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2022
E. Fita, Damrich, S., and Hamprecht, F. A., “The Algebraic Path Problem for Graph Metrics”, 39th International Conference on Machine Learning, PMLR. Proceedings , vol. 162. pp. 19178-19204, 2022.
Q. Garrido, Damrich, S., Jäger, A., Cerletti, D., Claassen, M., Najman, L., and Hamprecht, F. A., “Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder”, Bioinformatics, vol. 38 (Suppl 1), pp. i316-i324, 2022.
2021
M. Haußmann, “Bayesian Neural Networks for Probabilistic Machine Learning”. Heidelberg University, 2021.
A. Vijayan, Tofanelli, R., Strauss, S., Cerrone, L., Wolny, A., Strohmeier, J., Kreshuk, A., Hamprecht, F. A., Smith, R. S., and Schneitz, K., “A Digital 3D Reference Atlas Reveals Cellular Growth Patterns Shaping the Arabidopsis Ovule”, eLife, 2021.
E. Fita, Damrich, S., and Hamprecht, F. A., “Directed Probabilistic Watershed”, NeurIPS. Proceedings, vol. 34. 2021.PDF icon Technical Report (957.78 KB)
M. Kandemir, Agkül, A., Haußmann, M., and Ünal, G., “Evidential Turing Processes”. arXiv preprint, 2021.
E. Jenner, Fita, E., and Hamprecht, F. A., “Extensions of Karger's Algorithm: Why They Fail in Theory and How They Are Useful in Practice”, ICCV. Proceedings. pp. 4602-4611, 2021.PDF icon Technical Report (1.1 MB)
L. M. Schütz, Louveaux, M., Vilches-Barro, A., Bouziri, S., Cerrone, L., Wolny, A., Kreshuk, A., Hamprecht, F. A., and Maizel, A., “Integration of Cell Growth and Asymmetric Division during Lateral Root Initiation in Arabidopsis thaliana”, Plant and Cell Physiology, vol. 62, no. 8, pp. 1269-1279, 2021.
A. Andersson, Diego, F., Hamprecht, F. A., and Wählby, C., “ISTDECO: In Situ Transcriptomics Decoding by Deconvolution”, bioRxiv, 2021.
M. Haußmann, Gerwinn, S., Look, A., Rakitsch, B., and Kandemir, M., “Learning Partially Known Stochastic Dynamics with Empirical PAC Bayes”, International Conference on Artificial Intelligence and Statistics , vol. PMLR 130. pp. 478-486, 2021.
C. Pape, 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., “Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera”, BioEssays, vol. 43, no. 3, 2021.
F. C. Walter, Damrich, S., and Hamprecht, F. A., “MultiStar: Instance Segmentation of Overlapping Objects with Star-Convex Polygons”, ISBI. pp. 295-298, 2021.PDF icon Technical Report (1.83 MB)
D. Kotovenko, Wright, M., Heimbrecht, A., and Ommer, B., “Rethinking Style Transfer: From Pixels to Parameterized Brushstrokes”, Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (CVPR). 2021.
H. Arlt, 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., “Seipin forms a flexible cage at lipid droplet formation sites”. bioRxiv, 2021.
S. Damrich and Hamprecht, F. H., “UMAP does not reproduce high-dimensional similarities due to negative sampling”. arXiv preprint, 2021.
S. Damrich and Hamprecht, F. A., “On UMAP's True Loss Function”, NeurIPS. Proceedings, vol. 34. 2021.PDF icon Technical Report (1.87 MB)
M. Bellagente, Haußmann, M., Luchmann, M., and Plehn, T., “Understanding Event-Generation Networks via Uncertainties”. arXiv preprint, 2021.
B. Brattoli, Büchler, U., Dorkenwald, M., Reiser, P., Filli, L., Helmchen, F., Wahl, A. - S., and Ommer, B., “Unsupervised behaviour analysis and magnification (uBAM) using deep learning”, Nature Machine Intelligence, 2021.
2020
A. Wolny, 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., “Accurate and Versatile 3D Segmentation of Plant Tissues at Cellular Resolution”, eLife, vol. 9, 2020.
A. Krull, Hirsch, P., Rother, C., Schiffrin, A., and Krull, C., “Artificial-intelligence-driven scanning probe microscopy”, Communications Physics, vol. 3, 2020.
C. Schnörr, “Assignment Flows”, Handbook of Variational Methods for Nonlinear Geometric Data. Springer, p. 235—260, 2020.
M. Haußmann, Gerwinn, S., and Kandemir, M., “Bayesian Evidential Deep Learning with PAC Regularization ”, 3rd Symposium on Advances in Approximate Bayesian Inference . 2020.
S. Bollweg, Haußmann, M., Kasieczka, G., Luchmann, M., Plehn, T., and Thompson, J., “Deep-Learning Jets with Uncertainties and More”, SciPost Phys, vol. 8, no. 1, 2020.PDF icon Technical Report (1.65 MB)
E. Kirschbaum, Bailoni, A., and Hamprecht, F. A., “DISCo: Deep Learning, Instance Segmentation, and Correlations for Cell Segmentation in Calcium Imaging”, MICCAI. Proceedings. pp. 151-162, 2020.
T. M. Hehn, Kooij, J. F. P., and Hamprecht, F. A., “End-to-End Learning of Decision Trees and Forests”, International Journal of Computer Vision, vol. 128, pp. 997-1011, 2020.
T. M. Hehn, Kooij, J. F. P., and Hamprecht, F. A., “End-to-End Learning of Decision Trees and Forests”, International Journal of Computer Vision, vol. 128, pp. 997-1011, 2020.
S. Wolf, Hamprecht, F. A., and Funke, J., “Inpainting Networks Learn to Separate Cells in Microscopy Images”, BMCV. 2020.PDF icon Technical Report (357.23 KB)
S. Wolf, Hamprecht, F. A., and Funke, J., “Instance Separation Emerges from Inpainting”, arXiv preprint arXiv:2003.00891, 2020.
S. Wolf, Bailoni, A., Pape, C., Rahaman, N., Kreshuk, A., Köthe, U., and Hamprecht, F. A., “The Mutex Watershed and its Objective: Efficient, Parameter-Free Graph Partitioning”, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 43, pp. 3724-3738, 2020.PDF icon Technical Report (2.58 MB)
S. Haller, Prakash, M., Hutschenreiter, L., Pietzsch, T., Rother, C., Jug, F., Swoboda, P., and Savchynskyy, B., “A Primal-Dual Solver for Large-Scale Tracking-by-Assignment”, AISTATS 2020. 2020.PDF icon PDF (1.04 MB)
S. Haller, Prakash, M., Hutschenreiter, L., Pietzsch, T., Rother, C., Jug, F., Swoboda, P., and Savchynskyy, B., “A Primal-Dual Solver for Large-Scale Tracking-by-Assignment”, AISTATS 2020. 2020.PDF icon PDF (1.04 MB)
A. Bailoni, Pape, C., Wolf, S., Kreshuk, A., and Hamprecht, F. A., “Proposal-Free Volumetric Instance Segmentation from Latent Single-Instance Masks”, GCPR, vol. 12544. Springer, pp. 331-344, 2020.
S. Wolf, Li, Y., Pape, C., Bailoni, A., Kreshuk, A., and Hamprecht, F. A., “The Semantic Mutex Watershed for Efficient Bottom-Up Semantic Instance Segmentation”, ECCV. Proceedings. pp. 208-224, 2020.
2019
C. Schnörr, “Assignment Flows”, Variational Methods for Nonlinear Geometric Data and Applications. Springer, 2019.
M. Haußmann, Gerwinn, S., and Kandemir, M., “Bayesian Prior Networks with PAC Training”, arXiv preprint arXiv:1906.00816, 2019.

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