healthcare software developers

Abstract: 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.

Abstract: Electronic health record (EHR) foundation models trained on longitudinal patient trajectories have demonstrated strong performance across diverse clinical prediction tasks. However, their clinical reasoning capabilities remain constrained by next-token prediction on limited and incomplete EHR data. To address this, we propose a reinforcement learning (RL) fine-tuning framework that treats EHR foundation models as generative policies over patient trajectories. We formulate common clinical prediction problems (e.g., hospital readmission) as event-conditioned, time-windowed reasoning tasks. We then design time-aware, rollout-sensitive rewards to account for finite rollout lengths and temporally inconclusive outcomes. We find that RL fine-tuning consistently improves over pre-trained backbones and strong baselines. Notably, it enables smaller models to surpass larger pre-trained models in data-limited regimes and induces positive transfer across tasks. Further analysis shows that RL fine-tuned models generate trajectories with stronger structural and semantic alignment to ground truth and greater downstream utility.

Abstract: 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.

Abstract: Large language models are unreliable at arithmetic, which is a problem for clinical calculators where a single numerical error changes the recommendation. The standard response is to hardcode each calculator as a validated function, one at a time. We test an alternative: the model does not calculate. Instead, it writes case-specific Python that a restricted local executor runs as a deterministic solver, and the model's task reduces to deciding how to use it. We evaluate this Program-Solve interface on MedCalc-Bench Verified (1,100 cases, 55 calculators) against direct model arithmetic and a hand-written 22-calculator library, using Qwen2.5-7B and Qwen2.5-32B-AWQ, after auditing the benchmark's formulas against current clinical guidelines and flagging 16 of 55 with version, use or coefficient concerns. With formulas and gold variables supplied and both routes reading the whole note, handing off to the solver is not a reliable advantage at 7B (75.31% against 72.02%, a paired +3.29 points with a 95% calculator-cluster interval of [-3.49, 10.38]) but is one at 32B (90.53% against 83.47%, +7.05 [0.47, 14.60], clear of zero). The hand-written library is exact on its 440 supported cases but abstains elsewhere (40.0% overall). Adding an executor thus helps some open-weight models more than others even under matched formula, variable and note access, and is not a substitute for verified formulas or reliable variable extraction either way.

Abstract: Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

Abstract: The digitization of healthcare has generated vast, longitudinal, and multimodal patient records over a lifetime, yet fully exploiting these data to represent and predict patient state trajectories remains a critical challenge. Current AI models often struggle to capture the complex, irregular temporal dynamics and inherent stochasticity of real-world multimodal patient data. Existing AI approaches for modeling longitudinal patient records are predominantly discriminative, limited to a few modalities, constrained by closed categorical vocabularies, treating time as a monotonic inductive bias, or they are limited in forecasting future patient states. We introduce NOAH, a time-aware, task-agnostic, generative transformer model representing and forecasting the full multimodal patient journey. NOAH features a novel bidirectional time integration and a variational latent space to capture the continuous evolution of patient states and the stochasticity of clinical trajectories. Built from over 559 million clinical events from 431,000 hospital visits of 299,000 patients across the MIMIC dataset family, NOAH natively processes medical images, time-series and numeric signals, categorical events, as well as structured and unstructured clinical records. NOAH is the first truly holistic generative model in its field, enabling autoregressive forecasting with optional time control, zero-shot classification, and counterfactual intervention simulation. It generates highly informative and predictive patient state representations that demonstrate strong performance in probing for clinical outcomes, 15 ICD chapters, and 29 comorbidities, as well as in time-to-event prediction. Seamlessly handling diverse modalities and complex temporal dynamics, NOAH provides a versatile, task-agnostic, scalable foundation for intelligent predictive systems in personalized clinical care and digital medicine.

Abstract: The application of large language models (LLMs) to personalized medical assistants has garnered growing interest. However, existing medical benchmarks largely rely on static question answering with pre-selected evidence, leaving unclear whether LLMs can make reliable clinical decisions from real longitudinal electronic health records (EHRs). To bridge this gap, we introduce ObGynLongBench, a rule-grounded long-context EHR benchmark for obstetric and gynecologic decision-making, comprising 1,500 clinical decision-point cases from 976 real pregnancy EHR histories and traceable rules. Each case is anchored to a patient, a pregnancy-timeline point, and a pre-decision information boundary, enabling Evidence-only, Visit-level EHR, and History-level EHR evaluation. Evaluating 17 LLMs reveals a substantial Evidence-to-EHR Gap: models perform well when evidence is directly provided, but accuracy drops when evidence must be extracted from same-day records or full pre-decision EHR histories. Further analyses identify evidence utilization as a key bottleneck: performance decreases with longer EHR contexts and more complex evidence requirements, and earlier failures often predict later failures within the same patient history. Finally, active-search agents perform best among EHR access strategies, highlighting patient-specific evidence utilization as a central challenge for reliable personalized medical assistants. Resources are available at https://github.com/xiangjun2003/ObgynLongbench.

Abstract: Uncertainty arising from inter-observer variability in medical image segmentation plays an important role in developing treatment plans. Research in this area is inhibited by the lack of multiple annotations for large-scale medical datasets, especially for volumetric data, which suffers from additional scaling and computational complexity challenges. Flow matching has emerged as a powerful framework for generative modelling and has also been demonstrated to maintain strong performance when working with latent representations of images. In this work, we introduce a latent-to-latent flow technique for stochastic segmentation of medical volumes via encoded representations of both the image and label space. We evaluate our method on two challenging applications covering delineation uncertainty for radiotherapy planning and multiple organ structure segmentation, improving efficiency up to 14x compared with full resolution models while maintaining clinically relevant performance.