Development of a Structured Query Language and Natural Language Processing Algorithm to Identify Lung Nodules in a Cancer Centre

Natural Language Processing for the Identification of Incidental Lung Nodules in Computed Tomography Reports: A Quality Control Tool

PURPOSE

To evaluate the diagnostic performance of a natural language processing (NLP) model in detecting incidental lung nodules (ILNs) in unstructured chest computed tomography (CT) reports.

METHODS

All unstructured consecutive reports of chest CT scans performed at a tertiary hospital between 2020 and 2021 were retrospectively reviewed (n = 21,542) to train the NLP tool. Internal validation was performed using reference readings by two radiologists of both CT scans and reports, using a different external cohort of 300 chest CT scans. Second, external validation was performed in a cohort of all random unstructured chest CT reports from 57 different hospitals conducted in May 2022. A review by the same thoracic radiologists was used as the gold standard. The sensitivity, specificity, and accuracy were calculated.

RESULTS

Of 21,542 CT reports, 484 mentioned at least one ILN (mean age, 71 ± 17.6 [standard deviation] years; women, 52%) and were included in the training set. In the internal validation (n = 300), the NLP tool detected ILN with a sensitivity of 100.0% (95% CI, 97.6 to 100.0), a specificity of 95.9% (95% CI, 91.3 to 98.5), and an accuracy of 98.0% (95% CI, 95.7 to 99.3). In the external validation (n = 977), the NLP tool yielded a sensitivity of 98.4% (95% CI, 94.5 to 99.8), a specificity of 98.6% (95% CI, 97.5 to 99.3), and an accuracy of 98.6% (95% CI, 97.6 to 99.2). Twelve months after the initial reports, 8 (8.60%) patients had a final diagnosis of lung cancer, among which 2 (2.15%) would have been lost to follow-up without the NLP tool.

CONCLUSION

NLP can be used to identify ILNs in unstructured reports with high accuracy, allowing a timely recall of patients and a potential diagnosis of early-stage lung cancer that might have been lost to follow-up.

Developing electronic clinical quality measures to assess the cancer diagnostic process

OBJECTIVE

Measures of diagnostic performance in cancer are underdeveloped. Electronic clinical quality measures (eCQMs) to assess quality of cancer diagnosis could help quantify and improve diagnostic performance.

MATERIALS AND METHODS

We developed 2 eCQMs to assess diagnostic evaluation of red-flag clinical findings for colorectal (CRC; based on abnormal stool-based cancer screening tests or labs suggestive of iron deficiency anemia) and lung (abnormal chest imaging) cancer. The 2 eCQMs quantified rates of red-flag follow-up in CRC and lung cancer using electronic health record data repositories at 2 large healthcare systems. Each measure used clinical data to identify abnormal results, evidence of appropriate follow-up, and exclusions that signified follow-up was unnecessary. Clinicians reviewed 100 positive and 20 negative randomly selected records for each eCQM at each site to validate accuracy and categorized missed opportunities related to system, provider, or patient factors.

RESULTS

We implemented the CRC eCQM at both sites, while the lung cancer eCQM was only implemented at the VA due to lack of structured data indicating level of cancer suspicion on most chest imaging results at Geisinger. For the CRC eCQM, the rate of appropriate follow-up was 36.0% (26 746/74 314 patients) in the VA after removing clinical exclusions and 41.1% at Geisinger (1009/2461 patients; P < .001). Similarly, the rate of appropriate evaluation for lung cancer in the VA was 61.5% (25 166/40 924 patients). Reviewers most frequently attributed missed opportunities at both sites to provider factors (84 of 157).

CONCLUSIONS

We implemented 2 eCQMs to evaluate the diagnostic process in cancer at 2 large health systems. Health care organizations can use these eCQMs to monitor diagnostic performance related to cancer.

Performance of a rule-based semi-automated method to optimize chart abstraction for surveillance imaging among patients treated for non-small cell lung cancer

Background

We aim to develop and test performance of a semi-automated method (computerized query combined with manual review) for chart abstraction in the identification and characterization of surveillance radiology imaging for post-treatment non-small cell lung cancer patients.

Methods

A gold standard dataset consisting of 3011 radiology reports from 361 lung cancer patients treated at the Veterans Health Administration from 2008 to 2016 was manually created by an abstractor coding image type, image indication, and image findings. Computerized queries using a text search tool were performed to code reports. The primary endpoint of query performance was evaluated by sensitivity, positive predictive value (PPV), and F1 score. The secondary endpoint of efficiency compared semi-automated abstraction time to manual abstraction time using a separate dataset and the Wilcoxon rank-sum test.

Results

Query for image type demonstrated the highest sensitivity of 85%, PPV 95%, and F1 score 0.90. Query for image indication demonstrated sensitivity 72%, PPV 70%, and F1 score 0.71. The image findings queries ranged from sensitivity 75–85%, PPV 23–25%, and F1 score 0.36–0.37. Semi-automated abstraction with our best performing query (image type) improved abstraction times by 68% per patient compared to manual abstraction alone (from median 21.5 min (interquartile range 16.0) to 6.9 min (interquartile range 9.5), p < 0.005).

Conclusions

Semi-automated abstraction using the best performing query of image type improved abstraction efficiency while preserving data accuracy. The computerized query acts as a pre-processing tool for manual abstraction by restricting effort to relevant images. Determining image indication and findings requires the addition of manual review for a semi-automatic abstraction approach in order to ensure data accuracy.

The Role of Artificial Intelligence in Early Cancer Diagnosis

Improving the proportion of patients diagnosed with early-stage cancer is a key priority of the World Health Organisation. In many tumour groups, screening programmes have led to improvements in survival, but patient selection and risk stratification are key challenges. In addition, there are concerns about limited diagnostic workforces, particularly in light of the COVID-19 pandemic, placing a strain on pathology and radiology services. In this review, we discuss how artificial intelligence algorithms could assist clinicians in (1) screening asymptomatic patients at risk of cancer, (2) investigating and triaging symptomatic patients, and (3) more effectively diagnosing cancer recurrence. We provide an overview of the main artificial intelligence approaches, including historical models such as logistic regression, as well as deep learning and neural networks, and highlight their early diagnosis applications. Many data types are suitable for computational analysis, including electronic healthcare records, diagnostic images, pathology slides and peripheral blood, and we provide examples of how these data can be utilised to diagnose cancer. We also discuss the potential clinical implications for artificial intelligence algorithms, including an overview of models currently used in clinical practice. Finally, we discuss the potential limitations and pitfalls, including ethical concerns, resource demands, data security and reporting standards.