Interpretable phenotyping of Heart Failure patients with Dutch discharge letters
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| Main Authors: | , , , , , , , , |
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| Format: | Preprint |
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2025
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| author | Torri, Vittorio Boonstra, Machteld J. van de Veerdonk, Marielle C. Kalkman, Deborah N. Uijl, Alicia Ieva, Francesca Abu-Hanna, Ameen Asselbergs, Folkert W. Calixto, Iacer |
| author_facet | Torri, Vittorio Boonstra, Machteld J. van de Veerdonk, Marielle C. Kalkman, Deborah N. Uijl, Alicia Ieva, Francesca Abu-Hanna, Ameen Asselbergs, Folkert W. Calixto, Iacer |
| contents | Objective: Heart failure (HF) patients present with diverse phenotypes affecting treatment and prognosis. This study evaluates models for phenotyping HF patients based on left ventricular ejection fraction (LVEF) classes, using structured and unstructured data, assessing performance and interpretability.
Materials and Methods: The study analyzes all HF hospitalizations at both Amsterdam UMC hospitals (AMC and VUmc) from 2015 to 2023 (33,105 hospitalizations, 16,334 patients). Data from AMC were used for model training, and from VUmc for external validation. The dataset was unlabelled and included tabular clinical measurements and discharge letters. Silver labels for LVEF classes were generated by combining diagnosis codes, echocardiography results, and textual mentions. Gold labels were manually annotated for 300 patients for testing. Multiple Transformer-based (black-box) and Aug-Linear (white-box) models were trained and compared with baselines on structured and unstructured data. To evaluate interpretability, two clinicians annotated 20 discharge letters by highlighting information they considered relevant for LVEF classification. These were compared to SHAP and LIME explanations from black-box models and the inherent explanations of Aug-Linear models.
Results: BERT-based and Aug-Linear models, using discharge letters alone, achieved the highest classification results (AUC=0.84 for BERT, 0.81 for Aug-Linear on external validation), outperforming baselines. Aug-Linear explanations aligned more closely with clinicians' explanations than post-hoc explanations on black-box models.
Conclusions: Discharge letters emerged as the most informative source for phenotyping HF patients. Aug-Linear models matched black-box performance while providing clinician-aligned interpretability, supporting their use in transparent clinical decision-making. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2505_24619 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | Interpretable phenotyping of Heart Failure patients with Dutch discharge letters Torri, Vittorio Boonstra, Machteld J. van de Veerdonk, Marielle C. Kalkman, Deborah N. Uijl, Alicia Ieva, Francesca Abu-Hanna, Ameen Asselbergs, Folkert W. Calixto, Iacer Computation and Language Machine Learning 68T50 I.2.7; J.3 Objective: Heart failure (HF) patients present with diverse phenotypes affecting treatment and prognosis. This study evaluates models for phenotyping HF patients based on left ventricular ejection fraction (LVEF) classes, using structured and unstructured data, assessing performance and interpretability. Materials and Methods: The study analyzes all HF hospitalizations at both Amsterdam UMC hospitals (AMC and VUmc) from 2015 to 2023 (33,105 hospitalizations, 16,334 patients). Data from AMC were used for model training, and from VUmc for external validation. The dataset was unlabelled and included tabular clinical measurements and discharge letters. Silver labels for LVEF classes were generated by combining diagnosis codes, echocardiography results, and textual mentions. Gold labels were manually annotated for 300 patients for testing. Multiple Transformer-based (black-box) and Aug-Linear (white-box) models were trained and compared with baselines on structured and unstructured data. To evaluate interpretability, two clinicians annotated 20 discharge letters by highlighting information they considered relevant for LVEF classification. These were compared to SHAP and LIME explanations from black-box models and the inherent explanations of Aug-Linear models. Results: BERT-based and Aug-Linear models, using discharge letters alone, achieved the highest classification results (AUC=0.84 for BERT, 0.81 for Aug-Linear on external validation), outperforming baselines. Aug-Linear explanations aligned more closely with clinicians' explanations than post-hoc explanations on black-box models. Conclusions: Discharge letters emerged as the most informative source for phenotyping HF patients. Aug-Linear models matched black-box performance while providing clinician-aligned interpretability, supporting their use in transparent clinical decision-making. |
| title | Interpretable phenotyping of Heart Failure patients with Dutch discharge letters |
| topic | Computation and Language Machine Learning 68T50 I.2.7; J.3 |
| url | https://arxiv.org/abs/2505.24619 |