Fred Hamprecht

Quentin Garrido, Sebastian Damrich, Alexander Jäger et al.

Motivation: Single cell RNA sequencing (scRNA-seq) data makes studying the development of cells possible at unparalleled resolution. Given that many cellular differentiation processes are hierarchical, their scRNA-seq data is expected to be approximately tree-shaped in gene expression space. Inference and representation of this tree-structure in two dimensions is highly desirable for biological interpretation and exploratory analysis.Results:Our two contributions are an approach for identifying a meaningful tree structure from high-dimensional scRNA-seq data, and a visualization method respecting the tree-structure. We extract the tree structure by means of a density based minimum spanning tree on a vector quantization of the data and show that it captures biological information well. We then introduce DTAE, a tree-biased autoencoder that emphasizes the tree structure of the data in low dimensional space. We compare to other dimension reduction methods and demonstrate the success of our method both qualitatively and quantitatively on real and toy data.Availability: Our implementation relying on PyTorch and Higra is available at https://github.com/hci-unihd/DTAE.

Annika Reinke, Minu D. Tizabi, Carole H. Sudre et al.

While the importance of automatic image analysis is continuously increasing, recent meta-research revealed major flaws with respect to algorithm validation. Performance metrics are particularly key for meaningful, objective, and transparent performance assessment and validation of the used automatic algorithms, but relatively little attention has been given to the practical pitfalls when using specific metrics for a given image analysis task. These are typically related to (1) the disregard of inherent metric properties, such as the behaviour in the presence of class imbalance or small target structures, (2) the disregard of inherent data set properties, such as the non-independence of the test cases, and (3) the disregard of the actual biomedical domain interest that the metrics should reflect. This living dynamically document has the purpose to illustrate important limitations of performance metrics commonly applied in the field of image analysis. In this context, it focuses on biomedical image analysis problems that can be phrased as image-level classification, semantic segmentation, instance segmentation, or object detection task. The current version is based on a Delphi process on metrics conducted by an international consortium of image analysis experts from more than 60 institutions worldwide.

Steffen Wolf, Lukas Schott, Ullrich Köthe et al.

Learned boundary maps are known to outperform hand- crafted ones as a basis for the watershed algorithm. We show, for the first time, how to train watershed computation jointly with boundary map prediction. The estimator for the merging priorities is cast as a neural network that is con- volutional (over space) and recurrent (over iterations). The latter allows learning of complex shape priors. The method gives the best known seeded segmentation results on the CREMI segmentation challenge.

Xinghua Lou, Fred Hamprecht

Structured learning is appropriate when predicting structured outputs such as trees, graphs, or sequences. Most prior work requires the training set to consist of complete trees, graphs or sequences. Specifying such detailed ground truth can be tedious or infeasible for large outputs. Our main contribution is a large margin formulation that makes structured learning from only partially annotated data possible. The resulting optimization problem is non-convex, yet can be efficiently solve by concave-convex procedure (CCCP) with novel speedup strategies. We apply our method to a challenging tracking-by-assignment problem of a variable number of divisible objects. On this benchmark, using only 25% of a full annotation we achieve a performance comparable to a model learned with a full annotation. Finally, we offer a unifying perspective of previous work using the hinge, ramp, or max loss for structured learning, followed by an empirical comparison on their practical performance.