding Superior Image Quality , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2014.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2013
Book Chapters
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Moment Constraints in Convex Optimization for Segmentation and Tracking , Chapter in Advanced Topics in Computer Vision, Springer, 2013.
Journal Articles
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Spatially Varying Color Distributions for Interactive Multi-Label Segmentation , In IEEE Transactions on Pattern Analysis and Machine Intelligence, volume 35, 2013. (Code available)
Conference and Workshop Papers
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Tree Shape Priors with Connectivity Constraints using Convex Relaxation on General Graphs , In IEEE International Conference on Computer Vision (ICCV), 2013.
Oral Presentation [] Noise Reduction in Accelerated Diffusion Spectrum Imaging through Integration of SENSE Reconstruction into Joint Reconstruction in Combination with q-Space Compressed Sensing , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.
[] Phase Sensitive Reconstruction in Diffusion Spectrum Imaging Enabling Velocity Encoding and Unbiased Noise Distribution , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.
[] SNR-dependent Quality Assessment of Compressed-Sensing-Accelerated Diffusion Spectrum Imaging Using a Fiber Crossing Phantom , In International Society for Magnetic Resonance in Medicine (ISMRM) Annual Meeting, 2013.
[] Corrected Joint SENSE Reconstruction, Low-Rank Constraints, and Compressed-Sensing-Accelerated Diffusion Spectrum Imaging in Denoising and Kurtosis Tensor Estimation , In ISMRM Workshop on Diffusion as a Probe of Neural Tissue Microstructure, 2013.
[] Reconstruction, Regularization, and Quality in Diffusion MRI Using the Example of Accelerated Diffusion Spectrum Imaging , In 16th Annual Meeting of the German Chapter of the ISMRM, 2013.
Oral Presentation [] Line-Process-Based Joint SENSE Reconstruction of Diffusion Images with Intensity Inhomogeneity Correction and Noise Non-Stationarity Correction , In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013.
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 , In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2013.
Oral Presentation
Technical Reports
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Label Configuration Priors for Continuous Multi-Label Optimization , Technical report, , 2013.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2012
Journal Articles
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An image classification approach to analyze the suppression of plant immunity by the human pathogen Salmonella Typhimurium , In BMC Bioinformatics, volume 13, 2012.
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Image segmentation with one shape prior - A template-based formulation , In Image and Vision Computing, volume 30, 2012.
Conference and Workshop Papers
[] Comparison of Diffusion Kurtosis Tensor Estimation Methods in an Advanced Quality Assessment Framework , In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012.
[] Evaluation of DSI Imaging with Compressed Sensing under the Presence of Different Noise Levels on a Diffusion Phantom , In European Society for Magnetic Resonance in Medicine and Biology (ESMRMB) Annual Meeting, 2012.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2011
Journal Articles
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A Variational Approach to Vesicle Membrane Reconstruction from Fluorescence Imaging , In Pattern Recognition, volume 44, 2011.
Conference and Workshop Papers
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Pixel-based Classification Method for Detecting Unhealthy Regions in Leaf Images , In 6th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2011.
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A Convex Framework for Image Segmentation with Moment Constraints , In IEEE International Conference on Computer Vision (ICCV), 2011.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2010
Conference and Workshop Papers
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Probabilistic Classification of Disease Symptoms caused by Salmonella on Arabidopsis Plants , In 5th IEEE ISIF Workshop on Sensor Data Fusion: Trends, Solutions, Applications (SDF), 2010.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2009
Conference and Workshop Papers
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A Convex Relaxation Approach for Computing Minimal Partitions , In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 2009.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2008
Conference and Workshop Papers
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Fast and Exact Solution of Total Variation Models on the GPU , In CVPR Workshop on Visual Computer Vision on GPU's, 2008.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2007
Book Chapters
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Efficient kernel density estimation of shape and intensity priors for level set segmentation , Chapter in Parametric and Geometric Deformable Models: An application in Biomaterials and Medical Imagery (J. S. Suri, A. Farag, eds.), Springer, 2007.
Journal Articles
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A review of statistical approaches to level set segmentation: integrating color, texture, motion and shape , In International Journal of Computer Vision, volume 72, 2007.
Conference and Workshop Papers
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A probabilistic level set formulation for interactive organ segmentation , In Proc. of the SPIE Medical Imaging, 2007.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2006
Journal Articles
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Kernel density estimation and intrinsic alignment for shape priors in level set segmentation , In International Journal of Computer Vision, volume 69, 2006.
Conference and Workshop Papers
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4D shape priors for level set segmentation of the left myocardium in SPECT sequences , In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 4190, 2006.
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Nonparametric priors on the space of joint intensity distributions for non-rigid multi-modal image registration , In IEEE Conference on Computer Vision and Pattern Recognition (CVPR), volume 2, 2006.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2005
Conference and Workshop Papers
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Efficient kernel density estimation of shape and intensity priors for level set segmentation , In Medical Image Computing and Computer Assisted Intervention (MICCAI), volume 1, 2005.
2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2002
2002
Journal Articles
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Travelling waves of exitation in neural field models: Equivalence of rate descriptions and integrate-and-fire dynamics , In Neural Computation, volume 14, 2002.
