All Publications

2022
Fita, E, Damrich, S and Hamprecht, F A (2022). The Algebraic Path Problem for Graph Metrics. 39th International Conference on Machine Learning, PMLR. Proceedings . 162 19178-19204 Google Scholar BibTeX RTF EndNote XML
Garrido, Q, Damrich, S, Jäger, A, Cerletti, D, Claassen, M, Najman, L and Hamprecht, F A (2022). Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder. Bioinformatics. arXiv preprint. 38 (Suppl 1) i316-i324 DOI Google Scholar BibTeX RTF EndNote XML
Damrich, S (2022). Discovering Structure without Labels. Heidelberg University Google Scholar BibTeX RTF EndNote XML

2021
Arlt, H, Sui, X, Folger, B, Adams, C, Chen, X, Remme, R, Hamprecht, F A, DiMaio, F, Liao, M, Goodman, J M, Farese, R V and Walther, T C (2021). Seipin forms a flexible cage at lipid droplet formation sites. bioRxiv DOI Google Scholar BibTeX RTF EndNote XML
Jenner, E, Fita, E and Hamprecht, F A (2021). Extensions of Karger's Algorithm: Why They Fail in Theory and How They Are Useful in Practice. ICCV. Proceedings. 4602-4611 Google Scholar BibTeX RTF EndNote XML Technical Report (1.1 MB)
Schütz, L M, Louveaux, M, Vilches-Barro, A, Bouziri, S, Cerrone, L, Wolny, A, Kreshuk, A, Hamprecht, F A and Maizel, A (2021). Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana. Plant and Cell Physiology. 62 1269-1279 DOI Google Scholar BibTeX RTF EndNote XML
Damrich, S and Hamprecht, F A (2021). On UMAP's True Loss Function. NeurIPS. Proceedings. 34 Google Scholar BibTeX RTF EndNote XML Technical Report (1.87 MB)
Fita, E, Damrich, S and Hamprecht, F A (2021). Directed Probabilistic Watershed. NeurIPS. Proceedings. 34 Google Scholar BibTeX RTF EndNote XML Technical Report (957.78 KB)
Ruiz, A (2021). Deep K-Segments: A Generalization Of K-Means. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Haußmann, (2021). Bayesian Neural Networks for Probabilistic Machine Learning. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Bailoni, A (2021). Deep Learning for Graph-Based Image Instance Segmentation. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Pape, C (2021). Scalable Instance Segmentation for Microscopy. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Bellagente, M, Haußmann, M, Luchmann, M and Plehn, T (2021). Understanding Event-Generation Networks via Uncertainties. arXiv preprint. https://arxiv.org/abs/2104.04543v1 Google Scholar BibTeX RTF EndNote XML
Kandemir, M, Agkül, A, Haußmann, M and Ünal, G (2021). Evidential Turing Processes. arXiv preprint. https://arxiv.org/abs/2106.01216 Google Scholar BibTeX RTF EndNote XML
Haußmann, M, Gerwinn, S, Look, A, Rakitsch, B and Kandemir, M (2021). Learning Partially Known Stochastic Dynamics with Empirical PAC Bayes. International Conference on Artificial Intelligence and Statistics . PMLR 130 478-486 Google Scholar BibTeX RTF EndNote XML
Andersson, A, Diego, F, Hamprecht, F A and Wählby, C (2021). Istdeco: In Situ Transcriptomics Decoding By Deconvolution. bioRxiv Google Scholar BibTeX RTF EndNote XML
Damrich, S and Hamprecht, F H (2021). UMAP does not reproduce high-dimensional similarities due to negative sampling. arXiv preprint Google Scholar BibTeX RTF EndNote XML
Walter, F C, Damrich, S and Hamprecht, F A (2021). MultiStar: Instance Segmentation of Overlapping Objects with Star-Convex Polygons. ISBI. 295-298 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (1.83 MB)
Vijayan, A, Tofanelli, R, Strauss, S, Cerrone, L, Wolny, A, Strohmeier, J, Kreshuk, A, Hamprecht, F A, Smith, R S and Schneitz, K (2021). A Digital 3D Reference Atlas Reveals Cellular Growth Patterns Shaping the Arabidopsis Ovule. eLife DOI Google Scholar BibTeX RTF EndNote XML
Pape, C, Remme, R, Wolny, A, Olberg, S, Wolf, S, Cerrone, L, Cortese, M, Klaus, S, Lucic, B, Ullrich, S, Anders-Össwein, M, Wolf, S, Cerikan, B, Neufeldt, C J, Ganter, M, Schnitzler, P, Merle, U, Lusic, M, Boulant, S, Stanifer, M, Bartenschlager, R, Hamprecht, F A, Kreshuk, A, Tischer, C, Kräusslich, H - G, Müller, B and Laketa, V (2021). Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera. BioEssays. 43 DOI Google Scholar BibTeX RTF EndNote XML

2020
Wolf, S, Hamprecht, F A and Funke, J (2020). Instance Separation Emerges from Inpainting. arXiv preprint arXiv:2003.00891 Google Scholar BibTeX RTF EndNote XML
Hehn, T M, Kooij, J F P and Hamprecht, F A (2020). End-to-End Learning of Decision Trees and Forests. International Journal of Computer Vision. 128 997-1011 DOI Google Scholar BibTeX RTF EndNote XML
Bollweg, S, Haußmann, M, Kasieczka, G, Luchmann, M, Plehn, T and Thompson, J (2020). Deep-Learning Jets with Uncertainties and More. SciPost Phys. 8. https://scipost.org/10.21468/SciPostPhys.8.1.006 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (1.65 MB)
Wolf, S, Bailoni, A, Pape, C, Rahaman, N, Kreshuk, A, Köthe, U and Hamprecht, F A (2020). The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning. IEEE Transactions on Pattern Analysis and Machine Intelligence. 43 3724-3738 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (2.58 MB)
Wolf, S (2020). Machine Learning for Instance Segmentation. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Wolf, S, Li, Y, Pape, C, Bailoni, A, Kreshuk, A and Hamprecht, F A (2020). The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation. ECCV. Proceedings. 208-224 DOI Google Scholar BibTeX RTF EndNote XML
Wolf, S, Hamprecht, F A and Funke, J (2020). Inpainting Networks Learn to Separate Cells in Microscopy Images. BMCV Google Scholar BibTeX RTF EndNote XML Technical Report (357.23 KB)
Wolny, A, Cerrone, L, Vijayan, A, Tofanelli, R, Vilches-Barro, A, Louveaux, M, Wenzel, C, Strauss, S, Wilson-Sanchez, D, Lymbouridou, R, Steigleder, S S, Pape, C, Bailoni, A, Duran-Nebreda, S, Bassel, G W, Lohmann, J U, Tsiantis, M, Hamprecht, F A, Schneitz, K, Maizel, A and Kreshuk, A (2020). Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution. eLife. 9 DOI Google Scholar BibTeX RTF EndNote XML
Kirschbaum, E, Bailoni, A and Hamprecht, F A (2020). DISCo: Deep Learning, Instance Segmentation, and Correlations for Cell Segmentation in Calcium Imaging. MICCAI. Proceedings. 151-162 Google Scholar BibTeX RTF EndNote XML
Haußmann, M, Gerwinn, S and Kandemir, M (2020). Bayesian Evidential Deep Learning with PAC Regularization . 3rd Symposium on Advances in Approximate Bayesian Inference Google Scholar BibTeX RTF EndNote XML
Bailoni, A, Pape, C, Wolf, S, Kreshuk, A and Hamprecht, F A (2020). Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks. GCPR. Springer. 12544 331-344 DOI Google Scholar BibTeX RTF EndNote XML

2019
Bengio, Y, Deleu, T, Rahaman, N, Ke, R, Lachapelle, S, Bilaniuk, O, Goyal, A and Pal, C (2019). A Meta-Transfer Objective for Learning to Disentangle Causal Mechanisms. arXiv preprint arXiv:1901.10912 Google Scholar BibTeX RTF EndNote XML Technical Report (871.59 KB)
Kiefer, L, Storath, M and Weinmann, A (2019). An efficient algorithm for the piecewise affine-linear Mumford-Shah model based on a Taylor jet splitting. IEEE Transactions on Image Processing. 29 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (2.04 MB)
Berg, S, Kutra, D, Kroeger, T, Straehle, C N, Kausler, B X, Haubold, C, Schiegg, M, Ales, J, Beier, T, Rudy, M, Eren, K, Cervantes, J I, Xu, B, Beuttenmüller, F, Wolny, A, Zhang, C, Köthe, U, Hamprecht, F A and Kreshuk, A (2019). ilastik: interactive machine learning for (bio)image analysis. Nature Methods. 16 1226-1232 DOI Google Scholar BibTeX RTF EndNote XML
Haußmann, M, Gerwinn, S and Kandemir, M (2019). Bayesian Prior Networks with PAC Training. arXiv preprint arXiv:1906.00816 Google Scholar BibTeX RTF EndNote XML
Haußmann, M, Hamprecht, F A and Kandemir, M (2019). Deep Active Learning with Adaptive Acquisition. IJCAI. Proceedings. 2470-2476 DOI Google Scholar BibTeX RTF EndNote XML Technical Report (137.6 KB)
Cerrone, L, Zeilmann, A and Hamprecht, F A (2019). End-to-End Learned Random Walker for Seeded Image Segmentation. CVPR. Proceedings. 12559-12568 DOI Google Scholar BibTeX RTF EndNote XML
Ravindran, A (2019). Novel Deep Learning-Based Instance Segmentation Using Mutex Watershed For Microscopy Cell Images. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Li, J (2019). Robust Single Object Tracking Via Fully Convolutional Siamese Networks. Heidelberg University Google Scholar BibTeX RTF EndNote XML
Bendinger, A L, Debus, C, Glowa, C, Karger, C P, Peter, J and Storath, M (2019). Bolus arrival time estimation in dynamic contrast-enhanced magnetic resonance imaging of small animals based on spline models, in press. Physics in Medicine and Biology. 64 DOI Google Scholar BibTeX RTF EndNote XML

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