Automated feature extraction from MRI brain scans and diagnosis of Alzheimer's disease are ongoing challenges. With advances in 3D imaging technology, 3D data acquisition is becoming more viable and efficient than its 2D counterpart. Rather than using feature-based vectors, in this paper, for the first time, we suggest a pipeline to extract novel covariance-based descriptors from the cortical surface using the Ricci energy optimization. The covariance descriptors are components of the nonlinear manifold of symmetric positive-definite matrices, thus we focus on using the Gaussian radial basis function to apply manifold-based classification to the 3D shape problem. Applying this novel signature to the analysis of abnormal cortical brain morphometry allows for diagnosing Alzheimer's disease. Experimental studies performed on about two hundred 3D MRI brain models, gathered from Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate the effectiveness of our descriptors in achieving remarkable classification accuracy.
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Randomized trials are considered the gold standard for making informed decisions in medicine, yet they often lack generalizability to the patient populations in clinical practice. Observational studies, on the other hand, cover a broader patient population but are prone to various biases. Thus, before using an observational study for decision-making, it is crucial to benchmark its treatment effect estimates against those derived from a randomized trial. We propose a novel strategy to benchmark observational studies beyond the average treatment effect. First, we design a statistical test for the null hypothesis that the treatment effects estimated from the two studies, conditioned on a set of relevant features, differ up to some tolerance. We then estimate an asymptotically valid lower bound on the maximum bias strength for any subgroup in the observational study. Finally, we validate our benchmarking strategy in a real-world setting and show that it leads to conclusions that align with established medical knowledge.
The effective control of infectious diseases relies on accurate assessment of the impact of interventions, which is often hindered by the complex dynamics of the spread of disease. A Beta-Dirichlet switching state-space transmission model is proposed to track underlying dynamics of disease and evaluate the effectiveness of interventions simultaneously. As time evolves, the switching mechanism introduced in the susceptible-exposed-infected-recovered (SEIR) model is able to capture the timing and magnitude of changes in the transmission rate due to the effectiveness of control measures. The implementation of this model is based on a particle Markov Chain Monte Carlo algorithm, which can estimate the time evolution of SEIR states, switching states, and high-dimensional parameters efficiently. The efficacy of the proposed model and estimation procedure are demonstrated through simulation studies. With a real-world application to British Columbia's COVID-19 outbreak, the proposed switching state-space transmission model quantifies the reduction of transmission rate following interventions. The proposed model provides a promising tool to inform public health policies aimed at studying the underlying dynamics and evaluating the effectiveness of interventions during the spread of the disease.
Machine Learning (ML) has demonstrated its great potential on medical data analysis. Large datasets collected from diverse sources and settings are essential for ML models in healthcare to achieve better accuracy and generalizability. Sharing data across different healthcare institutions is challenging because of complex and varying privacy and regulatory requirements. Hence, it is hard but crucial to allow multiple parties to collaboratively train an ML model leveraging the private datasets available at each party without the need for direct sharing of those datasets or compromising the privacy of the datasets through collaboration. In this paper, we address this challenge by proposing Decentralized, Collaborative, and Privacy-preserving ML for Multi-Hospital Data (DeCaPH). It offers the following key benefits: (1) it allows different parties to collaboratively train an ML model without transferring their private datasets; (2) it safeguards patient privacy by limiting the potential privacy leakage arising from any contents shared across the parties during the training process; and (3) it facilitates the ML model training without relying on a centralized server. We demonstrate the generalizability and power of DeCaPH on three distinct tasks using real-world distributed medical datasets: patient mortality prediction using electronic health records, cell-type classification using single-cell human genomes, and pathology identification using chest radiology images. We demonstrate that the ML models trained with DeCaPH framework have an improved utility-privacy trade-off, showing it enables the models to have good performance while preserving the privacy of the training data points. In addition, the ML models trained with DeCaPH framework in general outperform those trained solely with the private datasets from individual parties, showing that DeCaPH enhances the model generalizability.
In driving tasks, the driver's situation awareness of the surrounding scenario is crucial for safety driving. However, current methods of measuring situation awareness mostly rely on subjective questionnaires, which interrupt tasks and lack non-intrusive quantification. To address this issue, our study utilizes objective gaze motion data to provide an interference-free quantification method for situation awareness. Three quantitative scores are proposed to represent three different levels of awareness: perception, comprehension, and projection, and an overall score of situation awareness is also proposed based on above three scores. To validate our findings, we conducted experiments where subjects performed driving tasks in a virtual reality simulated environment. All the four proposed situation awareness scores have clearly shown a significant correlation with driving performance. The proposed not only illuminates a new path for understanding and evaluating the situation awareness but also offers a satisfying proxy for driving performance.
Shariat et al previously investigated the possibility of predicting, from preoperative biomarkers and clinical data, which of any pair of patients would suffer recurrence of prostate cancer first. We wished to establish the extent to which predictions of time of relapse from such a model could be improved upon using Bayesian methodology. The same dataset was reanalysed using a Bayesian skew-Student mixture model. Predictions were made of which of any pair of patients would relapse first and of the time of relapse. The benefit of using these biomarkers relative to predictions made without them, was measured by the apparent Shannon information, using as prior a simple exponential attrition model of relapse time independent of input variables. Using half the dataset for training and the other half for testing, predictions of relapse time from the strict Cox model gave $-\infty$ nepers of apparent Shannon information, (it predicts that relapse can only occur at times when patients in the training set relapsed). Deliberately smoothed predictions from the Cox model gave -0.001 (-0.131 to +0.120) nepers, while the Bayesian model gave +0.109 (+0.021 to +0.192) nepers (mean, 2.5 to 97.5 centiles), being positive with posterior probability 0.993 and beating the blurred Cox model with posterior probability 0.927. These predictions from the Bayesian model thus outperform those of the Cox model, but the overall yield of predictive information leaves scope for improvement of the range of biomarkers in use. The Bayesian model presented here is the first such model for prostate cancer to consider the variation of relapse hazard with biomarker concentrations to be smooth, as is intuitive. It is also the first model to be shown to provide more apparent Shannon information than the Cox model and the first to be shown to provide positive apparent information relative to an exponential prior.
Recent genome-wide association studies (GWAS) have uncovered the genetic basis of complex traits, but show an under-representation of non-European descent individuals, underscoring a critical gap in genetic research. Here, we assess whether we can improve disease prediction across diverse ancestries using multiomic data. We evaluate the performance of Group-LASSO INTERaction-NET (glinternet) and pretrained lasso in disease prediction focusing on diverse ancestries in the UK Biobank. Models were trained on data from White British and other ancestries and validated across a cohort of over 96,000 individuals for 8 diseases. Out of 96 models trained, we report 16 with statistically significant incremental predictive performance in terms of ROC-AUC scores. These findings suggest that advanced statistical methods that borrow information across multiple ancestries may improve disease risk prediction, but with limited benefit.
Logistic regression is widely used in many areas of knowledge. Several works compare the performance of lasso and maximum likelihood estimation in logistic regression. However, part of these works do not perform simulation studies and the remaining ones do not consider scenarios in which the ratio of the number of covariates to sample size is high. In this work, we compare the discrimination performance of lasso and maximum likelihood estimation in logistic regression using simulation studies and applications. Variable selection is done both by lasso and by stepwise when maximum likelihood estimation is used. We consider a wide range of values for the ratio of the number of covariates to sample size. The main conclusion of the work is that lasso has a better discrimination performance than maximum likelihood estimation when the ratio of the number of covariates to sample size is high.
Open Information Extraction (OpenIE) represents a crucial NLP task aimed at deriving structured information from unstructured text, unrestricted by relation type or domain. This survey paper provides an overview of OpenIE technologies spanning from 2007 to 2024, emphasizing a chronological perspective absent in prior surveys. It examines the evolution of task settings in OpenIE to align with the advances in recent technologies. The paper categorizes OpenIE approaches into rule-based, neural, and pre-trained large language models, discussing each within a chronological framework. Additionally, it highlights prevalent datasets and evaluation metrics currently in use. Building on this extensive review, the paper outlines potential future directions in terms of datasets, information sources, output formats, methodologies, and evaluation metrics.
Image reconstruction is an essential step of every medical imaging method, including Photoacoustic Tomography (PAT), which is a promising modality of imaging, that unites the benefits of both ultrasound and optical imaging methods. Reconstruction of PAT images using conventional methods results in rough artifacts, especially when applied directly to sparse PAT data. In recent years, generative adversarial networks (GANs) have shown a powerful performance in image generation as well as translation, rendering them a smart choice to be applied to reconstruction tasks. In this study, we proposed an end-to-end method called DensePANet to solve the problem of PAT image reconstruction from sparse data. The proposed model employs a novel modification of UNet in its generator, called FD-UNet++, which considerably improves the reconstruction performance. We evaluated the method on various in-vivo and simulated datasets. Quantitative and qualitative results show the better performance of our model over other prevalent deep learning techniques.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
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