Clinical NLP

Natural language processing (NLP) models can detect depression-related language in text written near the time symptoms are measured, but whether pretrained transformers can predict depressive symptoms from text written twelve years earlier is largely untested. In the National Child Development Study, a British birth cohort, we predict probable depressive symptoms at age 23 from essays the same people wrote at age 11. Our baseline, a logistic regression on six childhood covariates, outperforms every text model that sees only the essay: seven fine-tuned transformers, a bag-of-words model, frozen embeddings and four zero-shot large language models. Its area under the receiver operating characteristic curve (AUC-ROC) is 0.737 against 0.670 for the best transformer on the primary seed, and no added text score detectably raises the baseline's AUC-ROC. None of the five domain-pretrained transformers detectably beats its general-domain control after Bonferroni correction. For long-horizon prediction, the baseline remains the model to beat.

This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2026. BioASQ is an international challenge series that supports progress in biomedical language processing tasks ranging from semantic indexing and information extraction to question answering and summarization. In 2026, BioASQ included six shared tasks: a) Task 14b on biomedical semantic question answering. b) Task Synergy14 on question answering for developing biomedical top- ics. c) Task MultiClinSum-2 on multilingual clinical summarization. d) Task BioNNE-R on extracting relations between nested named entities in Russian and English. e) Task ELCardioCC on clinical coding in cardiology. f) Task GutBrainIE on gut-brain interplay information extrac- tion. Across these six tasks, 87 distinct teams participated, submitting more than 1000 runs overall. As in previous editions, several submissions reached competitive performance, reflecting the continued progress of state-of-the-art methods across biomedical language processing tasks.

This paper describes the approach of the UniBuc team in tackling the SemEval 2024 Task 2: Safe Biomedical Natural Language Inference for Clinical Trials. We used SOLAR Instruct, without any fine-tuning, while focusing on input manipulation and tailored prompting. By customizing prompts for individual CTR sections, in both zero-shot and few-shots settings, we managed to achieve a consistency score of 0.72, ranking 14th in the leaderboard. Our thorough error analysis revealed that our model has a tendency to take shortcuts and rely on simple heuristics, especially when dealing with semantic-preserving changes.

This work addresses continuous depression-severity score prediction from clinical interview transcripts under data scarcity. We propose a sequential low-rank adaptation (LoRA) protocol for cross-scale transfer: a Qwen3 backbone with a bounded regression head is first fine-tuned on the English DAIC-WOZ dataset (189 avatar-mediated sessions, PHQ-8), and the adapter then initializes fine-tuning on the Chinese PDCH dataset (100 real clinical consultations, HAMD-17), where a reinitialised, scale-specific head predicts the clinician-assigned score. All configurations use patient-level stratified 5-fold, 2-repeat cross-validation. On the data-scarce HAMD-17 target, the sequential protocol attains the best point-estimate MAE , RMSE, and macro-$F_1$ on both 0.6B and 1.7B backbones, outperforming target-only training and non-LLM baselines---4.96/6.59/0.36 with Qwen3-0.6B and 4.38/5.62/0.46 with Qwen3-1.7B. Ablations suggest that correctly aligned source supervision gives the best point estimates (unsupervised exposure and shuffled-label controls also show partial gains), that native-Chinese target input outperforms machine-translated English input, and that the reversed order yields no clear gain within run-to-run variance. The study is an exploratory, single-site internal evaluation: it does not establish screening or diagnostic utility, nor separately identify the contribution of the scale, language, or paradigm shifts. To our knowledge, no prior study evaluates this specific DAIC-WOZ-to-PDCH sequential transfer setting.

Complex medical information is often difficult for patients to understand, making effective medical knowledge simplification essential for improving patient comprehension, informed decision-making, and health outcomes. Recent advances in large language models (LLMs) provide a promising approach for simplifying complex medical information into patient-friendly language; however, their effectiveness in real-world patient education remains insufficiently explored through human evaluation. To investigate their practical effectiveness, this paper presents a case study on diabetes knowledge simplification through the implementation and evaluation of MediClear, an LLM-based medical knowledge simplification system enhanced with Retrieval-Augmented Generation (RAG). Public diabetes-related articles from Diabetes Australia, WHO, American Diabetes Association (ADA), NIDDK, and AIHW are indexed in the RAG knowledge base to retrieve clinically grounded information, which is then simplified by the LLM into accessible patient explanations. We evaluate the generated responses using standard readability metrics, including the Flesch-Kincaid Grade Level (FKGL), and conduct a human study involving 10 participants. Results show that MediClear consistently reduces the reading level of generated responses to the recommended patient literacy range while achieving high user satisfaction and willingness for future use. This case study demonstrates the potential of LLMs to improve the accessibility of medical knowledge for patient education.

Background: To determine whether cross-lingual clinical annotation projection can be formulated as a text-preserving, document-level generative task that produces verifiable character-level annotations for multilingual clinical corpus construction, and to characterize its robustness and computational trade-offs relative to candidate-based projection pipelines. Methods: We developed a constrained LLM projection workflow that inserts entity tags directly into immutable target-language text, followed by deterministic validation and character-offset reconstruction. We evaluated it alongside supervised candidate-span projection and hybrid ML-LLM refinement for transferring Spanish Disease, Symptom, and Procedure annotations into six languages. Evaluation used MultiClinAI gold standard with strict span matching and character-overlap F1 Results: Direct LLM projection achieved the strongest and most consistent performance. GLM 5.2 obtained a mean Strict F1 of 0.9201 across 18 language-entity combinations, while locally deployable Gemma4:31B achieved 0.9133. The best LLM configuration improved Strict F1 over the previous state of the art in all 18 settings, by 0.0564-0.1512, yielding 55,416 grounded mentions with reconstructed offsets. Conclusions: Direct LLM-based projection enables high-quality multilingual clinical annotation transfer and provides a practical approach for extending clinical NLP resources to languages with fewer annotated datasets and language-specific tools. Combined with local inference and deterministic validation, it can substantially reduce expert time and cost for multilingual clinical corpus construction.

Clinical de-identification relies on accurately identifying personally identifiable information (PII). However, manually annotated datasets are costly to construct, while existing synthetic alternatives often provide limited details about their generation process or rely on relatively simple synthesis strategies. We introduce Meddies-PII-Dataset, a corpus of one million synthetic clinical documents spanning seventeen languages and nine PII labels. The documents are generated using attribute-conditioned prompts and validated through thirteen deterministic gates that enforce structural and annotation consistency. To evaluate the dataset's utility, we train Meddies-PII-Model, a BIOES token classifier, and compare it with existing PII extraction systems using exact-match entity-level F1. Meddies-PII-Model achieves the highest performance among the evaluated systems on all reported benchmarks, with a mean F1 of 0.827 across fifteen external benchmarks, compared with 0.658 for the strongest baseline. Upon acceptance, we will publicly release the dataset, benchmark suite, model, generation framework, and evaluation code to support research on multilingual clinical de-identification.

Clinical notes contain personally identifiable information (PII), restricting reuse for research and medical AI, especially when data cannot leave an institution. We developed MedDeID, an on-premises framework combining in-house annotation and synthetic-note generation with model training, inference, pseudonymisation and evaluation. On an independently annotated, adjudicated 300-note Dutch hospital benchmark, a hospital-trained compact transformer detected 98.9% of identifying text while redacting 0.24% of text outside annotated identifiers; a synthetic-only counterpart detected 96.1%. On 100 primary-care notes, the synthetic-trained model achieved higher recall than the hospital-trained model (90.3% versus 87.0%) and greater robustness to identifier-format perturbations. An English instantiation trained without real text detected 99.7% and 98.9% of annotated identifier characters on two external synthetic benchmarks. These results demonstrate transfer of the workflow to another language, but not clinical English performance. MedDeID provides a route to locally governed de-identification using real or synthetic training data.

Purpose: Accurate CT protocol selection is critical for diagnostic quality and patient safety, yet the current process is manual, time-consuming, and prone to inconsistencies. Prior Machine Learning methods using keywords or bag-of-words lack contextual understanding and perform poorly on rare protocols. We propose a decision support system using large language model (LLM) features to recommend protocols from free-text clinical indications, capturing clinical nuance and phrasing variation for more consistent, efficient selection. Methods: In this REB-approved retrospective study, 285,123 chest CT imaging requests from a large academic medical center (2017-2024) were split into training (228,099, 80%) and held-out test (57,024, 20%) sets. Each request included procedure names, clinical indication, HIS comments, and the selected protocol. Clinical text was embedded using a fine-tuned LLM, Meta's LLaMA-3.1-70B; these features input a logistic regression classifier predicting 18 protocol labels (e.g., PE, LDCT). Results: The pipeline achieved a weighted precision of 0.84, weighted F1-score of 0.81, and overall accuracy of 79% across 18 CT protocols. On 300 independent cases with expert consensus, the LLM reached an overall accuracy of 80% versus 83% for radiologists, with no significant difference (p = 0.263). Performance was comparable across most classes, with the LLM exceeding radiologists for some challenging categories, and entropy analyses indicated more balanced protocol use, suggesting reduced variability. Conclusion: An LLM-based recommendation system can leverage general knowledge from a large natural-text corpus to accurately assign chest CT protocols from free-text imaging requests, and may serve as a viable foundation for protocol recommendation tools where inputs require language understanding.

Assessing suicide risk from social media text is a small-data, high-stakes setting requiring not only severity prediction but also supporting evidence and clinically relevant risk and protective factors. Yet common NLP techniques, including model scaling, synthetic data, loss reweighting, ensembling, and threshold tuning, are often applied without testing whether their gains hold up under severe class imbalance, coupled outputs, and limited author-level data. We study 1,635 clinician-annotated posts and audit 31 pre-specified techniques from 7 methodological families through roughly 300 controlled experiments on author-disjoint partitions. We found no prior audit of this playbook in this regime. The findings guide a task-grounded system for three outputs: 4-level suicide risk, evidence spans, and 24 clinical risk and protective factors. Only 5 of 31 comparisons produced reliable gains. We reformulate factor prediction as entailment between each post and its codebook definitions, using an architecturally diverse ensemble with class-balanced training and score rescaling. Risk predictions condition a 7-model evidence tagger ensemble; evidence restricts symbolic risk rules; and a difficult risk class is routed separately. The factor predictor remains independent because risk evidence provides no additional factor signal. We also correct a mismatch between validation scores used for threshold fitting and test-time ensemble scores through deployment-consistent calibration, yielding the largest improvement to the factor system. The final system achieves 0.8203 for risk, 0.7953 for evidence, and 0.7045 macro-F1 for factors, with a 0.7781 composite, ranking third among 53 teams. We call the underlying principle task-conditioned technique selection: retain techniques only when task-specific knowledge, structure, or empirical evidence justifies them.

Sentence-level recognition of depression symptoms is challenging because similar expressions can differ in symptom relevance, and language-model inference is insufficiently grounded in diagnostic definitions. This study proposes a two-stage framework separating symptom-candidate generation from definition-grounded verification. A contrastively fine-tuned sentence encoder generates a symptom candidate per sentence, and a fine-tuned language model verifies whether the candidate is present or absent using the sentence, its context, and a candidate-specific diagnostic definition, checking its judgment against that definition before answering. Evaluated against encoder, inference-based, medical, and general LLM baselines and a matched single-stage supervised classifier, the proposed pipeline attains the best accuracy and F1 scores of all methods, with rationales matching expert-authored annotations. A preliminary clinical audit indicates moderate alignment with diagnostic definitions, with explanation quality strongly dependent on prediction correctness. The results support decomposing symptom recognition into candidate generation and definition-grounded verification, though performance remains limited for rare categories.

Patients with depression present with diverse symptom profiles, yet clinical practice routinely reduces this variation to a single severity score. Large language models (LLMs) can potentially capture various symptoms and their severity from patient speech. However, how depressive symptoms are represented inside LLMs remains poorly understood, limiting clinical trust. To examine whether internal model activations match clinician judgment, we analyzed the residual stream of Gemma-3-27B-PT using mechanistic interpretability techniques. Recording activations across symptom descriptions drawn from validated clinical instruments, we found that symptom groups geometrically separated the most at layer 21 across multiple distance metrics. Using Semantic Projection, we then projected held-out naturalistic text onto Symptom Vectors constructed from these instruments. The resulting per-symptom coefficients preserved clinician-annotated rank ordering across mood, somatic, and suicidality axes. Furthermore, a single depression vector in Layer 21 separates held-out depressive from non-depressive text (AUC = 0.789), which can be used as an emotional valence gate that restricts symptom projection to depressive speech. These results reveal a decorrelated, clinician-aligned symptom signal readable directly from internal activations, offering a mechanistic foundation for interpretable depression-assessment tools.

Crisis helplines assess suicide risk through structured interviews, a process that is slow and dependent on operator training and workload. Natural language processing could support risk assessment and call prioritization, but almost no work addresses Arabic-language helpline calls or operates within the privacy constraints of real helpline data. We analysed de-identified transcripts from Lebanon's National Lifeline for Emotional Support and Suicide Prevention. Audio never left the helpline: calls were transcribed on site with a speech recognition model for Levantine Arabic, and an Arabic named-entity recognition model removed identifying information locally. Only the de-identified transcripts were shared with the research team. Operators recorded the five suicidal ideation items of the Columbia Suicide Severity Rating Scale, which we combined into two binary outcomes: at-risk and high-risk. We also machine-translated the transcripts into English, giving a paired Arabic/English comparison. On each corpus, we fine-tuned five instruction-tuned large language models alongside six transformer encoder baselines (four Arabic, two English) and evaluated all models on a held-out test set. We included 383 calls: 373 for the at-risk task (52.3% positive) and 297 for the high-risk task (30.0% positive). The best Arabic model reached a macro-F1 of 81.19 and a ROC-AUC of 90.61 on high-risk; the best English model reached 85.00 and 92.59, identifying 88.9% of high-risk calls. In both languages, high-risk calls separated more cleanly than at-risk calls, and translation to English did not reduce the best observed performance. Suicide risk can be classified from de-identified Arabic transcripts without sending audio outside the helpline. The high-risk results support further testing as an operator-facing tool; lower-severity ideation proved the harder case.

Understanding how psychiatric patients subjectively experienced a clinical conversation is important for feedback and alliance-related process monitoring. While interviewers form post-session judgments about patient experience, these judgments do not always match patients' self-reports. Automatic approaches for predicting perceived interaction quality from conversation have been proposed, but it remains unclear whether such approaches can complement human judgment rather than simply replicate it. To address this gap, we evaluate a clinician-support framework in which post-session interviewer ratings are combined with automatic language-based predictions to estimate patient-reported interaction quality in free clinical interviews. We assess this integration across multiple standard model types, including Ridge, SVR, MLP, GRU, and BiLSTM, all trained on sentence embeddings extracted from dyadic transcripts of 107 free conversations between psychiatric patients and interviewers. Our results show that combining interviewer judgments with model predictions through simple averaging yields the strongest overall performance. The interviewer-only baseline reached a Pearson correlation of 0.365. Among fully automatic models, Ridge achieved the strongest Pearson correlation (r = 0.286), while BiLSTM achieved r = 0.270. The strongest result was obtained by BiLSTM interviewer integration (r = 0.403). Our findings suggest that automatic language analysis and interviewer judgment capture complementary aspects of patient experience and that their combination provides a more accurate approximation of the patient's own report than either source alone.

Artificial intelligence (AI) and natural language processing (NLP) are increasingly used to extract, integrate, and interpret biomedical knowledge relevant to cancer genomics, yet their translation into routine clinical oncology has been comparatively slow. The central challenge is not computational capability alone, but trustworthy integration into clinical workflows. This review examines how NLP and AI support the cancer genomics pipeline, from literature mining and automated variant interpretation to clinical trial matching, knowledge graph construction, and multimodal data integration. We identify four interrelated translational failure domains: evidence inconsistency, explainability and uncertainty, data governance and reproducibility, and interoperability. Rather than considering these challenges in isolation, we take a systems-level view, focusing on their interaction across the translational pathway. We propose a conceptual framework and roadmap for addressing these domains through rigorous validation, uncertainty-aware methods, interoperable infrastructures, regulatory alignment, and human oversight across the AI lifecycle. Progress toward routine clinical use will depend less on further improving model capability than on systematically addressing these interacting failure domains from development through deployment and post-deployment monitoring.

Biomedical Named Entity Recognition (NER) is fundamental to healthcare AI applications, including clinical decision support and medical information extraction. While corpora with Unified Medical Language System (UMLS) annotations, such as MedMentions, have driven progress in English biomedical NER, no comparable resource exists for Vietnamese. This paper presents En-ViMedNER, the first English-Vietnamese parallel biomedical NER corpus annotated with UMLS semantic types, which are language-neutral codes providing a shared cross-lingual label space and ensuring direct comparability with existing UMLS-based resources. The corpus contains 4,392 PubMed abstract pairs, 44,892 English-Vietnamese sentence pairs, and 202,949 aligned entity-mention pairs across 21 semantic types adapted from the MedMentions ST21pv dataset. To balance quality and scalability, we have constructed the corpus through automatic translation, expert post-editing, LLM-assisted label projection, and human verification and adjudication. We characterize En-ViMedNER as a large-scale silver-standard corpus with a human-audited and consensus-corrected mini-test subset. We evaluate En-ViMedNER in two settings: (i) Vietnamese-input/Vietnamese-output biomedical NER and (ii) English-input/Vietnamese-output cross-lingual NER. For Vietnamese NER, we benchmark Vietnamese-supervised encoder models, English-supervised multilingual encoder models, and prompt-based LLMs. The best model achieves an F1 score of 52.70 on the test set and 53.78 on the mini-test set. For cross-lingual NER, we benchmark encoder-decoder models and prompt-based LLMs. The best model achieves an F1 score of 45.44 on the mini-test set. We publicly release our corpus, corpus construction pipeline, and baseline models to facilitate future Vietnamese biomedical NLP research.

Many modern AI systems analyze conversational traces to infer aspects of human interaction and state, implicitly assuming that such information is recoverable from conversation. We study observability: whether a target is recoverable from conversational transcripts alone. Observability is difficult to assess because transcripts may provide only a partial view of many targets, and large-scale analysis requires model-based annotation, making true limits of the conversational signal hard to distinguish from annotator error. We therefore study clinical encounters, where patient-reported outcome measures (PROMs) provide an external anchor for patient state, and visits follow broadly structured patterns. We study observability of patient state and conversational phase structure using 439 real-world clinical encounter transcripts spanning 134 hours, including 245 ENT transcripts paired with 273 PROM surveys. We operationalize patient state using PROM scores for voice, cough, and swallowing; phase structure using conversational phase segmentation. To make these analyses credible at scale, we use a PHI-compliant GPT-5 deployment for transcript annotation and conduct 40 hours of manual validation, reducing the risk that apparent limits of observability simply reflect annotator error. Our core finding is an observability asymmetry: phase structure is observable and useful for characterizing clinical encounter organization, while patient state is only partially observable, even in a setting designed to elicit patient symptoms and experiences, cautioning against transcript-only inference of human state.

Mental health disorders are a leading cause of disability worldwide, yet Natural Language Processing (NLP) research for mental healthcare has remained concentrated in high-income, English-language settings. North Africa, and Algeria in particular, is largely absent from this literature despite its unique linguistic, historical, and healthcare context. We present the first conceptual framework examining the potential role of NLP within Algeria's mental healthcare system. Drawing on narrative synthesis of global NLP mental health research, Algerian healthcare literature, and low-resource NLP methodologies, we identify four structural barriers to mental healthcare: the language-of-care gap, geographic inequities in access, stigma-related barriers to help-seeking, and the absence of research and digital infrastructure. We then map existing NLP capabilities to each barrier, outlining their potential applications, implementation constraints, and the technical, institutional, and governance requirements necessary for deployment. Based on this analysis, we propose a research and policy roadmap that prioritizes data resources, multilingual language technologies, evaluation frameworks, and regulatory capacity. Although grounded in the Algerian context, the framework addresses challenges common to many multilingual, low-resource, and post-colonial settings. This work provides a foundation for future research on culturally and linguistically appropriate NLP for mental healthcare and offers a practical roadmap for developing responsible AI-enabled mental health systems in underrepresented regions.

Natural Language Processing (NLP) models predicting mental health outcomes rarely specify what they measure: contextual knowledge, emotional content, or syntactic structure. NLP Psychometrics treats psychological prediction from text as a psychometric problem, linking scores to interpretable linguistic evidence and testing beyond the training text format. Nine LLMs, conditioned on controlled personas (cognitive digital shadows), completed psychometric questionnaires with textual explanations per item. We extracted emotional profiles and syntactic-semantic structure via textual forma mentis networks, combined with personality and sociodemographic variables in ablated random forest (RF) regressors, using SHAP to identify which features drove performance and in which direction. Full RF models explained up to 70.8% of variance in life satisfaction (SWLS), 55.7% in depression (PHQ-9), and, for DASS-21, 68.5% depression, 76.0% anxiety, 72.4% stress. Sociodemographics alone explained no meaningful variance in depression, anxiety, or stress, but did so for life satisfaction, where emotion features and income were the strongest predictors; neuroticism and network topology instead dominated depression and anxiety, reversing direction between them. Without retraining, RF models separated diaries from low- and high-score personas ($r$ up to 0.91) and, using only network/emotion features, classified clinical from control participants in real transcripts with up to 68% accuracy. These results show the promise and limits of synthetic data: LLM personas can expose model biases, recover patterns consistent with clinical rumination, and support psychometric prediction from human text without a matched questionnaire, but cannot substitute for human validation. NLP Psychometrics makes these distinctions explicit, measurable, and testable through interpretable AI and network/emotional features.

Much clinical value is conveyed not through structured records but through communication: exchanges in which patients describe symptoms, clinicians reason and give instructions, ambulances hand over to emergency departments, and nurses pass on a shift. Such language differs from tabular data because meaning depends on speaker role, intent, causality, uncertainty, omission, and channel noise. Healthcare natural language processing must therefore interpret information as conveyed rather than coded. This requires well-annotated corpora, which are scarce because authentic exchanges are private, fragmented, and costly to annotate. Large language models offer a way forward by transforming clinical sources, such as records, diagnostic labels, symptom lists, or care plans, into written and transcribed communication for downstream models. We present a structured narrative survey organized by source representation, communication form and participants, generation method, and downstream task, complemented by thirteen novel case studies. These build clinical NLP systems for communication channels and languages without labeled real-world data, including EMS pre-arrival reports, field-radio casualty documentation, nurse handoffs, patient-portal triage, and low-resource discharge communication. They show that synthetic communication can bootstrap such systems. Findings include the competitiveness of fine-tuned encoder models over evaluated zero-shot baselines and the value of deliberately degraded communication for robustness. The main limitation is that most studies evaluate on held-out synthetic communication, while train-on-synthetic, test-on-authentic evidence remains limited. We conclude that syn-thetic clinical communication is becoming a practical research resource; establishing it as reusable clinical infrastructure will require authentic-data transfer, safety and external validation.

We introduce PlainMedScale, a topic-aligned medical corpus spanning four levels of comprehensibility in German and English, drawn from MSD (professional and consumer), Gesund.Bund, Apotheken Umschau Einfache Sprache, and the NHS. The four tiers correspond to distinct communicative functions --- reference, explanation, decision support, and access --- and move beyond the binary expert--lay contrast of prior corpora. In two pilot studies enabled by the alignments, we show that many readability metrics established on two registers fail to generalize across the full gradient, and that a SOTA open-weight LLM prompted for Plain Language still partially preserves the difficulty of its input. Code (https://github.com/GS-Uni-Heidelberg/PlainMedScale) and data (https://doi.org/10.5281/zenodo.21728290) are made available.

Early detection of mental health disorders is often limited by the lack of specialized resources in Spanish and the difficulty of analyzing long histories of social media posts. This paper addresses these challenges through three main contributions. First, we introduce three Spanish foundational models specifically adapted to the mental health domain through domain-specific pre-training. Second, we propose Incremental Context Expansion (ICE), an automatic relabeling methodology designed for early detection. ICE identifies the point at which cumulative messages provide enough evidence of a disorder, generating more informative training samples. Third, we provide a set of fine-tuned models using the samples generated with the ICE methodology for early risk detection tasks. Our results on three Spanish benchmarks show that combining these specialized models with ICE improves the state-of-the-art, reducing detection latency while maintaining high performance. All models are publicly available.

The reliance on unstructured free text for documenting clinical trial protocols creates a significant barrier to automated reasoning, cohort discovery, and trial simulation. The lack of formal structure obscures critical temporal phenotypes, such as dynamic eligibility criteria and event timing constraints. Although Temporal Ensemble Logic (TEL) offers an expressive framework for modeling these elements, manual encoding remains a prohibitive bottleneck. We introduce the CT-TEL workflow: a scalable pipeline leveraging Large Language Models (LLMs) to translate narrative clinical protocols into TEL formulas. We applied CT-TEL to generate logical models for 23 real-world trials from ClinicalTrials.gov. We evaluated translation fidelity via a back-translation approach, using LLMs to convert TEL formulas back into natural language and measuring semantic similarity against source texts. The resulting semantic retention suggests that LLMs may offer a pathway for mapping informal protocols to computable logic, providing preliminary evidence toward scalable clinical trial emulation within the emerging "Symbolic Biomedicine" paradigm championed by the corresponding author.

AI_LectureNote is a historical, readability-oriented post-ASR workflow for Korean-English medical lectures. It rewrites speech-to-text output into study transcripts while restoring Latin-script medical terms rather than Korean phonetic transliterations. We retrospectively evaluate the workflow on four author-recorded lectures across five conditions. In this pilot, post-processing raised the macro English-script rendering rate from 0.39 to 0.71 on the whisper-1 path and from 0.26 to 0.65 when applied to 3-minute chunked gpt-4o-transcribe output. However, English-script rendering did not imply semantic faithfulness: the two post-processed conditions showed semantic drift in 34 and 36 of 282 reference sentences and polarity failures in 11 and 13 of 101 polarity-cue rows. A descriptive cross-input comparison suggested different candidate failure patterns: polarity-failure sets overlapped more strongly across front-ends (Jaccard 0.60; 9 shared of 15 unioned failures) than general semantic-drift sets (Jaccard 0.23; 13 shared of 57 unioned drifts). This single-annotator pilot documents concrete failure modes rather than population rates and supports evaluating surface accuracy, term-script rendering, chunk-level script consistency, and medical-meaning preservation separately.

Federated learning (FL) enables multi-institutional training on clinical text without sharing raw data, but gradient inversion can reconstruct sensitive information from shared model updates. The extent of this leakage for radiology reports, and the role of tokenizer design, remains unclear. We quantify gradient-based text reconstruction in FL and compare privacy risk across three tokenizers with the model architecture held fixed. Six FL clients trained a GPT-2-style transformer (sequence length 32) on public radiology corpora (368,751 diagnostic reports, 98,206 discharge summaries, 1,500 MIMIC-CXR free-text reports) using the GPT-2, RadBERT, and LLaMA-2 tokenizers at batch sizes of 64, 128, and 256. Assuming an active malicious server that modifies the shared architecture before distribution, we applied analytic gradient inversion and measured reconstruction fidelity over five runs. Exact sentence reconstruction ranged from 31% to 44% across tokenizers (30.6-43.5% across the 27 tokenizer x dataset x batch-size cells). At batch size 64 on the Discharge dataset, accuracy was 42.1% (GPT-2), 42.3% (RadBERT), and 39.4% (LLaMA-2), decreasing to 37.3%, 37.2%, and 34.3% at batch size 256. S-BLEU declined as batch size grew (GPT-2: 0.44 to 0.33; RadBERT: 0.48 to 0.35). RadBERT yielded the highest reconstruction fidelity and recovered the most clinical terms (18.1% of a 1,440-term reference vocabulary, vs 12.5% for GPT-2 and 9.4% for LLaMA-2), yet no tokenizer prevented leakage. Substantial portions of report text are therefore recoverable from FL gradients even at larger batch sizes and with domain-specific tokenizers. Tokenizer design influences leakage severity and is a privacy-relevant decision, not only a utility one; safeguards such as secure aggregation and differential privacy are likely necessary to meet HIPAA and GDPR requirements for FL in radiology NLP.

Clinical notes contain many of the signs and symptoms that bring patients to care, yet this information rarely reaches structured fields. Existing extraction approaches either rely on context-insensitive rules that generate false positives or on supervised models that require substantial fine-tuning. We present Pythia, a multi-agent system that autonomously writes and optimizes extraction prompts for clinical concepts without manual prompt engineering or fine-tuning. Running on a locally hosted open-weights model, Pythia keeps clinical notes on local infrastructure and selects prompts using development-set sensitivity and specificity. We compared Pythia with a curated lexicon across 72 signs and symptoms from 400 clinical notes representing 387 patients. Development (n=300) and validation (n=100) sets were partitioned independently for each concept. Pythia achieved mean sensitivity of 0.76 and specificity of 0.95, compared with 0.82 and 0.76 for the lexicon, and matched or exceeded the lexicon on both metrics for 20 of 62 directly comparable concepts. For 14 concepts where the lexicon labeled every note positive, Pythia recovered mean specificity of 0.97 by requiring a present-tense, patient-attributed finding rather than any textual mention of a term. Specificity transferred from development to validation with minimal degradation across prevalences, whereas sensitivity transfer weakened below 5% prevalence, reaching a mean gap of 0.25 below 2% prevalence. A BERT classifier fine-tuned per concept on the same development set achieved mean sensitivity of 0.23 and collapsed to zero sensitivity for concepts below roughly 5% prevalence. These findings suggest that autonomous, fine-tuning-free prompt optimization can produce symptom extraction prompts that generalize effectively from development to validation while remaining deployable on local infrastructure.

Natural language processing (NLP) is a common method for supplying data to clinical research and decision making by extracting information from electronic medical records. Numerous textbooks and tutorials describe specific algorithms and applications for text processing, yet algorithmic knowledge is only one ingredient of a successful NLP project. Drawing on the available literature, this paper presents a stepwise approach that applies the Systems Development Life Cycle (SDLC) to projects that rely on data extraction through language processing.

We study inference-time pattern-memory gating in a production-scale clinical natural language processing (NLP) pipeline. The pipeline pairs a generator (Llama-3.3 70B) proposing extractions with a verifier (MMed-Llama-3.1 70B) accepting or rejecting them, over 167,034 PMC-Patients narratives, and adds a lightweight memory that learns at deployment which extractions to filter, so the verifier need not re-examine candidates already seen to fail. We report four findings. First, learning filtering rules directly from the verifier's rejections failed at full scale: the relation-extraction filter stayed empty despite 785,797 logged rejections, because they were spread too thinly across too many distinct forms to accumulate. Second, a simpler rule using a fixed clinical ontology produced the same filtering without the verifier, capturing 49,734 ontology-violating relations on a held-out 5,000-patient set. Third, of five versions of the question-answering filter, four failed for distinct, instructive reasons; the fifth succeeded by checking whether a patient's extracted entities support the question asked, and where it applies was 1.84 times likelier to flag an answer the verifier would reject than one it would accept. Fourth, one pattern held across all five: a filter is selective only when it tests the same evidence the verifier weighs, not when it imitates the verifier's output. Together these give a transferable result for any generator-verifier pipeline: the most natural memory design can fail silently at scale, and whether a pre-generation gate is selective is decided before any engineering effort, by whether its signal probes the question the verifier itself answers. Throughout, the system flags suspect extractions rather than deleting them, so every decision stays visible for clinical review. All code and test artefacts are released openly.

Medication errors, particularly dosing errors in clinical trials (CT), can lead to patient harm, adverse drug events and worse patient outcomes. Dosing errors are preventable, and early identification can improve trial integrity and mitigate subsequent clinical and financial burden. This study aims to detect dosing errors within CT protocols by evaluating text representations of trial information using transformer-based language models trained on biomedical corpora. CT textual data was encoded using several models, including ClinicalBERT, PubMedBERT, BioBERT, and MedCPT, and integrated with categorical features. These text embeddings were used as input to classical machine learning models and neural network architectures within an experimental framework. Performance was primarily assessed using ROC-AUC with respect to predicting dosage error. Under a logistic regression baseline, BioBERT consistently outperformed alternative encoders, achieving an ROC-AUC of 0.794, a 3.95% improvement over the ClinicalBERT baseline. Combining multiple embeddings did not yield improvements, indicating that domain alignment outweighs representational stacking. Gradient boosting models, support vector classifiers, logistic regression, and residual neural networks achieved the strongest performance for predicting dosage error, achieving ROC-AUCs: 0.821 to 0.853. Overall, the integration of domain-specific transformer embeddings with structured metadata enables discrimination of trials meeting a predefined elevated dosing error risk criterion, advancing safety monitoring and supporting informed regulatory decision-making.

Clinical machine learning increasingly relies on training corpora generated by large language models (LLMs) rather than annotated by clinicians, and such corpora are described and reused largely on the basis of their reported scale. We test whether volume reflects information content. Analysing the complete output of a multi-agent clinical extraction pipeline applied to 167,034 patient narratives, 2.51 billion generated tokens across the ten text-bearing channels of an eleven-channel pipeline, we introduce Provenance-based Redundancy Decomposition, a token-level classification of the entire output by source. Only 10.9% of the output is trainable-unique content while 79.4% is redundant; raw token count overstates information content by roughly ninefold. The redundancy arises through two distinct mechanisms, verbatim copying of source context into per-item fields, and duplication of generated text across records, of which only the former is losslessly removable. An independent, model-free analysis based on lossless compression confirms the redundancy, recovering the two mechanisms without reference to the provenance labels. One pipeline channel carries almost no redundancy, showing that the level of redundancy depends on how each channel is structured rather than being a fixed property of LLM extraction. Because uncorrected redundancy up-weights the longer, more complex presentations that generate the most items, it skews the token-level training distribution of the corpus, a property we measure directly. In a controlled downstream test, de-duplicating the corpus before adaptation improved a clinical encoder on external disease-recognition benchmarks at equal token budget, robustly across adaptation depths and replicated on a second benchmark, confirming that the redundancy carries a measurable cost beyond storage. The classification tool is released openly.