Multi-focus cluster labeling.

Document collections resulting from searches in the biomedical literature, for instance, in PubMed, are often so large that some organization of the returned information is necessary. Clustering is an efficient tool for organizing search results. To help the user to decide how to continue the search for relevant documents, the content of each cluster can be characterized by a set of representative keywords or cluster labels. As different users may have different interests, it can be desirable with solutions that make it possible to produce labels from a selection of different topical categories. We therefore introduce the concept of multi-focus cluster labeling to give users the possibility to get an overview of the contents through labels from multiple viewpoints. The concept for multi-focus cluster labeling has been established and has been demonstrated on three different document collections. We illustrate that multi-focus visualizations can give an overview of clusters along axes that general labels are not able to convey. The approach is generic and should be applicable to any biomedical (or other) domain with any selection of foci where appropriate focus vocabularies can be established. A user evaluation also indicates that such a multi-focus concept is useful.

User-Intended Doppler Measurement Type Prediction Combining CNNs With Smart Post-Processing.

Spectral Doppler measurements are an important part of the standard echocardiographic examination. These measurements give insight into myocardial motion and blood flow, providing clinicians with parameters for diagnostic decision making. Many of these measurements are performed automatically with high accuracy, increasing the efficiency of the diagnostic pipeline. However, full automation is not yet available because the user must manually select which measurement should be performed on each image. In this work, we develop a pipeline based on convolutional neural networks (CNNs) to automatically classify the measurement type from cardiac Doppler scans. We show how the multi-modal information in each spectral Doppler recording can be combined using a meta parameter post-processing mapping scheme and heatmaps to encode coordinate locations. Additionally, we experiment with several architectures to examine the tradeoff between accuracy, speed, and memory usage for resource-constrained environments. Finally, we propose a confidence metric using the values in the last fully connected layer of the network and show that our confidence metric can prevent many misclassifications. Our algorithm enables a fully automatic pipeline from acquisition to Doppler spectrum measurements. We achieve 96% accuracy on a test set drawn from separate clinical sites, indicating that the proposed method is suitable for clinical adoption.

Explaining decisions of deep neural networks used for fish age prediction.

Age-reading of fish otoliths (ear stones) is important for the sustainable management of fish resources. However, the procedure is challenging and requires experienced readers to carefully examine annual growth zones. In a recent study, convolutional neural networks (CNNs) have been demonstrated to perform reasonably well on automatically predicting fish age from otolith images. In the present study, we carefully investigate the prediction rule learned by such neural networks to provide insight into the features that identify certain fish age ranges. For this purpose, a recent technique for visualizing and analyzing the predictions of the neural networks was applied to different versions of the otolith images. The results indicate that supplementary knowledge about the internal structure improves the results for the youngest age groups, compared to using only the contour shape attribute of the otolith. However, the contour shape and size attributes are, in general, sufficient for older age groups. In addition, within specific age ranges we find that the network tends to focus on particular areas of the otoliths and that the most discriminating factors seem to be related to the central part and the outer edge of the otolith. Explaining age predictions from otolith images as done in this study will hopefully help build confidence in the potential of deep learning algorithms for automatic age prediction, as well as improve the quality of the age estimation.