Identifying Patient Populations in Texts Describing Drug Approvals Through Deep Learning–Based Information Extraction: Development of a Natural Language Processing Algorithm

Introduction

Recent developments in deep learning–based [1,2] natural language processing (NLP) have enabled transfer learning [3] to be used in automated or semiautomated information extraction using data sets as small as thousands or even sometimes hundreds of entries [4]. While a data set containing billions of words (the full Wikipedia and BooksCorpus content) is necessary to train models such as Bidirectional Encoder Representations from Transformers (BERT) [1], a state-of-the-art deep learning NLP model, fine-tuning this model can be successfully applied to much smaller data sets [4]. Small input data sets are often encountered in practice, and such methods allow applicability to a larger number of problems. Moreover, BERT has demonstrated state-of-the-art performances on a wide variety of tasks, including binary and multiclass classification on balanced and unbalanced data sets or question-answering data sets [1]. When data drift has to be expected, such stability is a strong differentiator.

Besides the fine-tuned BERT deep learning model, we develop a fit-for-purpose rule-based approach. We then compare results of both approaches, and the algorithm that performs best is applied to new data. The results are sent for review and curation to subject matter experts.

In the case study presented in this paper, the goal was to categorize and extract entities from descriptions of drug approvals that would allow us to link a particular patient population and clinical trials to a specific drug approval event. This linkage supports our aim of streamlining information extraction and aiding visualization of the competitive drug approval landscape.

We selected 6 drug targets of relevance to AstraZeneca’s Oncology portfolio and investigate the capability of NLP tools to extract an overview of the competitive landscape for these drug targets. The aim was to retrieve information defining the patient profile—specifically the approved line of therapy and stage of cancer—and references to the clinical trial or trials that support each drug approval.

Machine-learning and rule-based approaches, or their combination, have been used to extract cancer stage automatically from electronic medical records.

Shivade et al [5] and Meng et al [6] have reviewed automatic systems, rule- or machine-learning–based, applied to automatically identify patient phenotype, including but not limited to cancer stage and line of therapy.

A carefully crafted sequence of rule-based approaches and machine learning algorithms allowed cancer stage identification in McCowen et al’s [7] and Yim et al’s [8] studies. In Nguyen et al’s [9] study, a rule-based algorithm was compared to a machine learning approach based on support vector machine, and performances are found to be equivalent. A recent example is described by Hu et al [10], where fine-tuned BERT models were used to identify 14 different named entities and relations among entities. These are then fed to a rule-based postprocessing workflow that answers a list of 22 questions indicative of cancer stage. Most recently, CancerBERT [11] is a fine-tuned BERT-based deep learning model trained to extract 10 types of named entity recognition (NER) entities, including cancer stage.

Example applications of rule-based approaches used to extract line of therapy automatically are described previously [12-15]. In these studies, cancer stage and line of therapy are often expressed through several indicators that need to be identified individually and then combined. The nature of the documents in our case is less detailed, and a new methodology is needed. A single paragraph of text is available, which sometimes consists of 2 or 3 lines of text only, sometimes more (Figure 1). Stage can be mentioned explicitly, or information can be provided indirectly through words such as “advanced” or “metastatic.” A text describing an approval can cover only 1 cancer stage or a wide range of stages. As for line of therapy, a previous treatment or intervention (resection…) is sometimes mentioned, which helps narrow down the possibilities.

Finally, automatic information extraction of clinical trial characteristics has also been published using carefully crafted combinations of machine learning and rule-based approaches. The extracted information includes trial names as well as relevant information about patient populations enrolled in the trial [16,17]. In our case, we identified, among several trial names, those that lead to compound approval, hence the need for a specially crafted model.

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Methods

Data Set and Labeling Process

The BioMedTracker [18] database contains a repository of standardized drug approval events, reported across a number of indications and markets. Each event has a number of structured metadata associated with it (eg, disease, approval date, and approval region), as shown in the table in the top half of Figure 1. However, information relating to a more granular description of the patient population (including line of therapy and stage of disease) and any supportive clinical trial is constrained to the unstructured free-text section that is written by an analyst. This can be seen in the lower half of Figure 1. Texts describing drug approvals of interest were accessed programatically from the database using a Representative State Transfer application programing interface (API) query.

We focused on approval events in 6 drug targets, which were included sequentially as the project evolved. The drug targets taken into account were (1) EGFR (Epidermal Growth Factor Receptor), (2) human epidermal growth factor receptor 2/neu or ErbB-2, (3) Cytotoxic T-Lymphocyte Antigen 4, (4) Programed death-1 receptor/Programed death ligands (1 and 2), (5) Poly ADP-Ribose Polymerase, and (6) Bruton’s Tyrosine Kinase, which are all of relevance to AstraZeneca’s drug portfolio.

In terms of preprocessing, hyperlinks were deleted from input texts. Information about line of therapy and cancer stage was found in the first 2 paragraphs of text, so only these were considered for these tasks. The full text was used to identify trials leading to an approval.

A manual labeling process was applied to ensure consistency; 2 subject matter experts split the task of labeling 433 texts describing approvals, while an independent third labeler reviewed their work to ensure accuracy and consistency. The task is difficult as line of therapy and cancer stage are sometimes described indirectly. We used Label-studio [19] to perform the labeling task.

We found that both line of therapy and cancer stage showed a large number of possible classes in the data (Table 1), and for the purposes of model training, pooled some of these categories together to make the classification task more manageable.

The final list of refined classes was selected based on their frequency and an assessment of how useful an individual class would be to the project, as judged by a subject matter expert; this information was also used to assign an ordinal rank to each class, lower ranks corresponding to more common classes.

To map from the initial list to the final list, we developed a binning algorithm that chooses the training class with the highest rank that overlaps with the labeled class. For example, in Table 2, “Second line” was ranked third and “First line” was ranked fourth; therefore, a labeled class with the categories “First line; Second line; Third line” would have the training class value of “Second line.” The highest-ranked class was always assigned the null set. This functioned as the default value for when there is no overlapping training class in the labeled class.

Algorithmically, this means the following:

base_features = {(i,j,k), (i,k,l), (m,n), (k), …},

target_classes_reverse_order = {(i), (j,k), (j), (k), …}

text_target_class = null

for text in texts:

for base_feature in base_features:

for target_class in target_classes_reverse_order:

if base_feature in target_class:

text_target_class = target_class

NLP Algorithm Development

Off-the-shelf packages are available that return state-of-the-art results on many different benchmarking data sets. Here, we use the transformers library from huggingface [20,21].

We applied transfer learning [2] and fine-tuned a DistilBERT [22] model, a distilled version of BERT that runs faster while retaining comparable performance. We attempted to use BioBERT [4] because models adapted to medical literature have been shown to increase scores [23]; however, here, performance did not improve. Along these lines, we also fine-tuned a domain-adapted BERT-based model, using trial titles from the Trialtrove database as text and patient population categories that had been tagged by a Trialtrove analyst as the target. The performance of this model was disappointing, and we concluded that syntaxes were too different between Trialtrove titles and BioMedTracker approval descriptions, possibly because titles are too short to allow the model to learn.

Line of therapy and stage of cancer extraction are treated as classification problems, while trial identification is treated as a NER task. Preimplemented flows are available in the Hugging Face library [24,25] and we adapted them to our needs. Selecting only the first 2 paragraphs of text led to better results in the classification tasks, while using the full text was found to be best for the NER task, probably because information relating to the line of therapy or stage of cancer is located at the beginning of the text, while trials leading to approval can be found either at the beginning, or toward the end. We also deleted HTML tags, which generally correspond to hyperlinks leading to trial description.

As a benchmark, we developed a rule-based text mining approach on the same data. Subject matter experts gathered common examples of words and phrases that were associated with their choice of line of therapy or stage of cancer. These examples were used as a lookup list in the text-mining model.

The accuracy of the rule-based approach was then calculated and compared with the cross-validated accuracy from the deep learning approach. The highest score was considered as the winning model. Predictions using this winning model were used to prepopulate label-studio input to guide the labeling process when new texts describing approvals became available or new drug targets were taken into account.

Ethical Considerations

This study is exempt from human subjects’ research review as no human subjects were involved.

Results

Classification Tasks: Line and Stage

We observed the following results for the classification task.

For the BERT-based models, we display 5-fold cross-validated accuracy, defined in recent literature as the best available metric for classification [1,26]. This means that the data set is divided into 5 segments, which are successively considered as test data sets; we train the model on 4 segments, that is, 80% of the data, and test it on the remaining segment, that is, 20% of the data. Then the next data segment is considered as test data set. Finally, the 5 results are averaged.

We followed the methodology proposed in appendix A.3 of Devlin et al [1] and performed a grid search over batch size (possible values: 16 and 32), learning rate (possible values: 2e-5, 3e-5, and 5e-5), and number of epochs (possible values: 2, 3, and 4). Devlin et al [1] report in appendix A.3 that searching over these hyperparameters worked well across all tasks they worked on, which include binary and multiclass classifications, balanced and unbalanced data sets, and question answering tasks.

5-fold cross-validated accuracies (red line in Figure 2) generally increase with the number of texts describing approvals, similarly to benchmark data sets (Multimedia Appendix 1 [27-43] ). As a second observation, we notice some local decreases, similar to those observed for benchmark data sets, for example, TREC-6 or IMDB, for similar abscissas (Multimedia Appendix 1). Based on these 2 observations, benchmark data sets provide a good understanding of the fine-tuned BERT models’ behavior.

Due to the unbalanced data set, we also displayed the percentage of inputs from the largest class (green line). This percentage fluctuates through time as new drug targets are included sequentially. A simple algorithm that would place all entries in the largest class would return a score corresponding to the green curve. As an example, for stage of cancer, the proportion of the class corresponding to “stage III; stage IV” reached almost 65% during the project.

For the rule-based text mining model (blue line in Figure 2), accuracies decreased as new texts describing approvals were added to the database. This is in line with expectations: the dictionary of expressions was established early on and not modified, and new texts describing approvals can only bring more diversity in the expressions.

Marked changes at the end of the curves correspond to two key operational decisions: (1) labeling was refined and homogenized and (2) the number of different classes considered in the classification tasks was increased from 4 to 5 (all 5 lines from Table 2 for line of therapy and stage of cancer were taken into account instead of the first 4 lines only).

Current scores of 5-fold cross-validated accuracy were 61% for line of therapy with the fine-tuned BERT model and 60% for the rule-based approach. For cancer stage, they were 56% and 74%, respectively. These scores are displayed in Table 3. Although these scores may seem low, it is important to understand that each model performs multiclass classification with 5 classes each, so they are doing much better than random.

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Model Interpretability

Model interpretability is key in deep learning algorithms, and models whose results are well understood can be preferred to less interpretable, higher-accuracy models [44]. We use LIME [44] to understand what the classification models see in the data.

LIME results are generally easy to interpret, which builds confidence in the models. For line of therapy, the word “first” appeared repeatedly as the most important word for the class “First line,” and the word “maintenance” appeared often as the most important word for the class “Maintenance/Consolidation.” Figure 3 illustrates this observation on 1 typical example for the class “First line” (top). On the left-hand side of Figure 3, LIME displays scores corresponding to individual classes, and the highest score is the BERT-based model’s result. When the highest score is close to 1, the choice is unambiguous for the model (Figure 3, top, 99% for class First line). In other circumstances, the choice is more balanced (Figure 3, bottom), and in this second example, the model fails to predict the correct class. In the middle part of Figure 3, LIME displays words leading to decision with the most important word at the top and the least important word at the bottom. This ranking was obtained by LIME through deletion of randomly selected words in the text and the reevaluation of the final score. Words appearing with the color of the class reinforce the decision taken by the algorithm, while words displayed in blue weaken the decision. In the right part of Figure 3, LIME displays the input text and highlights the most important words.

Besides these straightforward cases, other words appear as important which are a lot less intuitive. For example, “Korea” was often identified as important in first line and “carcinoma” in second line. These examples show that biases can appear when applied to a new data set. We think that these biases will disappear or be attenuated when the number of inputs increases, something to be checked over time. Since a subject matter expert is involved to correct the results of the algorithm before they are used in the internal software, these possible biases are appropriately handled in the project (see section Deployment to production).

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NER Task: Clinical Study

To identify trials leading to an approval, we adopted a NER algorithm [45]. We selected 5-fold cross-validated F₁-score as a metric for this task, in agreement with recent literature [1,26] for NER tasks. F₁-scores are the harmonic mean of precision and recall and are classically used as a measure of success in NER tasks (unbalanced problems, where accuracy is not sufficient as a metric) [45]. We also applied the hyperparameters grid search strategy described for the classification tasks. In this project, we found that concatenating the BioMedTracker data set with another data set from the literature [46-48] and solving for all end points simultaneously was necessary to get a 5-fold cross-validated F₁-score of 87%, as reported in Table 3. Table 4 illustrates this process and summarizes the number of entities per class available in the merged data set when the merge is done with the wnut data set [48]. The improved scores are in agreement with previous work [49-52], which reports that “multitasking” improves NER results. However, multitask learning generally leads to a few percent increase in F₁-score. In this study, the F₁-score is null when we only use the BioMedTracker data set, and it reaches 87% when we concatenate this data set with one of the conll, ncbi, or wnut data sets [46-48].

Deployment to Production

Figure 4 illustrates the deployment to production of the 3 models described above. New texts describing approvals were collected automatically from the BioMedTracker API [18]. Predicted labels were calculated using both the rule-based text mining approach and the deep learning approach described above. The algorithm leading to the highest accuracy was selected, and its results are displayed.

The data set was then released both in internal software and to subject matter experts performing the labeling. Results that correspond to predictions are explicitly flagged as predictions to the user.

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Discussion

Principal Results

We have developed and put in 3 deep learning models corresponding to fine-tuned versions of the BERT model. Each model is designed to automatically analyze free text describing approvals taken out of the BioMedTracker database and answer one of the following questions: (1) Which line of therapy has the compound been approved for? (2) Which stage of cancer has the compound been approved for? (3) Which clinical trials have supported this approved indication? The first 2 questions have been addressed as classification tasks, while the third question was addressed as an NER task. For this purpose, we have used publicly available packages that allow fine-tuning the BERT model with relative ease [24,25], and we have used published grid search strategies for the hyperparameters [1].

Current scores of 5-fold cross-validated accuracy were 61% and 56% for line of therapy and cancer stage, respectively, and 87% 5-fold cross-validated F₁-scores for clinical trial. We have compared a rule-based approach for line of therapy and cancer stage, whose current scores are 60% and 74%, respectively.

The tasks described in this paper are challenging because they rely on a variety of subtly different text formulations. Hence, machine learning results help focus the analysis of the subject matter expert. For example, they help identify quickly unambiguous cases (top of Figure 3): the model scores high (99% for class “First line”), and the highlighted words indicate the reason for the decision (the words “first-line treatment” are highlighted in the text). The second example at the bottom of Figure 3 is more ambiguous, and the subject matter expert can focus on the analysis. Overall, the 3 machine learning models enable subject matter experts to leverage the results for deeper analysis and to accelerate information retrieval in a crowded clinical environment such as oncology.

Limitations

The main limitation of the application of deep learning to the BioMedTracker data set is the size of the labeled training data set, which currently is equal to 433 texts describing approvals. More training instances will become available when additional drug targets are considered or when new approval descriptions will be stored in the BioMedTracker database.

It also seems that our problem can be considered a complex problem if we take as a comparison point data sets from the literature used in Multimedia Appendix 1. Indeed, when we add more entry texts, accuracies increase slowly, at a rate similar to the Yahoo! Answers data set (40% accuracy with 200 entry texts and 77% accuracy for all 1.4 million texts).

This small number of training instances leads to relatively low scores for the 2 classification tasks: the current 5-fold cross-validated accuracies for line of therapy and stage of cancer are 61% and 56%, respectively. However, these accuracies are still much better than random choice alone because each model comprises 5 different classes.

Mitigation of these low accuracies for downstream, dependent systems is handled by the production pipeline, since a subject matter expert verifies and corrects the automatic labels produced by the deep learning model so as to return reliable results to end users.

Despite the lower accuracies seen for the classification tasks, subject matter experts reported that the labeling experience was improved by the presence of model predictions; even for a human, it is a nontrivial task to assess the approved populations for a large number of event descriptions.

Comparison With Previous Work

In this work, we address the problem of extracting information for competitive intelligence. NLP tools have been widely applied to extract information from electronic health records [5-15,16,17,53-55]. Even though the targets can be similar, for example, cancer stage or line of therapy, the nature of the documents is different, a lot less detailed in our case, and a new methodology is needed.

Conclusions

We have described the development and application of 3 deep learning models, fine-tuned from BERT [1]. They aim at extracting structured information from unstructured text, aiding information extraction and visualizations in downstream systems. The first model classifies the text describing the approval (Figure 1) in 1 of 5 categories corresponding to line of therapy. The second model performs the same task for cancer stage. The third model identifies trials in the paragraph only if they lead to the approval. We compared the results of these deep learning models to rule-based approaches for line of therapy and cancer stage.

In our case, although much better than random, accuracies achieved are insufficient for automation, and human intervention is necessary. We describe how we implement human intervention, which leads to a process that is effective for the users, subject matter experts, and machine learning engineers.

Accuracies are expected to improve through time as more training data become available. However, in the meantime, subject matter experts already find these results to be an insightful guide to labeling, saving much-needed time for extracting this information to support clinical insights and decision-making.