Incorporating causal knowledge and mechanisms is essential for refining causal models and improving downstream tasks such as designing new treatments. In this paper, we introduce a novel concept in causal discovery, termed interventional constraints, which differs fundamentally from interventional data. While interventional data require direct perturbations of variables, interventional constraints encode high-level causal knowledge in the form of inequality constraints on causal effects. For instance, in the Sachs dataset (Sachs et al.\ 2005), Akt has been shown to be activated by PIP3, meaning PIP3 exerts a positive causal effect on Akt. Existing causal discovery methods allow enforcing structural constraints (for example, requiring a causal path from PIP3 to Akt), but they may still produce incorrect causal conclusions such as learning that "PIP3 inhibits Akt". Interventional constraints bridge this gap by explicitly constraining the total causal effect between variable pairs, ensuring learned models respect known causal influences. To formalize interventional constraints, we propose a metric to quantify total causal effects for linear causal models and formulate the problem as a
Let $p(x)$ be the joint density of variables $X$, and let $ψ(x)= abla_x\log p(x)$ be its score field. Geometry constructed from $p$ and $ψ$ alone cannot identify causal direction: structural models with the same observational distribution have the same score geometry. I develop an interventional analogue. A hard intervention $\operatorname{do}(X_k=ξ)$ does not merely reweight the joint law; it restricts the distribution to the submanifold ${x_k=ξ}$. Its score should therefore be defined on the remaining $d-1$ free coordinates. I define causal influence $X_k\rightsquigarrow X_j$ as variation of the interventional marginal distribution of $X_j$ with $ξ$, and show that the corresponding derivative of the marginal interventional score gives a local sufficient condition for influence. Projecting the observational score onto admissible intervention directions does not generally recover causal response: two models may share the same observational score and admissible set yet respond differently. I therefore introduce an interventional response field supplied by structural information. A causal metric is defined as the Fisher information metric on a family of interventions with a common ta
Existing identification results in proximal causal inference often focus on marginal interventional distributions using standard outcome or treatment bridge functions. These methods do not generally identify joint interventional distributions that contain all proxy variables that were used to define the corresponding bridge functions. In many applications, however, these joint interventional distributions are a natural target of interest. We introduce extended bridge functions and derive new identification results for joint interventional distributions that may retain all relevant proxy variables. We then apply these results to proximal identification algorithms, where interventional kernels naturally arise as intermediate objects, yielding a generalized framework based on kernel operations.
We study the problem of learning robust discriminative representations of causally related latent variables given the underlying causal graph and a training set comprising passively collected observational data and interventional data obtained through targeted interventions on some of these latent variables. We desire to learn representations that are robust against the resulting interventional distribution shifts. Existing approaches treat observational and interventional data alike, ignoring the independence relations arising from these interventions, even with known underlying causal models. As a result, their representations lead to large predictive performance disparities between observational and interventional data. This performance disparity worsens when interventional training data is scarce. In this paper, (1) we first identify a strong correlation between this performance disparity and the representations' violation of statistical independence induced during interventions. (2) For linear models, we derive sufficient conditions on the proportion of interventional training data, for which enforcing statistical independence between representations of the intervened node and
Electronic health record (EHR) notes are dense medical documents containing large amounts of information, often filled with complex medical jargon. Highlighting all details in EHRs helps reduce the likelihood of missing crucial information by drawing attention to key content. This study proposes the design of a Cardiology Interface Terminology (CIT) to accurately highlight all details in EHR notes of cardiology patients. We introduce an innovative Machine Learning (ML) technique for the design of CIT. The ML technique requires training data. Manual preparation of such training data is time-consuming and expensive. The process of the CIT design includes three phases. In the first two phases, we innovatively derive a training data CIT to be used by the third phase, ML technique. We start by designing an initial CIT, composed of several components: the cardiology-related sub-hierarchies of SNOMED, other SNOMED concepts mined from EHRs of build set, and necessary components of terms e.g., medical abbreviations and medications. Utilizing an iterative process, fine-grained phrases containing initial CIT concepts are extracted from build set as CIT concept candidates. The candidate concep
In this paper we show how to exploit interventional data to acquire the joint conditional distribution of all the variables using the Maximum Entropy principle. To this end, we extend the Causal Maximum Entropy method to make use of interventional data in addition to observational data. Using Lagrange duality, we prove that the solution to the Causal Maximum Entropy problem with interventional constraints lies in the exponential family, as in the Maximum Entropy solution. Our method allows us to perform two tasks of interest when marginal interventional distributions are provided for any subset of the variables. First, we show how to perform causal feature selection from a mixture of observational and single-variable interventional data, and, second, how to infer joint interventional distributions. For the former task, we show on synthetically generated data, that our proposed method outperforms the state-of-the-art method on merging datasets, and yields comparable results to the KCI-test which requires access to joint observations of all variables.
Prior-data fitted networks (PFNs) have emerged as powerful foundation models for tabular causal inference, yet their extension to time series remains limited by the absence of synthetic data generators that provide interventional targets. Existing time series benchmarks generate observational data with ground-truth causal graphs but lack the interventional data required for training causal foundation models. To address this, we propose \textbf{CausalTimePrior}, a principled framework for generating synthetic temporal structural causal models (TSCMs) with paired observational and interventional time series. Our prior supports configurable causal graph structures, nonlinear autoregressive mechanisms, regime-switching dynamics, and multiple intervention types (hard, soft, time-varying). We demonstrate that PFNs trained on CausalTimePrior can perform in-context causal effect estimation on held-out TSCMs, establishing a pathway toward foundation models for time series causal inference.
Heart diseases remain a leading cause of morbidity and mortality worldwide, necessitating accurate and trustworthy differential diagnosis. However, existing artificial intelligence-based diagnostic methods are often limited by insufficient cardiology knowledge, inadequate support for complex reasoning, and poor interpretability. Here we present HeartAgent, a cardiology-specific agent system designed to support a reliable and explainable differential diagnosis. HeartAgent integrates customized tools and curated data resources and orchestrates multiple specialized sub-agents to perform complex reasoning while generating transparent reasoning trajectories and verifiable supporting references. Evaluated on the MIMIC dataset and a private electronic health records cohort, HeartAgent achieved over 36% and 20% improvements over established comparative methods, in top-3 diagnostic accuracy, respectively. Additionally, clinicians assisted by HeartAgent demonstrated gains of 26.9% in diagnostic accuracy and 22.7% in explanatory quality compared with unaided experts. These results demonstrate that HeartAgent provides reliable, explainable, and clinically actionable decision support for cardio
Biomedical text embeddings have primarily been developed using research literature from PubMed, yet clinical cardiology practice relies heavily on procedural knowledge and specialized terminology found in comprehensive textbooks rather than research abstracts. This research practice gap limits the effectiveness of existing embedding models for clinical applications incardiology. This study trained CardioEmbed, a domain-specialized embedding model based on Qwen3-Embedding-8B, using contrastive learning on a curated corpus of seven comprehensive cardiology textbooks totaling approximately 150,000 sentences after deduplication. The model employs InfoNCE loss with in-batch negatives and achieves 99.60% retrieval accuracy on cardiac-specific semantic retrieval tasks, a +15.94 percentage point improvement over MedTE, the current state-of-the-art medical embedding model. On MTEB medical benchmarks, the model obtained BIOSSES 0.77 Spearman and SciFact 0.61 NDCG@10, indicating competitive performance on related biomedical domains. Domain-specialized training on comprehensive clinical textbooks yields near-perfect cardiology retrieval (99.60% Acc@1), improving over MedTE by +15.94 percentage
Estimating causal effects of joint interventions on multiple variables is crucial in many domains, but obtaining data from such simultaneous interventions can be challenging. Our study explores how to learn joint interventional effects using only observational data and single-variable interventions. We present an identifiability result for this problem, showing that for a class of nonlinear additive outcome mechanisms, joint effects can be inferred without access to joint interventional data. We propose a practical estimator that decomposes the causal effect into confounded and unconfounded contributions for each intervention variable. Experiments on synthetic data demonstrate that our method achieves performance comparable to models trained directly on joint interventional data, outperforming a purely observational estimator.
Mechanistic interpretability often evaluates explanations by intervening on a model: swapping hidden states, patching activations, ablating components, or comparing a compressed model to the original one. These experiments are usually summarized by a point estimate, even though the evaluation may be monitored while it runs or adapted toward suspected failures. This makes it hard to tell whether a reported fidelity or patching effect is a stable causal claim or a consequence of finite sampling and evaluation choices. We introduce Certified Interventional Fidelity (CIF), a statistical layer for interventional interpretability evaluations. CIF first writes the quantity being reported as a causal estimand: an expectation of a bounded score over a stated input distribution and a stated intervention distribution. It then provides confidence intervals and anytime-valid confidence sequences for this estimand, including under adaptive intervention sampling via bounded mixture importance weighting. We instantiate CIF with Hoeffding-style sequences and variance-adaptive betting sequences, the latter reducing certification cost by 10-30x in our experiments. On MNIST abstractions and GPT-2 Smal
Domain-specific text embeddings are critical for clinical natural language processing, yet systematic comparisons across model architectures remain limited. This study evaluates ten transformer-based embedding models adapted for cardiology through Low-Rank Adaptation (LoRA) fine-tuning on 106,535 cardiology text pairs derived from authoritative medical textbooks. Results demonstrate that encoder-only architectures, particularly BioLinkBERT, achieve superior domain-specific performance (separation score: 0.510) compared to larger decoder-based models, while requiring significantly fewer computational resources. The findings challenge the assumption that larger language models necessarily produce better domain-specific embeddings and provide practical guidance for clinical NLP system development. All models, training code, and evaluation datasets are publicly available to support reproducible research in medical informatics.
Detecting and quantifying causality is a focal topic in the fields of science, engineering, and interdisciplinary studies. However, causal studies on non-intervention systems attract much attention but remain extremely challenging. Delay-embedding technique provides a promising approach. In this study, we propose a framework named Interventional Dynamical Causality (IntDC) in contrast to the traditional Constructive Dynamical Causality (ConDC). ConDC, including Granger causality, transfer entropy and convergence of cross-mapping, measures the causality by constructing a dynamical model without considering interventions. A computational criterion, Interventional Embedding Entropy (IEE), is proposed to measure causal strengths in an interventional manner. IEE is an intervened causal information flow but in the delay-embedding space. Further, the IEE theoretically and numerically enables the deciphering of IntDC solely from observational (non-interventional) time-series data, without requiring any knowledge of dynamical models or real interventions in the considered system. In particular, IEE can be applied to rank causal effects according to their importance and construct causal netw
Cardiovascular diseases are becoming increasingly prevalent in modern society, with a profound impact on global health and well-being. These Cardiovascular disorders are complex and multifactorial, influenced by genetic predispositions, lifestyle choices, and diverse socioeconomic and clinical factors. Information about these interrelated factors is dispersed across multiple types of textual data, including patient narratives, medical records, and scientific literature. Natural language processing (NLP) has emerged as a powerful approach for analysing such unstructured data, enabling healthcare professionals and researchers to gain deeper insights that may transform the diagnosis, treatment, and prevention of cardiac disorders. This review provides a comprehensive overview of NLP research in cardiology from 2014 to 2025. We systematically searched six literature databases for studies describing NLP applications across a range of cardiovascular diseases. After a rigorous screening process, we identified 265 relevant articles. Each study was analysed across multiple dimensions, including NLP paradigms, cardiology-related tasks, disease types, and data sources. Our findings reveal sub
The invariance properties of interventional distributions relative to the observational distribution, and how these properties allow us to refine Markov equivalence classes (MECs) of DAGs, is central to causal DAG discovery algorithms that use both interventional and observational data. Here, we show how the invariance properties of interventional DAG models, and the corresponding refinement of MECs into interventional MECs, can be generalized to mixed graphical models that allow for latent cofounders and selection variables. We first generalize interventional Markov equivalence to all formal independence models associated to loopless mixed graphs. For ancestral graphs, we prove the resulting interventional MECs admit a graphical characterization generalizing that of DAGs. We then define interventional distributions for acyclic directed mixed graph models, and prove that this generalization aligns with the graphical generalization of interventional Markov equivalence given for the formal independence models. This provides a framework for causal model discovery via observational and interventional data in the presence of latent confounders that applies even when the interventions ar
The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient diagnosis, disease progression monitoring, treatment effects assessment, prediction of future clinical events, etc. While contextualized language models have demonstrated impressive performance improvements for named entity recognition (NER) systems in English corpora, there remains a scarcity of research focused on clinical texts in low-resource languages. To bridge this gap, our study aims to develop multiple deep contextual embedding models to enhance clinical NER in the cardiology domain, as part of the BioASQ MultiCardioNER shared task. We explore the effectiveness of different monolingual and multilingual BERT-based models, trained on general domain text, for extracting disease and medication mentions from clinical case reports written in English, Spanish, and Italian. We achieved an F1-score of 77.88% on Spanish Diseases Recognition (SDR), 92.09% on Spanish Medications Recognition (SMR), 91.74% on English Medications Recognition (EMR), and 88.
We investigate the effectiveness of fine-tuning large language models (LLMs) on small medical datasets for text classification and named entity recognition tasks. Using a German cardiology report dataset and the i2b2 Smoking Challenge dataset, we demonstrate that fine-tuning small LLMs locally on limited training data can improve performance achieving comparable results to larger models. Our experiments show that fine-tuning improves performance on both tasks, with notable gains observed with as few as 200-300 training examples. Overall, the study highlights the potential of task-specific fine-tuning of LLMs for automating clinical workflows and efficiently extracting structured data from unstructured medical text.
Use real word data to evaluate the performance of the electrocardiographic markers of GEH as features in a machine learning model with Standard ECG features and Risk Factors in Predicting Outcome of patients in a population referred to a tertiary cardiology hospital. Patients forwarded to specific evaluation in a cardiology specialized hospital performed an ECG and a risk factor anamnesis. A series of follow up attendances occurred in periods of 6 months, 12 months and 15 months to check for cardiovascular related events (mortality or new nonfatal cardiovascular events (Stroke, MI, PCI, CS), as identified during 1-year phone follow-ups. The first attendance ECG was measured by a specialist and processed in order to obtain the global electric heterogeneity (GEH) using the Kors Matriz. The ECG measurements, GEH parameters and risk factors were combined for training multiple instances of XGBoost decision trees models. Each instance were optmized for the AUCPR and the instance with higher AUC is chosen as representative to the model. The importance of each parameter for the winner tree model was compared to better understand the improvement from using GEH parameters. The GEH parameters
This article investigates how translation memories (TM) can be created by translators or other language professionals in order to compile domain-specific parallel corpora , which can then be used in different scenarios, such as machine translation training and fine-tuning, TM leveraging, and/or large language model fine-tuning. The article introduces a semi-automatic TM preparation methodology leveraging primarily translation tools used by translators in favor of data quality and control by the translators. This semi-automatic methodology is then used to build a cardiology-based Turkish -> English corpus from bilingual abstracts of Turkish cardiology journals. The resulting corpus called TRENCARD Corpus has approximately 800,000 source words and 50,000 sentences. Using this methodology, translators can build their custom TMs in a reasonable time and use them in their bilingual data requiring tasks.
Modern machine learning approaches excel in static settings where a large amount of i.i.d. training data are available for a given task. In a dynamic environment, though, an intelligent agent needs to be able to transfer knowledge and re-use learned components across domains. It has been argued that this may be possible through causal models, aiming to mirror the modularity of the real world in terms of independent causal mechanisms. However, the true causal structure underlying a given set of data is generally not identifiable, so it is desirable to have means to quantify differences between models (e.g., between the ground truth and an estimate), on both the observational and interventional level. In the present work, we introduce the Interventional Kullback-Leibler (IKL) divergence to quantify both structural and distributional differences between models based on a finite set of multi-environment distributions generated by interventions from the ground truth. Since we generally cannot quantify all differences between causal models for every finite set of interventional distributions, we propose a sufficient condition on the intervention targets to identify subsets of observed va