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Cited by 616Machine Learning in HealthcareArtificial Intelligence in HealthcareElectronic Health Records Systems

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BEHRT: Transformer for Electronic Health Records

Open access
Li, Yikuan, Rao, Shishir, Solares, José Roberto Ayala, Hassaine, Abdelaali, Ramakrishnan, Rema, Canoy, Dexter, Zhu, Yajie, Rahimi, Kazem, Salimi-Khorshidi, Gholamreza·2020·Scientific Reports
DOI 10.1038/s41598-020-62922-yPMC PMC7189231
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Abstract

Today, despite decades of developments in medicine and the growing interest in precision healthcare, vast majority of diagnoses happen once patients begin to show noticeable signs of illness. Early indication and detection of diseases, however, can provide patients and carers with the chance of early intervention, better disease management, and efficient allocation of healthcare resources. The latest developments in machine learning (including deep learning) provides a great opportunity to address this unmet need. In this study, we introduce BEHRT: A deep neural sequence transduction model for electronic health records (EHR), capable of simultaneously predicting the likelihood of 301 conditions in one’s future visits. When trained and evaluated on the data from nearly 1.6 million individuals, BEHRT shows a striking improvement of 8.0–13.2% (in terms of average precision scores for different tasks), over the existing state-of-the-art deep EHR models. In addition to its scalability and superior accuracy, BEHRT enables personalised interpretation of its predictions; its flexible architecture enables it to incorporate multiple heterogeneous concepts (e.g., diagnosis, medication, measurements, and more) to further improve the accuracy of its predictions; its (pre-)training results in disease and patient representations can be useful for future studies (i.e., transfer learning).

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Crossref · 10.1038/s41598-020-62922-y

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Figure 1 Linkage and filtering of CPRD data. This flow lists all the key steps of our data cleaning and linkage procedure. At each step, the number of patients that are included is shown. As you can see, we started with nearly 8 million patients and our final data (used for training and evaluation of our models) consists of 1.6 million patients, each meeting our inclusion criteria.
Figure 1 Linkage and filtering of CPRD data. This flow lists all the key steps of our data cleaning and linkage procedure. At each step, the number of patients that are included is shown. As you can see, we started with nearly 8 million patients and our final data (used for training and evaluation of our models) consists of 1.6 million patients, each meeting our inclusion criteria.CC BY · PubMed Central
Figure 2 Preparation of CPRD data for BEHRT. An example patient’s EHR sequence can be seen in the figure, which consists of 8 visits. In each visit, the record can consist of concepts such as diagnoses, medications and measurements; all these values are artificial and for illustration purposes. For this study, we are only interested in age and diagnoses. Therefore, as shown in at the bottom of the figure, we have taken only the diagnosis and age subset of the record to form the necessary sequences. This resulting sequence is how we represent every patient’s EHR in our modelling process. Note that the visits shown in purple boxes are not going to be represented to the model, due to them lacking diagnoses.
Figure 2 Preparation of CPRD data for BEHRT. An example patient’s EHR sequence can be seen in the figure, which consists of 8 visits. In each visit, the record can consist of concepts such as diagnoses, medications and measurements; all these values are artificial and for illustration purposes. For this study, we are only interested in age and diagnoses. Therefore, as shown in at the bottom of the figure, we have taken only the diagnosis and age subset of the record to form the necessary sequences. This resulting sequence is how we represent every patient’s EHR in our modelling process. Note that the visits shown in purple boxes are not going to be represented to the model, due to them lacking diagnoses.CC BY · PubMed Central
Figure 3 BEHRT architecture. Using the artificial data shown in Fig. 2, section (a) shows how BEHRT sees one’s EHR. In addition to diagnosis and age, BEHRT also employs an encoding for an event’s positions (shown as POSITION) and an encoding for visit (shown as SEGMENT with A and B), which alternates between visits. The summation of all these embeddings results in a final embedding shown at the bottom of (a), which will be the latent contextual representation of one’s EHR at a given visit’s diagnosis. Section (b) on the other hand shows BEHRT’s Transformer-based architecture. It is first pre-trained by the MLM task, to learn the network parameters (including the disease embeddings) that can predict the masked disease tokens. When training the model in downstream tasks (i.e., T1 to T3 - detailed explanation can be found in section: Disease Prediction), the model finetunes the weights pre-trained in the MLM task and learns the weights for the classification layer (i.e., mapping T1 to the pooling layer and finally to the subsequent diseases classifier).
Figure 3 BEHRT architecture. Using the artificial data shown in Fig. 2, section (a) shows how BEHRT sees one’s EHR. In addition to diagnosis and age, BEHRT also employs an encoding for an event’s positions (shown as POSITION) and an encoding for visit (shown as SEGMENT with A and B), which alternates between visits. The summation of all these embeddings results in a final embedding shown at the bottom of (a), which will be the latent contextual representation of one’s EHR at a given visit’s diagnosis. Section (b) on the other hand shows BEHRT’s Transformer-based architecture. It is first pre-trained by the MLM task, to learn the network parameters (including the disease embeddings) that can predict the masked disease tokens. When training the model in downstream tasks (i.e., T1 to T3 - detailed explanation can be found in section: Disease Prediction), the model finetunes the weights pre-trained in the MLM task and learns the weights for the classification layer (i.e., mapping T1 to the pooling layer and finally to the subsequent diseases classifier).CC BY · PubMed Central
Figure 4 Visual investigation of the disease embedding. In this image we see a graph of disease embeddings projected in two dimensions where distance represents closeness of contextual association. The colors represent the Caliber chapter. Most associations are accepted by medical experts and maintain the gender-based divisions in illnesses, among other things. We zoom in and profile four clusters in this plot – shown in subfigures (A–D).
Figure 4 Visual investigation of the disease embedding. In this image we see a graph of disease embeddings projected in two dimensions where distance represents closeness of contextual association. The colors represent the Caliber chapter. Most associations are accepted by medical experts and maintain the gender-based divisions in illnesses, among other things. We zoom in and profile four clusters in this plot – shown in subfigures (A–D).CC BY · PubMed Central
Figure 5 The analysis of BEHRT’s self-attention. This figure shows the EHR history of patients (A and B), each presented as two identical columns (shown chronologically, going downwards) for the convenience of association analysis. The left side of the column represents the disease of interest and the right column indicates the corresponding associations to the highlighted disease on the left. The intensity of the blue on the right column represents the strength of the attention score – the stronger the intensity, the stronger the association and hence the stronger the attention score. The attention scores are specifically retrieved from the attention component of the last layer of BEHRT network.
Figure 5 The analysis of BEHRT’s self-attention. This figure shows the EHR history of patients (A and B), each presented as two identical columns (shown chronologically, going downwards) for the convenience of association analysis. The left side of the column represents the disease of interest and the right column indicates the corresponding associations to the highlighted disease on the left. The intensity of the blue on the right column represents the strength of the attention score – the stronger the intensity, the stronger the association and hence the stronger the attention score. The attention scores are specifically retrieved from the attention component of the last layer of BEHRT network.CC BY · PubMed Central
Figure 6 Disease-wise precision analysis. Each circle in these graphs represents a disease, and its colour and size denote the Caliber chapter and prevalence, respectively. Also, in these plots, we show APS and AUROC on the x- and y-axis, respectively. Therefore, the further right and higher a disease, the better BEHRT’s job at predicting its occurrence in the next 6 months. Subplot (A) illustrated the full results, and subplots (B and C) illustrate the best and worst sections of the plot, in terms of BEHRT’s performance.
Figure 6 Disease-wise precision analysis. Each circle in these graphs represents a disease, and its colour and size denote the Caliber chapter and prevalence, respectively. Also, in these plots, we show APS and AUROC on the x- and y-axis, respectively. Therefore, the further right and higher a disease, the better BEHRT’s job at predicting its occurrence in the next 6 months. Subplot (A) illustrated the full results, and subplots (B and C) illustrate the best and worst sections of the plot, in terms of BEHRT’s performance.CC BY · PubMed Central

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Research works printed but not linked: 3

  1. Choi, E., Bahadori, M. T., Schuetz, A., Stewart, W. F. & Sun, J. Doctor AI: Predicting Clinical Events via Recurrent Neural Networks. In Machine Learning for Healthcare Conference, 301–318 (2016).
  2. Zhu, M. Recall, precision and average precision. Dep. Stat. Actuar. Sci. Univ. Waterloo, Waterloo 2, 30 (2004).
  3. Vig, J. Visualizing Attention in Transformer-Based Language Representation Models. arXiv preprint arXiv:1904.02679 (2019). · arXiv

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Metadata

Authors
Li, Y., Rao, S., Solares, J. R. A., Hassaine, A., Ramakrishnan, R., Canoy, D., Zhu, Y., Rahimi, K., & Salimi-Khorshidi, G.
Affiliations
University of Oxford (GB)
Corresponding author
Rao, Shishir
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2020-04-28
Volume
10
Issue
1
Pages
7155-7155
ISSN
2045-2322 (ISSN-L)
DOI
10.1038/s41598-020-62922-y
PMC
PMC7189231
OpenAlex
W3017637887
Cited by
595
References
37
Citations by year
2026: 129 · 2025: 128 · 2024: 106 · 2023: 98 · 2022: 60 · 2021: 58 · 2020: 16
FWCI
22.80
Type
journal article
Language
en
Open access
Licence
Locations
  • Scientific Reports (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • UNSWorks (University of New South Wales, Sydney, Australia) (submittedVersion, cc-by)
  • arXiv (Cornell University) (cc-by)
Funders
  • DH | National Institute for Health Research
  • Oxford University | Oxford Martin School, University of Oxford
Topics
  • Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
  • Health Sciences › Health Professions › Health Information Management › Artificial Intelligence in Healthcare
  • Health Sciences › Health Professions › Health Information Management › Electronic Health Records Systems
Keywords
electronic health records, disease prediction, early disease detection, sequence-to-sequence models, transformer models, multi-task prediction, heterogeneous clinical data, interpretable prediction, patient representation learning, transfer learning
MeSH terms
Machine Learning, Algorithms, Humans, Electronic Health Records

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