Clinical Concept Extraction with Lexical Semantics to Support Automatic Annotation.

BackgroundDiabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected, DR can be treated to prevent further damage causing blindness. There is an increasing interest in developing artificial intelligence (AI) technologies to help detect DR using electronic health records. The lesion-related information documented in fundus image reports is a valuable resource that could help diagnoses of DR in clinical decision support systems. However, most studies for AI-based DR diagnoses are mainly based on medical images; there is limited studies to explore the lesion-related information captured in the free text image reports.MethodsIn this study, we examined two state-of-the-art transformer-based natural language processing (NLP) models, including BERT and RoBERTa, compared them with a recurrent neural network implemented using Long short-term memory (LSTM) to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and developed transformer-based NLP models for clinical concept extraction and relation extraction. We also examined the relation extraction under two settings including ‘gold-standard’ setting—where gold-standard concepts were used–and end-to-end setting.ResultsFor concept extraction, the BERT model pretrained with the MIMIC III dataset achieve the best performance (0.9503 and 0.9645 for strict/lenient evaluation). For relation extraction, BERT model pretrained using general English text achieved the best strict/lenient F1-score of 0.9316. The end-to-end system, BERT_general_e2e, achieved the best strict/lenient F1-score of 0.8578 and 0.8881, respectively. Another end-to-end system based on the RoBERTa architecture, RoBERTa_general_e2e, also achieved the same performance as BERT_general_e2e in strict scores.ConclusionsThis study demonstrated the efficiency of transformer-based NLP models for clinical concept extraction and relation extraction. Our results show that it’s necessary to pretrain transformer models using clinical text to optimize the performance for clinical concept extraction. Whereas, for relation extraction, transformers pretrained using general English text perform better.

The digitization of healthcare has been accompanied by a rapid expansion of electronic health records (EHRs); however, a significant proportion of critical patient data, specifically medication regimens, remains entrapped within unstructured clinical narratives. The inability to seamlessly compute this data hinders advancements in pharmacovigilance, clinical decision support, and population health management. This study presents a comprehensive, rigorous evaluation of the feasibility of deploying Large Language Models (LLMs) to automate the extraction of structured dosage information (Dose, Daily Frequency, Duration) from outpatient antimicrobial clinical notes sourced from the Collaboration to Harmonize Antimicrobial Registry Measures (CHARM) registry. We scrutinized the performance of five distinct open-weight architectures, namely GPT-OSS:20B, Gemma 2:9B, Mistral 7B, Qwen3:14B and Llama 3.2, across both Zero-Shot and Retrieval Augmented Generation (RAG)-based Few-Shot prompting paradigms. Our analysis reveals a fundamental architectural trade-off: the reasoning-optimized GPT-OSS:20B dominates the zero-shot landscape (F1 > 0.90) by leveraging abstract schema understanding, whereas the instruction-tuned Gemma 2:9B excels in the few-shot setting (F1 ~ 0.99), effectively utilizing examples as guardrails to surpass larger models. Conversely, smaller models (Mistral, Llama) exhibit a prohibitive “hallucination barrier,” rendering them unsafe for unsupervised clinical application. Furthermore, we identify “Inconsistent Unit Handling” and “Complex Temporal Logic” as persistent failure modes that resist simple scaling laws. This report provides a definitive framework for selecting model architectures based on the availability of few-shot examples and highlights the necessity of dynamic RAG strategies to achieve production-grade reliability in medical informatics.

Clinical concept extraction: A methodology review.

Vast amounts of clinically relevant text-based variables lie undiscovered and unexploited in electronic medical records (EMR). To exploit this untapped resource, and thus facilitate the discovery of informative covariates from unstructured clinical narratives, we have built a novel computational pipeline termed Text-based Exploratory Pattern Analyser for Prognosticator and Associator discovery (TEPAPA). This pipeline combines semantic-free natural language processing (NLP), regular expression induction, and statistical association testing to identify conserved text patterns associated with outcome variables of clinical interest. When we applied TEPAPA to a cohort of head and neck squamous cell carcinoma patients, plausible concepts known to be correlated with human papilloma virus (HPV) status were identified from the EMR text, including site of primary disease, tumour stage, pathologic characteristics, and treatment modalities. Similarly, correlates of other variables (including gender, nodal status, recurrent disease, smoking and alcohol status) were also reliably recovered. Using highly-associated patterns as covariates, a patient’s HPV status was classifiable using a bootstrap analysis with a mean area under the ROC curve of 0.861, suggesting its predictive utility in supporting EMR-based phenotyping tasks. These data support using this integrative approach to efficiently identify disease-associated factors from unstructured EMR narratives, and thus to efficiently generate testable hypotheses.

Model tuning or prompt Tuning? a study of large language models for clinical concept and relation extraction

Large Language Models (LLMs) hold the potential for clinical task-shifting by processing unstructured clinical text, enabling tasks such as clinical concept extraction and medical question answering from electronic health records. If implemented reliably, such approaches may benefit over-burdened healthcare systems, particularly in resource-limited settings and for traditionally overlooked populations, provided that local fine-tuning is supported by appropriate clinical and technical expertise. However, this powerful technology remains largely understudied in real-world contexts, particularly in the Global South. This study aims to assess whether openly available LLMs can be used reliably for processing medical notes in real-world settings in South Asia. We used publicly available LLMs to parse de-identified clinical notes from a large electronic health records (EHR) database in Pakistan, containing hospital records for 8.2 million patients. ChatGPT (GPT-3.5) as a general-purpose LLM, and GatorTron (base), BioMegatron, BioBert and ClinicalBERT as medical LLMs were evaluated when applied to these data, after fine-tuning them with (a) publicly available clinical datasets namely Informatics for Integrating Biology & the Bedside (I2B2) and National NLP Clinical Challenges (N2C2) for medical concept extraction (MCE) and emrQA for medical question answering (MQA), and (b) the local Pakistani de-identified EHR dataset, which includes inpatient Discharge Summaries (DS) and Subjective, Objective, Assessment, and Plan (SOAP) notes, as detailed in this paper. MCE models were applied to these clinical notes using both 3-label and 9-label formats, while MQA models were applied to medical questions. Internal and external validation performance was measured for (a) and (b) using F1 score, precision, recall, and accuracy for MCE and BLEU and ROUGE-L, which measure lexical and sequence similarity, for MQA. When clinical LLMs were not fine-tuned on the local EHR dataset, their performance during external validation on local data was notably poorer compared to internal validation on the dataset used for fine-tuning, with reductions of at least 15% in F1 scores for MCE and 35% in ROUGE-L and BLEU scores for MQA tasks. This suggests potential bias and highlights the inability of the medical LLMs to reliably handle the data distribution of the local population without further fine-tuning and adaptation. This trend persisted across two distinct natural language processing tasks: concept extraction and question answering, spanning a spectrum of task complexities. However, fine-tuning the LLMs with local EHR data significantly improved model performance across both tasks, yielding a 7.5% to 15% increase in the F1 score for MCE and a 27% to 53% increase in ROUGE-L and BLEU scores for MQA. Notably, ChatGPT, as a general-purpose LLM, stood out as an exception, demonstrating superior performance across all measured metrics on the local dataset compared to the publicly available dataset, with improvements ranging from 3% to 17% on the local EHR dataset, even without fine-tuning on the local data. Publicly available LLMs, predominantly trained on data from high-income regions, were found to be unreliable when applied in a real-world clinical setting in Pakistan. Fine-tuning them with local EHR data and regional clinical contexts improved their reliability, demonstrating a feasible adaptation strategy that is substantially less resource-intensive than training large language models from scratch. Close collaboration between local clinical and technical experts to curate and leverage more representative, inclusive, and unbiased medical datasets, can play a crucial role in further ensuring reliability of LLMs for resource-limited, overburdened settings, to be used in ways that are safe, fair, and beneficial for all.

Low self-esteem (LoST) is a latent yet critical psychosocial risk factor that predisposes individuals to depressive disorders. Although structured tools exist to assess self-esteem, their limited clinical adoption suggests that relevant indicators of LoST remain buried within unstructured clinical narratives. The scarcity of annotated clinical notes impedes the development of natural language processing (NLP) models for its detection. Manual chart reviews are labor-intensive and large language model (LLM)-driven (weak) labeling raises privacy concerns. Past studies demonstrate that NLP models trained on LLM-generated synthetic clinical notes achieve performance comparable to, and sometimes better than those trained on real notes. This highlights synthetic data’s utility for augmenting scarce clinical corpora while reducing privacy concerns. Prior efforts have leveraged social media data, such as Reddit, to identify linguistic markers of low self-esteem; however, the linguistic and contextual divergence between social media and clinical text limits the generalizability of these models. To address this gap, we present a novel framework that generates context-enhanced synthetic clinical notes from social media narratives and evaluates the utility of small language models for identifying expressions of low self-esteem. Our approach includes a mixed-method evaluation framework: (i) structure analysis, (ii) readability analysis, (iii) linguistic diversity, and (iv) contextual fidelity of LoST cues in source Reddit posts and synthetic notes. This work offers a scalable, privacy-preserving solution for synthetic data generation for early detection of psychosocial risks such as LoST and demonstrates a pathway for translating mental health signals in clinical notes into clinically actionable insights, thereby identifying patients at risk.

Low self-esteem (LoST) is a latent yet critical psychosocial risk factor that predisposes individuals to depressive disorders. Although structured tools exist to assess self-esteem, their limited clinical adoption suggests that relevant indicators of LoST remain buried within unstructured clinical narratives. The scarcity of annotated clinical notes impedes the development of natural language processing (NLP) models for its detection. Manual chart reviews are labor-intensive and large language model (LLM)-driven (weak) labeling raises privacy concerns. Past studies demonstrate that NLP models trained on LLM-generated synthetic clinical notes achieve performance comparable to, and sometimes better than those trained on real notes. This highlights synthetic data's utility for augmenting scarce clinical corpora while reducing privacy concerns. Prior efforts have leveraged social media data, such as Reddit, to identify linguistic markers of low self-esteem; however, the linguistic and contextual divergence between social media and clinical text limits the generalizability of these models. To address this gap, we present a novel framework that generates context-enhanced synthetic clinical notes from social media narratives and evaluates the utility of small language models for identifying expressions of low self-esteem. Our approach includes a mixed-method evaluation framework: (i) structure analysis, (ii) readability analysis, (iii) linguistic diversity, and (iv) contextual fidelity of LoST cues in source Reddit posts and synthetic notes. This work offers a scalable, privacy-preserving solution for synthetic data generation for early detection of psychosocial risks such as LoST and demonstrates a pathway for translating mental health signals in clinical notes into clinically actionable insights, thereby identifying patients at risk.

Since tangible applications of insights are being drawn from their current unprocessed form in clinical-narrative texts, clinical text mining-based NLP technologies find an increasing relevance as tools. Thus, depending on the means employed, we can vaguely designate as this: rule-based systems depending on medical lexicons and ontologies, machine-learning approaches, like supervised and unsupervised learning, and finally, deep-learning models, RNNs, and Transformer-based architectures like BERT. Applications of these methodologies include Named Entity Recognition, information extraction, sentiment analysis, and building a Clinical Decision Support System (CDSS). Clinical text mining uses NLP methodologies for unstructured clinical narratives and indeed opens limitless possibilities for more comprehensive data analysis in the health domain. It still faces challenges arising from the need to protect patient privacy, sparsity in publicly accessible and annotated datasets, and complexities brought forth by medical terminologies. Envisaged future research would enable avenues for developing multilingual clinical NLP models and frameworks of federated learning that maximize data-sharing opportunities whilst protecting the data from potential breaches as well as fusion of NLP with wearable health-monitored devices for real-time health assessments. This is an important area that needs to be tackled and a relevant avenue that must be explored for the future of clinical text mining to be able to improve patient health and quality of service.

Children seem to be relatively delayed in their comprehension of the verbal be-passive in English, compared to their acquisition of other constructions of object-movement such as wh-questions and unaccusatives. Prior work has found that children’s performance on these passives can be affected by the verb’s lexical semantics. Through a meta-analysis of experimental studies assessing English-speaking children’s age of acquisition for the verbal be- passive, we identify a developmental trajectory composed of five classes, where each class has a distinct lexical semantic profile. A Truth-Value Judgment (TVJ) Task assessing English-speaking children’s comprehension of verbal be-passives supports this developmental trajectory. Together, the meta-analysis and TVJ study underscore the importance of lexical semantics for understanding the development of the English verbal be-passive.

An accurate image retrieval technique is required due to the rapidly increasing number of images. It is important to implement image annotation techniques that are fast, simple, and, most importantly, automatically annotate. Image annotation has recently received much attention due to the massive rise in image data volume. Focusing on the agriculture field, this study implements automatic image annotation, namely, a repetitive annotation task technique, to classify the ripeness of oil palm fruit and recognize a variety of fruits. This approach assists farmers to enhance the classification of fruit methods and increase their production. This study proposes simple and effective models using a deep learning approach with You Only Look Once (YOLO) versions. The models were developed through transfer learning where the dataset was trained with 100 images of oil fruit palm and 400 images of a variety of fruit in RGB images. Model performance and accuracy of automatically annotating the images with 3500 fruits were examined. The results show that the annotation technique successfully annotated a large number of images accurately. The mAP result achieved for oil palm fruit was 98.7% and the variety of fruit was 99.5%.

New drug treatments are regularly approved, and it is challenging to remain up-to-date in this rapidly changing environment. Fast and accurate visualization is important to allow a global understanding of the drug market. Automation of this information extraction provides a helpful starting point for the subject matter expert, helps to mitigate human errors, and saves time. We aimed to semiautomate disease population extraction from the free text of oncology drug approval descriptions from the BioMedTracker database for 6 selected drug targets. More specifically, we intended to extract (1) line of therapy, (2) stage of cancer of the patient population described in the approval, and (3) the clinical trials that provide evidence for the approval. We aimed to use these results in downstream applications, aiding the searchability of relevant content against related drug project sources. We fine-tuned a state-of-the-art deep learning model, Bidirectional Encoder Representations from Transformers, for each of the 3 desired outputs. We independently applied rule-based text mining approaches. We compared the performances of deep learning and rule-based approaches and selected the best method, which was then applied to new entries. The results were manually curated by a subject matter expert and then used to train new models. The training data set is currently small (433 entries) and will enlarge over time when new approval descriptions become available or if a choice is made to take another drug target into account. The deep learning models achieved 61% and 56% 5-fold cross-validated accuracies for line of therapy and stage of cancer, respectively, which were treated as classification tasks. Trial identification is treated as a named entity recognition task, and the 5-fold cross-validated F1-score is currently 87%. Although the scores of the classification tasks could seem low, the models comprise 5 classes each, and such scores are a marked improvement when compared to random classification. Moreover, we expect improved performance as the input data set grows, since deep learning models need to be trained on a large enough amount of data to be able to learn the task they are taught. The rule-based approach achieved 60% and 74% 5-fold cross-validated accuracies for line of therapy and stage of cancer, respectively. No attempt was made to define a rule-based approach for trial identification. We developed a natural language processing algorithm that is currently assisting subject matter experts in disease population extraction, which supports health authority approvals. This algorithm achieves semiautomation, enabling subject matter experts to leverage the results for deeper analysis and to accelerate information retrieval in a crowded clinical environment such as oncology.

Diabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected early, DR can be treated to preventing further damage causing blindness, therefore, early detection is very important for the treatment of DR. There is an increasing interest in developing Al technologies to help early detection of DR using electronic health records (EHR). The detailed diagnoses information documented in image reports is a valuable resource that could help detect lesions from the medical image, thus helping early detection of DR. In this study, we examined two state-of-the-art transformer-based natural language processing models, including BERT and RoBERTa, to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and trained four transformer-based NLP models for clinical concept extraction. The experimental results show that the BERT model pretrained with the MIMIC III dataset achieved the best strict/lenient F1-score of 0.9503 and 0.9645, respectively.

Clinician notes are a rich source of patient information, but often contain inconsistencies due to varied writing styles, abbreviations, medical jargon, grammatical errors, and non-standard formatting. These inconsistencies hinder their direct use in patient care and degrade the performance of downstream computational applications that rely on these notes as input, such as quality improvement, population health analytics, precision medicine, clinical decision support, and research. We present a large-language-model (LLM) approach to the preprocessing of 1618 neurology notes. The LLM corrected spelling and grammatical errors, expanded acronyms, and standardized terminology and formatting, without altering clinical content. Expert review of randomly sampled notes confirmed that no significant information was lost. To evaluate downstream impact, we applied an ontology-based NLP pipeline (Doc2Hpo) to extract biomedical concepts from the notes before and after editing. F1 scores for Human Phenotype Ontology extraction improved from 0.40 to 0.61, confirming our hypothesis that better inputs yielded better outputs. We conclude that LLM-based preprocessing is an effective error correction strategy that improves data quality at the level of free text in clinical notes. This approach may enhance the performance of a broad class of downstream applications that derive their input from unstructured clinical documentation.

Lung cancer remains the leading cause of cancer-related mortality worldwide, highlighting the urgent need for earlier detection within real-world screening and patient management pathways. Recent advances in multi-omics technologies have created new opportunities for identifying biomarkers associated with early-stage lung cancer, particularly in high-risk populations under clinical surveillance. This review systematically evaluates early diagnostic biomarkers across multiple omics layers, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and microbiomics. It also summarises the application of artificial intelligence (AI), particularly machine learning and deep learning approaches, for integrating and analysing complex multi-omics datasets to support biomarker discovery and clinical decision-making. Multi-omics strategies are accelerating the identification of molecular signatures relevant to early lung cancer detection. AI-driven methods enable the extraction of latent patterns from high-dimensional data, facilitating risk stratification, diagnostic refinement, histological subtyping and treatment planning. The review highlights the clinical utility of these biomarkers and their potential incorporation into screening algorithms, as well as the development of AI-based clinical decision support systems (CDSS) aligned with real-world clinical workflows. However, major barriers to clinical translation remain, including multi-centre data heterogeneity, limited model interpretability affecting clinical trust, regulatory and cost-effectiveness challenges and insufficient validation in prospective cohorts. Emerging technologies, such as single-cell and spatial multi-omics, along with federated learning frameworks, offer promising solutions to bridge the gap between computational discovery and clinical implementation. The integration of AI and multi-omics approaches has the potential to advance risk-adapted and personalised early detection strategies for lung cancer.