The British journal of radiology · 2023
Transformer versus traditional natural language processing: how much data is enough for automated radiology report classification?
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Yang Eric, Li Matthew D, Raghavan Shruti, Deng Francis, Lang Min, Succi Marc D, Huang Ambrose J, Kalpathy-Cramer Jayashree
Аннотация
OBJECTIVES: Current state-of-the-art natural language processing (NLP) techniques use transformer deep-learning architectures, which depend on large training datasets. We hypothesized that traditional NLP techniques may outperform transformers for smaller radiology report datasets.
METHODS: We compared the performance of BioBERT, a deep-learning-based transformer model pre-trained on biomedical text, and three traditional machine-learning models (gradient boosted tree, random forest, and logistic regression) on seven classification tasks given free-text radiology reports. Tasks included detection of appendicitis, diverticulitis, bowel obstruction, and enteritis/colitis on abdomen/pelvis CT reports, ischemic infarct on brain CT/MRI reports, and medial and lateral meniscus tears on knee MRI reports (7,204 total annotated reports). The performance of NLP models on held-out test sets was compared after training using the full training set, and 2.5%, 10%, 25%, 50%, and 75% random subsets of the training data.
RESULTS: In all tested classification tasks, BioBERT performed poorly at smaller training sample sizes compared to non-deep-learning NLP models. Specifically, BioBERT required training on approximately 1,000 reports to perform similarly or better than non-deep-learning models. At around 1,250 to 1,500 training samples, the testing performance for all models began to plateau, where additional training data yielded minimal performance gain.
CONCLUSIONS: With larger sample sizes, transformer NLP models achieved superior performance in radiology report binary classification tasks. However, with smaller sizes (<1000) and more imbalanced training data, traditional NLP techniques performed better.
ADVANCES IN KNOWLEDGE: Our benchmarks can help guide clinical NLP researchers in selecting machine-learning models according to their dataset characteristics.
METHODS: We compared the performance of BioBERT, a deep-learning-based transformer model pre-trained on biomedical text, and three traditional machine-learning models (gradient boosted tree, random forest, and logistic regression) on seven classification tasks given free-text radiology reports. Tasks included detection of appendicitis, diverticulitis, bowel obstruction, and enteritis/colitis on abdomen/pelvis CT reports, ischemic infarct on brain CT/MRI reports, and medial and lateral meniscus tears on knee MRI reports (7,204 total annotated reports). The performance of NLP models on held-out test sets was compared after training using the full training set, and 2.5%, 10%, 25%, 50%, and 75% random subsets of the training data.
RESULTS: In all tested classification tasks, BioBERT performed poorly at smaller training sample sizes compared to non-deep-learning NLP models. Specifically, BioBERT required training on approximately 1,000 reports to perform similarly or better than non-deep-learning models. At around 1,250 to 1,500 training samples, the testing performance for all models began to plateau, where additional training data yielded minimal performance gain.
CONCLUSIONS: With larger sample sizes, transformer NLP models achieved superior performance in radiology report binary classification tasks. However, with smaller sizes (<1000) and more imbalanced training data, traditional NLP techniques performed better.
ADVANCES IN KNOWLEDGE: Our benchmarks can help guide clinical NLP researchers in selecting machine-learning models according to their dataset characteristics.