We introduce ChemPro, a progressive benchmark with 4100 natural language question-answer pairs in Chemistry, across 4 coherent sections of difficulty designed to assess the proficiency of Large Language Models (LLMs) in a broad spectrum of general chemistry topics. We include Multiple Choice Questions and Numerical Questions spread across fine-grained information recall, long-horizon reasoning, multi-concept questions, problem-solving with nuanced articulation, and straightforward questions in a balanced ratio, effectively covering Bio-Chemistry, Inorganic-Chemistry, Organic-Chemistry and Physical-Chemistry. ChemPro is carefully designed analogous to a student's academic evaluation for basic to high-school chemistry. A gradual increase in the question difficulty rigorously tests the ability of LLMs to progress from solving basic problems to solving more sophisticated challenges. We evaluate 45+7 state-of-the-art LLMs, spanning both open-source and proprietary variants, and our analysis reveals that while LLMs perform well on basic chemistry questions, their accuracy declines with different types and levels of complexity. These findings highlight the critical limitations of LLMs in
The competency of any intelligent agent is bounded by its formal account of the world in which it operates. Clinical AI lacks such an account. Existing frameworks address evaluation, regulation, or system design in isolation, without a shared model of the clinical world to connect them. We introduce the Clinical World Model, a framework that formalizes care as a tripartite interaction among Patient, Provider, and Ecosystem. To formalize how any agent, whether human or artificial, transforms information into clinical action, we develop parallel decision-making architectures for providers, patients, and AI agents, grounded in validated principles of clinical cognition. The Clinical AI Skill-Mix operationalizes competency through eight dimensions. Five define the clinical competency space (condition, phase, care setting, provider role, and task) and three specify how AI engages human reasoning (assigned authority, agent facing, and anchoring layer). The combinatorial product of these dimensions yields a space of billions of distinct competency coordinates. A central structural implication is that validation within one coordinate provides minimal evidence for performance in another, re
Clinical NLP increasingly relies on electronic health record (EHR) data to detect suicidal behaviors, treating clinical documentation as more reliable ground truth than social media. We argue that this framing obscures how EHR-based suicidality datasets encode a particular operationalization of suicidality, shaped by who authors the data, how episodes are bounded, and how ambiguity is resolved. We ground this argument in a case study of the ScAN dataset, built over MIMIC-III clinical notes. We show how governance constraints, ICD-based cohort selection, single-annotator labeling, and hospital-stay-level aggregation produce labels that reflect clinician-documented judgments, treat suicidality as a bounded episode, and assume that intent can be reliably inferred from documentation. A linguistic analysis demonstrates that identical labels subsume heterogeneous clinical framings differing in temporality, negation, and uncertainty. We argue that clinical NLP should examine the assumptions embedded in suicidality datasets before interpreting their labels as ground truth.
To enhance large language models (LLMs) for chemistry problem solving, several LLM-based agents augmented with tools have been proposed, such as ChemCrow and Coscientist. However, their evaluations are narrow in scope, leaving a large gap in understanding the benefits of tools across diverse chemistry tasks. To bridge this gap, we develop ChemToolAgent, an enhanced chemistry agent over ChemCrow, and conduct a comprehensive evaluation of its performance on both specialized chemistry tasks and general chemistry questions. Surprisingly, ChemToolAgent does not consistently outperform its base LLMs without tools. Our error analysis with a chemistry expert suggests that: For specialized chemistry tasks, such as synthesis prediction, we should augment agents with specialized tools; however, for general chemistry questions like those in exams, agents' ability to reason correctly with chemistry knowledge matters more, and tool augmentation does not always help.
We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.
We introduce SoftTiger, a clinical large language model (CLaM) designed as a foundation model for healthcare workflows. The narrative and unstructured nature of clinical notes is a major obstacle for healthcare intelligentization. We address a critical problem of structuring clinical notes into clinical data, according to international interoperability standards. We collect and annotate data for three subtasks, namely, international patient summary, clinical impression and medical encounter. We then supervised fine-tuned a state-of-the-art LLM using public and credentialed clinical data. The training is orchestrated in a way that the target model can first support basic clinical tasks such as abbreviation expansion and temporal information extraction, and then learn to perform more complex downstream clinical tasks. Moreover, we address several modeling challenges in the healthcare context, e.g., extra long context window. Our blind pairwise evaluation shows that SoftTiger outperforms other popular open-source models and GPT-3.5, comparable to Gemini-pro, with a mild gap from GPT-4. We believe that LLMs may become a step-stone towards healthcare digitalization and democratization.
Empiric antibiotic prescribing in high-risk clinical contexts often requires decision making under conditions of incomplete information, where inappropriate coverage or unjustified escalation may compromise safety and antimicrobial stewardship. While clinical decision-support systems have been proposed to assist in this process, many approaches lack explicit governance and evaluation mechanisms defining scope, abstention conditions, recommendation permissibility, and expected system behavior. This work specifies a governance and evaluation framework for deterministic clinical decision-support systems operating under explicitly constrained scope. Deterministic behavior is adopted to ensure that identical inputs yield identical outputs, supporting transparency, auditability, and conservative decision support in high-risk prescribing contexts. The framework treats governance as a first-class design component, separating clinical decision logic from rule-based mechanisms that determine whether a recommendation may be issued. Explicit abstention, deterministic stewardship constraints, and exclusion rules are formalized as core constructs. The framework defines an evaluation methodology
Developing AI models that are useful in clinical practice, requires efficient collaboration between clinicians and AI developers. This poses a practical challenge: clinicians must repeatedly communicate and refine their requirements with AI developers before those requirements can be translated into executable model development. This iterative process is time-consuming, and even after repeated discussion, misalignment may still exist because the two sides do not fully share each other's expertise. Coding agents may help close this gap. They can write and refine code on their own, and they carry working knowledge of both medicine and AI to understand commands formulated by both medical experts and developers. We present a prototype that lets clinicians drive AI development directly. A clinician describes the task in plain language, and the system turns the description into a working pipeline, refines it through repeated experiments together with the clinician, and returns a model that meets the stated clinical objective. Across five clinical tasks, the system reliably produces models that matched the clinician's request and reached competitive performance. Most notably, on chest rad
The spatial distribution of the chemical reservoirs in protoplanetary disks is key to elucidate the composition of planets, especially habitable ones. However, the partitioning of the main elements among the refractory and volatile phases is still elusive. Key parameters such as the carbon-to-oxygen C/O elemental ratio and the ionization fraction remain poorly constrained, with the latter potentially orders of magnitude lower than in the interstellar medium. Moreover, the thermal structure of the gas is also poorly known, despite its deep influence on gas-phase chemistry. In this context, ortho-to-para ratios could provide selective and sensitive probes. Recent ALMA observations have measured the spatially resolved column density of ortho-and para-H2CO in the transition disk orbiting TW Hya and derived the radial profile of the ortho-to-para ratio. Yet, current disk models do not include the nuclear-spin-resolved chemistry required to interpret these observations. The present work aims to fill this gap, by combining a parametric disk physical model of TW Hya with the UGAN network, updated to include a comprehensive description of the nuclear-spin-resolved chemistry of formaldehyde.
Multimodal scientific reasoning remains a significant challenge for large language models (LLMs), particularly in chemistry, where problem-solving relies on symbolic diagrams, molecular structures, and structured visual data. Here, we systematically evaluate 40 proprietary and open-source multimodal LLMs, including GPT-5, o3, Gemini-2.5-Pro, and Qwen2.5-VL, on a curated benchmark of Olympiad-style chemistry questions drawn from over two decades of U.S. National Chemistry Olympiad (USNCO) exams. These questions require integrated visual and textual reasoning across diverse modalities. We find that many models struggle with modality fusion, where in some cases, removing the image even improves accuracy, indicating misalignment in vision-language integration. Chain-of-Thought prompting consistently enhances both accuracy and visual grounding, as demonstrated through ablation studies and occlusion-based interpretability. Our results reveal critical limitations in the scientific reasoning abilities of current MLLMs, providing actionable strategies for developing more robust and interpretable multimodal systems in chemistry. This work provides a timely benchmark for measuring progress in
Digital Twins hold great potential to personalize clinical patient care, provided the concept is translated to meet specific requirements emerging from established clinical workflows. We present a general and unspecialized Digital Twin design combining knowledge graphs and ensemble learning to reflect the entire patient's clinical journey and assist clinicians in their decision-making. Such a design is predictive, modular, evolving, informed, interpretable and explainable, thus opening broad clinical applications.
Accelerated materials discovery is critical for addressing global challenges. However, developing new laboratory workflows relies heavily on real-world experimental trials, and this can hinder scalability because of the need for numerous physical make-and-test iterations. Here we present MATTERIX, a multiscale, graphics processing unit-accelerated robotic simulation framework designed to create high-fidelity digital twins of chemistry laboratories, thus accelerating workflow development. This multiscale digital twin simulates robotic physical manipulation, powder and liquid dynamics, device functionalities, heat transfer and basic chemical reaction kinetics. This is enabled by integrating realistic physics simulation and photorealistic rendering with a modular graphics processing unit-accelerated semantics engine, which models logical states and continuous behaviors to simulate chemistry workflows across different levels of abstraction. MATTERIX streamlines the creation of digital twin environments through open-source asset libraries and interfaces, while enabling flexible workflow design via hierarchical plan definition and a modular skill library that incorporates learning-based
Introduction: Semantic search, which retrieves documents based on conceptual similarity rather than keyword matching, offers substantial advantages for retrieval of clinical information. However, deploying semantic search across entire health systems, comprising hundreds of millions of clinical notes, presents formidable engineering, cost, and governance challenges that have prevented adoption. Methods: We deployed a semantic search system at a large children's hospital indexing 166 million clinical notes (484 million vectors) from 1.68 million patients. The system uses instruction-tuned qwen3-embedding-0.6B embeddings, stores vectors in a managed database with storage-optimized indexing, maintains full-text metadata in a low-latency key-value store, and operates within a HIPAA-compliant governance framework. We evaluated the system through three experiments: optimization of embedding model and chunking strategy using a physician-authored benchmark dataset, characterization of full-scale performance (cost, latency, retrieval quality), and clinical utility assessment via comparison of chart abstraction efficiency across three tasks. Results: The system delivers sub-second query late
We evaluate the impact of large language model-based clinical decision support in live care. In partnership with Penda Health, a network of primary care clinics in Nairobi, Kenya, we studied AI Consult, a tool that serves as a safety net for clinicians by identifying potential documentation and clinical decision-making errors. AI Consult integrates into clinician workflows, activating only when needed and preserving clinician autonomy. We conducted a quality improvement study, comparing outcomes for 39,849 patient visits performed by clinicians with or without access to AI Consult across 15 clinics. Visits were rated by independent physicians to identify clinical errors. Clinicians with access to AI Consult made relatively fewer errors: 16% fewer diagnostic errors and 13% fewer treatment errors. In absolute terms, the introduction of AI Consult would avert diagnostic errors in 22,000 visits and treatment errors in 29,000 visits annually at Penda alone. In a survey of clinicians with AI Consult, all clinicians said that AI Consult improved the quality of care they delivered, with 75% saying the effect was "substantial". These results required a clinical workflow-aligned AI Consult i
This paper is dedicated to the design and evaluation of the first AMR parser tailored for clinical notes. Our objective was to facilitate the precise transformation of the clinical notes into structured AMR expressions, thereby enhancing the interpretability and usability of clinical text data at scale. Leveraging the colon cancer dataset from the Temporal Histories of Your Medical Events (THYME) corpus, we adapted a state-of-the-art AMR parser utilizing continuous training. Our approach incorporates data augmentation techniques to enhance the accuracy of AMR structure predictions. Notably, through this learning strategy, our parser achieved an impressive F1 score of 88% on the THYME corpus's colon cancer dataset. Moreover, our research delved into the efficacy of data required for domain adaptation within the realm of clinical notes, presenting domain adaptation data requirements for AMR parsing. This exploration not only underscores the parser's robust performance but also highlights its potential in facilitating a deeper understanding of clinical narratives through structured semantic representations.
Bioinformatics platforms have significantly changed clinical diagnostics by facilitating the analysis of genomic data, thereby advancing personalized medicine and improving patient care. This study examines the integration, usage patterns, challenges, and impact of the Galaxy platform within clinical diagnostics laboratories. We employed a convergent parallel mixed-methods design, collecting quantitative survey data and qualitative insights from structured interviews with fifteen participants across various clinical roles. The findings indicate a wide adoption of Galaxy, with participants expressing high satisfaction due to its user-friendly interface and notable improvements in workflow efficiency and diagnostic accuracy. Challenges such as data security and training needs were also identified, highlighting the platform's role in simplifying complex data analysis tasks. This study contributes to understanding the transformative potential of Galaxy in clinical practice and offers recommendations for optimizing its integration and functionality. These insights are crucial for advancing clinical diagnostics and enhancing patient outcomes.
Despite the plethora of AI-based algorithms developed for anomaly detection in radiology, subsequent integration into clinical setting is rarely evaluated. In this work, we assess the applicability and utility of an AI-based model for brain aneurysm detection comparing the performance of two readers with different levels of experience (2 and 13 years). We aim to answer the following questions: 1) Do the readers improve their performance when assisted by the AI algorithm? 2) How much does the AI algorithm impact routine clinical workflow? We reuse and enlarge our open-access, Time-Of-Flight Magnetic Resonance Angiography dataset (N=460). We use 360 subjects for training/validating our algorithm and 100 as unseen test set for the reading session. Even though our model reaches state-of-the-art results on the test set (sensitivity=74%, false positive rate=1.6), we show that neither the junior nor the senior reader significantly increase their sensitivity (p=0.59, p=1, respectively). In addition, we find that reading time for both readers is significantly higher in the "AI-assisted" setting than in the "Unassisted" (+15 seconds, on average; p=3x10^(-4) junior, p=3x10^(-5) senior). The c
Efficient chemical kinetic model inference and application in combustion are challenging due to large ODE systems and widely separated time scales. Machine learning techniques have been proposed to streamline these models, though strong nonlinearity and numerical stiffness combined with noisy data sources make their application challenging. Here, we introduce ChemKANs, a novel neural network framework with applications both in model inference and simulation acceleration for combustion chemistry. ChemKAN's novel structure augments the generic Kolmogorov Arnold Network Ordinary Differential Equations (KAN-ODEs) with knowledge of the information flow through the relevant kinetic and thermodynamic laws. This chemistry-specific structure combined with the expressivity and rapid neural scaling of the underlying KAN-ODE algorithm instills in ChemKANs a strong inductive bias, streamlined training, and higher accuracy predictions compared to standard benchmarks, while facilitating parameter sparsity through shared information across all inputs and outputs. In a model inference investigation, we benchmark the robustness of ChemKANs to sparse data containing up to 15% added noise, and superfl
Specialised pre-trained language models are becoming more frequent in NLP since they can potentially outperform models trained on generic texts. BioBERT and BioClinicalBERT are two examples of such models that have shown promise in medical NLP tasks. Many of these models are overparametrised and resource-intensive, but thanks to techniques like Knowledge Distillation (KD), it is possible to create smaller versions that perform almost as well as their larger counterparts. In this work, we specifically focus on development of compact language models for processing clinical texts (i.e. progress notes, discharge summaries etc). We developed a number of efficient lightweight clinical transformers using knowledge distillation and continual learning, with the number of parameters ranging from 15 million to 65 million. These models performed comparably to larger models such as BioBERT and ClinicalBioBERT and significantly outperformed other compact models trained on general or biomedical data. Our extensive evaluation was done across several standard datasets and covered a wide range of clinical text-mining tasks, including Natural Language Inference, Relation Extraction, Named Entity Reco
Objective: Integrating EHR data with other resources is essential in rare disease research due to low disease prevalence. Such integration is dependent on the alignment of ontologies used for data annotation. The International Classification of Diseases (ICD) is used to annotate clinical diagnoses; the Human Phenotype Ontology (HPO) to annotate phenotypes. Although these ontologies overlap in biomedical entities described, the extent to which they are interoperable is unknown. We investigate how well aligned these ontologies are and whether such alignments facilitate EHR data integration. Materials and Methods: We conducted an empirical analysis of the coverage of mappings between ICD and HPO. We interpret this mapping coverage as a proxy for how easily clinical data can be integrated with research ontologies such as HPO. We quantify how exhaustively ICD codes are mapped to HPO by analyzing mappings in the UMLS Metathesaurus. We analyze the proportion of ICD codes mapped to HPO within a real-world EHR dataset. Results and Discussion: Our analysis revealed that only 2.2% of ICD codes have direct mappings to HPO in UMLS. Within our EHR dataset, less than 50% of ICD codes have mapping