Maximilian Nielsen

Maximilian Nielsen, Laura Wenderoth, Thilo Sentker et al.

Is self-supervised deep learning (DL) for medical image analysis already a serious alternative to the de facto standard of end-to-end trained supervised DL? We tackle this question for medical image classification, with a particular focus on one of the currently most limiting factors of the field: the (non-)availability of labeled data. Based on three common medical imaging modalities (bone marrow microscopy, gastrointestinal endoscopy, dermoscopy) and publicly available data sets, we analyze the performance of self-supervised DL within the self-distillation with no labels (DINO) framework. After learning an image representation without use of image labels, conventional machine learning classifiers are applied. The classifiers are fit using a systematically varied number of labeled data (1-1000 samples per class). Exploiting the learned image representation, we achieve state-of-the-art classification performance for all three imaging modalities and data sets with only a fraction of between 1% and 10% of the available labeled data and about 100 labeled samples per class.

Hümeyra Husseini-Wüsthoff, Sabine Riethdorf, Andreas Schneeweiss et al.

Detection and differentiation of circulating tumor cells (CTCs) and non-CTCs in blood draws of cancer patients pose multiple challenges. While the gold standard relies on tedious manual evaluation of an automatically generated selection of images, machine learning (ML) techniques offer the potential to automate these processes. However, human assessment remains indispensable when the ML system arrives at uncertain or wrong decisions due to an insufficient set of labeled training data. This study introduces a human-in-the-loop (HiL) strategy for improving ML-based CTC detection. We combine self-supervised deep learning and a conventional ML-based classifier and propose iterative targeted sampling and labeling of new unlabeled training samples by human experts. The sampling strategy is based on the classification performance of local latent space clusters. The advantages of the proposed approach compared to naive random sampling are demonstrated for liquid biopsy data from patients with metastatic breast cancer.

Aneeq Zia, Max Berniker, Rogerio Garcia Nespolo et al.

Robotic assisted (RA) surgery promises to transform surgical intervention. Intuitive Surgical is committed to fostering these changes and the machine learning models and algorithms that will enable them. With these goals in mind we have invited the surgical data science community to participate in a yearly competition hosted through the Medical Imaging Computing and Computer Assisted Interventions (MICCAI) conference. With varying changes from year to year, we have challenged the community to solve difficult machine learning problems in the context of advanced RA applications. Here we document the results of these challenges, focusing on surgical tool localization (SurgToolLoc). The publicly released dataset that accompanies these challenges is detailed in a separate paper arXiv:2501.09209 [1].

Nils Gessert, Maximilian Nielsen, Mohsin Shaikh et al.

In this paper, we describe our method for the ISIC 2019 Skin Lesion Classification Challenge. The challenge comes with two tasks. For task 1, skin lesions have to be classified based on dermoscopic images. For task 2, dermoscopic images and additional patient meta data have to be used. A diverse dataset of 25000 images was provided for training, containing images from eight classes. The final test set contains an additional, unknown class. We address this challenging problem with a simple, data driven approach by including external data with skin lesions types that are not present in the training set. Furthermore, multi-class skin lesion classification comes with the problem of severe class imbalance. We try to overcome this problem by using loss balancing. Also, the dataset contains images with very different resolutions. We take care of this property by considering different model input resolutions and different cropping strategies. To incorporate meta data such as age, anatomical site, and sex, we use an additional dense neural network and fuse its features with the CNN. We aggregate all our models with an ensembling strategy where we search for the optimal subset of models. Our best ensemble achieves a balanced accuracy of 74.2% using five-fold cross-validation. On the official test set our method is ranked first for both tasks with a balanced accuracy of 63.6% for task 1 and 63.4% for task 2.

Rüdiger Schmitz, Frederic Madesta, Maximilian Nielsen et al.

Histopathologic diagnosis relies on simultaneous integration of information from a broad range of scales, ranging from nuclear aberrations ($\approx \mathcal{O}(0.1{μm})$) through cellular structures ($\approx \mathcal{O}(10{μm})$) to the global tissue architecture ($\gtrapprox \mathcal{O}(1{mm})$). To explicitly mimic how human pathologists combine multi-scale information, we introduce a family of multi-encoder FCNs with deep fusion. We present a simple block for merging model paths with differing spatial scales in a spatial relationship-preserving fashion, which can readily be included in standard encoder-decoder networks. Additionally, a context classification gate block is proposed as an alternative for the incorporation of global context. Our experiments were performed on three publicly available whole-slide images of recent challenges (PAIP 2019, BACH 2020, CAMELYON 2016). The multi-scale architectures consistently outperformed the baseline single-scale U-Nets by a large margin. They benefit from local as well as global context and particularly a combination of both. If feature maps from different scales are fused, doing so in a manner preserving spatial relationships was found to be beneficial. Deep guidance by a context classification loss appeared to improve model training at low computational costs. All multi-scale models had a reduced GPU memory footprint compared to ensembles of individual U-Nets trained on different image scales. Additional path fusions were shown to be possible at low computational cost, opening up possibilities for further, systematic and task-specific architecture optimization. The findings demonstrate the potential of the presented family of human-inspired, end-to-end trainable, multi-scale multi-encoder FCNs to improve deep histopathologic diagnosis by extensive integration of largely different spatial scales.