A small note on variation in segmentation annotations

We report on the results of a small crowdsourcing experiment conducted at a workshop on machine learning for segmentation held at the Danish Bio Imaging network meeting 2020. During the workshop we asked participants to manually segment mitochondria in three 2D patches. The aim of the experiment was to illustrate that manual annotations should not be seen as the ground truth, but as a reference standard that is subject to substantial variation. In this note we show how the large variation we observed in the segmentations can be reduced by removing the annotators with worst pair-wise agreement. Having removed the annotators with worst performance, we illustrate that the remaining variance is semantically meaningful and can be exploited to obtain segmentations of cell boundary and cell interior

Locally orderless tensor networks for classifying two- and three-dimensional medical images

Tensor networks are factorisations of high rank tensors into networks of lower rank tensors and have primarily been used to analyse quantum many-body problems. Tensor networks have seen a recent surge of interest in relation to supervised learning tasks with a focus on image classification. In this work, we improve upon the matrix product state (MPS) tensor networks that can operate on one-dimensional vectors to be useful for working with 2D and 3D medical images. We treat small image regions as orderless, squeeze their spatial information into feature dimensions and then perform MPS operations on these locally orderless regions. These local representations are then aggregated in a hierarchical manner to retain global structure. The proposed locally orderless tensor network (LoTeNet) is compared with relevant methods on three datasets. The architecture of LoTeNet is fixed in all experiments and we show it requires lesser computational resources to attain performance on par or superior to the compared methods.Comment: Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) (see https://melba-journal.org). Source code at https://github.com/raghavian/LoTeNet_pytorch

Deep Learning from Label Proportions for Emphysema Quantification

We propose an end-to-end deep learning method that learns to estimate emphysema extent from proportions of the diseased tissue. These proportions were visually estimated by experts using a standard grading system, in which grades correspond to intervals (label example: 1-5% of diseased tissue). The proposed architecture encodes the knowledge that the labels represent a volumetric proportion. A custom loss is designed to learn with intervals. Thus, during training, our network learns to segment the diseased tissue such that its proportions fit the ground truth intervals. Our architecture and loss combined improve the performance substantially (8% ICC) compared to a more conventional regression network. We outperform traditional lung densitometry and two recently published methods for emphysema quantification by a large margin (at least 7% AUC and 15% ICC), and achieve near-human-level performance. Moreover, our method generates emphysema segmentations that predict the spatial distribution of emphysema at human level.Comment: Accepted to MICCAI 201

Multi-layered tensor networks for image classification

The recently introduced locally orderless tensor network (LoTeNet) for supervised image classification uses matrix product state (MPS) operations on grids of transformed image patches. The resulting patch representations are combined back together into the image space and aggregated hierarchically using multiple MPS blocks per layer to obtain the final decision rules. In this work, we propose a non-patch based modification to LoTeNet that performs one MPS operation per layer, instead of several patch-level operations. The spatial information in the input images to MPS blocks at each layer is squeezed into the feature dimension, similar to LoTeNet, to maximise retained spatial correlation between pixels when images are flattened into 1D vectors. The proposed multi-layered tensor network (MLTN) is capable of learning linear decision boundaries in high dimensional spaces in a multi-layered setting, which results in a reduction in the computation cost compared to LoTeNet without any degradation in performance.Comment: Updated version with exact computation costs. 6 pages. Accepted to the First Workshop on Quantum Tensor Networks in Machine Learning. In conjunction with 34th NeurIPS, 2020. Source code at https://github.com/raghavian/mlt