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Self-supervised pre-training of deep learning models with contrastive learning is a widely used technique in image analysis. Current findings indicate a strong potential for contrastive pre-training on medical images. However, further research is necessary to incorporate the particular characteristics of these images. We hypothesize that the similarity of medical images hinders the success of contrastive learning in the medical imaging domain. To this end, we investigate different strategies based on deep embedding, information theory, and hashing in order to identify and reduce redundancy in medical pre-training datasets. The effect of these different reduction strategies on contrastive learning is evaluated on two pre-training datasets and several downstream classification tasks. In all of our experiments, dataset reduction leads to a considerable performance gain in downstream tasks, e.g., an AUC score improvement from 0.78 to 0.83 for the COVID CT Classification Grand Challenge, 0.97 to 0.98 for the OrganSMNIST Classification Challenge and 0.73 to 0.83 for a brain hemorrhage classification task. Furthermore, pre-training is up to nine times faster due to the dataset reduction. In conclusion, the proposed approach highlights the importance of dataset quality and provides a transferable approach to improve contrastive pre-training for classification downstream tasks on medical images.

Processing histopathological Whole Slide Images (WSI) leads to massive storage requirements for clinics worldwide. Even after lossy image compression during image acquisition, additional lossy compression is frequently possible without substantially affecting the performance of deep learning-based (DL) downstream tasks. In this paper, we show that the commonly used JPEG algorithm is not best suited for further compression and we propose Stain Quantized Latent Compression (SQLC ), a novel DL based histopathology data compression approach. SQLC compresses staining and RGB channels before passing it through a compression autoencoder (CAE ) in order to obtain quantized latent representations for maximizing the compression. We show that our approach yields superior performance in a classification downstream task, compared to traditional approaches like JPEG, while image quality metrics like the Multi-Scale Structural Similarity Index (MS-SSIM) is largely preserved. Our method is online available.

Materials and methods: First, a dual-time approach was assessed, for which the CNN was provided sequences of the MRI that initially depicted new MM (diagnosis MRI) as well as of a prediagnosis MRI: inclusion of only contrast-enhanced T1-weighted images (CNNdual_ce) was compared with inclusion of also the native T1-weighted images, T2-weighted images, and FLAIR sequences of both time points (CNNdual_all).Second, results were compared with the corresponding single time approaches, in which the CNN was provided exclusively the respective sequences of the diagnosis MRI.Casewise diagnostic performance parameters were calculated from 5-fold cross-validation. Results: In total, 94 cases with 494 MMs were included. Overall, the highest diagnostic performance was achieved by inclusion of only the contrast-enhanced T1-weighted images of the diagnosis and of a prediagnosis MRI (CNNdual_ce, sensitivity = 73%, PPV = 25%, F1-score = 36%). Using exclusively contrast-enhanced T1-weighted images as input resulted in significantly less false-positives (FPs) compared with inclusion of further sequences beyond contrast-enhanced T1-weighted images (FPs = 5/7 for CNNdual_ce/CNNdual_all, P < 1e-5). Comparison of contrast-enhanced dual and mono time approaches revealed that exclusion of prediagnosis MRI significantly increased FPs (FPs = 5/10 for CNNdual_ce/CNNce, P < 1e-9).Approaches with only native sequences were clearly inferior to CNNs that were provided contrast-enhanced sequences. Conclusions: Automated MM detection on contrast-enhanced T1-weighted images performed with high sensitivity. Frequent FPs due to artifacts and vessels were significantly reduced by additional inclusion of prediagnosis MRI, but not by inclusion of further sequences beyond contrast-enhanced T1-weighted images. Future studies might investigate different change detection architectures for computer-aided detection.

In machine learning larger databases are usually associated with higher classification accuracy due to better generalization. This generalization may lead to non-optimal classifiers in some medical applications with highly variable expressions of pathologies. This paper presents a method for learning from a large training base by adaptively selecting optimal training samples for given input data. In this way heterogeneous databases are supported two-fold. First, by being able to deal with sparsely annotated data allows a quick inclusion of new data set and second, by training an input-dependent classifier. The proposed approach is evaluated using the SISS challenge. The proposed algorithm leads to a significant improvement of the classification accuracy.

We propose a new method that employs transfer learning techniques to effectively correct sampling selection errors introduced by sparse annotations during supervised learning for automated tumor segmentation. The practicality of current learning-based automated tissue classification approaches is severely impeded by their dependency on manually segmented training databases that need to be recreated for each scenario of application, site, or acquisition setup. The comprehensive annotation of reference datasets can be highly labor-intensive, complex, and error-prone. The proposed method derives high-quality classifiers for the different tissue classes from sparse and unambiguous annotations and employs domain adaptation techniques for effectively correcting sampling selection errors introduced by the sparse sampling. The new approach is validated on labeled, multi-modal MR images of 19 patients with malignant gliomas and by comparative analysis on the BraTS 2013 challenge data sets. Compared to training on fully labeled data, we reduced the time for labeling and training by a factor greater than 70 and 180 respectively without sacrificing accuracy. This dramatically eases the establishment and constant extension of large annotated databases in various scenarios and imaging setups and thus represents an important step towards practical applicability of learning-based approaches in tissue classification.

As with any physical instrument, hyperspectral cameras induce different kinds of noise in the acquired data. Therefore, Hyperspectral denoising is a crucial step for analyzing hyperspectral images (HSIs). Conventional computational methods rarely use GPUs to improve efficiency and are not fully open-source. Alternatively, deep learning-based methods are often open-source and use GPUs, but their training and utilization for real-world applications remain non-trivial for many researchers. Consequently, we propose HyDe: the first open-source, GPU-accelerated Python-based, hyperspectral image denoising toolbox, which aims to provide a large set of methods with an easy-to-use environment. HyDe includes a variety of methods ranging from low-rank wavelet-based methods to deep neural network (DNN) models. HyDe's interface dramatically improves the interoperability of these methods and the performance of the underlying functions. In fact, these methods maintain similar HSI denoising performance to their original implementations while consuming nearly ten times less energy. Furthermore, we present a method for training DNNs for denoising HSIs which are not spatially related to the training dataset, i.e., training on ground-level HSIs for denoising HSIs with other perspectives including airborne, drone-borne, and space-borne. To utilize the trained DNNs, we show a sliding window method to effectively denoise HSIs which would otherwise require more than 40 GB. The package can be found at: \urlhttps://github.com/Helmholtz-AI-Energy/HyDe.