This paper reviews state-of-the-art research solutions across the spectrum of medical imaging informatics, discusses clinical translation, and provides future directions for advancing clinical practice. More specifically, it summarizes advances in medical imaging acquisition technologies for different modalities, highlighting the necessity for efficient medical data management strategies in the context of AI in big healthcare data analytics. It then provides a synopsis of contemporary and emerging algorithmic methods for disease classification and organ/ tissue segmentation, focusing on AI and deep learning architectures that have already become the de facto approach. The clinical benefits of in-silico modelling advances linked with evolving 3D reconstruction and visualization applications are further documented. Concluding, integrative analytics approaches driven by associate research branches highlighted in this study promise to revolutionize imaging informatics as known today across the healthcare continuum for both radiology and digital pathology applications. The latter, is projected to enable informed, more accurate diagnosis, timely prognosis, and effective treatment planning, underpinning precision medicine.
Large language models (LLMs) have rapidly become important tools in Biomedical and Health Informatics (BHI), potentially enabling new ways to analyze data, treat patients, and conduct research. This study aims to provide a comprehensive overview of LLM applications in BHI, highlighting their transformative potential and addressing the associated ethical and practical challenges. We reviewed 1698 research articles from January 2022 to December 2023, categorizing them by research themes and diagnostic categories. Additionally, we conducted network analysis to map scholarly collaborations and research dynamics. Our findings reveal a substantial increase in the potential applications of LLMs to a variety of BHI tasks, including clinical decision support, patient interaction, and medical document analysis. Notably, LLMs are expected to be instrumental in enhancing the accuracy of diagnostic tools and patient care protocols. The network analysis highlights dense and dynamically evolving collaborations across institutions, underscoring the interdisciplinary nature of LLM research in BHI. A significant trend was the application of LLMs in managing specific disease categories, such as mental health and neurological disorders, demonstrating their potential to influence personalized medicine and public health strategies. LLMs hold promising potential to further transform biomedical research and healthcare delivery. While promising, the ethical implications and challenges of model validation call for rigorous scrutiny to optimize their benefits in clinical settings. This survey serves as a resource for stakeholders in healthcare, including researchers, clinicians, and policymakers, to understand the current state and future potential of LLMs in BHI.
Monika Ludlova, Kateřina Koudelková, Jitka Pallova
et al.
BackgroundWeight loss is a cornerstone of obesity treatment and diabetes mellitus type 2 (T2D) prevention, but its implementation in clinical practice is limited by its perceived burden and variability in response. Personalizing interventions to increase their success rate is an unmet clinical need.
ObjectiveIdentification of predictive factors associated with successful weight loss after sequential exercise in women with obesity.
MethodsThe study will consist of a 2-stage analytical approach, including a predictive validation study and a 2:1 randomized cross-over controlled trial. Women aged 25-45 years with obesity (BMI>30) will be included in the study. The intervention will consist of a progressive protocol of aerobic exercise on a treadmill and a bicycle ergometer. We will measure weight loss in terms of fat mass (FM) and fat-free mass (FFM), metabolic flexibility (MetFlex) as ΔRQ (change in respiratory quotient (VCO2/VO2) between basal and insulin-stimulated state during glucose clamp), insulin sensitivity, glucose tolerance, hemoglobin A1c, microbiome composition, and metabolomic signatures.
ResultsRecruitment for the trial began in January 2024. A total of 12 participants were enrolled and randomized. Among them 6 participants have completed the first phase of the A-arm and 6 participants have completed the control period of the B-arm and their intervention is ongoing. Recruitment is ongoing. We expect the preliminary data from this study to be completed in 2026.
ConclusionsThis intervention will investigate whether whole body and gut MetFlex can be further explored and used as ex ante predictors of successful weight loss following exercise intervention, providing proof of concept and paving the way for personalized lifestyle interventions.
Trial RegistrationClinicalTrials.gov NCT06329349; https://clinicaltrials.gov/study/NCT06329349
International Registered Report Identifier (IRRID)DERR1-10.2196/67570
Medicine, Computer applications to medicine. Medical informatics
Milena Engelke, Jorge Piano Simões, Laura Basso
et al.
Abstract Intensive longitudinal sampling enhances subjective data collection by capturing real-time, dynamic inputs in natural settings, complementing traditional methods. This study evaluates the feasibility of using daily self-reported app data to assess clinical improvement among tinnitus patients undergoing treatment. App data from a multi-center randomized clinical trial were analysed using time-series feature extraction and nested cross-validated ordinal regression with elastic net regulation to predict clinical improvement based on the Clinical Global Impression—Improvement scale (CGI-I). With 50% app compliance (N = 129, 8480 entries), the model demonstrated good fit to the test data (McFadden R2 = 0.82) suggesting its generalizability. Clinical improvement was associated with linear declines in tinnitus-related thoughts, jaw tension, tinnitus loudness, increases in happiness, and variability changes in tinnitus loudness and distress. These findings suggest that daily self-reported data on tinnitus symptoms is sensitive to treatment response and provides insights into specific symptom changes that occur during treatment.
Computer applications to medicine. Medical informatics
Abstract
BackgroundArtificial intelligence (AI) algorithms offer an effective solution to alleviate the burden of diabetic retinopathy (DR) screening in public health settings. However, there are challenges in translating diagnostic performance and its application when deployed in real-world conditions.
ObjectiveThis study aimed to assess the technical feasibility of integration and diagnostic performance of validated DR screening (DRS) AI algorithms in real-world outpatient public health settings.
MethodsPrior to integrating an AI algorithm for DR screening, the study involved several steps: (1) Five AI companies, including four from India and one international company, were invited to evaluate their diagnostic performance using low-cost nonmydriatic fundus cameras in public health settings; (2) The AI algorithms were prospectively validated on fundus images from 250 people with diabetes mellitus, captured by a trained optometrist in public health settings in Chandigarh Tricity in North India. The performance evaluation used diagnostic metrics, including sensitivity, specificity, and accuracy, compared to human grader assessments; (3) The AI algorithm with better diagnostic performance was integrated into a low-cost screening camera deployed at a community health center (CHC) in the Moga district of Punjab, India. For AI algorithm analysis, a trained health system optometrist captured nonmydriatic images of 343 patients.
ResultsThree web-based AI screening companies agreed to participate, while one declined and one chose to withdraw due to low specificity identified during the interim analysis. The three AI algorithms demonstrated variable diagnostic performance, with sensitivity (60%-80%) and specificity (14%-96%). Upon integration, the better-performing algorithm AI-3 (sensitivity: 68%, specificity: 96, and accuracy: 88·43%) demonstrated high sensitivity of image gradability (99.5%), DR detection (99.6%), and referral DR (79%) at the CHC.
ConclusionsThis study highlights the importance of systematic AI validation for responsible clinical integration, demonstrating the potential of DRS to improve health care access in resource-limited public health settings.
Computer applications to medicine. Medical informatics
Medical image segmentation is a pivotal task within the realms of medical image analysis and computer vision. While current methods have shown promise in accurately segmenting major regions of interest, the precise segmentation of boundary areas remains challenging. In this study, we propose a novel network architecture named CTO, which combines Convolutional Neural Networks (CNNs), Vision Transformer (ViT) models, and explicit edge detection operators to tackle this challenge. CTO surpasses existing methods in terms of segmentation accuracy and strikes a better balance between accuracy and efficiency, without the need for additional data inputs or label injections. Specifically, CTO adheres to the canonical encoder-decoder network paradigm, with a dual-stream encoder network comprising a mainstream CNN stream for capturing local features and an auxiliary StitchViT stream for integrating long-range dependencies. Furthermore, to enhance the model's ability to learn boundary areas, we introduce a boundary-guided decoder network that employs binary boundary masks generated by dedicated edge detection operators to provide explicit guidance during the decoding process. We validate the performance of CTO through extensive experiments conducted on seven challenging medical image segmentation datasets, namely ISIC 2016, PH2, ISIC 2018, CoNIC, LiTS17, and BTCV. Our experimental results unequivocally demonstrate that CTO achieves state-of-the-art accuracy on these datasets while maintaining competitive model complexity. The codes have been released at: https://github.com/xiaofang007/CTO.
We propose two novel loss functions, Multiplicative Loss and Confidence-Adaptive Multiplicative Loss, for semantic segmentation in medical and cellular images. Although Cross Entropy and Dice Loss are widely used, their additive combination is sensitive to hyperparameters and often performs suboptimally, especially with limited data. Medical images suffer from data scarcity due to privacy, ethics, and costly annotations, requiring robust and efficient training objectives. Our Multiplicative Loss combines Cross Entropy and Dice losses multiplicatively, dynamically modulating gradients based on prediction confidence. This reduces penalties for confident correct predictions and amplifies gradients for incorrect overconfident ones, stabilizing optimization. Building on this, Confidence-Adaptive Multiplicative Loss applies a confidence-driven exponential scaling inspired by Focal Loss, integrating predicted probabilities and Dice coefficients to emphasize difficult samples. This enhances learning under extreme data scarcity by strengthening gradients when confidence is low. Experiments on cellular and medical segmentation benchmarks show our framework consistently outperforms tuned additive and existing loss functions, offering a simple, effective, and hyperparameter-free mechanism for robust segmentation under challenging data limitations.
Paul Zaha, Lars Böcking, Simeon Allmendinger
et al.
Medical image segmentation is crucial for disease diagnosis and treatment planning, yet developing robust segmentation models often requires substantial computational resources and large datasets. Existing research shows that pre-trained and finetuned foundation models can boost segmentation performance. However, questions remain about how particular image preprocessing steps may influence segmentation performance across different medical imaging modalities. In particular, edges-abrupt transitions in pixel intensity-are widely acknowledged as vital cues for object boundaries but have not been systematically examined in the pre-training of foundation models. We address this gap by investigating to which extend pre-training with data processed using computationally efficient edge kernels, such as kirsch, can improve cross-modality segmentation capabilities of a foundation model. Two versions of a foundation model are first trained on either raw or edge-enhanced data across multiple medical imaging modalities, then finetuned on selected raw subsets tailored to specific medical modalities. After systematic investigation using the medical domains Dermoscopy, Fundus, Mammography, Microscopy, OCT, US, and XRay, we discover both increased and reduced segmentation performance across modalities using edge-focused pre-training, indicating the need for a selective application of this approach. To guide such selective applications, we propose a meta-learning strategy. It uses standard deviation and image entropy of the raw image to choose between a model pre-trained on edge-enhanced or on raw data for optimal performance. Our experiments show that integrating this meta-learning layer yields an overall segmentation performance improvement across diverse medical imaging tasks by 16.42% compared to models pre-trained on edge-enhanced data only and 19.30% compared to models pre-trained on raw data only.
The pursuit of groundbreaking health care innovations has led to the convergence of artificial intelligence (AI) and traditional Chinese medicine (TCM), thus marking a new frontier that demonstrates the promise of combining the advantages of ancient healing practices with cutting-edge advancements in modern technology. TCM, which is a holistic medical system with >2000 years of empirical support, uses unique diagnostic methods such as inspection, auscultation and olfaction, inquiry, and palpation. AI is the simulation of human intelligence processes by machines, especially via computer systems. TCM is experience oriented, holistic, and subjective, and its combination with AI has beneficial effects, which presumably arises from the perspectives of diagnostic accuracy, treatment efficacy, and prognostic veracity. The role of AI in TCM is highlighted by its use in diagnostics, with machine learning enhancing the precision of treatment through complex pattern recognition. This is exemplified by the greater accuracy of TCM syndrome differentiation via tongue images that are analyzed by AI. However, integrating AI into TCM also presents multifaceted challenges, such as data quality and ethical issues; thus, a unified strategy, such as the use of standardized data sets, is required to improve AI understanding and application of TCM principles. The evolution of TCM through the integration of AI is a key factor for elucidating new horizons in health care. As research continues to evolve, it is imperative that technologists and TCM practitioners collaborate to drive innovative solutions that push the boundaries of medical science and honor the profound legacy of TCM. We can chart a future course wherein AI-augmented TCM practices contribute to more systematic, effective, and accessible health care systems for all individuals.
Biomedical informatics can be considered as a multidisciplinary research and educational field situated at the intersection of computational sciences (including computer science, data science, mathematics, and statistics), biology, and medicine. In recent years, there have been advances in the field of biomedical informatics. The current article highlights some interesting state-of-the-art research outcomes in these fields. These include research outcomes in areas like (i) computational biology and medicine, (ii) explainable artificial intelligence (XAI) in biomedical research and clinical practice, (iii) machine learning (including deep learning) methods and application for bioinformatics and healthcare, (iv) imaging informatics, as well as (v) medical statistics and data science. Moreover, the current article also discusses some existing challenges and potential future directions for these research areas to advance the fields of biomedical informatics.
Lubomir M. Hadjiiski, Kenny H. Cha, H. Chan
et al.
Rapid advances in artificial intelligence (AI) and machine learning, and specifically in deep learning (DL) techniques, have enabled broad application of these methods in health care. The promise of the DL approach has spurred further interest in computer-aided diagnosis (CAD) development and applications using both "traditional" machine learning methods and newer DL-based methods. We use the term CAD-AI to refer to this expanded clinical decision support environment that uses traditional and DL-based AI methods. Numerous studies have been published to date on the development of machine learning tools for computer-aided, or AI-assisted, clinical tasks. However, most of these machine learning models are not ready for clinical deployment. It is of paramount importance to ensure that a clinical decision support tool undergoes proper training and rigorous validation of its generalizability and robustness before adoption for patient care in the clinic. To address these important issues, the American Association of Physicists in Medicine (AAPM) Computer-Aided Image Analysis Subcommittee (CADSC) is charged, in part, to develop recommendations on practices and standards for the development and performance assessment of computer-aided decision support systems. The committee has previously published two opinion papers on the evaluation of CAD systems and issues associated with user training and quality assurance of these systems in the clinic. With machine learning techniques continuing to evolve and CAD applications expanding to new stages of the patient care process, the current task group report considers the broader issues common to the development of most, if not all, CAD-AI applications and their translation from the bench to the clinic. The goal is to bring attention to the proper training and validation of machine learning algorithms that may improve their generalizability and reliability and accelerate the adoption of CAD-AI systems for clinical decision support.
Kim Nordmann, Stefanie Sauter, Marie-Christin Redlich
et al.
Background Germany's healthcare system provides high-quality, universal health coverage to almost all residents. However, a major challenge lies in the strong separation of healthcare structures, which hinders efficient interprofessional and intersectoral communication and collaboration. The mandatory nationwide implementation of the telematics infrastructure may offer a solution to enhance healthcare professionals’ communication and collaboration. Objective Our study aims to elicit participants’ perceptions of and attitudes towards the implementation and usage of the telematics infrastructure in fostering interprofessional communication and collaboration between home-care nursing services and general practitioner practices. Methods We conducted interviews with seven members of general practitioner practices and 10 in home-care nursing services. Using thematic content analysis, we identified five themes, of which four along with 10 subthemes were integrated into Greenhalgh et al.'s ‘nonadoption, abandonment, scale-up, spread and sustainability’ framework. Results Participants recognised the potential of digital technology to enhance interprofessional communication and collaboration. However, this potential largely depended on individual healthcare actors’ willingness to seek information, invest and adapt. Attitudes towards the telematics infrastructure varied widely from hopeful confidence to outright rejection. Home-care nursing services generally viewed the telematics infrastructure with optimism, while general practitioners expressed reservations, particularly due to technological disruptions, lack of user-friendliness, and organisational structures. Conclusion Our findings highlight the potential of digital technology to enhance interprofessional communication. Successful implementation of technological innovations, however, goes beyond technological aspects and involves social, political and organisational processes. Future implementation strategies for such innovations in healthcare should involve users early and ensure clear communication.
Computer applications to medicine. Medical informatics
Anomaly detection (AD) aims at detecting abnormal samples that deviate from the expected normal patterns. Generally, it can be trained merely on normal data, without a requirement for abnormal samples, and thereby plays an important role in rare disease recognition and health screening in the medical domain. Despite the emergence of numerous methods for medical AD, the lack of a fair and comprehensive evaluation causes ambiguous conclusions and hinders the development of this field. To address this problem, this paper builds a benchmark with unified comparison. Seven medical datasets with five image modalities, including chest X-rays, brain MRIs, retinal fundus images, dermatoscopic images, and histopathology images, are curated for extensive evaluation. Thirty typical AD methods, including reconstruction and self-supervised learning-based methods, are involved in comparison of image-level anomaly classification and pixel-level anomaly segmentation. Furthermore, for the first time, we systematically investigate the effect of key components in existing methods, revealing unresolved challenges and potential future directions. The datasets and code are available at https://github.com/caiyu6666/MedIAnomaly.
AI is the workhorse of modern data analytics and omnipresent across many sectors. Large Language Models and multi-modal foundation models are today capable of generating code, charts, visualizations, etc. How will these massive developments of AI in data analytics shape future data visualizations and visual analytics workflows? What is the potential of AI to reshape methodology and design of future visual analytics applications? What will be our role as visualization researchers in the future? What are opportunities, open challenges and threats in the context of an increasingly powerful AI? This Visualization Viewpoint discusses these questions in the special context of biomedical data analytics as an example of a domain in which critical decisions are taken based on complex and sensitive data, with high requirements on transparency, efficiency, and reliability. We map recent trends and developments in AI on the elements of interactive visualization and visual analytics workflows and highlight the potential of AI to transform biomedical visualization as a research field. Given that agency and responsibility have to remain with human experts, we argue that it is helpful to keep the focus on human-centered workflows, and to use visual analytics as a tool for integrating ``AI-in-the-loop''. This is in contrast to the more traditional term ``human-in-the-loop'', which focuses on incorporating human expertise into AI-based systems.
Segment Anything Model (SAM) has gained significant attention because of its ability to segment various objects in images given a prompt. The recently developed SAM 2 has extended this ability to video inputs. This opens an opportunity to apply SAM to 3D images, one of the fundamental tasks in the medical imaging field. In this paper, we extensively evaluate SAM 2's ability to segment both 2D and 3D medical images by first collecting 21 medical imaging datasets, including surgical videos, common 3D modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) as well as 2D modalities such as X-ray and ultrasound. Two evaluation settings of SAM 2 are considered: (1) multi-frame 3D segmentation, where prompts are provided to one or multiple slice(s) selected from the volume, and (2) single-frame 2D segmentation, where prompts are provided to each slice. The former only applies to videos and 3D modalities, while the latter applies to all datasets. Our results show that SAM 2 exhibits similar performance as SAM under single-frame 2D segmentation, and has variable performance under multi-frame 3D segmentation depending on the choices of slices to annotate, the direction of the propagation, the predictions utilized during the propagation, etc. We believe our work enhances the understanding of SAM 2's behavior in the medical field and provides directions for future work in adapting SAM 2 to this domain. Our code is available at: https://github.com/mazurowski-lab/segment-anything2-medical-evaluation.
Research in neural models inspired by mammal's visual cortex has led to many spiking neural networks such as pulse-coupled neural networks (PCNNs). These models are oscillating, spatio-temporal models stimulated with images to produce several time-based responses. This paper reviews PCNN's state of the art, covering its mathematical formulation, variants, and other simplifications found in the literature. We present several applications in which PCNN architectures have successfully addressed some fundamental image processing and computer vision challenges, including image segmentation, edge detection, medical imaging, image fusion, image compression, object recognition, and remote sensing. Results achieved in these applications suggest that the PCNN architecture generates useful perceptual information relevant to a wide variety of computer vision tasks.
Alireza Sadeghi Milani, Aaron Cecil-Xavier, Avinash Gupta
et al.
Abstract This article provides a systematic review of research related to Human–Computer Interaction techniques supporting training and learning in various domains including medicine, healthcare, and engineering. The focus is on HCI techniques involving Extended Reality (XR) technology which encompasses Virtual Reality, Augmented Reality, and Mixed Reality. HCI-based research is assuming more importance with the rapid adoption of XR tools and techniques in various training and learning contexts including education. There are many challenges in the adoption of HCI approaches, which results in a need to have a comprehensive and systematic review of such HCI methods in various domains. This article addresses this need by providing a systematic literature review of a cross-section of HCI approaches involving proposed so far. The PRISMA-guided search strategy identified 1156 articles for abstract review. Irrelevant abstracts were discarded. The whole body of each article was reviewed for the remaining articles, and those that were not linked to the scope of our specific issue were also eliminated. Following the application of inclusion/exclusion criteria, 69 publications were chosen for review. This article has been divided into the following sections: Introduction; Research methodology; Literature review; Threats of validity; Future research and Conclusion. Detailed classifications (pertaining to HCI criteria and concepts, such as affordance; training, and learning techniques) have also been included based on different parameters based on the analysis of research techniques adopted by various investigators. The article concludes with a discussion of the key challenges for this HCI area along with future research directions. A review of the research outcomes from these publications underscores the potential for greater success when such HCI-based approaches are adopted during such 3D-based training interactions. Such a higher degree of success may be due to the emphasis on the design of user-friendly (and user-centric) training environments, interactions, and processes that positively impact the cognitive abilities of users and their respective learning/training experiences. We discovered data validating XR-HCI as an ascending method that brings a new paradigm by enhancing skills and safety while reducing costs and learning time through replies to three exploratory study questions. We believe that the findings of this study will aid academics in developing new research avenues that will assist XR-HCI applications to mature and become more widely adopted.
Abstract Background Liquid chromatography–mass spectrometry is widely used in untargeted metabolomics for composition profiling. In multi-run analysis scenarios, features of each run are aligned into consensus features by feature alignment algorithms to observe the intensity variations across runs. However, most of the existing feature alignment methods focus more on accurate retention time correction, while underestimating the importance of feature matching. None of the existing methods can comprehensively consider feature correspondences among all runs and achieve optimal matching. Results To comprehensively analyze feature correspondences among runs, we propose G-Aligner, a graph-based feature alignment method for untargeted LC–MS data. In the feature matching stage, G-Aligner treats features and potential correspondences as nodes and edges in a multipartite graph, considers the multi-run feature matching problem an unbalanced multidimensional assignment problem, and provides three combinatorial optimization algorithms to find optimal matching solutions. In comparison with the feature alignment methods in OpenMS, MZmine2 and XCMS on three public metabolomics benchmark datasets, G-Aligner achieved the best feature alignment performance on all the three datasets with up to 9.8% and 26.6% increase in accurately aligned features and analytes, and helped all comparison software obtain more accurate results on their self-extracted features by integrating G-Aligner to their analysis workflow. G-Aligner is open-source and freely available at https://github.com/CSi-Studio/G-Aligner under a permissive license. Benchmark datasets, manual annotation results, evaluation methods and results are available at https://doi.org/10.5281/zenodo.8313034 Conclusions In this study, we proposed G-Aligner to improve feature matching accuracy for untargeted metabolomics LC–MS data. G-Aligner comprehensively considered potential feature correspondences between all runs, converting the feature matching problem as a multidimensional assignment problem (MAP). In evaluations on three public metabolomics benchmark datasets, G-Aligner achieved the highest alignment accuracy on manual annotated and popular software extracted features, proving the effectiveness and robustness of the algorithm.
Computer applications to medicine. Medical informatics, Biology (General)
Angona Biswas, MD Abdullah Al Nasim, Md Shahin Ali
et al.
The development of medical science greatly depends on the increased utilization of machine learning algorithms. By incorporating machine learning, the medical imaging field can significantly improve in terms of the speed and accuracy of the diagnostic process. Computed tomography (CT), magnetic resonance imaging (MRI), X-ray imaging, ultrasound imaging, and positron emission tomography (PET) are the most commonly used types of imaging data in the diagnosis process, and machine learning can aid in detecting diseases at an early stage. However, training machine learning models with limited annotated medical image data poses a challenge. The majority of medical image datasets have limited data, which can impede the pattern-learning process of machine-learning algorithms. Additionally, the lack of labeled data is another critical issue for machine learning. In this context, active learning techniques can be employed to address the challenge of limited annotated medical image data. Active learning involves iteratively selecting the most informative samples from a large pool of unlabeled data for annotation by experts. By actively selecting the most relevant and informative samples, active learning reduces the reliance on large amounts of labeled data and maximizes the model's learning capacity with minimal human labeling effort. By incorporating active learning into the training process, medical imaging machine learning models can make more efficient use of the available labeled data, improving their accuracy and performance. This approach allows medical professionals to focus their efforts on annotating the most critical cases, while the machine learning model actively learns from these annotated samples to improve its diagnostic capabilities.