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1. Empowering Variational Inference with Predictive Features: Application to Disease Suptypying

   Ardavan Saeedi, Payman Yadollahpour ( January 2021 , Proceedings of Machine Learning Research)

   null (Ed.)

   Probabilistic topic models, have been widely deployed for various applications such as learning disease or tissue subtypes. Yet, learning the parameters of such models is usually an ill-posed problem and may result in losing valuable information about disease severity. A common approach is to add a discriminative loss term to the generative model’s loss in order to learn a representation that is also predictive of disease severity. However, finding a balance between these two losses is not straightforward. We propose an alternative way in this paper. We develop a framework which allows for incorporating external covariates into the generative model’s approximate posterior. These covariates can have more discriminative power for disease severity compared to the representation that we extract from the posterior distribution. For instance, they can be features extracted from a neural network which predicts disease severity from CT images. Effectively, we enforce the generative model’s approximate posterior to reside in the subspace of these discriminative covariates. We illustrate our method’s application on a large-scale lung CT study of Chronic Obstructive Pulmonary Disease (COPD), a highly heterogeneous disease. We aim at identifying tissue subtypes by using a variant of topic model as a generative model. We quantitatively evaluate the predictive performance of the inferred subtypes and demonstrate that our method outperforms or performs on par with some reasonable baselines. We also show that some of the discovered subtypes are correlated with genetic measurements, suggesting that the identified subtypes may characterize the disease’s underlying etiology. 

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2. Early Diagnosis and Real-Time Monitoring of Regional Lung Function Changes to Prevent Chronic Obstructive Pulmonary Disease Progression to Severe Emphysema

   https://doi.org/10.3390/jcm10245811  

   Jung, Tony ; Vij, Neeraj ( December 2021 , Journal of Clinical Medicine)

   First- and second-hand exposure to smoke or air pollutants is the primary cause of chronic obstructive pulmonary disease (COPD) pathogenesis, where genetic and age-related factors predispose the subject to the initiation and progression of obstructive lung disease. Briefly, airway inflammation, specifically bronchitis, initiates the lung disease, leading to difficulty in breathing (dyspnea) and coughing as initial symptoms, followed by air trapping and inhibition of the flow of air into the lungs due to damage to the alveoli (emphysema). In addition, mucus obstruction and impaired lung clearance mechanisms lead to recurring acute exacerbations causing progressive decline in lung function, eventually requiring lung transplant and other lifesaving interventions to prevent mortality. It is noteworthy that COPD is much more common in the population than currently diagnosed, as only 16 million adult Americans were reported to be diagnosed with COPD as of 2018, although an additional 14 million American adults were estimated to be suffering from COPD but undiagnosed by the current standard of care (SOC) diagnostic, namely the spirometry-based pulmonary function test (PFT). Thus, the main issue driving the adverse disease outcome and significant mortality for COPD is lack of timely diagnosis in the early stages of the disease. The current treatment regime for COPD emphysema is most effective when implemented early, on COPD onset, where alleviating symptoms and exacerbations with timely intervention(s) can prevent steep lung function decline(s) and disease progression to severe emphysema. Therefore, the key to efficiently combatting COPD relies on early detection. Thus, it is important to detect early regional pulmonary function and structural changes to monitor modest disease progression for implementing timely interventions and effectively eliminating emphysema progression. Currently, COPD diagnosis involves using techniques such as COPD screening questionnaires, PFT, arterial blood gas analysis, and/or lung imaging, but these modalities are limited in their capability for early diagnosis and real-time disease monitoring of regional lung function changes. Hence, promising emerging techniques, such as X-ray phase contrast, photoacoustic tomography, ultrasound computed tomography, electrical impedance tomography, the forced oscillation technique, and the impulse oscillometry system powered by robust artificial intelligence and machine learning analysis capability are emerging as novel solutions for early detection and real time monitoring of COPD progression for timely intervention. We discuss here the scope, risks, and limitations of current SOC and emerging COPD diagnostics, with perspective on novel diagnostics providing real time regional lung function monitoring, and predicting exacerbation and/or disease onset for prognosis-based timely intervention(s) to limit COPD–emphysema progression. 

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3. Fractional Dynamics Foster Deep Learning of COPD Stage Prediction

   https://doi.org/10.1002/advs.202203485  

   Yin, Chenzhong ; Udrescu, Mihai ; Gupta, Gaurav ; Cheng, Mingxi ; Lihu, Andrei ; Udrescu, Lucretia ; Bogdan, Paul ; Mannino, David M. ; Mihaicuta, Stefan ( February 2023 , Advanced Science)

   Chronic obstructive pulmonary disease (COPD) is one of the leading causes of death worldwide. Current COPD diagnosis (i.e., spirometry) could be unreliable because the test depends on an adequate effort from the tester and testee. Moreover, the early diagnosis of COPD is challenging. The authors address COPD detection by constructing two novel physiological signals datasets (4432 records from 54 patients in the WestRo COPD dataset and 13824 medical records from 534 patients in the WestRo Porti COPD dataset). The authors demonstrate their complex coupled fractal dynamical characteristics and perform a fractional‐order dynamics deep learning analysis to diagnose COPD. The authors found that the fractional‐order dynamical modeling can extract distinguishing signatures from the physiological signals across patients with all COPD stages—from stage 0 (healthy) to stage 4 (very severe). They use the fractional signatures to develop and train a deep neural network that predicts COPD stages based on the input features (such as thorax breathing effort, respiratory rate, or oxygen saturation). The authors show that the fractional dynamic deep learning model (FDDLM) achieves a COPD prediction accuracy of 98.66% and can serve as a robust alternative to spirometry. The FDDLM also has high accuracy when validated on a dataset with different physiological signals.

    

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4. Bayesian inference of networks across multiple sample groups and data types

   https://doi.org/10.1093/biostatistics/kxy078  

   Shaddox, Elin ; Peterson, Christine B ; Stingo, Francesco C ; Hanania, Nicola A ; Cruickshank-Quinn, Charmion ; Kechris, Katerina ; Bowler, Russell ; Vannucci, Marina ( December 2018 , Biostatistics)

   null (Ed.)

   Summary In this article, we develop a graphical modeling framework for the inference of networks across multiple sample groups and data types. In medical studies, this setting arises whenever a set of subjects, which may be heterogeneous due to differing disease stage or subtype, is profiled across multiple platforms, such as metabolomics, proteomics, or transcriptomics data. Our proposed Bayesian hierarchical model first links the network structures within each platform using a Markov random field prior to relate edge selection across sample groups, and then links the network similarity parameters across platforms. This enables joint estimation in a flexible manner, as we make no assumptions on the directionality of influence across the data types or the extent of network similarity across the sample groups and platforms. In addition, our model formulation allows the number of variables and number of subjects to differ across the data types, and only requires that we have data for the same set of groups. We illustrate the proposed approach through both simulation studies and an application to gene expression levels and metabolite abundances on subjects with varying severity levels of chronic obstructive pulmonary disease. Bayesian inference; Chronic obstructive pulmonary disease (COPD); Data integration; Gaussian graphical model; Markov random field prior; Spike and slab prior. 

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5. Out-Clinic Pulmonary Disease Evaluation via Acoustic Sensing and Multi-Task Learning on Commodity Smartphones

   https://doi.org/10.1145/3560905.3568437  

   Yin, Xiangyu ; Huang, Kai ; Forno, Erick ; Chen, Wei ; Huang, Heng ; Gao, Wei ( November 2022 , Proceedings of the 20th ACM Conference on Embedded Networked Sensor Systems)

   Pulmonary diseases, such as asthma and Chronic Obstructive Pulmonary Disease (COPD), constitute a major public health challenge. The disease symptoms, including airway obstruction and inflammation, usually result in changes in airway mechanical properties, such as the caliber and impedance of the airway. To measure such airway properties for disease evaluation and diagnosis purposes, pulmonary function tests (PFT) has been widely adopted. However, most existing PFT systems require expensive and cumbersome hardware that are impossible to be used out of clinic. To allow out-clinic continuous pulmonary disease evaluation, in this paper we present AWARE, a new sensing and AI system that supports accurate and reliable PFT using commodity smartphones. AWARE uses a smartphone to transmit acoustic signals and reconstructs the profile of human airway based on the analysis of reflected acoustic waves captured from the smartphone's microphone. The subject's pulmonary condition is then evaluated by a multi-task learning model that integrates both the airway measurements and the subject's lung function records as the ground truth. Evaluations on 75 human subjects demonstrate that AWARE has the capability to achieve 80% accuracy on distinguishing between humans with healthy pulmonary function and with asthma symptoms. 

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