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Purpose: Radiology reports mostly contain free-text, which makes it challenging to obtain structured data. Natural language processing (NLP) techniques transform free-text reports into machine-readable document vectors that are important for creating reliable, scalable methods for data analysis. The aim of this study is to classify unstructured radiograph reports according to fractures of the distal fibula and to find the best text mining method.
Materials & Methods: We established a novel German language report dataset: a designated search engine was used to identify radiographs of the ankle and the reports were manually labeled according to fractures of the distal fibula. This data was used to establish a machine learning pipeline, which implemented the text representation methods bag-of-words (BOW), term frequency-inverse document frequency (TF-IDF), principal component analysis (PCA), non-negative matrix factorization (NMF), latent Dirichlet allocation (LDA), and document embedding (doc2vec). The extracted document vectors were used to train neural networks (NN), support vector machines (SVM), and logistic regression (LR) to recognize distal fibula fractures. The results were compared via cross-tabulations of the accuracy (acc) and area under the curve (AUC).
Results: In total, 3268 radiograph reports were included, of which 1076 described a fracture of the distal fibula. Comparison of the text representation methods showed that BOW achieved the best results (AUC = 0.98; acc = 0.97), followed by TF-IDF (AUC = 0.97; acc = 0.96), NMF (AUC = 0.93; acc = 0.92), PCA (AUC = 0.92; acc = 0.9), LDA (AUC = 0.91; acc = 0.89) and doc2vec (AUC = 0.9; acc = 0.88). When comparing the different classifiers, NN (AUC = 0,91) proved to be superior to SVM (AUC = 0,87) and LR (AUC = 0,85).
Conclusion: An automated classification of unstructured reports of radiographs of the ankle can reliably detect findings of fractures of the distal fibula. A particularly suitable feature extraction method is the BOW model.
Key Points:
- The aim was to classify unstructured radiograph reports according to distal fibula fractures.
- Our automated classification system can reliably detect fractures of the distal fibula.
- A particularly suitable feature extraction method is the BOW model.
The Logical Observation Identifiers, Names and Codes (LOINC) is a common terminology used for standardizing laboratory terms. Within the consortium of the HiGHmed project, LOINC is one of the central terminologies used for health data sharing across all university sites. Therefore, linking the LOINC codes to the site-specific tests and measures is one crucial step to reach this goal. In this work we report our ongoing efforts in implementing LOINC to our laboratory information system and research infrastructure, as well as our challenges and the lessons learned. 407 local terms could be mapped to 376 LOINC codes of which 209 are already available to routine laboratory data. In our experience, mapping of local terms to LOINC is a widely manual and time consuming process for reasons of language and expert knowledge of local laboratory procedures.