Background
In the era of datafication, it is important that medical data are accurate and structured for multiple applications. Especially data for oncological staging need to be accurate to stage ...and treat a patient, as well as population-level surveillance and outcome assessment. To support data extraction from free-text radiological reports, Dutch natural language processing (NLP) algorithm was built to quantify T-stage of pulmonary tumors according to the tumor node metastasis (TNM) classification. This structuring tool was translated and validated on English radiological free-text reports. A rule-based algorithm to classify T-stage was trained and validated on, respectively, 200 and 225 English free-text radiological reports from diagnostic computed tomography (CT) obtained for staging of patients with lung cancer. The automated T-stage extracted by the algorithm from the report was compared to manual staging. A graphical user interface was built for training purposes to visualize the results of the algorithm by highlighting the extracted concepts and its modifying context.
Results
Accuracy of the T-stage classifier was 0.89 in the validation set, 0.84 when considering the T-substages, and 0.76 when only considering tumor size. Results were comparable with the Dutch results (respectively, 0.88, 0.89 and 0.79). Most errors were made due to ambiguity issues that could not be solved by the rule-based nature of the algorithm.
Conclusions
NLP can be successfully applied for staging lung cancer from free-text radiological reports in different languages. Focused introduction of machine learning should be introduced in a hybrid approach to improve performance.
Reports are the standard way of communication between the radiologist and the referring clinician. Efforts are made to improve this communication by, for instance, introducing standardization and ...structured reporting. Natural Language Processing (NLP) is another promising tool which can improve and enhance the radiological report by processing free text. NLP as such adds structure to the report and exposes the information, which in turn can be used for further analysis. This paper describes pre-processing and processing steps and highlights important challenges to overcome in order to successfully implement a free text mining algorithm using NLP tools and machine learning in a small language area, like Dutch. A rule-based algorithm was constructed to classify T-stage of pulmonary oncology from the original free text radiological report, based on the items tumor size, presence and involvement according to the 8th TNM classification system. PyContextNLP, spaCy and regular expressions were used as tools to extract the correct information and process the free text. Overall accuracy of the algorithm for evaluating T-stage was 0,83 in the training set and 0,87 in the validation set, which shows that the approach in this pilot study is promising. Future research with larger datasets and external validation is needed to be able to introduce more machine learning approaches and perhaps to reduce required input efforts of domain-specific knowledge. However, a hybrid NLP approach will probably achieve the best results.
Natural language processing (NLP) is thought to be a promising solution to extract and store concepts from free text in a structured manner for data mining purposes. This is also true for radiology ...reports, which still consist mostly of free text. Accurate and complete reports are very important for clinical decision support, for instance, in oncological staging. As such, NLP can be a tool to structure the content of the radiology report, thereby increasing the report's value.
This study describes the implementation and validation of an N-stage classifier for pulmonary oncology. It is based on free-text radiological chest computed tomography reports according to the tumor, node, and metastasis (TNM) classification, which has been added to the already existing T-stage classifier to create a combined TN-stage classifier.
SpaCy, PyContextNLP, and regular expressions were used for proper information extraction, after additional rules were set to accurately extract N-stage.
The overall TN-stage classifier accuracy scores were 0.84 and 0.85, respectively, for the training (N=95) and validation (N=97) sets. This is comparable to the outcomes of the T-stage classifier (0.87-0.92).
This study shows that NLP has potential in classifying pulmonary oncology from free-text radiological reports according to the TNM classification system as both the T- and N-stages can be extracted with high accuracy.
Manual cohort building from radiology reports can be tedious. Natural Language Processing (NLP) can be used for automated cohort building. In this study, we have developed and validated an NLP ...approach based on deep learning (DL) to select lung cancer reports from a thoracic disease management group cohort.
4064 radiology reports (CT and PET/CT) of a thoracic disease management group reported between 2014 and 2016 were used. These reports were anonymised, cleaned, text normalized and split into a training, testing, and validation set. External validation was performed on radiology reports from the MIMIC-III clinical database. We used three DL models, namely, Bi-LSTM_simple, Bi-LSTM_dropout, and Pre-trained _BERT model to predict if a report concerned lung cancer. We studied the effect of minority oversampling on all models.
Without oversampling, the F1 scores at 95% CI for Bi-LSTM_simple, Bi-LSTM_dropout and BERT were 0.89, 0.90, and 0.86; with oversampling, the F1 scores were 0.94, 0.94, and 0.9, on internal validation. On external validation the F1-scores of Bi-LSTM_simple, Bi-LSTM_dropout and BERT models were 0.63, 0.77 and 0.80 without oversampling and 0.72, 0.78 and 0.77 with oversampling.
Pre-trained BERT model and Bi-LSTM_dropout models to predict a lung cancer report showed consistent performance on internal and external validation with the BERT model exhibiting superior performance. The overall F1 score decreased on external validation for both Bi-LSTM models with the Bi-LSTM_simple model showing a more significant drop. All models showed some improvement on minority oversampling.
Natural language processing (NLP) can be used to process and structure free text, such as (free text) radiological reports. In radiology, it is important that reports are complete and accurate for ...clinical staging of, for instance, pulmonary oncology. A computed tomography (CT) or positron emission tomography (PET)-CT scan is of great importance in tumor staging, and NLP may be of additional value to the radiological report when used in the staging process as it may be able to extract the T and N stage of the 8th tumor–node–metastasis (TNM) classification system. The purpose of this study is to evaluate a new TN algorithm (TN-PET-CT) by adding a layer of metabolic activity to an already existing rule-based NLP algorithm (TN-CT). This new TN-PET-CT algorithm is capable of staging chest CT examinations as well as PET-CT scans. The study design made it possible to perform a subgroup analysis to test the external validation of the prior TN-CT algorithm. For information extraction and matching, pyContextNLP, SpaCy, and regular expressions were used. Overall TN accuracy score of the TN-PET-CT algorithm was 0.73 and 0.62 in the training and validation set (
N
= 63,
N
= 100). The external validation of the TN-CT classifier (
N
= 65) was 0.72. Overall, it is possible to adjust the TN-CT algorithm into a TN-PET-CT algorithm. However, outcomes highly depend on the accuracy of the report, the used vocabulary, and its context to express, for example, uncertainty. This is true for both the adjusted PET-CT algorithm and for the CT algorithm when applied in another hospital.
Rising incidence and mortality of cancer have led to an incremental amount of research in the field. To learn from preexisting data, it has become important to capture maximum information related to ...disease type, stage, treatment, and outcomes. Medical imaging reports are rich in this kind of information but are only present as free text. The extraction of information from such unstructured text reports is labor-intensive. The use of Natural Language Processing (NLP) tools to extract information from radiology reports can make it less time-consuming as well as more effective. In this study, we have developed and compared different models for the classification of lung carcinoma reports using clinical concepts. This study was approved by the institutional ethics committee as a retrospective study with a waiver of informed consent. A clinical concept-based classification pipeline for lung carcinoma radiology reports was developed using rule-based as well as machine learning models and compared. The machine learning models used were XGBoost and two more deep learning model architectures with bidirectional long short-term neural networks. A corpus consisting of 1700 radiology reports including computed tomography (CT) and positron emission tomography/computed tomography (PET/CT) reports were used for development and testing. Five hundred one radiology reports from MIMIC-III Clinical Database version 1.4 was used for external validation. The pipeline achieved an overall F1 score of 0.94 on the internal set and 0.74 on external validation with the rule-based algorithm using expert input giving the best performance. Among the machine learning models, the Bi-LSTM_dropout model performed better than the ML model using XGBoost and the Bi-LSTM_simple model on internal set, whereas on external validation, the Bi-LSTM_simple model performed relatively better than other 2. This pipeline can be used for clinical concept-based classification of radiology reports related to lung carcinoma from a huge corpus and also for automated annotation of these reports.
Performing image feature extraction in radiation oncology is often dependent on the organ and tumor delineations provided by clinical staff. These delineation names are free text DICOM metadata ...fields resulting in undefined information, which requires effort to use in large-scale image feature extraction efforts. In this work we present a scale-able solution to overcome these naming convention challenges with a REST service using Semantic Web technology to convert this information to linked data. As a proof of concept an open source software is used to compute radiation oncology image features. The results of this work can be found in a public Bitbucket repository.
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