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Oct 31

Artificial Intelligence-derived Vascular Age from Photoplethysmography: A Novel Digital Biomarker for Cardiovascular Health

With the increasing availability of wearable devices, photoplethysmography (PPG) has emerged as a promising non-invasive tool for monitoring human hemodynamics. We propose a deep learning framework to estimate vascular age (AI-vascular age) from PPG signals, incorporating a distribution-aware loss to address biases caused by imbalanced data. The model was developed using data from the UK Biobank (UKB), with 98,672 participants in the development cohort and 113,559 participants (144,683 data pairs) for clinical evaluation. After adjusting for key confounders, individuals with a vascular age gap (AI-vascular age minus calendar age) exceeding 9 years had a significantly higher risk of major adverse cardiovascular and cerebrovascular events (MACCE) (HR = 2.37, p < 0.005) and secondary outcomes, including diabetes (HR = 2.69, p < 0.005), hypertension (HR = 2.88, p < 0.005), coronary heart disease (HR = 2.20, p < 0.005), heart failure (HR = 2.15, p < 0.005), myocardial infarction (HR = 2.51, p < 0.005), stroke (HR = 2.55, p < 0.005), and all-cause mortality (HR = 2.51, p < 0.005). Conversely, participants with a vascular age gap below -9 years exhibited a significantly lower incidence of these outcomes. We further evaluated the longitudinal applicability of AI-vascular age using serial PPG data from the UKB, demonstrating its value in risk stratification by leveraging AI-vascular age at two distinct time points to predict future MACCE incidence. External validation was performed on a MIMIC-III-derived cohort (n = 2,343), where each one-year increase in vascular age gap was significantly associated with elevated in-hospital mortality risk (OR = 1.02, p < 0.005). In conclusion, our study establishes AI-vascular age as a novel, non-invasive digital biomarker for cardiovascular health assessment.

  • 5 authors
·
Feb 18

ISLES 2024: The first longitudinal multimodal multi-center real-world dataset in (sub-)acute stroke

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

  • 18 authors
·
Aug 20, 2024

From time-series to complex networks: Application to the cerebrovascular flow patterns in atrial fibrillation

A network-based approach is presented to investigate the cerebrovascular flow patterns during atrial fibrillation (AF) with respect to normal sinus rhythm (NSR). AF, the most common cardiac arrhythmia with faster and irregular beating, has been recently and independently associated with the increased risk of dementia. However, the underlying hemodynamic mechanisms relating the two pathologies remain mainly undetermined so far; thus the contribution of modeling and refined statistical tools is valuable. Pressure and flow rate temporal series in NSR and AF are here evaluated along representative cerebral sites (from carotid arteries to capillary brain circulation), exploiting reliable artificially built signals recently obtained from an in silico approach. The complex network analysis evidences, in a synthetic and original way, a dramatic signal variation towards the distal/capillary cerebral regions during AF, which has no counterpart in NSR conditions. At the large artery level, networks obtained from both AF and NSR hemodynamic signals exhibit elongated and chained features, which are typical of pseudo-periodic series. These aspects are almost completely lost towards the microcirculation during AF, where the networks are topologically more circular and present random-like characteristics. As a consequence, all the physiological phenomena at microcerebral level ruled by periodicity - such as regular perfusion, mean pressure per beat, and average nutrient supply at cellular level - can be strongly compromised, since the AF hemodynamic signals assume irregular behaviour and random-like features. Through a powerful approach which is complementary to the classical statistical tools, the present findings further strengthen the potential link between AF hemodynamic and cognitive decline.

  • 3 authors
·
Sep 26, 2017

Heart Disease Detection using Vision-Based Transformer Models from ECG Images

Heart disease, also known as cardiovascular disease, is a prevalent and critical medical condition characterized by the impairment of the heart and blood vessels, leading to various complications such as coronary artery disease, heart failure, and myocardial infarction. The timely and accurate detection of heart disease is of paramount importance in clinical practice. Early identification of individuals at risk enables proactive interventions, preventive measures, and personalized treatment strategies to mitigate the progression of the disease and reduce adverse outcomes. In recent years, the field of heart disease detection has witnessed notable advancements due to the integration of sophisticated technologies and computational approaches. These include machine learning algorithms, data mining techniques, and predictive modeling frameworks that leverage vast amounts of clinical and physiological data to improve diagnostic accuracy and risk stratification. In this work, we propose to detect heart disease from ECG images using cutting-edge technologies, namely vision transformer models. These models are Google-Vit, Microsoft-Beit, and Swin-Tiny. To the best of our knowledge, this is the initial endeavor concentrating on the detection of heart diseases through image-based ECG data by employing cuttingedge technologies namely, transformer models. To demonstrate the contribution of the proposed framework, the performance of vision transformer models are compared with state-of-the-art studies. Experiment results show that the proposed framework exhibits remarkable classification results.

  • 4 authors
·
Oct 19, 2023

Phase-shifted remote photoplethysmography for estimating heart rate and blood pressure from facial video

Human health can be critically affected by cardiovascular diseases, such as hypertension, arrhythmias, and stroke. Heart rate and blood pressure are important biometric information for the monitoring of cardiovascular system and early diagnosis of cardiovascular diseases. Existing methods for estimating the heart rate are based on electrocardiography and photoplethyomography, which require contacting the sensor to the skin surface. Moreover, catheter and cuff-based methods for measuring blood pressure cause inconvenience and have limited applicability. Therefore, in this thesis, we propose a vision-based method for estimating the heart rate and blood pressure. This thesis proposes a 2-stage deep learning framework consisting of a dual remote photoplethysmography network (DRP-Net) and bounded blood pressure network (BBP-Net). In the first stage, DRP-Net infers remote photoplethysmography (rPPG) signals for the acral and facial regions, and these phase-shifted rPPG signals are utilized to estimate the heart rate. In the second stage, BBP-Net integrates temporal features and analyzes phase discrepancy between the acral and facial rPPG signals to estimate SBP and DBP values. To improve the accuracy of estimating the heart rate, we employed a data augmentation method based on a frame interpolation model. Moreover, we designed BBP-Net to infer blood pressure within a predefined range by incorporating a scaled sigmoid function. Our method resulted in estimating the heart rate with the mean absolute error (MAE) of 1.78 BPM, reducing the MAE by 34.31 % compared to the recent method, on the MMSE-HR dataset. The MAE for estimating the systolic blood pressure (SBP) and diastolic blood pressure (DBP) were 10.19 mmHg and 7.09 mmHg. On the V4V dataset, the MAE for the heart rate, SBP, and DBP were 3.83 BPM, 13.64 mmHg, and 9.4 mmHg, respectively.

  • 2 authors
·
Jan 9, 2024

Enhancing Adverse Drug Event Detection with Multimodal Dataset: Corpus Creation and Model Development

The mining of adverse drug events (ADEs) is pivotal in pharmacovigilance, enhancing patient safety by identifying potential risks associated with medications, facilitating early detection of adverse events, and guiding regulatory decision-making. Traditional ADE detection methods are reliable but slow, not easily adaptable to large-scale operations, and offer limited information. With the exponential increase in data sources like social media content, biomedical literature, and Electronic Medical Records (EMR), extracting relevant ADE-related information from these unstructured texts is imperative. Previous ADE mining studies have focused on text-based methodologies, overlooking visual cues, limiting contextual comprehension, and hindering accurate interpretation. To address this gap, we present a MultiModal Adverse Drug Event (MMADE) detection dataset, merging ADE-related textual information with visual aids. Additionally, we introduce a framework that leverages the capabilities of LLMs and VLMs for ADE detection by generating detailed descriptions of medical images depicting ADEs, aiding healthcare professionals in visually identifying adverse events. Using our MMADE dataset, we showcase the significance of integrating visual cues from images to enhance overall performance. This approach holds promise for patient safety, ADE awareness, and healthcare accessibility, paving the way for further exploration in personalized healthcare.

  • 5 authors
·
May 24, 2024

ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

  • 25 authors
·
Jun 14, 2022

CADICA: a new dataset for coronary artery disease detection by using invasive coronary angiography

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

  • 7 authors
·
Feb 1, 2024

Enhanced Mortality Prediction In Patients With Subarachnoid Haemorrhage Using A Deep Learning Model Based On The Initial CT Scan

PURPOSE: Subarachnoid hemorrhage (SAH) entails high morbidity and mortality rates. Convolutional neural networks (CNN), a form of deep learning, are capable of generating highly accurate predictions from imaging data. Our objective was to predict mortality in SAH patients by processing the initial CT scan on a CNN based algorithm. METHODS: Retrospective multicentric study of a consecutive cohort of patients with SAH between 2011-2022. Demographic, clinical and radiological variables were analyzed. Pre-processed baseline CT scan images were used as the input for training a CNN using AUCMEDI Framework. Our model's architecture leverages the DenseNet-121 structure, employing transfer learning principles. The output variable was mortality in the first three months. Performance of the model was evaluated by statistical parameters conventionally used in studies involving artificial intelligence methods. RESULTS: Images from 219 patients were processed, 175 for training and validation of the CNN and 44 for its evaluation. 52%(115/219) of patients were female, and the median age was 58(SD=13.06) years. 18.5%(39/219) were idiopathic SAH. Mortality rate was 28.5%(63/219). The model showed good accuracy at predicting mortality in SAH patients exclusively using the images of the initial CT scan (Accuracy=74%, F1=75% and AUC=82%). CONCLUSION: Modern image processing techniques based on AI and CNN make possible to predict mortality in SAH patients with high accuracy using CT scan images as the only input. These models might be optimized by including more data and patients resulting in better training, development and performance on tasks which are beyond the skills of conventional clinical knowledge.

  • 9 authors
·
Aug 25, 2023

Site-Level Fine-Tuning with Progressive Layer Freezing: Towards Robust Prediction of Bronchopulmonary Dysplasia from Day-1 Chest Radiographs in Extremely Preterm Infants

Bronchopulmonary dysplasia (BPD) is a chronic lung disease affecting 35% of extremely low birth weight infants. Defined by oxygen dependence at 36 weeks postmenstrual age, it causes lifelong respiratory complications. However, preventive interventions carry severe risks, including neurodevelopmental impairment, ventilator-induced lung injury, and systemic complications. Therefore, early BPD prognosis and prediction of BPD outcome is crucial to avoid unnecessary toxicity in low risk infants. Admission radiographs of extremely preterm infants are routinely acquired within 24h of life and could serve as a non-invasive prognostic tool. In this work, we developed and investigated a deep learning approach using chest X-rays from 163 extremely low-birth-weight infants (leq32 weeks gestation, 401-999g) obtained within 24 hours of birth. We fine-tuned a ResNet-50 pretrained specifically on adult chest radiographs, employing progressive layer freezing with discriminative learning rates to prevent overfitting and evaluated a CutMix augmentation and linear probing. For moderate/severe BPD outcome prediction, our best performing model with progressive freezing, linear probing and CutMix achieved an AUROC of 0.78 pm 0.10, balanced accuracy of 0.69 pm 0.10, and an F1-score of 0.67 pm 0.11. In-domain pre-training significantly outperformed ImageNet initialization (p = 0.031) which confirms domain-specific pretraining to be important for BPD outcome prediction. Routine IRDS grades showed limited prognostic value (AUROC 0.57 pm 0.11), confirming the need of learned markers. Our approach demonstrates that domain-specific pretraining enables accurate BPD prediction from routine day-1 radiographs. Through progressive freezing and linear probing, the method remains computationally feasible for site-level implementation and future federated learning deployments.

  • 16 authors
·
Jul 16

DS6, Deformation-aware Semi-supervised Learning: Application to Small Vessel Segmentation with Noisy Training Data

Blood vessels of the brain provide the human brain with the required nutrients and oxygen. As a vulnerable part of the cerebral blood supply, pathology of small vessels can cause serious problems such as Cerebral Small Vessel Diseases (CSVD). It has also been shown that CSVD is related to neurodegeneration, such as Alzheimer's disease. With the advancement of 7 Tesla MRI systems, higher spatial image resolution can be achieved, enabling the depiction of very small vessels in the brain. Non-Deep Learning-based approaches for vessel segmentation, e.g., Frangi's vessel enhancement with subsequent thresholding, are capable of segmenting medium to large vessels but often fail to segment small vessels. The sensitivity of these methods to small vessels can be increased by extensive parameter tuning or by manual corrections, albeit making them time-consuming, laborious, and not feasible for larger datasets. This paper proposes a deep learning architecture to automatically segment small vessels in 7 Tesla 3D Time-of-Flight (ToF) Magnetic Resonance Angiography (MRA) data. The algorithm was trained and evaluated on a small imperfect semi-automatically segmented dataset of only 11 subjects; using six for training, two for validation, and three for testing. The deep learning model based on U-Net Multi-Scale Supervision was trained using the training subset and was made equivariant to elastic deformations in a self-supervised manner using deformation-aware learning to improve the generalisation performance. The proposed technique was evaluated quantitatively and qualitatively against the test set and achieved a Dice score of 80.44 pm 0.83. Furthermore, the result of the proposed method was compared against a selected manually segmented region (62.07 resultant Dice) and has shown a considerable improvement (18.98\%) with deformation-aware learning.

  • 10 authors
·
Jun 18, 2020

PVBM: A Python Vasculature Biomarker Toolbox Based On Retinal Blood Vessel Segmentation

Introduction: Blood vessels can be non-invasively visualized from a digital fundus image (DFI). Several studies have shown an association between cardiovascular risk and vascular features obtained from DFI. Recent advances in computer vision and image segmentation enable automatising DFI blood vessel segmentation. There is a need for a resource that can automatically compute digital vasculature biomarkers (VBM) from these segmented DFI. Methods: In this paper, we introduce a Python Vasculature BioMarker toolbox, denoted PVBM. A total of 11 VBMs were implemented. In particular, we introduce new algorithmic methods to estimate tortuosity and branching angles. Using PVBM, and as a proof of usability, we analyze geometric vascular differences between glaucomatous patients and healthy controls. Results: We built a fully automated vasculature biomarker toolbox based on DFI segmentations and provided a proof of usability to characterize the vascular changes in glaucoma. For arterioles and venules, all biomarkers were significant and lower in glaucoma patients compared to healthy controls except for tortuosity, venular singularity length and venular branching angles. Conclusion: We have automated the computation of 11 VBMs from retinal blood vessel segmentation. The PVBM toolbox is made open source under a GNU GPL 3 license and is available on physiozoo.com (following publication).

  • 6 authors
·
Jul 31, 2022

Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neurovascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two non-invasive angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited datasets with annotations on CoW anatomy, especially for CTA. Therefore, we organized the TopCoW challenge with the release of an annotated CoW dataset. The TopCoW dataset is the first public dataset with voxel-level annotations for 13 CoW vessel components, enabled by virtual reality technology. It is also the first large dataset using 200 pairs of MRA and CTA from the same patients. As part of the benchmark, we invited submissions worldwide and attracted over 250 registered participants from six continents. The submissions were evaluated on both internal and external test datasets of 226 scans from over five centers. The top performing teams achieved over 90% Dice scores at segmenting the CoW components, over 80% F1 scores at detecting key CoW components, and over 70% balanced accuracy at classifying CoW variants for nearly all test sets. The best algorithms also showed clinical potential in classifying fetal-type posterior cerebral artery and locating aneurysms with CoW anatomy. TopCoW demonstrated the utility and versatility of CoW segmentation algorithms for a wide range of downstream clinical applications with explainability. The annotated datasets and best performing algorithms have been released as public Zenodo records to foster further methodological development and clinical tool building.

  • 113 authors
·
Dec 29, 2023

Distilling Large Language Models for Biomedical Knowledge Extraction: A Case Study on Adverse Drug Events

Large language models (LLMs), such as GPT-4, have demonstrated remarkable capabilities across a wide range of tasks, including health applications. In this paper, we study how LLMs can be used to scale biomedical knowledge curation. We find that while LLMs already possess decent competency in structuring biomedical text, by distillation into a task-specific student model through self-supervised learning, substantial gains can be attained over out-of-box LLMs, with additional advantages such as cost, efficiency, and white-box model access. We conduct a case study on adverse drug event (ADE) extraction, which is an important area for improving care. On standard ADE extraction evaluation, a GPT-3.5 distilled PubMedBERT model attained comparable accuracy as supervised state-of-the-art models without using any labeled data. Despite being over 1,000 times smaller, the distilled model outperformed its teacher GPT-3.5 by over 6 absolute points in F1 and GPT-4 by over 5 absolute points. Ablation studies on distillation model choice (e.g., PubMedBERT vs BioGPT) and ADE extraction architecture shed light on best practice for biomedical knowledge extraction. Similar gains were attained by distillation for other standard biomedical knowledge extraction tasks such as gene-disease associations and protected health information, further illustrating the promise of this approach.

  • 11 authors
·
Jul 12, 2023 1

Coping with Information Loss and the Use of Auxiliary Sources of Data: A Report from the NISS Ingram Olkin Forum Series on Unplanned Clinical Trial Disruptions

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

  • 12 authors
·
Jun 22, 2022

Sensing Cardiac Health Across Scenarios and Devices: A Multi-Modal Foundation Model Pretrained on Heterogeneous Data from 1.7 Million Individuals

Cardiac biosignals, such as electrocardiograms (ECG) and photoplethysmograms (PPG), are of paramount importance for the diagnosis, prevention, and management of cardiovascular diseases, and have been extensively used in a variety of clinical tasks. Conventional deep learning approaches for analyzing these signals typically rely on homogeneous datasets and static bespoke models, limiting their robustness and generalizability across diverse clinical settings and acquisition protocols. In this study, we present a cardiac sensing foundation model (CSFM) that leverages advanced transformer architectures and a generative, masked pretraining strategy to learn unified representations from vast, heterogeneous health records. Our model is pretrained on an innovative multi-modal integration of data from multiple large-scale datasets (including MIMIC-III-WDB, MIMIC-IV-ECG, and CODE), comprising cardiac signals and the corresponding clinical or machine-generated text reports from approximately 1.7 million individuals. We demonstrate that the embeddings derived from our CSFM not only serve as effective feature extractors across diverse cardiac sensing scenarios, but also enable seamless transfer learning across varying input configurations and sensor modalities. Extensive evaluations across diagnostic tasks, demographic information recognition, vital sign measurement, clinical outcome prediction, and ECG question answering reveal that CSFM consistently outperforms traditional one-modal-one-task approaches. Notably, CSFM exhibits robust performance across multiple ECG lead configurations from standard 12-lead systems to single-lead setups, and in scenarios where only ECG, only PPG, or a combination thereof is available. These findings highlight the potential of CSFM as a versatile and scalable solution, for comprehensive cardiac monitoring.

  • 13 authors
·
Jun 23

SzCORE as a benchmark: report from the seizure detection challenge at the 2025 AI in Epilepsy and Neurological Disorders Conference

Reliable automatic seizure detection from long-term EEG remains a challenge, as current machine learning models often fail to generalize across patients or clinical settings. Manual EEG review remains the clinical standard, underscoring the need for robust models and standardized evaluation. To rigorously assess algorithm performance, we organized a challenge using a private dataset of continuous EEG recordings from 65 subjects (4,360 hours). Expert neurophysiologists annotated the data, providing ground truth for seizure events. Participants were required to detect seizure onset and duration, with evaluation based on event-based metrics, including sensitivity, precision, F1-score, and false positives per day. The SzCORE framework ensured standardized evaluation. The primary ranking criterion was the event-based F1-score, reflecting clinical relevance by balancing sensitivity and false positives. The challenge received 30 submissions from 19 teams, with 28 algorithms evaluated. Results revealed wide variability in performance, with a top F1-score of 43% (sensitivity 37%, precision 45%), highlighting the ongoing difficulty of seizure detection. The challenge also revealed a gap between reported performance and real-world evaluation, emphasizing the importance of rigorous benchmarking. Compared to previous challenges and commercial systems, the best-performing algorithm in this contest showed improved performance. Importantly, the challenge platform now supports continuous benchmarking, enabling reproducible research, integration of new datasets, and clinical evaluation of seizure detection algorithms using a standardized framework.

  • 4 authors
·
May 19

LoRA-based methods on Unet for transfer learning in Subarachnoid Hematoma Segmentation

Aneurysmal subarachnoid hemorrhage (SAH) is a life-threatening neurological emergency with mortality rates exceeding 30%. Transfer learning from related hematoma types represents a potentially valuable but underexplored approach. Although Unet architectures remain the gold standard for medical image segmentation due to their effectiveness on limited datasets, Low-Rank Adaptation (LoRA) methods for parameter-efficient transfer learning have been rarely applied to convolutional neural networks in medical imaging contexts. We implemented a Unet architecture pre-trained on computed tomography scans from 124 traumatic brain injury patients across multiple institutions, then fine-tuned on 30 aneurysmal SAH patients from the University of Michigan Health System using 3-fold cross-validation. We developed a novel CP-LoRA method based on tensor CP-decomposition and introduced DoRA variants (DoRA-C, convDoRA, CP-DoRA) that decompose weight matrices into magnitude and directional components. We compared these approaches against existing LoRA methods (LoRA-C, convLoRA) and standard fine-tuning strategies across different modules on a multi-view Unet model. LoRA-based methods consistently outperformed standard Unet fine-tuning. Performance varied by hemorrhage volume, with all methods showing improved accuracy for larger volumes. CP-LoRA achieved comparable performance to existing methods while using significantly fewer parameters. Over-parameterization with higher ranks consistently yielded better performance than strictly low-rank adaptations. This study demonstrates that transfer learning between hematoma types is feasible and that LoRA-based methods significantly outperform conventional Unet fine-tuning for aneurysmal SAH segmentation.

  • 7 authors
·
Aug 3

Enhancing End Stage Renal Disease Outcome Prediction: A Multi-Sourced Data-Driven Approach

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

  • 2 authors
·
Oct 1, 2024

The Alzheimer's Disease Prediction Of Longitudinal Evolution (TADPOLE) Challenge: Results after 1 Year Follow-up

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

  • 96 authors
·
Feb 9, 2020

MALADE: Orchestration of LLM-powered Agents with Retrieval Augmented Generation for Pharmacovigilance

In the era of Large Language Models (LLMs), given their remarkable text understanding and generation abilities, there is an unprecedented opportunity to develop new, LLM-based methods for trustworthy medical knowledge synthesis, extraction and summarization. This paper focuses on the problem of Pharmacovigilance (PhV), where the significance and challenges lie in identifying Adverse Drug Events (ADEs) from diverse text sources, such as medical literature, clinical notes, and drug labels. Unfortunately, this task is hindered by factors including variations in the terminologies of drugs and outcomes, and ADE descriptions often being buried in large amounts of narrative text. We present MALADE, the first effective collaborative multi-agent system powered by LLM with Retrieval Augmented Generation for ADE extraction from drug label data. This technique involves augmenting a query to an LLM with relevant information extracted from text resources, and instructing the LLM to compose a response consistent with the augmented data. MALADE is a general LLM-agnostic architecture, and its unique capabilities are: (1) leveraging a variety of external sources, such as medical literature, drug labels, and FDA tools (e.g., OpenFDA drug information API), (2) extracting drug-outcome association in a structured format along with the strength of the association, and (3) providing explanations for established associations. Instantiated with GPT-4 Turbo or GPT-4o, and FDA drug label data, MALADE demonstrates its efficacy with an Area Under ROC Curve of 0.90 against the OMOP Ground Truth table of ADEs. Our implementation leverages the Langroid multi-agent LLM framework and can be found at https://github.com/jihyechoi77/malade.

  • 7 authors
·
Aug 3, 2024

Applying Dimensionality Reduction as Precursor to LSTM-CNN Models for Classifying Imagery and Motor Signals in ECoG-Based BCIs

Motor impairments, frequently caused by neurological incidents like strokes or traumatic brain injuries, present substantial obstacles in rehabilitation therapy. This research aims to elevate the field by optimizing motor imagery classification algorithms within Brain-Computer Interfaces (BCIs). By improving the efficiency of BCIs, we offer a novel approach that holds significant promise for enhancing motor rehabilitation outcomes. Utilizing unsupervised techniques for dimensionality reduction, namely Uniform Manifold Approximation and Projection (UMAP) coupled with K-Nearest Neighbors (KNN), we evaluate the necessity of employing supervised methods such as Long Short-Term Memory (LSTM) and Convolutional Neural Networks (CNNs) for classification tasks. Importantly, participants who exhibited high KNN scores following UMAP dimensionality reduction also achieved high accuracy in supervised deep learning (DL) models. Due to individualized model requirements and massive neural training data, dimensionality reduction becomes an effective preprocessing step that minimizes the need for extensive data labeling and supervised deep learning techniques. This approach has significant implications not only for targeted therapies in motor dysfunction but also for addressing regulatory, safety, and reliability concerns in the rapidly evolving BCI field.

  • 1 authors
·
Nov 22, 2023

Demystifying Large Language Models for Medicine: A Primer

Large language models (LLMs) represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

  • 23 authors
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Oct 24, 2024

SpiroLLM: Finetuning Pretrained LLMs to Understand Spirogram Time Series with Clinical Validation in COPD Reporting

Chronic Obstructive Pulmonary Disease (COPD), a major chronic respiratory disease with persistent airflow limitation, is a leading global cause of disability and mortality. Respiratory spirogram time series, routinely collected during pulmonary function tests (PFTs), play a critical role in the early detection of repsiratory diseases and in monitoring lung function over time. However, most current AI models for COPD diagnosis are limited to outputting classification results without providing a rationale for their diagnostic process, while current Large Language Models (LLMs) cannot understand spirograms yet, which severely limits their clinical trust and adoption. To tackle this challenge, we leverage a cohort of 234,028 individuals from the UK Biobank (UKB) to propose SpiroLLM, the first multimodal large language model that can understand spirogram. The model extracts morphological features from respiratory curves via a SpiroEncoder and aligns them with PFT numerical values in a unified latent space using a SpiroProjector, ultimately empowering a large language model to generate a comprehensive diagnostic report. Experimental results confirm that SpiroLLM achieved a diagnostic AUROC of 0.8980 (95% CI: 0.8820-0.9132). In a robustness test with missing core data, it maintained a 100% valid response rate, far surpassing the 13.4% of a text-only model and showcasing the superiority of its multimodal design. This work demonstrates the substantial potential of deeply fusing physiological signals with large language models, establishing a new paradigm for the next generation of interpretable and reliable clinical decision support tools.

  • 8 authors
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Jul 21

Improved Robustness for Deep Learning-based Segmentation of Multi-Center Myocardial Perfusion MRI Datasets Using Data Adaptive Uncertainty-guided Space-time Analysis

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

  • 11 authors
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Aug 8, 2024

Mythological Medical Machine Learning: Boosting the Performance of a Deep Learning Medical Data Classifier Using Realistic Physiological Models

Objective: To determine if a realistic, but computationally efficient model of the electrocardiogram can be used to pre-train a deep neural network (DNN) with a wide range of morphologies and abnormalities specific to a given condition - T-wave Alternans (TWA) as a result of Post-Traumatic Stress Disorder, or PTSD - and significantly boost performance on a small database of rare individuals. Approach: Using a previously validated artificial ECG model, we generated 180,000 artificial ECGs with or without significant TWA, with varying heart rate, breathing rate, TWA amplitude, and ECG morphology. A DNN, trained on over 70,000 patients to classify 25 different rhythms, was modified the output layer to a binary class (TWA or no-TWA, or equivalently, PTSD or no-PTSD), and transfer learning was performed on the artificial ECG. In a final transfer learning step, the DNN was trained and cross-validated on ECG from 12 PTSD and 24 controls for all combinations of using the three databases. Main results: The best performing approach (AUROC = 0.77, Accuracy = 0.72, F1-score = 0.64) was found by performing both transfer learning steps, using the pre-trained arrhythmia DNN, the artificial data and the real PTSD-related ECG data. Removing the artificial data from training led to the largest drop in performance. Removing the arrhythmia data from training provided a modest, but significant, drop in performance. The final model showed no significant drop in performance on the artificial data, indicating no overfitting. Significance: In healthcare, it is common to only have a small collection of high-quality data and labels, or a larger database with much lower quality (and less relevant) labels. The paradigm presented here, involving model-based performance boosting, provides a solution through transfer learning on a large realistic artificial database, and a partially relevant real database.

  • 6 authors
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Dec 28, 2021

Predicting sepsis in multi-site, multi-national intensive care cohorts using deep learning

Despite decades of clinical research, sepsis remains a global public health crisis with high mortality, and morbidity. Currently, when sepsis is detected and the underlying pathogen is identified, organ damage may have already progressed to irreversible stages. Effective sepsis management is therefore highly time-sensitive. By systematically analysing trends in the plethora of clinical data available in the intensive care unit (ICU), an early prediction of sepsis could lead to earlier pathogen identification, resistance testing, and effective antibiotic and supportive treatment, and thereby become a life-saving measure. Here, we developed and validated a machine learning (ML) system for the prediction of sepsis in the ICU. Our analysis represents the largest multi-national, multi-centre in-ICU study for sepsis prediction using ML to date. Our dataset contains 156,309 unique ICU admissions, which represent a refined and harmonised subset of five large ICU databases originating from three countries. Using the international consensus definition Sepsis-3, we derived hourly-resolved sepsis label annotations, amounting to 26,734 (17.1%) septic stays. We compared our approach, a deep self-attention model, to several clinical baselines as well as ML baselines and performed an extensive internal and external validation within and across databases. On average, our model was able to predict sepsis with an AUROC of 0.847 pm 0.050 (internal out-of sample validation) and 0.761 pm 0.052 (external validation). For a harmonised prevalence of 17%, at 80% recall our model detects septic patients with 39% precision 3.7 hours in advance.

  • 8 authors
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Jul 12, 2021

A Comprehensive Benchmark for COVID-19 Predictive Modeling Using Electronic Health Records in Intensive Care

The COVID-19 pandemic has posed a heavy burden to the healthcare system worldwide and caused huge social disruption and economic loss. Many deep learning models have been proposed to conduct clinical predictive tasks such as mortality prediction for COVID-19 patients in intensive care units using Electronic Health Record (EHR) data. Despite their initial success in certain clinical applications, there is currently a lack of benchmarking results to achieve a fair comparison so that we can select the optimal model for clinical use. Furthermore, there is a discrepancy between the formulation of traditional prediction tasks and real-world clinical practice in intensive care. To fill these gaps, we propose two clinical prediction tasks, Outcome-specific length-of-stay prediction and Early mortality prediction for COVID-19 patients in intensive care units. The two tasks are adapted from the naive length-of-stay and mortality prediction tasks to accommodate the clinical practice for COVID-19 patients. We propose fair, detailed, open-source data-preprocessing pipelines and evaluate 17 state-of-the-art predictive models on two tasks, including 5 machine learning models, 6 basic deep learning models and 6 deep learning predictive models specifically designed for EHR data. We provide benchmarking results using data from two real-world COVID-19 EHR datasets. One dataset is publicly available without needing any inquiry and another dataset can be accessed on request. We provide fair, reproducible benchmarking results for two tasks. We deploy all experiment results and models on an online platform. We also allow clinicians and researchers to upload their data to the platform and get quick prediction results using our trained models. We hope our efforts can further facilitate deep learning and machine learning research for COVID-19 predictive modeling.

  • 7 authors
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Sep 16, 2022

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

  • 58 authors
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Mar 28, 2024

AIMI: Leveraging Future Knowledge and Personalization in Sparse Event Forecasting for Treatment Adherence

Adherence to prescribed treatments is crucial for individuals with chronic conditions to avoid costly or adverse health outcomes. For certain patient groups, intensive lifestyle interventions are vital for enhancing medication adherence. Accurate forecasting of treatment adherence can open pathways to developing an on-demand intervention tool, enabling timely and personalized support. With the increasing popularity of smartphones and wearables, it is now easier than ever to develop and deploy smart activity monitoring systems. However, effective forecasting systems for treatment adherence based on wearable sensors are still not widely available. We close this gap by proposing Adherence Forecasting and Intervention with Machine Intelligence (AIMI). AIMI is a knowledge-guided adherence forecasting system that leverages smartphone sensors and previous medication history to estimate the likelihood of forgetting to take a prescribed medication. A user study was conducted with 27 participants who took daily medications to manage their cardiovascular diseases. We designed and developed CNN and LSTM-based forecasting models with various combinations of input features and found that LSTM models can forecast medication adherence with an accuracy of 0.932 and an F-1 score of 0.936. Moreover, through a series of ablation studies involving convolutional and recurrent neural network architectures, we demonstrate that leveraging known knowledge about future and personalized training enhances the accuracy of medication adherence forecasting. Code available: https://github.com/ab9mamun/AIMI.

  • 3 authors
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Mar 20 2

Microscale stress-geometry interactions in an additively manufactured NiTi cardiovascular stent: A synchrotron dual imaging tomography and diffraction study

This study explores cardiovascular stents fabricated using laser powder bed fusion (LPBF); an emerging method to offer patient-specific customisable parts. Here, the shape memory alloy NiTi, in a near equiatomic composition, was investigated to deconvolve the material response from macroscopic component effects. Specifically, stress-geometry interactions were revealed, in-situ, for a minaturised cardiovascular stent subjected to an externally applied cylindrical stress whilst acquiring synchrotron X-ray imaging and diffraction data. The approach enabled the collection of spatially resolved micromechanical deformation data; the formation of stress-induced martensite and R-phase was evident, occurring in locations near junctions between stent ligaments where stress concentrations exist. In the as-fabricated condition, hardness maps were obtained through nanoindentation, demonstrating that the localised deformation and deformation patterning is further controlled by porosity and microstructural heterogeneity. Electron backscatter diffraction (EBSD) supported these observations, showing a finer grain structure near stent junctions with higher associated lattice curvature. These features, combined with stress concentrations when loaded will initiate localised phase transformations. If the stent was subjected to repeated loading, representing in-vivo conditions, these regions would be susceptible to cyclic damage through transformation memory loss, leading to premature component failure. This study highlights the challenges that must be addressed for the post-processing treatment of LABF-processed stents for healthcare-related applications.

  • 11 authors
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Dec 12, 2023

Learning from Two Decades of Blood Pressure Data: Demography-Specific Patterns Across 75 Million Patient Encounters

Hypertension remains a global health concern with a rising prevalence, necessitating effective monitoring and understanding of blood pressure (BP) dynamics. This study delves into the wealth of information derived from BP measurement, a crucial approach in informing our understanding of hypertensive trends. Numerous studies have reported on the relationship between BP variation and various factors. In this research, we leveraged an extensive dataset comprising 75 million records spanning two decades, offering a unique opportunity to explore and analyze BP variations across demographic features such as age, race, and gender. Our findings revealed that gender-based BP variation was not statistically significant, challenging conventional assumptions. Interestingly, systolic blood pressure (SBP) consistently increased with age, while diastolic blood pressure (DBP) displayed a distinctive peak in the forties age group. Moreover, our analysis uncovered intriguing similarities in the distribution of BP among some of the racial groups. This comprehensive investigation contributes to the ongoing discourse on hypertension and underscores the importance of considering diverse demographic factors in understanding BP variations. Our results provide valuable insights that may inform personalized healthcare approaches tailored to specific demographic profiles.

  • 4 authors
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Feb 2, 2024

A Survey on Medical Large Language Models: Technology, Application, Trustworthiness, and Future Directions

With the advent of Large Language Models (LLMs), medical artificial intelligence (AI) has experienced substantial technological progress and paradigm shifts, highlighting the potential of LLMs to streamline healthcare delivery and improve patient outcomes. Considering this rapid technical progress, in this survey, we trace the recent advances of Medical Large Language Models (Med-LLMs), including the background, key findings, and mainstream techniques, especially for the evolution from general-purpose models to medical-specialized applications. Firstly, we delve into the foundational technology of Med-LLMs, indicating how general models can be progressively adapted and refined for the complicated medical tasks. Secondly, the wide-ranging applications of Med-LLMs are investigated across various healthcare domains, as well as an up-to-date review of existing Med-LLMs. The transformative impact of these models on daily medical practice is evident through their ability to assist clinicians, educators, and patients. Recognizing the importance of responsible innovation, we discuss the challenges associated with ensuring fairness, accountability, privacy, and robustness. Ethical considerations, rigorous evaluation methodologies, and the establishment of regulatory frameworks are crucial for building trustworthiness in the real-world system. We emphasize the need for ongoing scrutiny and development to maintain high standards of safety and reliability. Finally, we anticipate possible future trajectories for Med-LLMs, identifying key avenues for prudent expansion. By consolidating these insights, our review aims to provide professionals and researchers with a thorough understanding of the strengths and limitations of Med-LLMs, fostering a balanced and ethical approach to their integration into the healthcare ecosystem.

  • 9 authors
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Jun 5, 2024

The Psychogenic Machine: Simulating AI Psychosis, Delusion Reinforcement and Harm Enablement in Large Language Models

Background: Emerging reports of "AI psychosis" are on the rise, where user-LLM interactions may exacerbate or induce psychosis or adverse psychological symptoms. Whilst the sycophantic and agreeable nature of LLMs can be beneficial, it becomes a vector for harm by reinforcing delusional beliefs in vulnerable users. Methods: Psychosis-bench is a novel benchmark designed to systematically evaluate the psychogenicity of LLMs comprises 16 structured, 12-turn conversational scenarios simulating the progression of delusional themes(Erotic Delusions, Grandiose/Messianic Delusions, Referential Delusions) and potential harms. We evaluated eight prominent LLMs for Delusion Confirmation (DCS), Harm Enablement (HES), and Safety Intervention(SIS) across explicit and implicit conversational contexts. Findings: Across 1,536 simulated conversation turns, all LLMs demonstrated psychogenic potential, showing a strong tendency to perpetuate rather than challenge delusions (mean DCS of 0.91 pm0.88). Models frequently enabled harmful user requests (mean HES of 0.69 pm0.84) and offered safety interventions in only roughly a third of applicable turns (mean SIS of 0.37 pm0.48). 51 / 128 (39.8%) of scenarios had no safety interventions offered. Performance was significantly worse in implicit scenarios, models were more likely to confirm delusions and enable harm while offering fewer interventions (p < .001). A strong correlation was found between DCS and HES (rs = .77). Model performance varied widely, indicating that safety is not an emergent property of scale alone. Conclusion: This study establishes LLM psychogenicity as a quantifiable risk and underscores the urgent need for re-thinking how we train LLMs. We frame this issue not merely as a technical challenge but as a public health imperative requiring collaboration between developers, policymakers, and healthcare professionals.

  • 5 authors
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Sep 13

PRISM: Patient Records Interpretation for Semantic Clinical Trial Matching using Large Language Models

Clinical trial matching is the task of identifying trials for which patients may be potentially eligible. Typically, this task is labor-intensive and requires detailed verification of patient electronic health records (EHRs) against the stringent inclusion and exclusion criteria of clinical trials. This process is manual, time-intensive, and challenging to scale up, resulting in many patients missing out on potential therapeutic options. Recent advancements in Large Language Models (LLMs) have made automating patient-trial matching possible, as shown in multiple concurrent research studies. However, the current approaches are confined to constrained, often synthetic datasets that do not adequately mirror the complexities encountered in real-world medical data. In this study, we present the first, end-to-end large-scale empirical evaluation of clinical trial matching using real-world EHRs. Our study showcases the capability of LLMs to accurately match patients with appropriate clinical trials. We perform experiments with proprietary LLMs, including GPT-4 and GPT-3.5, as well as our custom fine-tuned model called OncoLLM and show that OncoLLM, despite its significantly smaller size, not only outperforms GPT-3.5 but also matches the performance of qualified medical doctors. All experiments were carried out on real-world EHRs that include clinical notes and available clinical trials from a single cancer center in the United States.

  • 13 authors
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Apr 23, 2024 1

Boosting EfficientNets Ensemble Performance via Pseudo-Labels and Synthetic Images by pix2pixHD for Infection and Ischaemia Classification in Diabetic Foot Ulcers

Diabetic foot ulcers are a common manifestation of lesions on the diabetic foot, a syndrome acquired as a long-term complication of diabetes mellitus. Accompanying neuropathy and vascular damage promote acquisition of pressure injuries and tissue death due to ischaemia. Affected areas are prone to infections, hindering the healing progress. The research at hand investigates an approach on classification of infection and ischaemia, conducted as part of the Diabetic Foot Ulcer Challenge (DFUC) 2021. Different models of the EfficientNet family are utilized in ensembles. An extension strategy for the training data is applied, involving pseudo-labeling for unlabeled images, and extensive generation of synthetic images via pix2pixHD to cope with severe class imbalances. The resulting extended training dataset features 8.68 times the size of the baseline and shows a real to synthetic image ratio of 1:3. Performances of models and ensembles trained on the baseline and extended training dataset are compared. Synthetic images featured a broad qualitative variety. Results show that models trained on the extended training dataset as well as their ensemble benefit from the large extension. F1-Scores for rare classes receive outstanding boosts, while those for common classes are either not harmed or boosted moderately. A critical discussion concretizes benefits and identifies limitations, suggesting improvements. The work concludes that classification performance of individual models as well as that of ensembles can be boosted utilizing synthetic images. Especially performance for rare classes benefits notably.

  • 3 authors
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Nov 30, 2021

CE-SSL: Computation-Efficient Semi-Supervised Learning for ECG-based Cardiovascular Diseases Detection

The label scarcity problem is the main challenge that hinders the wide application of deep learning systems in automatic cardiovascular diseases (CVDs) detection using electrocardiography (ECG). Tuning pre-trained models alleviates this problem by transferring knowledge learned from large datasets to downstream small datasets. However, bottlenecks in computational efficiency and detection performance limit its clinical applications. It is difficult to improve the detection performance without significantly sacrificing the computational efficiency during model training. Here, we propose a computation-efficient semi-supervised learning paradigm (CE-SSL) for robust and computation-efficient CVDs detection using ECG. It enables a robust adaptation of pre-trained models on downstream datasets with limited supervision and high computational efficiency. First, a random-deactivation technique is developed to achieve robust and fast low-rank adaptation of pre-trained weights. Subsequently, we propose a one-shot rank allocation module to determine the optimal ranks for the update matrices of the pre-trained weights. Finally, a lightweight semi-supervised learning pipeline is introduced to enhance model performance by leveraging labeled and unlabeled data with high computational efficiency. Extensive experiments on four downstream datasets demonstrate that CE-SSL not only outperforms the state-of-the-art methods in multi-label CVDs detection but also consumes fewer GPU footprints, training time, and parameter storage space. As such, this paradigm provides an effective solution for achieving high computational efficiency and robust detection performance in the clinical applications of pre-trained models under limited supervision. Code and Supplementary Materials are available at https://github.com/KAZABANA/CE-SSL

  • 7 authors
·
Jun 20, 2024

The Ethics of ChatGPT in Medicine and Healthcare: A Systematic Review on Large Language Models (LLMs)

With the introduction of ChatGPT, Large Language Models (LLMs) have received enormous attention in healthcare. Despite their potential benefits, researchers have underscored various ethical implications. While individual instances have drawn much attention, the debate lacks a systematic overview of practical applications currently researched and ethical issues connected to them. Against this background, this work aims to map the ethical landscape surrounding the current stage of deployment of LLMs in medicine and healthcare. Electronic databases and preprint servers were queried using a comprehensive search strategy. Studies were screened and extracted following a modified rapid review approach. Methodological quality was assessed using a hybrid approach. For 53 records, a meta-aggregative synthesis was performed. Four fields of applications emerged and testify to a vivid exploration phase. Advantages of using LLMs are attributed to their capacity in data analysis, personalized information provisioning, support in decision-making, mitigating information loss and enhancing information accessibility. However, we also identifies recurrent ethical concerns connected to fairness, bias, non-maleficence, transparency, and privacy. A distinctive concern is the tendency to produce harmful misinformation or convincingly but inaccurate content. A recurrent plea for ethical guidance and human oversight is evident. Given the variety of use cases, it is suggested that the ethical guidance debate be reframed to focus on defining what constitutes acceptable human oversight across the spectrum of applications. This involves considering diverse settings, varying potentials for harm, and different acceptable thresholds for performance and certainty in healthcare. In addition, a critical inquiry is necessary to determine the extent to which the current experimental use of LLMs is necessary and justified.

  • 2 authors
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Mar 21, 2024

A Deep Learning Model for Coronary Artery Segmentation and Quantitative Stenosis Detection in Angiographic Images

Coronary artery disease (CAD) is a leading cause of cardiovascular-related mortality, and accurate stenosis detection is crucial for effective clinical decision-making. Coronary angiography remains the gold standard for diagnosing CAD, but manual analysis of angiograms is prone to errors and subjectivity. This study aims to develop a deep learning-based approach for the automatic segmentation of coronary arteries from angiographic images and the quantitative detection of stenosis, thereby improving the accuracy and efficiency of CAD diagnosis. We propose a novel deep learning-based method for the automatic segmentation of coronary arteries in angiographic images, coupled with a dynamic cohort method for stenosis detection. The segmentation model combines the MedSAM and VM-UNet architectures to achieve high-performance results. After segmentation, the vascular centerline is extracted, vessel diameter is computed, and the degree of stenosis is measured with high precision, enabling accurate identification of arterial stenosis. On the mixed dataset (including the ARCADE, DCA1, and GH datasets), the model achieved an average IoU of 0.6308, with sensitivity and specificity of 0.9772 and 0.9903, respectively. On the ARCADE dataset, the average IoU was 0.6303, with sensitivity of 0.9832 and specificity of 0.9933. Additionally, the stenosis detection algorithm achieved a true positive rate (TPR) of 0.5867 and a positive predictive value (PPV) of 0.5911, demonstrating the effectiveness of our model in analyzing coronary angiography images. SAM-VMNet offers a promising tool for the automated segmentation and detection of coronary artery stenosis. The model's high accuracy and robustness provide significant clinical value for the early diagnosis and treatment planning of CAD. The code and examples are available at https://github.com/qimingfan10/SAM-VMNet.

  • 6 authors
·
Jun 1, 2024

Did You Really Just Have a Heart Attack? Towards Robust Detection of Personal Health Mentions in Social Media

Millions of users share their experiences on social media sites, such as Twitter, which in turn generate valuable data for public health monitoring, digital epidemiology, and other analyses of population health at global scale. The first, critical, task for these applications is classifying whether a personal health event was mentioned, which we call the (PHM) problem. This task is challenging for many reasons, including typically short length of social media posts, inventive spelling and lexicons, and figurative language, including hyperbole using diseases like "heart attack" or "cancer" for emphasis, and not as a health self-report. This problem is even more challenging for rarely reported, or frequent but ambiguously expressed conditions, such as "stroke". To address this problem, we propose a general, robust method for detecting PHMs in social media, which we call WESPAD, that combines lexical, syntactic, word embedding-based, and context-based features. WESPAD is able to generalize from few examples by automatically distorting the word embedding space to most effectively detect the true health mentions. Unlike previously proposed state-of-the-art supervised and deep-learning techniques, WESPAD requires relatively little training data, which makes it possible to adapt, with minimal effort, to each new disease and condition. We evaluate WESPAD on both an established publicly available Flu detection benchmark, and on a new dataset that we have constructed with mentions of multiple health conditions. Our experiments show that WESPAD outperforms the baselines and state-of-the-art methods, especially in cases when the number and proportion of true health mentions in the training data is small.

  • 2 authors
·
Feb 25, 2018

Generalization in Healthcare AI: Evaluation of a Clinical Large Language Model

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

  • 6 authors
·
Feb 14, 2024

An Electrocardiogram Foundation Model Built on over 10 Million Recordings with External Evaluation across Multiple Domains

Artificial intelligence (AI) has demonstrated significant potential in ECG analysis and cardiovascular disease assessment. Recently, foundation models have played a remarkable role in advancing medical AI. The development of an ECG foundation model holds the promise of elevating AI-ECG research to new heights. However, building such a model faces several challenges, including insufficient database sample sizes and inadequate generalization across multiple domains. Additionally, there is a notable performance gap between single-lead and multi-lead ECG analyses. We introduced an ECG Foundation Model (ECGFounder), a general-purpose model that leverages real-world ECG annotations from cardiology experts to broaden the diagnostic capabilities of ECG analysis. ECGFounder was trained on over 10 million ECGs with 150 label categories from the Harvard-Emory ECG Database, enabling comprehensive cardiovascular disease diagnosis through ECG analysis. The model is designed to be both an effective out-of-the-box solution, and a to be fine-tunable for downstream tasks, maximizing usability. Importantly, we extended its application to lower rank ECGs, and arbitrary single-lead ECGs in particular. ECGFounder is applicable to supporting various downstream tasks in mobile monitoring scenarios. Experimental results demonstrate that ECGFounder achieves expert-level performance on internal validation sets, with AUROC exceeding 0.95 for eighty diagnoses. It also shows strong classification performance and generalization across various diagnoses on external validation sets. When fine-tuned, ECGFounder outperforms baseline models in demographic analysis, clinical event detection, and cross-modality cardiac rhythm diagnosis. The trained model and data will be publicly released upon publication through the bdsp.io. Our code is available at https://github.com/bdsp-core/ECGFounder

  • 9 authors
·
Oct 5, 2024

Beyond Benchmarks: Dynamic, Automatic And Systematic Red-Teaming Agents For Trustworthy Medical Language Models

Ensuring the safety and reliability of large language models (LLMs) in clinical practice is critical to prevent patient harm and promote trustworthy healthcare applications of AI. However, LLMs are advancing so rapidly that static safety benchmarks often become obsolete upon publication, yielding only an incomplete and sometimes misleading picture of model trustworthiness. We demonstrate that a Dynamic, Automatic, and Systematic (DAS) red-teaming framework that continuously stress-tests LLMs can reveal significant weaknesses of current LLMs across four safety-critical domains: robustness, privacy, bias/fairness, and hallucination. A suite of adversarial agents is applied to autonomously mutate test cases, identify/evolve unsafe-triggering strategies, and evaluate responses, uncovering vulnerabilities in real time without human intervention. Applying DAS to 15 proprietary and open-source LLMs revealed a stark contrast between static benchmark performance and vulnerability under adversarial pressure. Despite a median MedQA accuracy exceeding 80\%, 94\% of previously correct answers failed our dynamic robustness tests. We observed similarly high failure rates across other domains: privacy leaks were elicited in 86\% of scenarios, cognitive-bias priming altered clinical recommendations in 81\% of fairness tests, and we identified hallucination rates exceeding 66\% in widely used models. Such profound residual risks are incompatible with routine clinical practice. By converting red-teaming from a static checklist into a dynamic stress-test audit, DAS red-teaming offers the surveillance that hospitals/regulators/technology vendors require as LLMs become embedded in patient chatbots, decision-support dashboards, and broader healthcare workflows. Our framework delivers an evolvable, scalable, and reliable safeguard for the next generation of medical AI.

  • 21 authors
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Jul 30

The Role of AI in Early Detection of Life-Threatening Diseases: A Retinal Imaging Perspective

Retinal imaging has emerged as a powerful, non-invasive modality for detecting and quantifying biomarkers of systemic diseases-ranging from diabetes and hypertension to Alzheimer's disease and cardiovascular disorders but current insights remain dispersed across platforms and specialties. Recent technological advances in optical coherence tomography (OCT/OCTA) and adaptive optics (AO) now deliver ultra-high-resolution scans (down to 5 {\mu}m ) with superior contrast and spatial integration, allowing early identification of microvascular abnormalities and neurodegenerative changes. At the same time, AI-driven and machine learning (ML) algorithms have revolutionized the analysis of large-scale retinal datasets, increasing sensitivity and specificity; for example, deep learning models achieve > 90 \% sensitivity for diabetic retinopathy and AUC = 0.89 for the prediction of cardiovascular risk from fundus photographs. The proliferation of mobile health technologies and telemedicine platforms further extends access, reduces costs, and facilitates community-based screening and longitudinal monitoring. Despite these breakthroughs, translation into routine practice is hindered by heterogeneous imaging protocols, limited external validation of AI models, and integration challenges within clinical workflows. In this review, we systematically synthesize the latest OCT/OCT and AO developments, AI/ML approaches, and mHealth/Tele-ophthalmology initiatives and quantify their diagnostic performance across disease domains. Finally, we propose a roadmap for multicenter protocol standardization, prospective validation trials, and seamless incorporation of retinal screening into primary and specialty care pathways-paving the way for precision prevention, early intervention, and ongoing treatment of life-threatening systemic diseases.

  • 3 authors
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May 27

ClinBench-HPB: A Clinical Benchmark for Evaluating LLMs in Hepato-Pancreato-Biliary Diseases

Hepato-pancreato-biliary (HPB) disorders represent a global public health challenge due to their high morbidity and mortality. Although large language models (LLMs) have shown promising performance in general medical question-answering tasks, the current evaluation benchmarks are mostly derived from standardized examinations or manually designed questions, lacking HPB coverage and clinical cases. To address these issues, we systematically eatablish an HPB disease evaluation benchmark comprising 3,535 closed-ended multiple-choice questions and 337 open-ended real diagnosis cases, which encompasses all the 33 main categories and 465 subcategories of HPB diseases defined in the International Statistical Classification of Diseases, 10th Revision (ICD-10). The multiple-choice questions are curated from public datasets and synthesized data, and the clinical cases are collected from prestigious medical journals, case-sharing platforms, and collaborating hospitals. By evalauting commercial and open-source general and medical LLMs on our established benchmark, namely ClinBench-HBP, we find that while commercial LLMs perform competently on medical exam questions, they exhibit substantial performance degradation on HPB diagnosis tasks, especially on complex, inpatient clinical cases. Those medical LLMs also show limited generalizability to HPB diseases. Our results reveal the critical limitations of current LLMs in the domain of HPB diseases, underscoring the imperative need for future medical LLMs to handle real, complex clinical diagnostics rather than simple medical exam questions. The benchmark will be released at https://clinbench-hpb.github.io.

  • 6 authors
·
May 30

Large Language Models to Identify Social Determinants of Health in Electronic Health Records

Social determinants of health (SDoH) have an important impact on patient outcomes but are incompletely collected from the electronic health records (EHR). This study researched the ability of large language models to extract SDoH from free text in EHRs, where they are most commonly documented, and explored the role of synthetic clinical text for improving the extraction of these scarcely documented, yet extremely valuable, clinical data. 800 patient notes were annotated for SDoH categories, and several transformer-based models were evaluated. The study also experimented with synthetic data generation and assessed for algorithmic bias. Our best-performing models were fine-tuned Flan-T5 XL (macro-F1 0.71) for any SDoH, and Flan-T5 XXL (macro-F1 0.70). The benefit of augmenting fine-tuning with synthetic data varied across model architecture and size, with smaller Flan-T5 models (base and large) showing the greatest improvements in performance (delta F1 +0.12 to +0.23). Model performance was similar on the in-hospital system dataset but worse on the MIMIC-III dataset. Our best-performing fine-tuned models outperformed zero- and few-shot performance of ChatGPT-family models for both tasks. These fine-tuned models were less likely than ChatGPT to change their prediction when race/ethnicity and gender descriptors were added to the text, suggesting less algorithmic bias (p<0.05). At the patient-level, our models identified 93.8% of patients with adverse SDoH, while ICD-10 codes captured 2.0%. Our method can effectively extracted SDoH information from clinic notes, performing better compare to GPT zero- and few-shot settings. These models could enhance real-world evidence on SDoH and aid in identifying patients needing social support.

  • 14 authors
·
Aug 11, 2023

FunnelNet: An End-to-End Deep Learning Framework to Monitor Digital Heart Murmur in Real-Time

Objective: Heart murmurs are abnormal sounds caused by turbulent blood flow within the heart. Several diagnostic methods are available to detect heart murmurs and their severity, such as cardiac auscultation, echocardiography, phonocardiogram (PCG), etc. However, these methods have limitations, including extensive training and experience among healthcare providers, cost and accessibility of echocardiography, as well as noise interference and PCG data processing. This study aims to develop a novel end-to-end real-time heart murmur detection approach using traditional and depthwise separable convolutional networks. Methods: Continuous wavelet transform (CWT) was applied to extract meaningful features from the PCG data. The proposed network has three parts: the Squeeze net, the Bottleneck, and the Expansion net. The Squeeze net generates a compressed data representation, whereas the Bottleneck layer reduces computational complexity using a depthwise-separable convolutional network. The Expansion net is responsible for up-sampling the compressed data to a higher dimension, capturing tiny details of the representative data. Results: For evaluation, we used four publicly available datasets and achieved state-of-the-art performance in all datasets. Furthermore, we tested our proposed network on two resource-constrained devices: a Raspberry PI and an Android device, stripping it down into a tiny machine learning model (TinyML), achieving a maximum of 99.70%. Conclusion: The proposed model offers a deep learning framework for real-time accurate heart murmur detection within limited resources. Significance: It will significantly result in more accessible and practical medical services and reduced diagnosis time to assist medical professionals. The code is publicly available at TBA.

  • 6 authors
·
May 9, 2024

A Machine Learning Approach for Identifying Anatomical Biomarkers of Early Mild Cognitive Impairment

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

  • 6 authors
·
May 29, 2024

Real-time accident detection and physiological signal monitoring to enhance motorbike safety and emergency response

Rapid urbanization and improved living standards have led to a substantial increase in the number of vehicles on the road, consequently resulting in a rise in the frequency of accidents. Among these accidents, motorbike accidents pose a particularly high risk, often resulting in serious injuries or deaths. A significant number of these fatalities occur due to delayed or inadequate medical attention. To this end, we propose a novel automatic detection and notification system specifically designed for motorbike accidents. The proposed system comprises two key components: a detection system and a physiological signal monitoring system. The detection system is integrated into the helmet and consists of a microcontroller, accelerometer, GPS, GSM, and Wi-Fi modules. The physio-monitoring system incorporates a sensor for monitoring pulse rate and SpO_{2} saturation. All collected data are presented on an LCD display and wirelessly transmitted to the detection system through the microcontroller of the physiological signal monitoring system. If the accelerometer readings consistently deviate from the specified threshold decided through extensive experimentation, the system identifies the event as an accident and transmits the victim's information -- including the GPS location, pulse rate, and SpO_{2} saturation rate -- to the designated emergency contacts. Preliminary results demonstrate the efficacy of the proposed system in accurately detecting motorbike accidents and promptly alerting emergency contacts. We firmly believe that the proposed system has the potential to significantly mitigate the risks associated with motorbike accidents and save lives.

  • 7 authors
·
Mar 27, 2024

AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease

Objective: We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). Materials and Methods: We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000-2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting, and then pretrained a BERT model for AD (AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. The embeddings of all the sections of a patient's notes processed by AD-BERT were combined by MaxPooling to compute the probability of MCI-to-AD progression. For replication, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. Results: Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.8170 and F1 score of 0.4178 on NMEDW dataset and AUC of 0.8830 and F1 score of 0.6836 on WCM dataset. Conclusion: We developed a deep learning framework using BERT models which provide an effective solution for prediction of MCI-to-AD progression using clinical note analysis.

  • 12 authors
·
Nov 6, 2022

EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical Text

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

  • 11 authors
·
Apr 16, 2023

A Toolbox for Surfacing Health Equity Harms and Biases in Large Language Models

Large language models (LLMs) hold immense promise to serve complex health information needs but also have the potential to introduce harm and exacerbate health disparities. Reliably evaluating equity-related model failures is a critical step toward developing systems that promote health equity. In this work, we present resources and methodologies for surfacing biases with potential to precipitate equity-related harms in long-form, LLM-generated answers to medical questions and then conduct an empirical case study with Med-PaLM 2, resulting in the largest human evaluation study in this area to date. Our contributions include a multifactorial framework for human assessment of LLM-generated answers for biases, and EquityMedQA, a collection of seven newly-released datasets comprising both manually-curated and LLM-generated questions enriched for adversarial queries. Both our human assessment framework and dataset design process are grounded in an iterative participatory approach and review of possible biases in Med-PaLM 2 answers to adversarial queries. Through our empirical study, we find that the use of a collection of datasets curated through a variety of methodologies, coupled with a thorough evaluation protocol that leverages multiple assessment rubric designs and diverse rater groups, surfaces biases that may be missed via narrower evaluation approaches. Our experience underscores the importance of using diverse assessment methodologies and involving raters of varying backgrounds and expertise. We emphasize that while our framework can identify specific forms of bias, it is not sufficient to holistically assess whether the deployment of an AI system promotes equitable health outcomes. We hope the broader community leverages and builds on these tools and methods towards realizing a shared goal of LLMs that promote accessible and equitable healthcare for all.

  • 30 authors
·
Mar 18, 2024

ECGNet: A generative adversarial network (GAN) approach to the synthesis of 12-lead ECG signals from single lead inputs

Electrocardiography (ECG) signal generation has been heavily explored using generative adversarial networks (GAN) because the implementation of 12-lead ECGs is not always feasible. The GAN models have achieved remarkable results in reproducing ECG signals but are only designed for multiple lead inputs and the features the GAN model preserves have not been identified-limiting the generated signals use in cardiovascular disease (CVD)-predictive models. This paper presents ECGNet which is a procedure that generates a complete set of 12-lead ECG signals from any single lead input using a GAN framework with a bidirectional long short-term memory (LSTM) generator and a convolutional neural network (CNN) discriminator. Cross and auto-correlation analysis performed on the generated signals identifies features conserved during the signal generation-i.e., features that can characterize the unique-nature of each signal and thus likely indicators of CVD. Finally, by using ECG signals annotated with the CVD-indicative features detailed by the correlation analysis as inputs for a CVD-onset-predictive CNN model, we overcome challenges preventing the prediction of multiple-CVD targets. Our models are experimented on 15s 12-lead ECG dataset recorded using MyoVista's wavECG. Functional outcome data for each patient is recorded and used in the CVD-predictive model. Our best GAN model achieves state-of-the-art accuracy with Frechet Distance (FD) scores of 4.73, 4.89, 5.18, 4.77, 4.71, and 5.55 on the V1-V6 pre-cordial leads respectively and shows strength in preserving the P-Q segments and R-peaks in the generated signals. To the best of our knowledge, ECGNet is the first to predict all of the remaining eleven leads from the input of any single lead.

  • 3 authors
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Sep 23, 2023