arXiv subjects

Bram van Es

Publications and source records attributed to Bram van Es.

5 recordsLinked to original sources

arXiv2026

Multilingual Artificial Datasets for AI-Driven Cardiology: the CliTe and ParaCliTe corpora

Background and Aims. Comparable, multilingual, validated cardiology corpora are critical to advance trustworthy natural language processing (NLP) models for cardiology but such resources are scarce due to privacy concerns. This study aimed to cover this gap by presenting suitable artificial corpus creation guidelines and by releasing 3 multilanguage corpora. Methods. Following purpose-specific publicly-available corpus construction guidelines, cardiologists from 7 European hospitals generated artificial clinical records in Czech, Dutch, English, Italian, Romanian, Spanish and Swedish, ensuring clinical diversity and sex balance, resulting in the CliTe corpus. A CliTe subset underwent a multi-stage manual translation into the other 6 languages, resulting in the parallel ParaCliTe corpus, while the remaining reports were automatically translated, constituting ParaCliTe Silver. Results. CliTe is a collection of 699 artificial cardiology reports, mostly outpatient notes (340 documents), discharge reports (263), and inpatient notes (89), describing fictional patients with ischaemic heart disease (199 patients), heart failure (188), and valvular disease (79), among others. ParaCliTe contains reports from 94 fictitious patients, each available in seven languages with sentence-level alignment, resulting in 658 documents. The corpus mainly comprises discharge reports (322 documents), and outpatient (196) and inpatient (140) notes, describing patients with heart failure (399 documents), ischaemic heart disease (287), and valvular disease (238). Empirical results illustrate the utility of ParaCliTe and highlight the limitations of state-of-the-art NLP models adapted to the cardiology domain. Conclusions. The creation of multilingual, equitable and realistic corpora of artificial patients capable of strengthening NLP performance for cardiology is feasible when supported by detailed guidelines.

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arXiv2026

CardioLM: A multilingual suite of small language models for the cardiology domain

Background: Cardiovascular care generates large volumes of clinical free-text documentation in local languages. However, clinical natural language processing (NLP) resources remain concentrated in English, and no existing benchmark is cardiology-specific, multilingual, and broad in entity coverage. Methods: We present two contributions. The first is CardioCCC, a corpus of 508 cardiology case reports originally published in Spanish and extended to Czech, Dutch, English, Italian, Romanian, and Swedish through machine translation, annotation projection, and clinician review, with annotations covering diseases, symptoms, procedures, and medications. The second is CardioLM, comprising CardioBERTa, a set of language-specific encoders obtained by continued pretraining on cardiology and biomedical corpora, and CardioNER, a set of named entity recognition (NER) models fine-tuned on CardioCCC. Results: Cardiology-specific pretraining reduced pseudo-perplexity by up to a factor of eight, yet changed strict span-level F1 by at most 0.04, with benefits concentrated in languages whose backbones lacked biomedical coverage. The jointly trained multilingual XLM-RoBERTa-large models achieved the best strict F1 in nearly every language and entity type, exceeding the strongest monolingual system by up to 0.13 F1. A large share of residual errors concerned boundary detection: relaxed matching recovered 0.10-0.23 F1 for disease, procedure, and symptom, but only 0.01-0.07 for medication. Clinicians rated CardioNER well above a rule- and dictionary-based baseline, with the mean rating across entity types rising from 26% to 73%. Conclusions: Specialty-specific pretraining is not the decisive factor for downstream entity recognition, whereas multilingual joint training yields the strongest results in nearly all settings and a simpler deployment path for multi-country clinical information extraction.

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arXiv2026

Automatic Cardiac Risk Management Classification using large-context Electronic Patients Health Records

To overcome the limitations of manual administrative coding in geriatric Cardiovascular Risk Management, this study introduces an automated classification framework leveraging unstructured Electronic Health Records (EHRs). Using a dataset of 3,482 patients, we benchmarked three distinct modeling paradigms on longitudinal Dutch clinical narratives: classical machine learning baselines, specialized deep learning architectures optimized for large-context sequences, and general-purpose generative Large Language Models (LLMs) in a zero-shot setting. Additionally, we evaluated a late fusion strategy to integrate unstructured text with structured medication embeddings and anthropometric data. Our analysis reveals that the custom Transformer architecture outperforms both traditional methods and generative \acs{llm}s, achieving the highest F1-scores and Matthews Correlation Coefficients. These findings underscore the critical role of specialized hierarchical attention mechanisms in capturing long-range dependencies within medical texts, presenting a robust, automated alternative to manual workflows for clinical risk stratification.

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arXiv2024

Diagnosis extraction from unstructured Dutch echocardiogram reports using span- and document-level characteristic classification

Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa$.$nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa$.$nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa$.$nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.

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arXiv2022

Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methods

As structured data are often insufficient, labels need to be extracted from free text in electronic health records when developing models for clinical information retrieval and decision support systems. One of the most important contextual properties in clinical text is negation, which indicates the absence of findings. We aimed to improve large scale extraction of labels by comparing three methods for negation detection in Dutch clinical notes. We used the Erasmus Medical Center Dutch Clinical Corpus to compare a rule-based method based on ContextD, a biLSTM model using MedCAT and (finetuned) RoBERTa-based models. We found that both the biLSTM and RoBERTa models consistently outperform the rule-based model in terms of F1 score, precision and recall. In addition, we systematically categorized the classification errors for each model, which can be used to further improve model performance in particular applications. Combining the three models naively was not beneficial in terms of performance. We conclude that the biLSTM and RoBERTa-based models in particular are highly accurate accurate in detecting clinical negations, but that ultimately all three approaches can be viable depending on the use case at hand.

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