The robust extraction of numeric values from clinical narratives is a well known problem in clinical data warehouses. In this paper we describe a dynamic and domain-independent approach to deliver numerical described values from clinical narratives. In contrast to alternative systems, we neither use manual defined rules nor any kind of ontologies or nomenclatures. Instead we propose a topic-based system, that tackles the information extraction as a text classification problem. Hence we use machine learning to identify the crucial context features of a topicspecific numeric value by a given set of example sentences, so that the manual effort reduces to the selection of appropriate sample sentences. We describe context features of a certain numeric value by term frequency vectors which are generated by multiple document segmentation procedures. Due to this simultaneous segmentation approaches, there can be more than one context vector for a numeric value. In those cases, we choose the context vector with the highest classification confidence and suppress the rest.To test our approach, we used a dataset from a german hospital containing 12 743 narrative reports about laboratory results of Leukemia patients. We used Support Vector Machines (SVM) for classification and achieved an average accuracy of 96% on a manually labeled subset of 2073 documents, using 10-fold cross validation. This is a significant improvement over an alternative rule based system.
Purpose To improve automated lung segmentation on 2D lung MR images using balanced augmentation and artificially-generated consolidations for training of a convolutional neural network (CNN). Materials and methods From 233 healthy volunteers and 100 patients, 1891 coronal MR images were acquired. Of these, 1666 images without consolidations were used to build a binary semantic CNN for lung segmentation and 225 images (187 without consolidations, 38 with consolidations) were used for testing. To increase CNN performance of segmenting lung parenchyma with consolidations, balanced augmentation was performed and artificially-generated consolidations were added to all training images. The proposed CNN (CNNBal/Cons) was compared to two other CNNs: CNNUnbal/NoCons—without balanced augmentation and artificially-generated consolidations and CNNBal/NoCons—with balanced augmentation but without artificially-generated consolidations. Segmentation results were assessed using Sørensen-Dice coefficient (SDC) and Hausdorff distance coefficient. Results Regarding the 187 MR test images without consolidations, the mean SDC of CNNUnbal/NoCons (92.1 ± 6% (mean ± standard deviation)) was significantly lower compared to CNNBal/NoCons (94.0 ± 5.3%, P = 0.0013) and CNNBal/Cons (94.3 ± 4.1%, P = 0.0001). No significant difference was found between SDC of CNNBal/Cons and CNNBal/NoCons (P = 0.54). For the 38 MR test images with consolidations, SDC of CNNUnbal/NoCons (89.0 ± 7.1%) was not significantly different compared to CNNBal/NoCons (90.2 ± 9.4%, P = 0.53). SDC of CNNBal/Cons (94.3 ± 3.7%) was significantly higher compared to CNNBal/NoCons (P = 0.0146) and CNNUnbal/NoCons (P = 0.001). Conclusions Expanding training datasets via balanced augmentation and artificially-generated consolidations improved the accuracy of CNNBal/Cons, especially in datasets with parenchymal consolidations. This is an important step towards a robust automated postprocessing of lung MRI datasets in clinical routine.
Accurate fully automated lung segmentation is needed to facilitate Fourier-Decomposition employment-based techniques in clinical routine among different centers. However, the lung parenchyma segmentation remains challenging for convolutional neural networks (CNN) when consolidations are present. To improve training balanced augmentation (BA) and artificially-generated consolidations (AGC) were introduced. The proposed CNN was compared to conventional CNNs without BA and AGC using Sørensen-Dice coefficient (SDC) and Hausdorff coefficient (HD). The SDC / HD of the proposed model is significantly higher (p of 0.0001 and p of 0.0146 / p of 0.0009 and p of 0.0152) when compared to CNNs without BA and AGC.
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