Auto-Rad: End-to-End Report Generation from Lumber Spine MRI Using Vision–Language Model
Abstract
:1. Introduction
2. Related Works
3. Methodology
3.1. Dataset
3.2. Text Transformation Using GPT-4
Prompt Engineering Approach
- Initial prompt structure: The initial prompt presented to GPT-4 for each report contained the full clinical note as input, followed by an instruction to “rephrase into a coherent, single-paragraph summary focusing on the assessment”.Prompt example:
“L4-L5: diffuse disc bulge noted, compressing the thecal sac and exit canals. Convert this to a coherent paragraph summarizing the key assessment findings”.
- Challenges in text transformation:
- −
- Inconsistent terminology: Radiologists often used varying terms to describe similar findings (e.g., “No significant thecal sac compression” vs. “adequate thecal sac”). This inconsistency required refinement in the prompts to encourage GPT-4 to use standardized language.
- −
- Abbreviations and shorthand: Reports contained medical shorthand (e.g., “thecal sac” as “TS”), which was not always uniformly understood by GPT-4. To address this, prompts were modified to ask GPT-4 to expand medical abbreviations where possible.
- −
- Spelling and grammatical errors: The model’s performance was occasionally hindered by spelling errors in the raw data, necessitating additional preprocessing instructions to GPT-4 to ensure it corrected these issues while maintaining the original meaning.
- Prompt development and standardization: We refined the prompts iteratively in order to reach a standardized template for this task. Outputs were evaluated for coherence and clinical accuracy, with adjustments made to ensure inclusion of critical details like muscle spasms, disc herniation, bulging, thecal sac compression, and Ligamentum flavum hypertrophy. The final standardized prompt directed GPT-4 to summarize and rephrase reports, correct spelling/grammar, expand abbreviations, and maintain consistent terminology.
- −
- Final standard template for prompt: “Given the radiologist’s clinical assessment report below, rephrase and transform the information into a structured, coherent paragraph that corrects any spelling or grammatical errors, expands abbreviations, and maintains clinical accuracy. Ensure the paragraph clearly communicates key findings related to disc conditions, nerve root compressions, muscle spasms, and any other relevant observations. Please use consistent terminology, avoid omitting any clinical details, and format the output as a concise paragraph”.
3.3. Stratified Topic-Based Data Splitting
3.4. Report Generation Model
3.5. Evaluation Process
- Diagnostic completeness (DC): Defined as the fraction of original diagnoses reflected in the report produced by the model, it essentially determines the presence of original diagnostic content from the radiologist’s report in the output generated by the model.
- Novel diagnostic detection (NDD): Measures the proportion of new diagnoses found in the report generated by the model but absent in the original radiologist’s report. Assesses whether the model has added any diagnostic content not initially found in the original report.
- Diagnostic correspondence (DCorr): Represents the percentage of discrepancies in the diagnoses between the model-generated and the original reports. Assesses the degree of agreement between the diagnoses in the reports generated by the model and the original diagnoses from the radiologist’s report.
4. Results
4.1. Model Evaluation
4.2. Empirical Evaluation
4.3. Evaluation of Topic Distribution
5. Discussion
5.1. Comparison
5.2. Limitations and Future Directions
5.3. Utility of ARRG for Lumbar Spine Diagnosis
6. Conclusions
- We demonstrate that VL models, initially pre-trained using natural images for captioning, can be refined for assessing radiographs and generating reports for specific diseases (for example, LSS).
- We show that VL models can be fine-tuned with a small number of samples for generating diagnostic reports from radiographs.
- We built an end-to-end system (Auto-Rad) utilizing semistructured clinician notes, transforming them into coherent paragraphs for model training with the assistance of advanced language models.
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Appendix A. Examples of Generated Reports
Original Report | Generated Report |
---|---|
Correctly generated reports | |
The LSS (lumbosacral spine) MRI reveals the presence of a mild disc bulge but no significant stenosis. | The MRI of the lumbar spine shows no evidence of significant spinal stenosis or nerve root impingement. |
The MRI findings reveal a feature of left-sided nerve root impingement with moderate compression due to a central disc protrusion. | The lumbar sacral spine MRI shows a right paracentral disc herniation with moderate nerve compression. |
The lumbar sacral spine MRI reveals a specific feature of degenerative disc disease but no evidence of herniation. | The MRI scan reveals no evidence of disc herniation or nerve compression in the lumbar region. |
Moderate disc bulge with mild impingement but no severe nerve compression is observed. | The MRI indicates a moderate disc bulge without severe nerve compression. |
Mild bulging observed at L4-L5 level, not leading to severe spinal stenosis. | There is mild disc bulging noted at L4-L5 without significant stenosis. |
Small disc protrusion at L3-L4 level but no nerve compression. | A small disc protrusion is noted at L3-L4, but it does not affect the nerve roots. |
Degenerative changes seen in the lumbar spine but no signs of nerve impingement. | The lumbar spine shows degenerative changes without nerve root compression. |
Incorrectly generated reports | |
Evidence of severe canal stenosis at L3-L4 due to a large disc herniation. | The MRI scan is unremarkable with no significant findings. |
Significant foraminal stenosis with nerve root compression detected on the left side. | No disc herniation or compression noted in the lumbar spine. |
Central disc protrusion at L5-S1 with moderate thecal sac impingement. | The MRI shows normal alignment with no abnormalities. |
Severe disc bulging at L4-L5 level with nerve compression noted. | Lumbar spine appears healthy with no signs of disc bulging. |
The MRI reveals degenerative changes with significant disc herniation compressing the thecal sac. | No abnormalities detected in the MRI scan. |
Diffuse disc bulge at multiple levels, leading to moderate stenosis. | No evidence of stenosis or disc bulging in the MRI. |
Mild disc herniation at L2-L3 causing nerve root impingement. | MRI findings show no signs of nerve root compression or disc herniation. |
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Metric | Score | Type |
---|---|---|
ROUGE-1 (F1) | 0.447 | NLG |
ROUGE-2 (F1) | 0.185 | NLG |
ROUGE-L (F1) | 0.299 | NLG |
ROUGE-Lsum (F1) | 0.299 | NLG |
BLEU | 0.110 | NLG |
METEOR | 0.370 | NLG |
BERTScore (F1) | 0.886 | NLG |
Perplexity | 1.045 | NLG |
CIDEr | 0.081 | NLG |
SPICE | 0.288 | NLG |
DC | 24.7% | Empirical |
NDD | 69.8% | Empirical |
DCorr | 26.8% | Empirical |
JSD | 0.391 | Topic Level |
EMD | 0.009 | Topic Level |
Model | Data (Images, Reports) | BLEU-1 | BLEU-2 | BLEU-3 | BLEU-4 | METEOR | ROUGE | CIDEr |
---|---|---|---|---|---|---|---|---|
GIT-base | Lumbar Spine MRI (1545, 515) | 0.3827 | 0.1461 | 0.0676 | 0.0382 | 0.3699 | 0.4570 | 0.0805 |
CNN–LSTM–ATT [45] | Bladder Cancer (1000, 5000) | 0.912 | 0.829 | 0.750 | 0.677 | 0.396 | 0.701 | 0.0204 |
CNN–HLSTM–DualLSTM–ATT [46] | IU X-Ray (7470, 3955) | 0.373 | 0.246 | 0.175 | 0.126 | 0.163 | 0.315 | 0.359 |
CNN–HLSTM–RL [47] | MIMIC-CXR (327,281, 141,783) | 0.313 | 0.206 | 0.146 | 0.103 | 0.146 | 0.306 | 1.046 |
Condition GPT2 [48] | IU X-Ray (7470, 7470) | 0.387 | 0.245 | 0.166 | 0.111 | 0.164 | 0.289 | 0.257 |
Reinforce CNN–LSTM [49] | IU X-Ray (7470, 7470) and MIMIC-CXR | 0.412 | 0.279 | 0.206 | 0.157 | 0.179 | 0.342 | 0.411 |
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Yeasin, M.; Moinuddin, K.A.; Havugimana, F.; Wang, L.; Park, P. Auto-Rad: End-to-End Report Generation from Lumber Spine MRI Using Vision–Language Model. J. Clin. Med. 2024, 13, 7092. https://doi.org/10.3390/jcm13237092
Yeasin M, Moinuddin KA, Havugimana F, Wang L, Park P. Auto-Rad: End-to-End Report Generation from Lumber Spine MRI Using Vision–Language Model. Journal of Clinical Medicine. 2024; 13(23):7092. https://doi.org/10.3390/jcm13237092
Chicago/Turabian StyleYeasin, Mohammed, Kazi Ashraf Moinuddin, Felix Havugimana, Lijia Wang, and Paul Park. 2024. "Auto-Rad: End-to-End Report Generation from Lumber Spine MRI Using Vision–Language Model" Journal of Clinical Medicine 13, no. 23: 7092. https://doi.org/10.3390/jcm13237092
APA StyleYeasin, M., Moinuddin, K. A., Havugimana, F., Wang, L., & Park, P. (2024). Auto-Rad: End-to-End Report Generation from Lumber Spine MRI Using Vision–Language Model. Journal of Clinical Medicine, 13(23), 7092. https://doi.org/10.3390/jcm13237092