arXiv subjects

Philip Müller

Publications and source records attributed to Philip Müller.

25 records · Page 2Linked to original sources

arXiv2023

Interpretable 2D Vision Models for 3D Medical Images

Training Artificial Intelligence (AI) models on 3D images presents unique challenges compared to the 2D case: Firstly, the demand for computational resources is significantly higher, and secondly, the availability of large datasets for pre-training is often limited, impeding training success. This study proposes a simple approach of adapting 2D networks with an intermediate feature representation for processing 3D images. Our method employs attention pooling to learn to assign each slice an importance weight and, by that, obtain a weighted average of all 2D slices. These weights directly quantify the contribution of each slice to the contribution and thus make the model prediction inspectable. We show on all 3D MedMNIST datasets as benchmark and two real-world datasets consisting of several hundred high-resolution CT or MRI scans that our approach performs on par with existing methods. Furthermore, we compare the in-built interpretability of our approach to HiResCam, a state-of-the-art retrospective interpretability approach.

eess.IV↗

arXiv2023

Anatomy-Driven Pathology Detection on Chest X-rays

Pathology detection and delineation enables the automatic interpretation of medical scans such as chest X-rays while providing a high level of explainability to support radiologists in making informed decisions. However, annotating pathology bounding boxes is a time-consuming task such that large public datasets for this purpose are scarce. Current approaches thus use weakly supervised object detection to learn the (rough) localization of pathologies from image-level annotations, which is however limited in performance due to the lack of bounding box supervision. We therefore propose anatomy-driven pathology detection (ADPD), which uses easy-to-annotate bounding boxes of anatomical regions as proxies for pathologies. We study two training approaches: supervised training using anatomy-level pathology labels and multiple instance learning (MIL) with image-level pathology labels. Our results show that our anatomy-level training approach outperforms weakly supervised methods and fully supervised detection with limited training samples, and our MIL approach is competitive with both baseline approaches, therefore demonstrating the potential of our approach.

cs.CV↗

arXiv2023

Interactive and Explainable Region-guided Radiology Report Generation

The automatic generation of radiology reports has the potential to assist radiologists in the time-consuming task of report writing. Existing methods generate the full report from image-level features, failing to explicitly focus on anatomical regions in the image. We propose a simple yet effective region-guided report generation model that detects anatomical regions and then describes individual, salient regions to form the final report. While previous methods generate reports without the possibility of human intervention and with limited explainability, our method opens up novel clinical use cases through additional interactive capabilities and introduces a high degree of transparency and explainability. Comprehensive experiments demonstrate our method's effectiveness in report generation, outperforming previous state-of-the-art models, and highlight its interactive capabilities. The code and checkpoints are available at https://github.com/ttanida/rgrg .

cs.CV↗

arXiv2023

Robust Detection Outcome: A Metric for Pathology Detection in Medical Images

Detection of pathologies is a fundamental task in medical imaging and the evaluation of algorithms that can perform this task automatically is crucial. However, current object detection metrics for natural images do not reflect the specific clinical requirements in pathology detection sufficiently. To tackle this problem, we propose Robust Detection Outcome (RoDeO); a novel metric for evaluating algorithms for pathology detection in medical images, especially in chest X-rays. RoDeO evaluates different errors directly and individually, and reflects clinical needs better than current metrics. Extensive evaluation on the ChestX-ray8 dataset shows the superiority of our metrics compared to existing ones. We released the code at https://github.com/FeliMe/RoDeO and published RoDeO as pip package (rodeometric).

cs.CV↗

arXiv2023

The Role of Local Alignment and Uniformity in Image-Text Contrastive Learning on Medical Images

Image-text contrastive learning has proven effective for pretraining medical image models. When targeting localized downstream tasks like semantic segmentation or object detection, additional local contrastive losses that align image regions with sentences have shown promising results. We study how local contrastive losses are related to global (per-sample) contrastive losses and which effects they have on localized medical downstream tasks. Based on a theoretical comparison, we propose to remove some components of local losses and replace others by a novel distribution prior which enforces uniformity of representations within each sample. We empirically study this approach on chest X-ray tasks and find it to be very effective, outperforming methods without local losses on 12 of 18 tasks.

cs.CV↗

arXiv2022

Joint Learning of Localized Representations from Medical Images and Reports

Contrastive learning has proven effective for pre-training image models on unlabeled data with promising results for tasks such as medical image classification. Using paired text (like radiological reports) during pre-training improves the results even further. Still, most existing methods target image classification downstream tasks and may not be optimal for localized tasks like semantic segmentation or object detection. We therefore propose Localized representation learning from Vision and Text (LoVT), to our best knowledge, the first text-supervised pre-training method that targets localized medical imaging tasks. Our method combines instance-level image-report contrastive learning with local contrastive learning on image region and report sentence representations. We evaluate LoVT and commonly used pre-training methods on an evaluation framework of 18 localized tasks on chest X-rays from five public datasets. LoVT performs best on 10 of the 18 studied tasks making it the preferred method of choice for localized tasks.

cs.CV↗

arXiv2021

Rotation-Equivariant Deep Learning for Diffusion MRI

Convolutional networks are successful, but they have recently been outperformed by new neural networks that are equivariant under rotations and translations. These new networks work better because they do not struggle with learning each possible orientation of each image feature separately. So far, they have been proposed for 2D and 3D data. Here we generalize them to 6D diffusion MRI data, ensuring joint equivariance under 3D roto-translations in image space and the matching 3D rotations in $q$-space, as dictated by the image formation. Such equivariant deep learning is appropriate for diffusion MRI, because microstructural and macrostructural features such as neural fibers can appear at many different orientations, and because even non-rotation-equivariant deep learning has so far been the best method for many diffusion MRI tasks. We validate our equivariant method on multiple-sclerosis lesion segmentation. Our proposed neural networks yield better results and require fewer scans for training compared to non-rotation-equivariant deep learning. They also inherit all the advantages of deep learning over classical diffusion MRI methods. Our implementation is available at https://github.com/philip-mueller/equivariant-deep-dmri and can be used off the shelf without understanding the mathematical background.

cs.CV↗