Paloma Rabaey

Paloma Rabaey, Stefan Heytens, Thomas Demeester

Clinical information extraction, which involves structuring clinical concepts from unstructured medical text, remains a challenging problem that could benefit from the inclusion of tabular background information available in electronic health records. Existing open-source datasets lack explicit links between structured features and clinical concepts in the text, motivating the need for a new research dataset. We introduce SimSUM, a benchmark dataset of 10,000 simulated patient records that link unstructured clinical notes with structured background variables. Each record simulates a patient encounter in the domain of respiratory diseases and includes tabular data (e.g., symptoms, diagnoses, underlying conditions) generated from a Bayesian network whose structure and parameters are defined by domain experts. A large language model (GPT-4o) is prompted to generate a clinical note describing the encounter, including symptoms and relevant context. These notes are annotated with span-level symptom mentions. We conduct an expert evaluation to assess note quality and run baseline predictive models on both the tabular and textual data. The SimSUM dataset is primarily designed to support research on clinical information extraction in the presence of tabular background variables, which can be linked through domain knowledge to concepts of interest to be extracted from the text -- namely, symptoms in the case of SimSUM. Secondary uses include research on the automation of clinical reasoning over both tabular data and text, causal effect estimation in the presence of tabular and/or textual confounders, and multi-modal synthetic data generation. SimSUM is not intended for training clinical decision support systems or production-grade models, but rather to facilitate reproducible research in a simplified and controlled setting.

Yeonsu Kwon, Jiho Kim, Junseong Choi et al.

Data consistency between unstructured clinical notes and structured tables in Electronic Health Records (EHRs) is essential for patient safety and clinical decision-making. However, existing work on note-table consistency verification mainly relies on surface-level matching of numeric values or simple events. Such approaches fail to capture the reasoning underlying real-world EHR documentation, including clinical interpretation, event relations, and temporal changes. To address this gap, we introduce EHR-ReasonCon, a reasoning-intensive benchmark for note-table consistency verification. Built on MIMIC-III with expert-guided annotations, it comprises 8,048 entities derived from clinical notes and provides high-quality ground-truth labels. The annotation protocol is supported by specialized table-exploration tools to ensure systematic evidence retrieval and reliable consistency assessment. We also propose EHR-Inspector, an LLM-based framework that segments notes, extracts anchor entities and temporal references, and uses table-exploration tools to verify consistency against structured tables. Evaluated using expert-validated LLM-as-a-judge metrics under harsh and lenient criteria, EHR-Inspector achieves state-of-the-art performance across multiple model backbones. Analyses further demonstrate the effectiveness of its components and highlight differences from human verification.

Paloma Rabaey, Cedric De Boom, Thomas Demeester

Bayesian Networks may be appealing for clinical decision-making due to their inclusion of causal knowledge, but their practical adoption remains limited as a result of their inability to deal with unstructured data. While neural networks do not have this limitation, they are not interpretable and are inherently unable to deal with causal structure in the input space. Our goal is to build neural networks that combine the advantages of both approaches. Motivated by the perspective to inject causal knowledge while training such neural networks, this work presents initial steps in that direction. We demonstrate how a neural network can be trained to output conditional probabilities, providing approximately the same functionality as a Bayesian Network. Additionally, we propose two training strategies that allow encoding the independence relations inferred from a given causal structure into the neural network. We present initial results in a proof-of-concept setting, showing that the neural model acts as an understudy to its Bayesian Network counterpart, approximating its probabilistic and causal properties.

Jong Hak Moon, Geon Choi, Paloma Rabaey et al.

Radiology reports convey detailed clinical observations and capture diagnostic reasoning that evolves over time. However, existing evaluation methods are limited to single-report settings and rely on coarse metrics that fail to capture fine-grained clinical semantics and temporal dependencies. We introduce LUNGUAGE,a benchmark dataset for structured radiology report generation that supports both single-report evaluation and longitudinal patient-level assessment across multiple studies. It contains 1,473 annotated chest X-ray reports, each reviewed by experts, and 80 of them contain longitudinal annotations to capture disease progression and inter-study intervals, also reviewed by experts. Using this benchmark, we develop a two-stage framework that transforms generated reports into fine-grained, schema-aligned structured representations, enabling longitudinal interpretation. We also propose LUNGUAGESCORE, an interpretable metric that compares structured outputs at the entity, relation, and attribute level while modeling temporal consistency across patient timelines. These contributions establish the first benchmark dataset, structuring framework, and evaluation metric for sequential radiology reporting, with empirical results demonstrating that LUNGUAGESCORE effectively supports structured report evaluation. The code is available at: https://github.com/SuperSupermoon/Lunguage

Henri Arno, Paloma Rabaey, Thomas Demeester

One of the central goals of causal machine learning is the accurate estimation of heterogeneous treatment effects from observational data. In recent years, meta-learning has emerged as a flexible, model-agnostic paradigm for estimating conditional average treatment effects (CATE) using any supervised model. This paper examines the performance of meta-learners when the confounding variables are expressed in text. Through synthetic data experiments, we show that learners using pre-trained text representations of confounders, in addition to tabular background variables, achieve improved CATE estimates compared to those relying solely on the tabular variables, particularly when sufficient data is available. However, due to the entangled nature of the text embeddings, these models do not fully match the performance of meta-learners with perfect confounder knowledge. These findings highlight both the potential and the limitations of pre-trained text representations for causal inference and open up interesting avenues for future research.

Paloma Rabaey, Jong Hak Moon, Jung-Oh Lee et al.

Radiology reports are invaluable for clinical decision-making and hold great potential for automated analysis when structured into machine-readable formats. These reports often contain uncertainty, which we categorize into two distinct types: (i) Explicit uncertainty reflects doubt about the presence or absence of findings, conveyed through hedging phrases. These vary in meaning depending on the context, making rule-based systems insufficient to quantify the level of uncertainty for specific findings; (ii) Implicit uncertainty arises when radiologists omit parts of their reasoning, recording only key findings or diagnoses. Here, it is often unclear whether omitted findings are truly absent or simply unmentioned for brevity. We address these challenges with a two-part framework. We quantify explicit uncertainty by creating an expert-validated, LLM-based reference ranking of common hedging phrases, and mapping each finding to a probability value based on this reference. In addition, we model implicit uncertainty through an expansion framework that systematically adds characteristic sub-findings derived from expert-defined diagnostic pathways for 14 common diagnoses. Using these methods, we release Lunguage++, an expanded, uncertainty-aware version of the Lunguage benchmark of fine-grained structured radiology reports. This enriched resource enables uncertainty-aware image classification, faithful diagnostic reasoning, and new investigations into the clinical impact of diagnostic uncertainty.

Alexander Decruyenaere, Heidelinde Dehaene, Paloma Rabaey et al.

Recent advances in generative models facilitate the creation of synthetic data to be made available for research in privacy-sensitive contexts. However, the analysis of synthetic data raises a unique set of methodological challenges. In this work, we highlight the importance of inferential utility and provide empirical evidence against naive inference from synthetic data, whereby synthetic data are treated as if they were actually observed. Before publishing synthetic data, it is essential to develop statistical inference tools for such data. By means of a simulation study, we show that the rate of false-positive findings (type 1 error) will be unacceptably high, even when the estimates are unbiased. Despite the use of a previously proposed correction factor, this problem persists for deep generative models, in part due to slower convergence of estimators and resulting underestimation of the true standard error. We further demonstrate our findings through a case study.

Max Hallemeesch, Marija Pizurica, Paloma Rabaey et al.

Cancer diagnosis and prognosis primarily depend on clinical parameters such as age and tumor grade, and are increasingly complemented by molecular data, such as gene expression, from tumor sequencing. However, sequencing is costly and delays oncology workflows. Recent advances in Deep Learning allow to predict molecular information from morphological features within Whole Slide Images (WSIs), offering a cost-effective proxy of the molecular markers. While promising, current methods lack the robustness to fully replace direct sequencing. Here we aim to improve existing methods by introducing a model-agnostic framework that allows to inject prior knowledge on gene-gene interactions into Deep Learning architectures, thereby increasing accuracy and robustness. We design the framework to be generic and flexibly adaptable to a wide range of architectures. In a case study on breast cancer, our strategy leads to an average increase of 983 significant genes (out of 25,761) across all 18 experiments, with 14 generalizing to an increase on an independent dataset. Our findings reveal a high potential for injection of prior knowledge to increase gene expression prediction performance from WSIs across a wide range of architectures.

Alexander Decruyenaere, Heidelinde Dehaene, Paloma Rabaey et al.

While synthetic data hold great promise for privacy protection, their statistical analysis poses significant challenges that necessitate innovative solutions. The use of deep generative models (DGMs) for synthetic data generation is known to induce considerable bias and imprecision into synthetic data analyses, compromising their inferential utility as opposed to original data analyses. This bias and uncertainty can be substantial enough to impede statistical convergence rates, even in seemingly straightforward analyses like mean calculation. The standard errors of such estimators then exhibit slower shrinkage with sample size than the typical 1 over root-$n$ rate. This complicates fundamental calculations like p-values and confidence intervals, with no straightforward remedy currently available. In response to these challenges, we propose a new strategy that targets synthetic data created by DGMs for specific data analyses. Drawing insights from debiased and targeted machine learning, our approach accounts for biases, enhances convergence rates, and facilitates the calculation of estimators with easily approximated large sample variances. We exemplify our proposal through a simulation study on toy data and two case studies on real-world data, highlighting the importance of tailoring DGMs for targeted data analysis. This debiasing strategy contributes to advancing the reliability and applicability of synthetic data in statistical inference.

Paloma Rabaey, Adrick Tench, Stefan Heytens et al.

Electronic health records (EHRs) form an invaluable resource for training clinical decision support systems. To leverage the potential of such systems in high-risk applications, we need large, structured tabular datasets on which we can build transparent feature-based models. While part of the EHR already contains structured information (e.g. diagnosis codes, medications, and lab results), much of the information is contained within unstructured text (e.g. discharge summaries and nursing notes). In this work, we propose a method for multi-modal patient-level information extraction that leverages both the tabular features available in the patient's EHR (using an expert-informed Bayesian network) as well as clinical notes describing the patient's symptoms (using neural text classifiers). We propose the use of virtual evidence augmented with a consistency node to provide an interpretable, probabilistic fusion of the models' predictions. The consistency node improves the calibration of the final predictions compared to virtual evidence alone, allowing the Bayesian network to better adjust the neural classifier's output to handle missing information and resolve contradictions between the tabular and text data. We show the potential of our method on the SimSUM dataset, a simulated benchmark linking tabular EHRs with clinical notes through expert knowledge.

Paloma Rabaey, Johannes Deleu, Stefan Heytens et al.

Bayesian networks are well-suited for clinical reasoning on tabular data, but are less compatible with natural language data, for which neural networks provide a successful framework. This paper compares and discusses strategies to augment Bayesian networks with neural text representations, both in a generative and discriminative manner. This is illustrated with simulation results for a primary care use case (diagnosis of pneumonia) and discussed in a broader clinical context.