Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Continuous-Time Deep Glioma Growth Models

The ability to estimate how a tumor might evolve in the future could have tremendous clinical benefits, from improved treatment decisions to better dose distribution in radiation therapy. Recent work has approached the glioma growth modeling problem via deep learning and variational inference, thus learning growth dynamics entirely from a real patient data distribution. So far, this approach was constrained to predefined image acquisition intervals and sequences of fixed length, which limits its applicability in more realistic scenarios. We overcome these limitations by extending Neural Processes, a class of conditional generative models for stochastic time series, with a hierarchical multi-scale representation encoding including a spatio-temporal attention mechanism. The result is a learned growth model that can be conditioned on an arbitrary number of observations, and that can produce a distribution of temporally consistent growth trajectories on a continuous time axis. On a dataset of 379 patients, the approach successfully captures both global and finer-grained variations in the images, exhibiting superior performance compared to other learned growth models.

GP-ConvCNP: Better Generalization for Convolutional Conditional Neural Processes on Time Series Data

Neural Processes (NPs) are a family of conditional generative models that are able to model a distribution over functions, in a way that allows them to perform predictions at test time conditioned on a number of context points. A recent addition to this family, Convolutional Conditional Neural Processes (ConvCNP), have shown remarkable improvement in performance over prior art, but we find that they sometimes struggle to generalize when applied to time series data. In particular, they are not robust to distribution shifts and fail to extrapolate observed patterns into the future. By incorporating a Gaussian Process into the model, we are able to remedy this and at the same time improve performance within distribution. As an added benefit, the Gaussian Process reintroduces the possibility to sample from the model, a key feature of other members in the NP family.

The Federated Tumor Segmentation (FeTS) Challenge

This manuscript describes the first challenge on Federated Learning, namely the Federated Tumor Segmentation (FeTS) challenge 2021. International challenges have become the standard for validation of biomedical image analysis methods. However, the actual performance of participating (even the winning) algorithms on "real-world" clinical data often remains unclear, as the data included in challenges are usually acquired in very controlled settings at few institutions. The seemingly obvious solution of just collecting increasingly more data from more institutions in such challenges does not scale well due to privacy and ownership hurdles. Towards alleviating these concerns, we are proposing the FeTS challenge 2021 to cater towards both the development and the evaluation of models for the segmentation of intrinsically heterogeneous (in appearance, shape, and histology) brain tumors, namely gliomas. Specifically, the FeTS 2021 challenge uses clinically acquired, multi-institutional magnetic resonance imaging (MRI) scans from the BraTS 2020 challenge, as well as from various remote independent institutions included in the collaborative network of a real-world federation (https://www.fets.ai/). The goals of the FeTS challenge are directly represented by the two included tasks: 1) the identification of the optimal weight aggregation approach towards the training of a consensus model that has gained knowledge via federated learning from multiple geographically distinct institutions, while their data are always retained within each institution, and 2) the federated evaluation of the generalizability of brain tumor segmentation models "in the wild", i.e. on data from institutional distributions that were not part of the training datasets.

A Case for the Score: Identifying Image Anomalies using Variational Autoencoder Gradients

Through training on unlabeled data, anomaly detection has the potential to impact computer-aided diagnosis by outlining suspicious regions. Previous work on deep-learning-based anomaly detection has primarily focused on the reconstruction error. We argue instead, that pixel-wise anomaly ratings derived from a Variational Autoencoder based score approximation yield a theoretically better grounded and more faithful estimate. In our experiments, Variational Autoencoder gradient-based rating outperforms other approaches on unsupervised pixel-wise tumor detection on the BraTS-2017 dataset with a ROC-AUC of 0.94.

High- and Low-level image component decomposition using VAEs for improved reconstruction and anomaly detection

Variational Auto-Encoders have often been used for unsupervised pretraining, feature extraction and out-of-distribution and anomaly detection in the medical field. However, VAEs often lack the ability to produce sharp images and learn high-level features. We propose to alleviate these issues by adding a new branch to conditional hierarchical VAEs. This enforces a division between higher-level and lower-level features. Despite the additional computational overhead compared to a normal VAE it results in sharper and better reconstructions and can capture the data distribution similarly well (indicated by a similar or slightly better OoD detection performance).

Unsupervised Anomaly Localization using Variational Auto-Encoders

An assumption-free automatic check of medical images for potentially overseen anomalies would be a valuable assistance for a radiologist. Deep learning and especially Variational Auto-Encoders (VAEs) have shown great potential in the unsupervised learning of data distributions. In principle, this allows for such a check and even the localization of parts in the image that are most suspicious. Currently, however, the reconstruction-based localization by design requires adjusting the model architecture to the specific problem looked at during evaluation. This contradicts the principle of building assumption-free models. We propose complementing the localization part with a term derived from the Kullback-Leibler (KL)-divergence. For validation, we perform a series of experiments on FashionMNIST as well as on a medical task including >1000 healthy and >250 brain tumor patients. Results show that the proposed formalism outperforms the state of the art VAE-based localization of anomalies across many hyperparameter settings and also shows a competitive max performance.

Context-encoding Variational Autoencoder for Unsupervised Anomaly Detection

Unsupervised learning can leverage large-scale data sources without the need for annotations. In this context, deep learning-based auto encoders have shown great potential in detecting anomalies in medical images. However, state-of-the-art anomaly scores are still based on the reconstruction error, which lacks in two essential parts: it ignores the model-internal representation employed for reconstruction, and it lacks formal assertions and comparability between samples. We address these shortcomings by proposing the Context-encoding Variational Autoencoder (ceVAE) which combines reconstruction- with density-based anomaly scoring. This improves the sample- as well as pixel-wise results. In our experiments on the BraTS-2017 and ISLES-2015 segmentation benchmarks, the ceVAE achieves unsupervised ROC-AUCs of 0.95 and 0.89, respectively, thus outperforming state-of-the-art methods by a considerable margin.

nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation

The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.

Exploiting the potential of unlabeled endoscopic video data with self-supervised learning

Surgical data science is a new research field that aims to observe all aspects of the patient treatment process in order to provide the right assistance at the right time. Due to the breakthrough successes of deep learning-based solutions for automatic image annotation, the availability of reference annotations for algorithm training is becoming a major bottleneck in the field. The purpose of this paper was to investigate the concept of self-supervised learning to address this issue. Our approach is guided by the hypothesis that unlabeled video data can be used to learn a representation of the target domain that boosts the performance of state-of-the-art machine learning algorithms when used for pre-training. Core of the method is an auxiliary task based on raw endoscopic video data of the target domain that is used to initialize the convolutional neural network (CNN) for the target task. In this paper, we propose the re-colorization of medical images with a generative adversarial network (GAN)-based architecture as auxiliary task. A variant of the method involves a second pre-training step based on labeled data for the target task from a related domain. We validate both variants using medical instrument segmentation as target task. The proposed approach can be used to radically reduce the manual annotation effort involved in training CNNs. Compared to the baseline approach of generating annotated data from scratch, our method decreases exploratively the number of labeled images by up to 75% without sacrificing performance. Our method also outperforms alternative methods for CNN pre-training, such as pre-training on publicly available non-medical or medical data using the target task (in this instance: segmentation). As it makes efficient use of available (non-)public and (un-)labeled data, the approach has the potential to become a valuable tool for CNN (pre-)training.