Clinical NLP

Automated classification of clinical transcriptions into medical specialties is essential for routing, coding, and clinical decision support, yet prior work on the widely used MTSamples benchmark suffers from severe data leakage caused by applying SMOTE oversampling before train test splitting. We first document this methodological flaw and establish a leakage free benchmark across 40 medical specialties (4966 records), revealing that the true task difficulty is substantially higher than previously reported. We then introduce CLiGNet (Clinical Label Interaction Graph Network), a neural architecture that combines a Bio ClinicalBERT text encoder with a two layer Graph Convolutional Network operating on a specialty label graph constructed from semantic similarity and ICD 10 chapter priors. Per label attention gates fuse document and label graph representations, trained with focal binary cross entropy loss to handle extreme class imbalance (181 to 1 ratio). Across seven baselines ranging from TF IDF classifiers to Clinical Longformer, CLiGNet without calibration achieves the highest macro F1 of 0.279, with an ablation study confirming that the GCN label graph provides the single largest component gain (increase of 0.066 macro F1). Adding per label Platt scaling calibration yields an expected calibration error of 0.007, demonstrating a principled trade off between ranking performance and probability reliability. We provide comprehensive failure analysis covering pairwise specialty confusions, rare class behaviour, document length effects, and token level Integrated Gradients attribution, offering actionable insights for clinical NLP system deployment.

The development of clinical natural language processing (NLP) systems is severely hampered by the sensitive nature of medical records, which restricts data sharing under stringent privacy regulations, particularly in France and the broader European Union. To address this gap, we introduce PARHAF, a large open-source corpus of clinical documents in French. PARHAF comprises expert-authored clinical reports describing realistic yet entirely fictitious patient cases, making it anonymous and freely shareable by design. The corpus was developed using a structured protocol that combined clinician expertise with epidemiological guidance from the French National Health Data System (SNDS), ensuring broad clinical coverage. A total of 104 medical residents across 18 specialties authored and peer-reviewed the reports following predefined clinical scenarios and document templates. The corpus contains 7394 clinical reports covering 5009 patient cases across a wide range of medical and surgical specialties. It includes a general-purpose component designed to approximate real-world hospitalization distributions, and four specialized subsets that support information-extraction use cases in oncology, infectious diseases, and diagnostic coding. Documents are released under a CC-BY open license, with a portion temporarily embargoed to enable future benchmarking under controlled conditions. PARHAF provides a valuable resource for training and evaluating French clinical language models in a fully privacy-preserving setting, and establishes a replicable methodology for building shareable synthetic clinical corpora in other languages and health systems.

Ambient AI generates draft clinical notes from patient-clinician conversations, often using lay or consumer-oriented phrasing to support patient understanding instead of standardized clinical terminology. How clinicians revise these drafts for professional documentation conventions remains unclear. We quantified clinician editing for consumer-to- clinical normalization using a dictionary-confirmed transformation framework. We analyzed 71,173 AI-draft and finalized-note section pairs from 34,726 encounters. Confirmed transformations were defined as replacing a consumer expression with its dictionary-mapped clinical equivalent in the same section. Editing significantly reduced terminology density across all sections (p < 0.001). The Assessment and Plan accounted for the largest transformation volume (59.3%). Our analysis identified 7,576 transformation events across 4,114 note sections (5.8%), representing 1.2% consumer-term deletions. Transformation intensity varied across individual clinicians (p < 0.001). Overall, clinician post-editing demonstrates consistent shifts from conversational phrasing toward standardized, section- appropriate clinical terminology, supporting section-aware ambient AI design.

Gender-based violence (GBV) is a major public health issue, with the World Health Organization estimating that one in three women experiences physical or sexual violence by an intimate partner during her lifetime. In Brazil, although healthcare professionals are legally required to report such cases, underreporting remains significant due to difficulties in identifying abuse and limited integration between public information systems. This study investigates whether FrameNet-based semantic annotation of open-text fields in electronic medical records can support the identification of patterns of GBV. We compare the performance of an SVM classifier for GBV cases trained on (1) frame-annotated text, (2) annotated text combined with parameterized data, and (3) parameterized data alone. Quantitative and qualitative analyses show that models incorporating semantic annotation outperform categorical models, achieving over 0.3 improvement in F1 score and demonstrating that domain-specific semantic representations provide meaningful signals beyond structured demographic data. The findings support the hypothesis that semantic analysis of clinical narratives can enhance early identification strategies and support more informed public health interventions.

Efficient classification of surgical procedures by urgency is paramount to optimize patient care and resource allocation within healthcare systems. This study introduces an unsupervised neural network approach to automatically categorize surgical transcriptions into three urgency levels: immediate, urgent, and elective. Leveraging BioClinicalBERT, a domain-specific language model, surgical transcripts are transformed into high-dimensional embeddings that capture their semantic nuances. These embeddings are subsequently clustered using both K-means and Deep Embedding Clustering (DEC) algorithms, in which DEC demonstrates superior performance in the formation of cohesive and well-separated clusters. To ensure clinical relevance and accuracy, the clustering results undergo validation through the Modified Delphi Method, which involves expert review and refinement. Following validation, a neural network that integrates Bidirectional Long Short-Term Memory (BiLSTM) layers with BioClinicalBERT embeddings is developed for classification tasks. The model is rigorously evaluated using cross-validation and metrics such as accuracy, precision, recall, and F1-score, which achieve robust performance and demonstrate strong generalization capabilities on unseen data. This unsupervised framework not only addresses the challenge of limited labeled data but also provides a scalable and reliable solution for real-time surgical prioritization, which ultimately enhances operational efficiency and patient outcomes in dynamic medical environments.

The rapid expansion of electronic health record (EHR) systems has generated large volumes of unstructured clinical narratives that contain valuable information for disease identification, patient cohort discovery, and clinical decision support. Extracting structured knowledge from these free-text documents remains challenging because clinical language is highly specialized, labeled datasets are limited, and full fine-tuning of large pretrained language models can require substantial computational resources. Efficient adaptation strategies are therefore essential for practical clinical natural language processing applications. This study proposes a parameter-efficient selective fine-tuning framework for adapting GPT-2 to clinical text classification tasks. Instead of updating the entire pretrained model, the majority of network parameters are frozen, and only the final Transformer block, the final layer normalization module, and a lightweight classification head are updated during training. This design substantially reduces the number of trainable parameters while preserving the contextual representation capabilities learned during pretraining. The proposed approach is evaluated using radiology reports from the MIMIC-IV-Note dataset with automatically derived CheXpert-style labels. Experiments on 50,000 radiology reports demonstrate that selective fine-tuning achieves approximately 91% classification accuracy while updating fewer than 6% of the model parameters. Comparative experiments with head-only training and full-model fine-tuning show that the proposed method provides a favorable balance between predictive performance and computational efficiency. These results indicate that selective fine-tuning offers an efficient and scalable framework for clinical text classification.

Free-style text is still one of the common ways in which data is registered in real environments, like legal procedures and medical records. Because of that, there have been significant efforts in the area of natural language processing to convert these texts into a structured format, which standard machine learning methods can then exploit. One of the most popular methods to embed text into a vectorial representation is the Contrastive Language-Image Pre-training model (CLIP), which was trained using both image and text. Although the representations computed by CLIP have been very successful in zero-show and few-shot learning problems, they still have problems when applied to a particular domain. In this work, we use a fuzzy rule-based classification system along with some standard text procedure techniques to map some of our features of interest to the space created by a CLIP model. Then, we discuss the rules and associations obtained and the importance of each feature considered. We apply this approach in two different data domains, clinical reports and film reviews, and compare the results obtained individually and when considering both. Finally, we discuss the limitations of this approach and how it could be further improved.

Depression is underdiagnosed in primary care, yet timely identification remains critical. Recorded clinical encounters, increasingly common with digital scribing technologies, present an opportunity to detect depression from naturalistic dialogue. We investigated automated depression detection from 1,108 audio-recorded primary care encounters in the Establishing Focus study, with depression defined by PHQ-9 (n=253 depressed, n=855 non-depressed). We compared three supervised approaches, Sentence-BERT + Logistic Regression (LR), LIWC+LR and ModernBERT, against a zero-shot GPT-OSS. GPT-OSS achieved the strongest performance (AUPRC=0.510, AUROC=0.774), with LIWC+LR competitive among supervised models (AUPRC=0.500, AUROC=0.742). Combined dyadic transcripts outperformed single-speaker configurations, with providers linguistically mirroring patients in depression encounters, an additive signal not captured by either speaker alone. Meaningful detection is achievable from the first 128 patient tokens (AUPRC=0.356, AUROC=0.675), supporting in-the-moment clinical decision support. These findings argue for passively collected clinical audio as a low-burden complement to existing screening workflows.

Accessing sensitive patient data for machine learning is challenging due to privacy concerns. Datasets with annotations of personally identifiable information are crucial for developing and testing anonymization systems to enable safe data sharing that complies with privacy regulations. Since accessing real patient data is a bottleneck, synthetic data offers an efficient solution for data scarcity, bypassing privacy regulations that apply to real data. Moreover, neural machine translation can help to create high-quality data for low-resource languages by translating validated real or synthetic data from a high-resource language. In this work, we create a multilingual anonymization benchmark in ten languages, using a machine translation methodology that preserves the original annotations and renders names of cities and people in a culturally and contextually appropriate form in each target language. Our evaluation study with medical professionals confirms the quality of the translations, both in general and with respect to the translation and adaptation of personal information. Our benchmark with over 2,500 annotations of personal information can be used in many applications, including training annotators, validating annotations across institutions without legal complications, and helping improve the performance of automatic personal information detection. We make our benchmark and annotation guidelines available for further research.

Case Report Forms (CRFs) collect data about patients and are at the core of well-established practices to conduct research in clinical settings. With the recent progress of language technologies, there is an increasing interest in automatic CRF-filling from clinical notes, mostly based on the use of Large Language Models (LLMs). However, there is a general scarcity of annotated CRF data, both for training and testing LLMs, which limits the progress on this task. As a step in the direction of providing such data, we present a new dataset of clinical notes from an Italian Emergency Department annotated with respect to a pre-defined CRF containing 134 items to be filled. We provide an analysis of the data, define the CRF-filling task and metric for its evaluation, and report on pilot experiments where we use an open-source state-of-the-art LLM to automatically execute the task. Results of the case-study show that (i) CRF-filling from real clinical notes in Italian can be approached in a zero-shot setting; (ii) LLMs' results are affected by biases (e.g., a cautious behaviour favours "unknown" answers), which need to be corrected.

Patient-generated text such as secure messages, surveys, and interviews contains rich expressions of the patient voice (PV), reflecting communicative behaviors and social determinants of health (SDoH). Traditional qualitative coding frameworks are labor intensive and do not scale to large volumes of patient-authored messages across health systems. Existing machine learning (ML) and natural language processing (NLP) approaches provide partial solutions but often treat patient-centered communication (PCC) and SDoH as separate tasks or rely on models not well suited to patient-facing language. We introduce PVminer, a domain-adapted NLP framework for structuring patient voice in secure patient-provider communication. PVminer formulates PV detection as a multi-label, multi-class prediction task integrating patient-specific BERT encoders (PV-BERT-base and PV-BERT-large), unsupervised topic modeling for thematic augmentation (PV-Topic-BERT), and fine-tuned classifiers for Code, Subcode, and Combo-level labels. Topic representations are incorporated during fine-tuning and inference to enrich semantic inputs. PVminer achieves strong performance across hierarchical tasks and outperforms biomedical and clinical pre-trained baselines, achieving F1 scores of 82.25% (Code), 80.14% (Subcode), and up to 77.87% (Combo). An ablation study further shows that author identity and topic-based augmentation each contribute meaningful gains. Pre-trained models, source code, and documentation will be publicly released, with annotated datasets available upon request for research use.

Psychological corpora in NLP are collections of texts used to analyze human psychology, emotions, and mental health. These texts allow researchers to study psychological constructs, identify patterns related to mental health problems and analyze emotional language. However, collecting accurate mental health data from social media can be challenging due to the assumptions made by data collectors. A more effective approach involves gathering data through open-ended questions and then assessing participants' mental health status using self-report screening surveys. This method was successfully employed for English, a language with a lot of psychological NLP resources. However, the same cannot be stated for Romanian, which currently has no open-source mental health corpus. To address this gap, we have collected the first open-source corpus focused on depression and anxiety in Romanian, by utilizing a form with 6 open-ended questions along with the standardized PHQ-9 and GAD-7 screening questionnaires. Although the PsihoRo corpus contains texts from only 205 respondents, it represents an important first step toward understanding and analyzing mental health issues within the Romanian population. We employ statistical analysis, text analysis using Romanian LIWC, emotion detection, and topic modeling to identify the most important features of this newly introduced resource for the NLP community. The data is publicly available at https://huggingface.co/datasets/Alegzandra/PsihoRo.

Background: Clinical named entity recognition tools commonly map free text to Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs). For many downstream tasks, however, the clinically meaningful unit is not a single CUI but a concept set comprising related synonyms, subtypes, and associated concepts. Constructing these sets is labour-intensive, inconsistently performed, and poorly supported by existing tools. Methods We present CUICurate, a graph-based retrieval-augmented generation (GraphRAG) framework for automated UMLS concept set curation. A UMLS knowledge graph (KG) was constructed and embedded for semantic retrieval. Candidate CUIs were retrieved using graph-based expansion and then filtered and classified using large language models (GPT-5 and Qwen3-32B). The framework was evaluated on five lexically heterogeneous clinical concepts against a manually curated concept sets and gold-standard concept sets. Results CUICurate produced substantially larger and more complete concept sets than the manual benchmarks. A single retrieval configuration across concepts achieved high recall of definitive concepts with manageable candidate sets. GPT-5 outperformed manual curation for all concepts and retained at least 95% of definitive gold-standard CUIs, while Qwen3-32B achieved comparable but slightly lower performance. Many missed concepts were not observed in 10,000 MIMIC-III notes. CUICurate infrastructure and end-to-end processing was inexpensive and stable across runs. Conclusions CUICurate offers a scalable, reproducible and cost-efficient approach for generating clinician-reviewable UMLS concept sets tailored to clinical natural language processing and phenotyping applications.

Large Language Models (LLMs) consistently excel in diverse medical Natural Language Processing (NLP) tasks, yet their substantial computational requirements often limit deployment in real-world healthcare settings. In this work, we investigate whether "small" LLMs (around one billion parameters) can effectively perform medical tasks while maintaining competitive accuracy. We evaluate models from three major families-Llama-3, Gemma-3, and Qwen3-across 20 clinical NLP tasks among Named Entity Recognition, Relation Extraction, Case Report Form Filling, Question Answering, and Argument Mining. We systematically compare a range of adaptation strategies, both at inference time (few-shot prompting, constraint decoding) and at training time (supervised fine-tuning, continual pretraining). Fine-tuning emerges as the most effective approach, while the combination of few-shot prompting and constraint decoding offers strong lower-resource alternatives. Our results show that small LLMs can match or even surpass larger baselines, with our best configuration based on Qwen3-1.7B achieving an average score +9.2 points higher than Qwen3-32B. We release a comprehensive collection of all the publicly available Italian medical datasets for NLP tasks, together with our top-performing models. Furthermore, we release an Italian dataset of 126M words from the Emergency Department of an Italian Hospital, and 175M words from various sources that we used for continual pre-training.

Text-based telemedicine has become an increasingly used mode of care, requiring clinicians to deliver medical advice clearly and effectively in writing. As platforms increasingly rely on patient ratings and feedback, clinicians face growing pressure to maintain satisfaction scores, even though these evaluations often reflect communication quality more than clinical accuracy. We analyse patient satisfaction signals in Romanian text-based telemedicine. Using a sample of anonymised text-based telemedicine consultations, we model feedback as a binary outcome, treating thumbs-up responses as positive and grouping negative or absent feedback into the other class. We extract from doctor responses interpretable, predominantly language-agnostic features (e.g., length, structural characteristics, readability proxies), along with Romanian LIWC psycholinguistic features and politeness/hedging markers where available. We train a classifier with a time-based split and perform SHAP-based analyses, which indicate that metadata dominates prediction, functioning as a strong prior, while characteristics of the response text provide a smaller but actionable signal. In subgroup correlation analyses, politeness and hedging are consistently associated with positive patient feedback, whereas lexical diversity shows a negative association.

This paper presents system description for Arabic medical text classification across 82 distinct categories. Our primary architecture utilizes a fine-tuned AraBERTv2 encoder enhanced with a hybrid pooling strategies, combining attention and mean representations, and multi-sample dropout for robust regularization. We systematically benchmark this approach against a suite of multilingual and Arabic-specific encoders, as well as several large-scale causal decoders, including zero-shot re-ranking via Llama 3.3 70B and feature extraction from Qwen 3B hidden states. Our findings demonstrate that specialized bidirectional encoders significantly outperform causal decoders in capturing the precise semantic boundaries required for fine-grained medical text classification. We show that causal decoders, optimized for next-token prediction, produce sequence-biased embeddings that are less effective for categorization compared to the global context captured by bidirectional attention. Despite significant class imbalance and label noise identified within the training data, our results highlight the superior semantic compression of fine-tuned encoders for specialized Arabic NLP tasks. Final performance metrics on the test set, including Accuracy and Macro-F1, are reported and discussed.

Patients' expectations towards their treatment have a substantial effect on the treatments' success. While primarily studied in clinical settings, online patient platforms like medical subreddits may hold complementary insights: treatment expectations that patients feel unnecessary or uncomfortable to share elsewhere. Despite this, no studies examine what type of expectations users discuss online and how they express them. Presumably this is because expectations have not been studied in natural language processing (NLP) before. Therefore, we introduce the task of Expectation Detection, arguing that expectations are relevant for many applications, including opinion mining and product design. Subsequently, we present a case study for the medical domain, where expectations are particularly crucial to extract. We contribute RedHOTExpect, a corpus of Reddit posts (4.5K posts) to study expectations in this context. We use a large language model (LLM) to silver-label the data and validate its quality manually (label accuracy ~78%). Based on this, we analyze which linguistic patterns characterize expectations and explore what patients expect and why. We find that optimism and proactive framing are more pronounced in posts about physical or treatment-related illnesses compared to mental-health contexts, and that in our dataset, patients mostly discuss benefits rather than negative outcomes. The RedHOTExpect corpus can be obtained from https://www.ims.uni-stuttgart.de/data/RedHOTExpect

Clinical documentation can contain emotionally charged language with stigmatizing or privileging valences. We present a framework for detecting and classifying such language as stigmatizing, privileging, or neutral. We constructed a curated lexicon of biased terms scored for emotional valence. We then used lexicon-based matching to extract text chunks from OB-GYN delivery notes (Mount Sinai Hospital, NY) and MIMIC-IV discharge summaries across multiple specialties. Three clinicians annotated all chunks, enabling characterization of valence patterns across specialties and healthcare systems. We benchmarked multiple classification strategies (zero-shot prompting, in-context learning, and supervised fine-tuning) across encoder-only models (GatorTron) and generative large language models (Llama). Fine-tuning with lexically primed inputs consistently outperformed prompting approaches. GatorTron achieved an F1 score of 0.96 on the OB-GYN test set, outperforming larger generative models while requiring minimal prompt engineering and fewer computational resources. External validation on MIMIC-IV revealed limited cross-domain generalizability (F1 < 0.70, 44% drop). Training on the broader MIMIC-IV dataset improved generalizability when testing on OB-GYN (F1 = 0.71, 11% drop), but at the cost of reduced precision. Our findings demonstrate that fine-tuning outperforms prompting for emotional valence classification and that models must be adapted to specific medical specialties to achieve clinically appropriate performance. The same terms can carry different emotional valences across specialties: words with clinical meaning in one context may be stigmatizing in another. For bias detection, where misclassification risks undermining clinician trust or perpetuating patient harm, specialty-specific fine-tuning is essential to capture these semantic shifts. * Equal contribution.

This tutorial focused on Healthcare Domain Applications of NLP, what we have achieved around HealthcareNLP, and the challenges that lie ahead for the future. Existing reviews in this domain either overlook some important tasks, such as synthetic data generation for addressing privacy concerns, or explainable clinical NLP for improved integration and implementation, or fail to mention important methodologies, including retrieval augmented generation and the neural symbolic integration of LLMs and KGs. In light of this, the goal of this tutorial is to provide an introductory overview of the most important sub-areas of a patient- and resource-oriented HealthcareNLP, with three layers of hierarchy: data/resource layer: annotation guidelines, ethical approvals, governance, synthetic data; NLP-Eval layer: NLP tasks such as NER, RE, sentiment analysis, and linking/coding with categorised methods, leading to explainable HealthAI; patients layer: Patient Public Involvement and Engagement (PPIE), health literacy, translation, simplification, and summarisation (also NLP tasks), and shared decision-making support. A hands-on session will be included in the tutorial for the audience to use HealthcareNLP applications. The target audience includes NLP practitioners in the healthcare application domain, NLP researchers who are interested in domain applications, healthcare researchers, and students from NLP fields. The type of tutorial is "Introductory to CL/NLP topics (HealthcareNLP)" and the audience does not need prior knowledge to attend this. Tutorial materials: https://github.com/4dpicture/HealthNLP

Large language models (LLMs) show promise in medical applications, but their ability to detect and correct errors in clinical texts remains under-evaluated, particularly beyond English. We introduce MedRECT, a bilingual benchmark for Japanese and English that formulates medical error handling as three subtasks: error detection, error sentence extraction, and error correction. MedRECT-ja contains 663 samples derived from the Japanese Medical Licensing Examinations, while the separately sourced MedRECT-en contains 458 samples curated from MEDEC. We evaluate 11 LLMs across 17 configurations that cover proprietary and open-weight models, medical-domain specialization, and multiple reasoning settings. Qwen3-32B scores higher in its thinking mode than in its non-thinking mode on error detection F1 and sentence extraction accuracy in both subsets, with sentence extraction accuracy higher by 24.5 percentage points on MedRECT-ja and 10.3 on MedRECT-en. Several leading general-purpose reasoning models outperform all three evaluated medical-domain models on these two subtasks. Most models have lower point estimates on the Japanese subset, although absolute scores are not directly comparable because the subsets differ in source material and error distributions. LoRA fine-tuning yields higher sentence extraction accuracy and higher point estimates on all three reference-based correction similarity metrics in both languages. MedRECT provides an open, reusable evaluation resource for studying medical error correction and reasoning across Japanese and English. Our dataset and code are available at https://github.com/pfnet-research/medrect.

Thematic analysis (TA) is a widely used qualitative approach for uncovering latent meanings in unstructured text data. TA provides valuable insights in healthcare but is resource-intensive. Large Language Models (LLMs) have been introduced to perform TA, yet their applications in high-stakes healthcare settings, particularly for qualitative clinical interview analysis, remain limited. Here, we propose TAMA: A Human-AI Collaborative Thematic Analysis framework using Multi-Agent LLMs for clinical interviews. We leverage the scalability and coherence of multi-agent systems through structured conversations between agents and coordinate the expertise of cardiac experts in TA. Using interview transcripts from parents of children with Anomalous Aortic Origin of a Coronary Artery (AAOCA), a rare congenital heart disease, we demonstrate that TAMA outperforms single-agent LLM TA approaches, achieving higher thematic hit rate, coverage, and distinctiveness. TAMA demonstrates strong potential for automated TA in clinical settings by leveraging multi-agent LLM systems with human-in-the-loop integration by enhancing quality while significantly reducing manual workload. The full implementation is publicly available at https://github.com/Charlie-Yi-SJ/TAMA.

Large language models (LLMs) are increasingly used in medical fields. In mental health support, the early identification of linguistic markers associated with mental health conditions can provide valuable support to mental health professionals, and reduce long waiting times for patients. Despite the benefits of LLMs for mental health support, there is limited research on their application in mental health systems for languages other than English. Our study addresses this gap by focusing on the detection of depression severity in Greek through user-generated posts which are automatically translated from English. Our results show that GPT3.5-turbo is not very successful in identifying the severity of depression in English, and it has a varying performance in Greek as well. Our study underscores the necessity for further research, especially in languages with less resources. Also, careful implementation is necessary to ensure that LLMs are used effectively in mental health platforms, and human supervision remains crucial to avoid misdiagnosis.