The rapidly increasing volume of electronic health record (EHR) data underscores a pressing need to unlock biomedical knowledge from unstructured clinical texts to support advancements in data-driven clinical systems, including patient diagnosis, disease progression monitoring, treatment effects assessment, prediction of future clinical events, etc. While contextualized language models have demonstrated impressive performance improvements for named entity recognition (NER) systems in English corpora, there remains a scarcity of research focused on clinical texts in low-resource languages. To bridge this gap, our study aims to develop multiple deep contextual embedding models to enhance clinical NER in the cardiology domain, as part of the BioASQ MultiCardioNER shared task. We explore the effectiveness of different monolingual and multilingual BERT-based models, trained on general domain text, for extracting disease and medication mentions from clinical case reports written in English, Spanish, and Italian. We achieved an F1-score of 77.88% on Spanish Diseases Recognition (SDR), 92.09% on Spanish Medications Recognition (SMR), 91.74% on English Medications Recognition (EMR), and 88.
Coronary Artery Disease (CAD) remains a leading cause of morbidity and mortality worldwide. Early detection is critical to recover patient outcomes and decrease healthcare costs. In recent years, machine learning (ML) advancements have shown significant potential in enhancing the accuracy of CAD diagnosis. This study investigates the application of ML algorithms to improve the detection of CAD by analyzing patient data, including clinical features, imaging, and biomarker profiles. Bi-directional Long Short-Term Memory (Bi-LSTM), Gated Recurrent Units (GRU), and a hybrid of Bi-LSTM+GRU were trained on large datasets to predict the presence of CAD. Results demonstrated that these ML models outperformed traditional diagnostic methods in sensitivity and specificity, offering a robust tool for clinicians to make more informed decisions. The experimental results show that the hybrid model achieved an accuracy of 97.07%. By integrating advanced data preprocessing techniques and feature selection, this study ensures optimal learning and model performance, setting a benchmark for the application of ML in CAD diagnosis. The integration of ML into CAD detection presents a promising avenue for
Rankings of scholarly journals based on citation data are often met with skepticism by the scientific community. Part of the skepticism is due to disparity between the common perception of journals' prestige and their ranking based on citation counts. A more serious concern is the inappropriate use of journal rankings to evaluate the scientific influence of authors. This paper focuses on analysis of the table of cross-citations among a selection of Statistics journals. Data are collected from the Web of Science database published by Thomson Reuters. Our results suggest that modelling the exchange of citations between journals is useful to highlight the most prestigious journals, but also that journal citation data are characterized by considerable heterogeneity, which needs to be properly summarized. Inferential conclusions require care in order to avoid potential over-interpretation of insignificant differences between journal ratings. Comparison with published ratings of institutions from the UK's Research Assessment Exercise shows strong correlation at aggregate level between assessed research quality and journal citation `export scores' within the discipline of Statistics.
Detecting duplicate patient participation in clinical trials is a major challenge because repeated patients can undermine the credibility and accuracy of the trial's findings and result in significant health and financial risks. Developing accurate automated speaker verification (ASV) models is crucial to verify the identity of enrolled individuals and remove duplicates, but the size and quality of data influence ASV performance. However, there has been limited investigation into the factors that can affect ASV capabilities in clinical environments. In this paper, we bridge the gap by conducting analysis of how participant demographic characteristics, audio quality criteria, and severity level of Alzheimer's disease (AD) impact the performance of ASV utilizing a dataset of speech recordings from 659 participants with varying levels of AD, obtained through multiple speech tasks. Our results indicate that ASV performance: 1) is slightly better on male speakers than on female speakers; 2) degrades for individuals who are above 70 years old; 3) is comparatively better for non-native English speakers than for native English speakers; 4) is negatively affected by clinician interference,
Neuromuscular diseases (NMDs) cause a significant burden for both healthcare systems and society. They can lead to severe progressive muscle weakness, muscle degeneration, contracture, deformity and progressive disability. The NMDs evaluated in this study often manifest in early childhood. As subtypes of disease, e.g. Duchenne Muscular Dystropy (DMD) and Spinal Muscular Atrophy (SMA), are difficult to differentiate at the beginning and worsen quickly, fast and reliable differential diagnosis is crucial. Photoacoustic and ultrasound imaging has shown great potential to visualize and quantify the extent of different diseases. The addition of automatic classification of such image data could further improve standard diagnostic procedures. We compare deep learning-based 2-class and 3-class classifiers based on VGG16 for differentiating healthy from diseased muscular tissue. This work shows promising results with high accuracies above 0.86 for the 3-class problem and can be used as a proof of concept for future approaches for earlier diagnosis and therapeutic monitoring of NMDs.
Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity.
Dermatological conditions affect 1.9 billion people globally, yet accurate diagnosis remains challenging due to limited specialist availability and complex clinical presentations. Family history significantly influences skin disease susceptibility and treatment responses, but is often underutilized in diagnostic processes. This research addresses the critical question: How can AI-powered systems integrate family history data with clinical imaging to enhance dermatological diagnosis while supporting clinical trial validation and real-world implementation? We developed a comprehensive multi-modal AI framework that combines deep learning-based image analysis with structured clinical data, including detailed family history patterns. Our approach employs interpretable convolutional neural networks integrated with clinical decision trees that incorporate hereditary risk factors. The methodology includes prospective clinical trials across diverse healthcare settings to validate AI-assisted diagnosis against traditional clinical assessment. In this work, validation was conducted with healthcare professionals to assess AI-assisted outputs against clinical expectations; prospective clinical
Background Chronic kidney disease (CKD) induces muscle wasting and a reduction in the maximum voluntary force (MVF). Little is known about the neuromuscular fatigability in CKD patients, defined as the reduction of muscle force capacities during exercise. Neuromuscular fatigability is a crucial physical parameter of the daily living. The quantification of explosive force has been shown to be a sensitive means to assess neuromuscular fatigability. Thus, our study used explosive force estimates to assess neuromuscular fatigability in elderly CKD patients. Methods Inclusion criteria for CKD patients were age $\ge$ 60 years old and glomerular filtration rate (GFR) < 45 mL/ min/1.73 m 2 not on dialysis, and those for controls were GFR > 60 mL/min/1.73 m 2 , age and diabetes matched. The fatigability protocol focused on a handgrip task coupled with surface electromyography (sEMG). Scalars were extracted from the rate of force development (RFD): absolute and normalized time periods (50, 75, 100, 150 and 200 ms, RFD 50 , RFD 75 , RFD 100 , RFD 150 and RFD 200 , respectively), peak RFD (RFD peak in absolute; NRFD peak normalized), timeto-peak RFD (t-RFD peak) and the relative force at
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.
Alzheimer's disease (AD) is a prominent, worldwide, age-related neurodegenerative disease that currently has no systemic treatment. Strong evidence suggests that permeable amyloid-beta peptide (Abeta) oligomers, astrogliosis and reactive astrocytosis cause neuronal damage in AD. A large amount of Abeta is secreted by astrocytes, which contributes to the total Abeta deposition in the brain. This suggests that astrocytes may also play a role in AD, leading to increased attention to their dynamics and associated mechanisms. Therefore, in the present study, we developed and evaluated novel stochastic models for Abeta growth using ADNI data to predict the effect of astrocytes on AD progression in a clinical trial. In the AD case, accurate prediction is required for a successful clinical treatment plan. Given that AD studies are observational in nature and involve routine patient visits, stochastic models provide a suitable framework for modelling AD. Using the approximate Bayesian computation (ABC) approach, the AD etiology may be modelled as a multi-state disease process. As a result, we use this approach to examine the weak and strong influence of astrocytes at multiple disease progre
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
The ability to predict the future trajectory of a patient is a key step toward the development of therapeutics for complex diseases such as Alzheimer's disease (AD). However, most machine learning approaches developed for prediction of disease progression are either single-task or single-modality models, which can not be directly adopted to our setting involving multi-task learning with high dimensional images. Moreover, most of those approaches are trained on a single dataset (i.e. cohort), which can not be generalized to other cohorts. We propose a novel multimodal multi-task deep learning model to predict AD progression by analyzing longitudinal clinical and neuroimaging data from multiple cohorts. Our proposed model integrates high dimensional MRI features from a 3D convolutional neural network with other data modalities, including clinical and demographic information, to predict the future trajectory of patients. Our model employs an adversarial loss to alleviate the study-specific imaging bias, in particular the inter-study domain shifts. In addition, a Sharpness-Aware Minimization (SAM) optimization technique is applied to further improve model generalization. The proposed m
Using the Scopus dataset (1996-2007) a grand matrix of aggregated journal-journal citations was constructed. This matrix can be compared in terms of the network structures with the matrix contained in the Journal Citation Reports (JCR) of the Institute of Scientific Information (ISI). Since the Scopus database contains a larger number of journals and covers also the humanities, one would expect richer maps. However, the matrix is in this case sparser than in the case of the ISI data. This is due to (i) the larger number of journals covered by Scopus and (ii) the historical record of citations older than ten years contained in the ISI database. When the data is highly structured, as in the case of large journals, the maps are comparable, although one may have to vary a threshold (because of the differences in densities). In the case of interdisciplinary journals and journals in the social sciences and humanities, the new database does not add a lot to what is possible with the ISI databases.
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
Progressive cognitive decline spanning across decades is characteristic of Alzheimer's disease (AD). Various predictive models have been designed to realize its early onset and study the long-term trajectories of cognitive test scores across populations of interest. Research efforts have been geared towards superimposing patients' cognitive test scores with the long-term trajectory denoting gradual cognitive decline, while considering the heterogeneity of AD. Multiple trajectories representing cognitive assessment for the long-term have been developed based on various parameters, highlighting the importance of classifying several groups based on disease progression patterns. In this study, a novel method capable of self-organized prediction, classification, and the overlay of long-term cognitive trajectories based on short-term individual data was developed, based on statistical and differential equation modeling. We validated the predictive accuracy of the proposed method for the long-term trajectory of cognitive test score results on two cohorts: the Alzheimer's Disease Neuroimaging Initiative (ADNI) study and the Japanese ADNI study. We also presented two practical illustrations
Modelling the progression of Degenerative Diseases (DD) is essential for detection, prevention, and treatment, yet it remains challenging due to the heterogeneity in disease trajectories among individuals. Factors such as demographics, genetic conditions, and lifestyle contribute to diverse phenotypical manifestations, necessitating patient stratification based on these variations. Recent methods like Subtype and Stage Inference (SuStaIn) have advanced unsupervised stratification of disease trajectories, but they face potential limitations in robustness, interpretability, and temporal granularity. To address these challenges, we introduce Disease Progression Modelling and Stratification (DP-MoSt), a novel probabilistic method that optimises clusters of continuous trajectories over a long-term disease time-axis while estimating the confidence of trajectory sub-types for each biomarker. We validate DP-MoSt using both synthetic and real-world data from the Parkinson's Progression Markers Initiative (PPMI). Our results demonstrate that DP-MoSt effectively identifies both sub-trajectories and subpopulations, and is a promising alternative to current state-of-the-art models.
A number of journal classification systems have been developed in bibliometrics since the launch of the Citation Indices by the Institute of Scientific Information (ISI) in the 1960s. These systems are used to normalize citation counts with respect to field-specific citation patterns. The best known system is the so-called "Web-of-Science Subject Categories" (WCs). In other systems papers are classified by algorithmic solutions. Using the Journal Citation Reports 2014 of the Science Citation Index and the Social Science Citation Index (n of journals = 11,149), we examine options for developing a new system based on journal classifications into subject categories using aggregated journal-journal citation data. Combining routines in VOSviewer and Pajek, a tree-like classification is developed. At each level one can generate a map of science for all the journals subsumed under a category. Nine major fields are distinguished at the top level. Further decomposition of the social sciences is pursued for the sake of example with a focus on journals in information science (LIS) and science studies (STS). The new classification system improves on alternative options by avoiding the problem
Estimating brain age (BA) from T1-weighted magnetic resonance images (MRIs) provides a powerful framework for quantifying anatomical brain aging. Whereas global BA (GBA) summarizes overall brain health, local BA (LBA) provides cortically specific patterns of aging at the subject level. Although previous studies have examined anatomical contributors to GBA, to our knowledge, no framework has been established to estimate LBA using cortical morphology. To address this gap, we introduce a graph neural network (GNN) that uses morphometric features$\unicode{x2013}$cortical thickness, surface area, curvature, gray/white matter intensity ratio (GWR), sulcal depth$\unicode{x2013}$to estimate LBA across the cortical surface at high spatial resolution (mean inter-vertex distance = 1.37 mm). Trained on cortical surface meshes extracted from the MRIs of cognitively normal (CN) adults (N = 14,423), our model achieves lower mean absolute error (MAE) than the existing state-of-the-art while identifying more biologically plausible patterns of aging in Alzheimer's disease (AD) on the ADNI dataset. Association cortices emerge as primary sites of morphometric aging in CNs, whereas mild cognitive impai
Although Alzheimer's disease (AD) cannot be reversed or cured, timely diagnosis can significantly reduce the burden of treatment and care. Current research on AD diagnosis models usually regards the diagnosis task as a typical classification task with two primary assumptions: 1) All target categories are known a priori; 2) The diagnostic strategy for each patient is consistent, that is, the number and type of model input data for each patient are the same. However, real-world clinical settings are open, with complexity and uncertainty in terms of both subjects and the resources of the medical institutions. This means that diagnostic models may encounter unseen disease categories and need to dynamically develop diagnostic strategies based on the subject's specific circumstances and available medical resources. Thus, the AD diagnosis task is tangled and coupled with the diagnosis strategy formulation. To promote the application of diagnostic systems in real-world clinical settings, we propose OpenClinicalAI for direct AD diagnosis in complex and uncertain clinical settings. This is the first powerful end-to-end model to dynamically formulate diagnostic strategies and provide diagnost
Using "Analyze Results" at the Web of Science, one can directly generate overlays onto global journal maps of science. The maps are based on the 10,000+ journals contained in the Journal Citation Reports (JCR) of the Science and Social Science Citation Indices (2011). The disciplinary diversity of the retrieval is measured in terms of Rao-Stirling's "quadratic entropy." Since this indicator of interdisciplinarity is normalized between zero and one, the interdisciplinarity can be compared among document sets and across years, cited or citing. The colors used for the overlays are based on Blondel et al.'s (2008) community-finding algorithms operating on the relations journals included in JCRs. The results can be exported from VOSViewer with different options such as proportional labels, heat maps, or cluster density maps. The maps can also be web-started and/or animated (e.g., using PowerPoint). The "citing" dimension of the aggregated journal-journal citation matrix was found to provide a more comprehensive description than the matrix based on the cited archive. The relations between local and global maps and their different functions in studying the sciences in terms of journal lit