Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma
Abstract Background Predictive modeling with longitudinal electronic health record (EHR) data offers great promise for accelerating personalized medicine and better informs clinical decision-making. Recently, deep learning models have achieved state-of-the-art performance for many healthcare predict...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2019-11-01
|
| Series: | BMC Medical Informatics and Decision Making |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12911-019-0951-4 |
| _version_ | 1818452656816914432 |
|---|---|
| author | Rawan AlSaad Qutaibah Malluhi Ibrahim Janahi Sabri Boughorbel |
| author_facet | Rawan AlSaad Qutaibah Malluhi Ibrahim Janahi Sabri Boughorbel |
| author_sort | Rawan AlSaad |
| collection | DOAJ |
| description | Abstract Background Predictive modeling with longitudinal electronic health record (EHR) data offers great promise for accelerating personalized medicine and better informs clinical decision-making. Recently, deep learning models have achieved state-of-the-art performance for many healthcare prediction tasks. However, deep models lack interpretability, which is integral to successful decision-making and can lead to better patient care. In this paper, we build upon the contextual decomposition (CD) method, an algorithm for producing importance scores from long short-term memory networks (LSTMs). We extend the method to bidirectional LSTMs (BiLSTMs) and use it in the context of predicting future clinical outcomes using patients’ EHR historical visits. Methods We use a real EHR dataset comprising 11071 patients, to evaluate and compare CD interpretations from LSTM and BiLSTM models. First, we train LSTM and BiLSTM models for the task of predicting which pre-school children with respiratory system-related complications will have asthma at school-age. After that, we conduct quantitative and qualitative analysis to evaluate the CD interpretations produced by the contextual decomposition of the trained models. In addition, we develop an interactive visualization to demonstrate the utility of CD scores in explaining predicted outcomes. Results Our experimental evaluation demonstrate that whenever a clear visit-level pattern exists, the models learn that pattern and the contextual decomposition can appropriately attribute the prediction to the correct pattern. In addition, the results confirm that the CD scores agree to a large extent with the importance scores generated using logistic regression coefficients. Our main insight was that rather than interpreting the attribution of individual visits to the predicted outcome, we could instead attribute a model’s prediction to a group of visits. Conclusion We presented a quantitative and qualitative evidence that CD interpretations can explain patient-specific predictions using CD attributions of individual visits or a group of visits. |
| first_indexed | 2024-12-14T21:26:34Z |
| format | Article |
| id | doaj.art-d3caeba424064e0dabd8ee0601ae5322 |
| institution | Directory Open Access Journal |
| issn | 1472-6947 |
| language | English |
| last_indexed | 2024-12-14T21:26:34Z |
| publishDate | 2019-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Informatics and Decision Making |
| spelling | doaj.art-d3caeba424064e0dabd8ee0601ae53222022-12-21T22:46:47ZengBMCBMC Medical Informatics and Decision Making1472-69472019-11-0119111110.1186/s12911-019-0951-4Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthmaRawan AlSaad0Qutaibah Malluhi1Ibrahim Janahi2Sabri Boughorbel3Machine Learning Group, Sidra MedicineDepartment of Computer Science and Engineering, Qatar UniversityDivision of Pediatric Pulmonology, Sidra MedicineMachine Learning Group, Sidra MedicineAbstract Background Predictive modeling with longitudinal electronic health record (EHR) data offers great promise for accelerating personalized medicine and better informs clinical decision-making. Recently, deep learning models have achieved state-of-the-art performance for many healthcare prediction tasks. However, deep models lack interpretability, which is integral to successful decision-making and can lead to better patient care. In this paper, we build upon the contextual decomposition (CD) method, an algorithm for producing importance scores from long short-term memory networks (LSTMs). We extend the method to bidirectional LSTMs (BiLSTMs) and use it in the context of predicting future clinical outcomes using patients’ EHR historical visits. Methods We use a real EHR dataset comprising 11071 patients, to evaluate and compare CD interpretations from LSTM and BiLSTM models. First, we train LSTM and BiLSTM models for the task of predicting which pre-school children with respiratory system-related complications will have asthma at school-age. After that, we conduct quantitative and qualitative analysis to evaluate the CD interpretations produced by the contextual decomposition of the trained models. In addition, we develop an interactive visualization to demonstrate the utility of CD scores in explaining predicted outcomes. Results Our experimental evaluation demonstrate that whenever a clear visit-level pattern exists, the models learn that pattern and the contextual decomposition can appropriately attribute the prediction to the correct pattern. In addition, the results confirm that the CD scores agree to a large extent with the importance scores generated using logistic regression coefficients. Our main insight was that rather than interpreting the attribution of individual visits to the predicted outcome, we could instead attribute a model’s prediction to a group of visits. Conclusion We presented a quantitative and qualitative evidence that CD interpretations can explain patient-specific predictions using CD attributions of individual visits or a group of visits.http://link.springer.com/article/10.1186/s12911-019-0951-4InterpretabilityDeep learningPredictive modelsElectronic health record |
| spellingShingle | Rawan AlSaad Qutaibah Malluhi Ibrahim Janahi Sabri Boughorbel Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma BMC Medical Informatics and Decision Making Interpretability Deep learning Predictive models Electronic health record |
| title | Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma |
| title_full | Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma |
| title_fullStr | Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma |
| title_full_unstemmed | Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma |
| title_short | Interpreting patient-Specific risk prediction using contextual decomposition of BiLSTMs: application to children with asthma |
| title_sort | interpreting patient specific risk prediction using contextual decomposition of bilstms application to children with asthma |
| topic | Interpretability Deep learning Predictive models Electronic health record |
| url | http://link.springer.com/article/10.1186/s12911-019-0951-4 |
| work_keys_str_mv | AT rawanalsaad interpretingpatientspecificriskpredictionusingcontextualdecompositionofbilstmsapplicationtochildrenwithasthma AT qutaibahmalluhi interpretingpatientspecificriskpredictionusingcontextualdecompositionofbilstmsapplicationtochildrenwithasthma AT ibrahimjanahi interpretingpatientspecificriskpredictionusingcontextualdecompositionofbilstmsapplicationtochildrenwithasthma AT sabriboughorbel interpretingpatientspecificriskpredictionusingcontextualdecompositionofbilstmsapplicationtochildrenwithasthma |