Emergency departments (EDs) operate under time pressure, generating multimodal data such as clinical conversations, triage notes, and discharge documents. Recent advances in natural language processing (NLP), particularly pretrained transformers and large language models, have created new opportunities to support language and time-intensive stages of emergency care. Yet existing surveys map clinical NLP across the broader hospital workflow or focus on specific tasks. This survey analyses 46 papers spanning the three phases of ED: triage, diagnosis, and disposition, covering tasks such as triage classification, clinical summarisation, automatic diagnosis, report generation, and discharge documentation. We examine modelling paradigms, evaluation practices, and emerging benchmarks and shared tasks. Across tasks, we identify common trends, including a shift from task-specific neural architectures to pretrained language models, growing interest in interactive clinical systems, and increasing attention to clinically grounded evaluation. Finally, we detail open challenges such as limited generalisability, noisy clinical inputs, and workflow constraints that inform future ED-NLP research.
Advances in multimodal large language models (MLLMs) are extending radiological artificial intelligence (AI) beyond task-specific image analysis toward multimodal understanding and reasoning. Volumetric radiology, however, presents a fundamental representational mismatch: clinical interpretation often requires full-volume spatial context and acquisition-dependent quantitative information, whereas current MLLMs are commonly conditioned on selected two-dimensional (2D) images, compressed visual representations, or report-derived text. Reliable volumetric radiology AI therefore requires representations that preserve task-relevant three-dimensional (3D) information and systems that can access, verify, and integrate this information across clinical workflows. In this Review, we examine more than 200 publications through July 2026. We organize the literature around volumetric representation and multimodal understanding at the model level, agentic orchestration at the system level, and their links to clinical applications and evaluation. We review volumetric foundation models, language alignment and compression strategies, and agentic systems that extend MLLMs through planning, tools, memory, and workflow interaction. We distinguish settings in which selected 2D views or report-mediated reasoning may suffice from those that warrant native volumetric modeling. We also introduce a Claim-Design-Validation framework to assess whether technical, workflow, and clinical claims are matched by appropriate design and validation. Across the literature, native volumetric modeling and agentic capabilities depend on the spatial, quantitative, contextual, and workflow requirements of the intended task. Clinical credibility requires faithful volumetric representation, traceable system behavior, claim-aligned validation, and clearly defined human oversight in realistic workflows.
Accurate localization and segmentation of the optic disc (OD) are important for retinal image analysis and glaucoma assessment, yet remain challenging due to variations in illumination, pathology, vascular interference, and poorly defined boundaries. This structured methodological review examines the evolution of OD segmentation from classical image-processing and deformable models to contemporary artificial intelligence (AI)-based approaches. A structured literature search and study-selection process was used to identify representative studies spanning major methodological developments. The review first summarizes commonly used fundus-image datasets, then organizes classical methods by principal mechanisms, including intensity and thresholding, histogram and entropy analysis, morphology, geometric and Hough-transform methods, filtering and feature operators, texture- and region-based approaches, and active-contour and level-set models. This paper pays particular attention to the assumptions, strengths, limitations, and complementary roles of these methods in OD localization and boundary delineation. Representative AI approaches are subsequently examined to illustrate the transition from handcrafted features and explicitly defined priors to learned representations, Transformer-based segmentation, boundary- and shape-aware learning, promptable segmentation, and retinal foundation models. Across these methodological generations, several core segmentation principles persist, including region-of-interest localization, multiscale representation, geometric and anatomical constraints, and boundary regularization, although their implementation has shifted from predefined operators to learned modules, losses, prompts, and pretrained representations. The review further identifies boundary ambiguity, anatomical variability, domain shift, and cross-dataset generalization as continuing challenges.
Accurate protein structure prediction is fundamental to structural biology because protein structure underlies molecular function and provides a basis for mechanistic interpretation. Recent advances in deep learning have transformed the field from multiple sequence alignment (MSA)-driven monomer folding into broader frameworks capable of modeling protein complexes and increasingly heterogeneous molecular systems. Existing reviews have summarized this progress from the perspectives of representative models, application domains, and protein design. Building on these efforts, this review focuses on the methodological evolution of the field itself. It examines recent developments through three closely related dimensions: representations and data, architectures and learning strategies, and confidence and evaluation. Within this perspective, the field is organized into four methodological phases and three cross-cutting transitions: from explicit evolutionary coupling features and early contact prediction to learned sequence representations in AlphaFold2, RoseTTAFold, and ESMFold; from protein-only monomer folding to increasingly integrated modeling of heterogeneous molecular systems in AlphaFold-Multimer, RoseTTAFoldNA, and AlphaFold3; and, more recently, from prediction-oriented structure inference to design-oriented generative modeling in RFdiffusion and related frameworks. This framework provides a clearer understanding of how methodological shifts have shaped the capabilities, limitations, and practical roles of recent models.
Computational approaches to drug discovery involve multiple sub-problems, and among them, drug-target binding affinity prediction plays an important role. Despite recent advances, accurately predicting binding affinity remains an open research area. The major objective of our paper is to perform a comprehensive review and comparative analysis of recent machine learning methods for drug-target binding affinity prediction, with a focus on identifying strengths, limitations, and research gaps. We review representative recent deep learning approaches that use common benchmark datasets and evaluation metrics, covering a range of neural network architectures and representation strategies. In addition, we analyze seven widely used benchmark datasets and commonly adopted evaluation metrics for drug-target binding affinity prediction. Our analysis indicates that although many methods report strong performance on standard benchmarks, their effectiveness is often influenced by dataset bias and limited evaluation settings. Furthermore, most methods exhibit reduced performance in cold-start scenarios, highlighting challenges in generalization. We identify several limitations of current approaches, including dataset imbalance, the lack of standardized evaluation, limited real-world applicability, and challenges in cold-start scenarios. We also discuss future research directions, including better dataset design, more robust evaluation methods, improved handling of cold-start problems, and the integration of multimodal representations.
Francesca Pia Panaccione, Eugenio Lomurno, Matteo Matteuccieess.IV cs.AI cs.CV cs.LG
Controllable generation guided by external knowledge is a key requirement in modern generative deep learning applications, enabling the synthesis of samples with explicit constraints on semantic content, structural properties, and variability. In 3D Computed Tomography (CT), such control is essential for clinical applications, including data augmentation, privacy-preserving data sharing, and the simulation of specific anatomical or pathological scenarios. While research on conditional 3D CT generation has expanded rapidly, the diversity of existing approaches makes systematic comparison difficult and obscures fundamental design choices. In this survey, we propose a conditioning-centric taxonomy that organizes the literature along three orthogonal dimensions: the type of external knowledge (K), the knowledge integration paradigm (I), and the generative architecture (A). This factorization defines an explicit design space (K x I x A) that provides a unified perspective on prior work. Using this framework, we systematize existing methods, identify dominant trends and recurring design patterns, and highlight underexplored regions of the design space that point toward promising directions for future research.
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.
In recent years, generative AI has attracted significant public attention, and its use has been rapidly expanding across a wide range of domains. From creative tasks such as text summarization, idea generation, and source code generation, to the streamlining of medical support tasks like diagnostic report generation and summarization, AI is now deeply involved in many areas. Today's breadth of AI applications is clearly distinct from what was seen before generative AI gained widespread recognition. Representative generative AI services include DALL-E 3 (OpenAI, California, USA) and Stable Diffusion (Stability AI, London, England, UK) for image generation, ChatGPT (OpenAI, California, USA), and Gemini (Google, California, USA) for text generation. The rise of generative AI has been influenced by advances in deep learning models and the scaling up of data, models, and computational resources based on the scaling laws. Moreover, the emergence of foundation models, which are trained on large-scale datasets and possess general-purpose knowledge applicable to various downstream tasks, is creating a new paradigm in AI development. These shifts brought about by generative AI and foundation models also profoundly impact medical image processing, fundamentally changing the framework for AI development in healthcare. This paper provides an overview of diffusion models used in image generation AI and large language models (LLMs) used in text generation AI, and introduces their applications in medical support. This paper also discusses foundation models, which are gaining attention alongside generative AI, including their construction methods and applications in the medical field. Finally, the paper explores how to develop foundation models and high-performance AI for medical support by fully utilizing national data and computational resources.
Zhaoyan Chen, Zhongxiu Cong, Zhuanfeng Jin +7cs.CV
Medical world models offer a framework for extending medical artificial intelligence beyond static prediction by representing evolving patient states and modelling how they change over time and in response to clinical interventions. This Review defines the conceptual boundaries, technical foundations, application domains, and evidence requirements of the field through a structured narrative synthesis with reproducible evidence mapping.We screened 1,455 unique records and assembled a corpus of 98 sources, including 14 studies that met a strict empirical definition of a medical world model. The field is organised around four capabilities: patient state representation, temporal dynamics modelling, intervention-conditioned simulation, and clinician-supervised planning. Evidence spans medical imaging, longitudinal electronic health records, treatment response modelling, physiological and multimodal state modelling, ultrasound and surgical interaction, and population and health-system simulation; clinical digital twins are treated as a cross-cutting integration framework.Current studies provide early evidence of technical feasibility for trajectory forecasting and comparison of candidate interventions, but most remain retrospective, task-specific, or preclinical. The evidence base is further limited by incomplete longitudinal intervention data, inconsistent action semantics, limited causal identifiability, long-horizon error accumulation, inadequate uncertainty estimation, and limited external validation. Clinical translation will therefore depend on precise intervention representations, robust causal and mechanistic grounding, calibrated trajectory-level uncertainty, safety-constrained planning, and prospective multicentre validation against clinically meaningful endpoints.
Color Fundus Photography (CFP) is a primary non-invasive imaging modality for large-scale screening of ophthalmic and systemic diseases. Existing surveys mainly summarize task-specific algorithms, datasets, or preprocessing techniques independently, lacking a unified perspective on their co-evolution with modern artificial intelligence. This review provides an integrated overview of CFP AI through the interplay of dataset evolution, preprocessing paradigms, and modeling frameworks. We show that CFP datasets have evolved from small single-center collections with task-specific labels to large multi-center resources featuring multimodal pairings and longitudinal clinical records. Preprocessing has progressed from conventional image enhancement to neural data-engineering pipelines, hardware-aware token optimization, and self-supervised imputation for incomplete electronic health records (EHRs). Meanwhile, modeling has advanced from convolutional neural networks (CNNs) to vision foundation models, state space models (SSMs), and multimodal expert architectures. At the multimodal frontier, CFP is increasingly integrated with EHRs and longitudinal patient information, enabling more comprehensive clinical reasoning beyond isolated image analysis. We conclude that future progress depends on the collaborative optimization of datasets, preprocessing, and multimodal modeling, providing a roadmap toward robust clinical deployment, improved cross-domain generalization, and resource-efficient edge intelligence.
Image inpainting aims to reconstruct missing or corrupted regions of an image while preserving as much as possible, visual and semantic consistency. In medical imaging, this task is particularly important because artifacts, missing information, and pathological alterations can compromise diagnostic reliability and downstream clinical applications. Recently, diffusion models have emerged as state-of-the-art generative approaches for medical image inpainting due to their ability to generate anatomically consistent reconstructions. This survey presents a systematic review of diffusion-based methods for medical image inpainting, covering the main architectures, applications, datasets, and evaluation strategies reported across 60 studies. In addition, we propose a taxonomy for diffusion-based approaches. The analysis reveals a rapid growth of research interest in diffusion-based medical image inpainting, with denoising diffusion probabilistic models and latent diffusion models emerging as the dominant architectures. The reviewed studies mainly focus on artifact removal, data augmentation, pseudo-healthy tissue reconstruction, and anomaly detection, particularly in magnetic resonance imaging and computed tomography imaging. Overall, diffusion models demonstrate strong performance in producing anatomically plausible reconstructions and aiding downstream clinical tasks. However, the review also highlights important challenges, including the lack of standardized benchmarks, limited dataset diversity, and restricted validation procedures across diverse clinical applications and imaging scenarios.
The growing ability of large language models and vision language models to jointly interpret and reason over images and text is reshaping medical agents, moving them from task specific predictors toward autonomous systems that perceive, reason, plan, remember, and act in clinical environments. This work departs from the capability first perspective of existing literature and instead begins from clinical deployment, asking what tasks, contamination resistant benchmarks, and interactive training environments are required before medical agents can be trusted in practice. Medical agents are formalized as sequential decision making systems under partial observability, together with a three level autonomy taxonomy spanning assisted, cooperative, and fully autonomous operation. The field is organized along a unified scaling spine consisting of framework scaling, capability scaling, and environment scaling. Within this framework, clinical environment scaling, the integration of tools, data, and clinical gyms, is identified as the most actionable yet underexplored direction for agents operating in PACS, EHR, and FHIR ecosystems. Clinical self evolution, where agents improve through interaction with their environments rather than parameter scaling alone, is further positioned as a key research frontier, drawing insights from self improving agents, agent gyms, and test time compute scaling. Applications across radiology, pathology, ophthalmology, and hospital workflows are examined together with deployment challenges including hallucination, cascading failures, and fairness. By consolidating more than 300 references, with particular emphasis on advances from 2025 to 2026, this work provides a roadmap toward trustworthy, self improving medical imaging systems for real clinical practice.
Large language models (LLMs) have emerged as important tools in healthcare, showing growing potential for clinical reasoning and patient care. This survey examines recent progress in medical LLMs, focusing on reasoning applications and requirements. We present a dual-view approach that connects clinical practice with computational methods. On the clinical side, we establish a five-level competency scheme following Miller's Pyramid, progressing from knowledge recall to dynamic case management. On the computational side, we link deductive, inductive, and abductive reasoning patterns to common medical goals and tasks. We also introduce a benchmark dataset spanning five levels of medical reasoning capability and report results on 18 state-of-the-art models, revealing that medical specialist models excel in diagnosis-centric tasks while general models lead in decision support and dialogue. We conclude by discussing current progress and open challenges, including data limitations, hallucination, and grounding issues, and outline directions toward safer, more reliable, and workflow-ready systems.
Medical diagnosis and treatment are dynamic processes in which patient states evolve over time and clinical interventions alter future outcomes. Although current medical AI can detect disease, estimate risk and generate reports, many systems still return static labels or scores, offering limited insight into how illness may progress or how alternative interventions may reshape its trajectory. Medical world models adapt the world-model idea from artificial intelligence to healthcare by learning internal simulators of patient-state dynamics. Their long-term goal is to help clinicians anticipate deterioration, compare treatment-conditioned futures and tailor care to individual patients. Yet relevant work remains scattered across foundation models, longitudinal modelling, disease simulation, treatment-effect estimation, reinforcement learning and digital twins. To bridge this gap, this review outlines a roadmap for advancing medical AI from isolated diagnosis and prediction toward medical world models that simulate disease evolution and support intervention decisions. This roadmap is organized around three coupled capabilities: patient-state construction, clinical dynamics modelling and intervention decision support. Across representative systems, the comparison highlights what each capability contributes and how partial components can be integrated into more mature perception--dynamics--planning systems. Finally, we identify the challenges involved in turning plausible rollouts into clinically useful simulators. Related literature is available at https://github.com/1999kevin/awesome_medical_world_models.
Medical image segmentation plays a critical role in clinical diagnostics, treatment planning, disease monitoring, and neurological disorder identification. This article presents a comprehensive review of its systematic development, covering widely used public datasets, representative methods built on the U-Net, Transformer, and SAM architectures, and key evaluation metrics with their differences, followed by an analysis of major challenges from multiple perspectives. Unlike surveys that focus on a single model family or a specific clinical application, this review organizes U-Net-, Transformer-, and SAM-based methods within a unified analytical framework, with a particular focus on their effectiveness in improving segmentation accuracy and efficiency. This work aims to guide future research and support clinical translation of medical image segmentation, with all related resources publicly available in our GitHub repository: https://github.com/andrew-pengyu/Awsome_MedSeg/tree/main.
Haniye Sherafatmandjoo, Mohammad Akbari, Zahed Rahmatics.LG
Knowledge graphs (KGs) have emerged as a promising solution for integrating and reasoning over complex biomedical and clinical data in healthcare. By representing structured relationships among entities such as diseases, drugs, symptoms, and patient records, KGs provide a semantic backbone for decision-making, prediction, recommendation, and personalized care. Recent advances have demonstrated their utility across diverse medical applications--including clinical decision support systems, disease and treatment outcome prediction, health recommender systems, precision medicine, and medical question answering--where KGs often enhance interpretability, semantic coherence, and patient-specific reasoning. In parallel, a growing body of work focuses on medical KG generation itself, proposing frameworks that construct graphs from EHRs, clinical narratives, biomedical literature, and web resources using ontologies, semantic web technologies, deep-learning-based information extraction, and hybrid neuro-symbolic pipelines. Despite this progress, significant challenges remain, including limited and fragmented knowledge coverage, difficulties in aligning heterogeneous data sources, the fragility of current reasoning and representation-learning methods on dense multi-relational graphs, and unresolved issues related to privacy, bias, and accountability. This survey reviews and categorizes current research on KGs in medicine along both application-oriented and methodology-oriented dimensions, discusses their benefits and technical foundations, and outlines key limitations and open research directions. By analyzing trends, architectures, and evaluation practices, this work aims to guide future developments in KG-driven medical AI systems and support their safe and effective integration into healthcare environments.
Recent developments in brain recording are driving a demand for machine learning tools capable of decoding the latent structure of large populations of neurons. In this paper, we provide a comprehensive survey that outlines the trajectory of Latent Variable Models (LVMs) from early state-space models to more recent deep generative models. We organize the literature into three closely related domains: (1) Single-Region Latent Dynamics, which includes models such as linear dynamical systems to more complex dynamics represented by Recurrent Neural Networks (RNNs) and Neural Ordinary Differential Equations (ODEs); (2) Multi-Region Communication, which employs probabilistic as well as subspace methods to study how information is transferred across different brain areas considering synaptic propagation delays and network connectivity; and (3) Behavior-Aligned Modeling, which seeks to disentangle neural activity related to task performance from other internal states via supervised or contrastive learning. This survey also includes large-scale neural foundation models, such as Transformers and diffusion models, that rely on large-scale pre-training for optimal performance across subjects. Finally, we conclude and discuss benchmarks, evaluation criteria, and open challenges, such as the ability to identify causal links or directionality of communication, to facilitate future research for bridging interpretable brain dynamics with reliable neural decoding.
Background: Dermatology AI has mainly focused on image-based diagnosis, while chronic disease workflows have received less attention. We surveyed Indian dermatologists to map routine clinical challenges, with a focus on atopic dermatitis (AD), and assess current AI use. Methods: A nationwide cross-sectional survey commissioned by the Society for Eczema Studies included 377 practicing Indian dermatologists. The survey assessed clinical challenges, AD workflow barriers, AI use, adoption barriers, and ethical concerns. Analyses used descriptive statistics, chi-square tests, false discovery rate correction, and multivariable logistic regression. Results: Patient adherence (61.3%) and treatment planning in difficult or refractory cases (57.0%) were reported more often than diagnostic uncertainty (48.0%). In AD care, severity scoring was reported as a challenge by 47.7% and had the lowest satisfaction among measured workflow areas. Current AI use was reported by 49.9%, most often involving general large language models for literature synthesis, documentation, and academic tasks rather than specialized image analysis. Barriers differed by experience: dermatologists with more than 20 years of practice more often cited lack of training, while those with 5 years or less more often cited lack of clinical utility after trying AI tools. AI users were more likely than non-users to report concern about patient self-misdiagnosis and anxiety, which remained significant after adjustment for experience and academic affiliation. Conclusion: Respondents reported using general-purpose AI mainly for cognitive and administrative tasks, while their clinical needs centered on chronic disease management and AD workflow support. Clinician-supervised workflow tools may be more useful than standalone diagnostic applications.
Optical Coherence Tomography (OCT) has become one of the most used imaging modality in ophthalmology. It provides high-resolution, non-invasive visualization of retinal microarchitecture. The automated analysis of OCT images through representation learning has emerged as a central research frontier. This has mainly been driven by the clinical need to process large acquisition volumes. The objective is to reduce the reliance on expert annotation, and improve diagnostic consistency across devices and populations. This survey provides a comprehensive and structured review of representation learning methods for retinal OCT image analysis. It covers the period from early deep learning approaches to the most recent developments in foundation models and vision-language systems. We organize the literature along a principled taxonomy of learning paradigms, encompassing supervised learning with CNN-based and transformer-based architectures, self-supervised and semi-supervised methods, generative approaches, as well as 3D volumetric modeling, multimodal representation learning, and large-scale pretrained foundation models. For each paradigm, we analyze the core methodological contributions, identify persistent limitations, and trace the connections between successive approaches. We further provide a structured overview of publicly available OCT datasets, discuss evaluation protocol considerations, and present a unified problem formulation that situates each learning paradigm within a common mathematical framework. Building on this analysis, we identify and discuss the most pressing open research directions emerging in the literature. This includes volumetric foundation model pretraining, uncertainty-aware representation learning, federated and privacy-preserving training, fairness and bias mitigation, concept-based interpretability,...