Templated Text Synthesis for Expert-Guided Multi-Label Extraction from Radiology Reports
Abstract
:1. Introduction
- Building on our work in [3], we propose to use templates to strategically augment the training dataset with rare cases obtained from a medical knowledge graph and with difficult cases obtained from rules created by human experts during the course of manual annotation, enabling expert-guided learning via text data synthesis.
- We analyse the impact of the vocabulary arising from domain-specific pre-training of BERT, and show why this improves accuracy.
- We perform extensive validation of our methods, including a prospective validation on data which was unseen at the point of annotating the training dataset, and show that our methods enable improved generalisation and a convenient mechanism for adaptation.
2. Related Work
2.1. Radiology Report Labelling
2.2. Pre-Training for Text Deep Learning Models
2.3. Text Data Synthesis
3. Materials and Methods
3.1. NHS GGC Dataset
3.2. Templates for Text Data Synthesis
3.2.1. Generic Templates
3.2.2. Combining Templates
3.2.3. Knowledge Injection into Templates
3.2.4. Protocol-Derived Templates
3.2.5. Synthetic Dataset Summary
3.3. Models
3.3.1. BERT Pre-Training Variants
3.3.2. ALARM-Based Models
4. Results
4.1. What Impact Does the Pre-Training Dataset Have on Task Accuracy?
4.2. What Impact Does Data Synthesis Have on Task Accuracy?
4.3. What Impact Does Data Synthesis Have on Task Accuracy for Prospective Data?
4.4. Comparison of the Proposed Method with a Rules-Based System
5. Discussion
5.1. Difference in Accuracy between Phase 1 and Phase 2 Test Data
5.2. Limitations of the Comparison with EdIE-R
5.3. Synthetic Data Distribution
5.4. Utilising Templates in an Online Learning Setting
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ALARM | automated labelling using an attention model for radiology reports of MRI scans |
BERT | bidirectional encoder representations from transformers |
BioBERT | bidirectional encoder representations from transformers for biomedical text mining |
CAML | convolutional attention for multi-label classification |
CNS | central nervous system |
CPU | central processing unit |
CSVD | cerebral small vessel disease |
CT | computed tomography |
CUI | concept unique identifier |
EdiE-R | Edinburgh information extraction for radiology reports |
GGC | Greater Glasgow and Clyde |
GHz | giga hertz |
GPU | graphics processing unit |
iCAIRD | Industrial Centre for AI Research in digital Diagnostics |
MIMIC | medical information mart for intensive care |
NHS | national health service |
NLI | natural language inference |
NLP | natural language processing |
NLTK | natural language toolkit |
OOV | out of vocabulary |
PubMedBERT | bidirectional encoder representations from transformers pre-trained using PubMed |
RSNA | Radiological Society of North America |
UKRI | United Kingdom Research and Innovation |
UMLS | unified medical language system |
VRAM | video random access memory |
Appendix A. Training and Inference Times
Training | Inference Time | |||
---|---|---|---|---|
Model Architecture | Pre-Trained Weights | # Parameters | Time [s] | [s/sample] |
BERT | BERT [4] | 109,586,824 | ||
BERT | BioBERT [20] | 108,414,856 | ||
BERT | PubMedBERT [9] | 109,586,824 | ||
ALARM + per-label attention | BERT | 127,985,800 | ||
ALARM + per-label attention | BioBERT | 126,813,832 | ||
ALARM + per-label attention | PubMedBERT | 127,985,800 |
Appendix B. Label Details
Train | Validation | Ind. Test | Prosp. Test | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Finding | + | ? | − | + | ? | − | + | ? | − | + | ? | − |
Hypodensity | 164 | - | - | 91 | - | - | 358 | 9 | - | 143 | 4 | - |
Hyperdensity | 35 | 3 | 5 | 23 | 1 | 1 | 85 | 9 | 11 | 45 | 5 | 5 |
Dilatation | 33 | 8 | - | 13 | 2 | 1 | 48 | 16 | - | 32 | - | 1 |
Collection | 13 | - | 26 | 4 | 1 | 14 | 14 | 2 | 43 | 11 | 1 | 31 |
Mass effect | 24 | - | 11 | 12 | 1 | 13 | 60 | 1 | 39 | 35 | - | 20 |
Midline shift | 21 | - | 13 | 8 | - | 10 | 52 | - | 39 | 19 | - | 21 |
Effacement | 28 | 1 | 1 | 11 | - | - | 52 | - | 4 | 21 | - | - |
Herniation | 16 | - | 4 | 2 | - | 3 | 23 | - | 16 | 11 | 2 | 4 |
Loss of differentiation | 14 | - | 6 | 7 | 1 | - | 41 | 1 | 4 | 13 | - | 3 |
Compression | 11 | - | - | 7 | - | 1 | 16 | - | 2 | 5 | - | 2 |
Oedema | 10 | - | - | 12 | - | - | 35 | 3 | 4 | 11 | 3 | 4 |
Artefact | 6 | - | - | 2 | - | - | 16 | 2 | - | 18 | 1 | - |
Swelling | 2 | - | - | 1 | - | - | 7 | - | - | 7 | - | - |
Malacic changes | 2 | - | - | - | - | - | 15 | - | - | 18 | - | - |
Gliosis | 2 | - | - | - | - | - | 14 | - | 1 | 5 | - | - |
Train | Validation | Ind. Test | Prosp. Test | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Impression | + | ? | − | + | ? | − | + | ? | − | + | ? | − |
Haemorrhage/Haematoma | 160 | 7 | 136 | 97 | 7 | 74 | 338 | 20 | 289 | 116 | 8 | 151 |
Infarct/Ischaemia | 150 | 24 | 57 | 93 | 19 | 37 | 386 | 60 | 145 | 190 | 20 | 69 |
Cerebral small vessel disease | 60 | 2 | 1 | 37 | - | 2 | 149 | 5 | 2 | 97 | - | 1 |
Lesion | 11 | - | 47 | 1 | 1 | 35 | 8 | - | 127 | 13 | 2 | 72 |
Involution/Atrophy | 54 | 1 | - | 50 | 2 | 3 | 129 | 1 | 1 | 69 | 1 | 1 |
Hydrocephalus | 13 | 3 | 13 | 5 | 2 | 11 | 21 | 3 | 33 | 13 | - | 22 |
Calcification | 18 | 1 | - | 4 | 1 | - | 24 | 1 | - | 16 | 2 | - |
Vessel occlusion | 6 | 7 | 1 | 7 | 3 | - | 16 | 13 | - | 6 | 7 | 1 |
Fracture | 1 | - | 10 | - | - | 6 | - | 1 | 21 | 14 | - | 19 |
Evidence of surgery/intervention | 10 | - | - | 3 | 1 | - | 5 | - | - | 26 | - | - |
Aneurysm | 6 | 1 | - | - | 2 | - | 3 | 1 | - | 3 | 1 | - |
Tumour | 2 | - | 3 | - | 2 | - | 7 | 4 | 1 | 3 | 4 | 1 |
Cavernoma | - | 2 | - | - | - | - | 2 | 1 | - | - | - | - |
Congenital abnormality | - | 1 | - | 2 | 2 | - | 4 | 2 | - | 1 | 1 | - |
Cyst | - | 1 | - | 1 | - | - | 3 | 1 | - | 4 | 1 | - |
Abscess | - | 1 | - | - | - | - | - | - | - | - | - | - |
Infection | - | - | - | - | - | - | - | - | - | 6 | 5 | - |
Pneumocephalus | - | - | - | - | - | - | - | - | - | 9 | - | 3 |
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Dataset | # Patients | # Reports | # Sentences | |
---|---|---|---|---|
Phase 1 (Initial) | Training | 138 | 138 | 839 |
Validation | 92 | 92 | 515 | |
Test—Independent | 317 | 317 | 1950 | |
Phase 2 (Prospective) | Test—Prospective | 197 | 200 | 1411 |
Test—Unlabelled | 10,112 | 27,940 | 228,170 |
Comparison | Cohen’s Kappa | F1 Micro | F1 Macro |
---|---|---|---|
Annotator 1 vs. Annotator 2 | 0.900 | 0.945 | 0.897 |
Annotator 1 vs. Reviewed | 0.918 | 0.953 | 0.865 |
Annotator 2 vs. Reviewed | 0.970 | 0.983 | 0.939 |
# Generated | # Generated | |||
---|---|---|---|---|
Data Synthesis Method | # Templates | Template [Label] | Sentences | |
Baselines | Random insertion | - | - | 840 |
Random deletion | - | - | 840 | |
Templated data synthesis | Simple templates | 3 | 99 | |
Permuted templates | 6 | 198 | ||
Combined templates | 1 | 400 | (UB) | |
Protocol-derived templates | 4 | 400 | + (UB) |
Model Architecture | Pre-Trained Weights | F1 Micro | F1 Macro |
---|---|---|---|
BERT | BERT [4] | ||
BERT | BioBERT [20] | ||
BERT | PubMedBERT [9] | ||
ALARM + per-label attention | BERT | ||
ALARM + per-label attention | BioBERT | ||
ALARM + per-label attention | PubMedBERT |
# Words Not in Vocabulary (% of Total) | ||||
---|---|---|---|---|
Model | Train | Validation | Test | All |
BERT | 356 (34%) | 236 (30%) | 539 (37%) | 710 (39%) |
BioBERT | 400 (38%) | 268 (34%) | 594 (41%) | 784 (43%) |
PubMedBERT | 211 (20%) | 148 (19%) | 370 (26%) | 496 (27%) |
Input Word | BERT Tokeniser Output | PubMedBERT Tokeniser Output | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
haemorrhage | (5) | ha | ## em | ## or | ## r | ## hage | (1) | haemorrhage | |||
hydrocephalus | (5) | h | ## ydro | ## ce | ## pha | ## lus | (1) | hydrocephalus | |||
haematoma | (4) | ha | ## ema | ## tom | ## a | (2) | haemat | ## oma | |||
hyperdensity | (4) | h | ## yper | ## den | ## sity | (4) | hyper | ## den | ## si | ## ty | |
hypodensity | (5) | h | ## y | ## po | ## den | ## sity | (4) | hypo | ## den | ## si | ## ty |
All Labels | Tumour | |||
---|---|---|---|---|
Data Synthesis Method | F1 Micro | F1 Macro | F1 Micro | |
Real data only | ||||
Baselines | Random word deletion | |||
Random stop word insertion | ||||
Templated data synthesis | [Label names] Simple templates | |||
+[Label names] Permuted templates | ||||
+[Label names] Combined templates | ||||
+[UMLS synonyms] Simple & Permuted | ||||
Ablations | Template synthesis only, label names | |||
Template synthesis only, inc. UMLS synonyms |
All Labels | Infection | ||
---|---|---|---|
Data Synthesis Method | F1 Micro | F1 Macro | F1 Micro |
Real data only | |||
Generic templates | |||
Protocol-derived templates |
Haemorrhage | Ischaemia | CSVD | Atrophy | Tumour | ||
---|---|---|---|---|---|---|
Model | F1 Macro | F1 Micro | F1 Micro | F1 Micro | F1 Micro | F1 Micro |
EdIE-R [11] | ||||||
Our model, real data only | ||||||
Our model |
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Schrempf, P.; Watson, H.; Park, E.; Pajak, M.; MacKinnon, H.; Muir, K.W.; Harris-Birtill, D.; O’Neil, A.Q. Templated Text Synthesis for Expert-Guided Multi-Label Extraction from Radiology Reports. Mach. Learn. Knowl. Extr. 2021, 3, 299-317. https://doi.org/10.3390/make3020015
Schrempf P, Watson H, Park E, Pajak M, MacKinnon H, Muir KW, Harris-Birtill D, O’Neil AQ. Templated Text Synthesis for Expert-Guided Multi-Label Extraction from Radiology Reports. Machine Learning and Knowledge Extraction. 2021; 3(2):299-317. https://doi.org/10.3390/make3020015
Chicago/Turabian StyleSchrempf, Patrick, Hannah Watson, Eunsoo Park, Maciej Pajak, Hamish MacKinnon, Keith W. Muir, David Harris-Birtill, and Alison Q. O’Neil. 2021. "Templated Text Synthesis for Expert-Guided Multi-Label Extraction from Radiology Reports" Machine Learning and Knowledge Extraction 3, no. 2: 299-317. https://doi.org/10.3390/make3020015