Exploring explainable AI features in the vocal biomarkers of lung disease.

This review delves into the burgeoning field of explainable artificial intelligence (XAI) in the detection and analysis of lung diseases through vocal biomarkers. Lung diseases, often elusive in their early stages, pose a significant public health challenge. Recent advancements in AI have ushered in innovative methods for early detection, yet the black-box nature of many AI models limits their clinical applicability. XAI emerges as a pivotal tool, enhancing transparency and interpretability in AI-driven diagnostics. This review synthesizes current research on the application of XAI in analyzing vocal biomarkers for lung diseases, highlighting how these techniques elucidate the connections between specific vocal features and lung pathology. We critically examine the methodologies employed, the types of lung diseases studied, and the performance of various XAI models. The potential for XAI to aid in early detection, monitor disease progression, and personalize treatment strategies in pulmonary medicine is emphasized. Furthermore, this review identifies current challenges, including data heterogeneity and model generalizability, and proposes future directions for research. By offering a comprehensive analysis of explainable AI features in the context of lung disease detection, this review aims to bridge the gap between advanced computational approaches and clinical practice, paving the way for more transparent, reliable, and effective diagnostic tools.

Interpretable clinical phenotypes among patients hospitalized with COVID-19 using cluster analysis.

Background: Multiple clinical phenotypes have been proposed for coronavirus disease (COVID-19), but few have used multimodal data. Using clinical and imaging data, we aimed to identify distinct clinical phenotypes in patients admitted with COVID-19 and to assess their clinical outcomes. Our secondary objective was to demonstrate the clinical applicability of this method by developing an interpretable model for phenotype assignment. Methods: We analyzed data from 547 patients hospitalized with COVID-19 at a Canadian academic hospital. We processed the data by applying a factor analysis of mixed data (FAMD) and compared four clustering algorithms: k-means, partitioning around medoids (PAM), and divisive and agglomerative hierarchical clustering. We used imaging data and 34 clinical variables collected within the first 24 h of admission to train our algorithm. We conducted a survival analysis to compare the clinical outcomes across phenotypes. With the data split into training and validation sets (75/25 ratio), we developed a decision-tree-based model to facilitate the interpretation and assignment of the observed phenotypes. Results: Agglomerative hierarchical clustering was the most robust algorithm. We identified three clinical phenotypes: 79 patients (14%) in Cluster 1, 275 patients (50%) in Cluster 2, and 203 (37%) in Cluster 3. Cluster 2 and Cluster 3 were both characterized by a low-risk respiratory and inflammatory profile but differed in terms of demographics. Compared with Cluster 3, Cluster 2 comprised older patients with more comorbidities. Cluster 1 represented the group with the most severe clinical presentation, as inferred by the highest rate of hypoxemia and the highest radiological burden. Intensive care unit (ICU) admission and mechanical ventilation risks were the highest in Cluster 1. Using only two to four decision rules, the classification and regression tree (CART) phenotype assignment model achieved an AUC of 84% (81.5-86.5%, 95 CI) on the validation set. Conclusions: We conducted a multidimensional phenotypic analysis of adult inpatients with COVID-19 and identified three distinct phenotypes associated with different clinical outcomes. We also demonstrated the clinical usability of this approach, as phenotypes can be accurately assigned using a simple decision tree. Further research is still needed to properly incorporate these phenotypes in the management of patients with COVID-19.

Machine Learning Models for the Automatic Detection of Exercise Thresholds in Cardiopulmonary Exercising Tests: From Regression to Generation to Explanation.

The cardiopulmonary exercise test (CPET) constitutes a gold standard for the assessment of an individual's cardiovascular fitness. A trend is emerging for the development of new machine-learning techniques applied to the automatic process of CPET data. Some of these focus on the precise task of detecting the exercise thresholds, which represent important physiological parameters. Three are the major challenges tackled by this contribution: (A) regression (i.e., the process of correctly identifying the exercise intensity domains and their crossing points); (B) generation (i.e., the process of artificially creating a CPET data file ex-novo); and (C) explanation (i.e., proving an interpretable explanation about the output of the machine learning model). The following methods were used for each challenge: (A) a convolutional neural network adapted for multi-variable time series; (B) a conditional generative adversarial neural network; and (C) visual explanations and calculations of model decisions have been conducted using cooperative game theory (Shapley's values). The results for the regression, generation, and explanatory techniques for AI-assisted CPET interpretation are presented here in a unique framework for the first time: (A) machine learning techniques reported an expert-level accuracy in the classification of exercise intensity domains; (B) experts are not able to substantially differentiate between a real vs an artificially generated CPET; and (C) Shapley's values can provide an explanation about the choices of the algorithms in terms of ventilatory variables. With the aim to increase their technology-readiness level, all the models discussed in this contribution have been incorporated into a free-to-use Python package called pyoxynet (ver. 12.1). This contribution should therefore be of interest to major players operating in the CPET device market and engineering.

Consistency of Feature Importance Algorithms for Interpretable EEG Abnormality Detection.

Recent advances in machine learning show great potential for automatic detection of abnormalities in electroencephalography (EEG). While simple and interpretable models combined with expert-comprehensible input features offer full control of the decision making process, these methods commonly lag behind complex deep learning and feature extraction methods in terms of performance. Here we study a feasibility of a bridging solution, where deep learning is combined with interpretable input and an algorithm computing the importance of particular EEG features in the decision process. We built a convolutional neural network with multi-channel EEG frequency bands as input and investigated four different methods for feature importance attribution: Layer-wise Relevance Propagation (LRP), DeepLIFT, Integrated Gradients (IG) and Guided GradCAM. Our analysis showed consistency between the first three methods, and deviating attributions of the fourth method, suggesting the importance of using a package of methods together to ensure the robustness of medical interpretation.

CoVEffect: interactive system for mining the effects of SARS-CoV-2 mutations and variants based on deep learning.

BACKGROUND: Literature about SARS-CoV-2 widely discusses the effects of variations that have spread in the past 3 years. Such information is dispersed in the texts of several research articles, hindering the possibility of practically integrating it with related datasets (e.g., millions of SARS-CoV-2 sequences available to the community). We aim to fill this gap, by mining literature abstracts to extract-for each variant/mutation-its related effects (in epidemiological, immunological, clinical, or viral kinetics terms) with labeled higher/lower levels in relation to the nonmutated virus. RESULTS: The proposed framework comprises (i) the provisioning of abstracts from a COVID-19-related big data corpus (CORD-19) and (ii) the identification of mutation/variant effects in abstracts using a GPT2-based prediction model. The above techniques enable the prediction of mutations/variants with their effects and levels in 2 distinct scenarios: (i) the batch annotation of the most relevant CORD-19 abstracts and (ii) the on-demand annotation of any user-selected CORD-19 abstract through the CoVEffect web application (http://gmql.eu/coveffect), which assists expert users with semiautomated data labeling. On the interface, users can inspect the predictions and correct them; user inputs can then extend the training dataset used by the prediction model. Our prototype model was trained through a carefully designed process, using a minimal and highly diversified pool of samples. CONCLUSIONS: The CoVEffect interface serves for the assisted annotation of abstracts, allowing the download of curated datasets for further use in data integration or analysis pipelines. The overall framework can be adapted to resolve similar unstructured-to-structured text translation tasks, which are typical of biomedical domains.

A Trust-Based Methodology to Evaluate Deep Learning Models for Automatic Diagnosis of Ocular Toxoplasmosis from Fundus Images.

In the automatic diagnosis of ocular toxoplasmosis (OT), Deep Learning (DL) has arisen as a powerful and promising approach for diagnosis. However, despite the good performance of the models, decision rules should be interpretable to elicit trust from the medical community. Therefore, the development of an evaluation methodology to assess DL models based on interpretability methods is a challenging task that is necessary to extend the use of AI among clinicians. In this work, we propose a novel methodology to quantify the similarity between the decision rules used by a DL model and an ophthalmologist, based on the assumption that doctors are more likely to trust a prediction that was based on decision rules they can understand. Given an eye fundus image with OT, the proposed methodology compares the segmentation mask of OT lesions labeled by an ophthalmologist with the attribution matrix produced by interpretability methods. Furthermore, an open dataset that includes the eye fundus images and the segmentation masks is shared with the community. The proposal was tested on three different DL architectures. The results suggest that complex models tend to perform worse in terms of likelihood to be trusted while achieving better results in sensitivity and specificity.

Driftage: a multi-agent system framework for concept drift detection.

BACKGROUND: The amount of data and behavior changes in society happens at a swift pace in this interconnected world. Consequently, machine learning algorithms lose accuracy because they do not know these new patterns. This change in the data pattern is known as concept drift. There exist many approaches for dealing with these drifts. Usually, these methods are costly to implement because they require (i) knowledge of drift detection algorithms, (ii) software engineering strategies, and (iii) continuous maintenance concerning new drifts. RESULTS: This article proposes to create Driftage: a new framework using multi-agent systems to simplify the implementation of concept drift detectors considerably and divide concept drift detection responsibilities between agents, enhancing explainability of each part of drift detection. As a case study, we illustrate our strategy using a muscle activity monitor of electromyography. We show a reduction in the number of false-positive drifts detected, improving detection interpretability, and enabling concept drift detectors' interactivity with other knowledge bases. CONCLUSION: We conclude that using Driftage, arises a new paradigm to implement concept drift algorithms with multi-agent architecture that contributes to split drift detection responsability, algorithms interpretability and more dynamic algorithms adaptation.

Utility of deep learning super-resolution in the context of osteoarthritis MRI biomarkers.

BACKGROUND: Super-resolution is an emerging method for enhancing MRI resolution; however, its impact on image quality is still unknown. PURPOSE: To evaluate MRI super-resolution using quantitative and qualitative metrics of cartilage morphometry, osteophyte detection, and global image blurring. STUDY TYPE: Retrospective. POPULATION: In all, 176 MRI studies of subjects at varying stages of osteoarthritis. FIELD STRENGTH/SEQUENCE: Original-resolution 3D double-echo steady-state (DESS) and DESS with 3× thicker slices retrospectively enhanced using super-resolution and tricubic interpolation (TCI) at 3T. ASSESSMENT: A quantitative comparison of femoral cartilage morphometry was performed for the original-resolution DESS, the super-resolution, and the TCI scans in 17 subjects. A reader study by three musculoskeletal radiologists assessed cartilage image quality, overall image sharpness, and osteophytes incidence in all three sets of scans. A referenceless blurring metric evaluated blurring in all three image dimensions for the three sets of scans. STATISTICAL TESTS: Mann-Whitney U-tests compared Dice coefficients (DC) of segmentation accuracy for the DESS, super-resolution, and TCI images, along with the image quality readings and blurring metrics. Sensitivity, specificity, and diagnostic odds ratio (DOR) with 95% confidence intervals compared osteophyte detection for the super-resolution and TCI images, with the original-resolution as a reference. RESULTS: DC for the original-resolution (90.2 ± 1.7%) and super-resolution (89.6 ± 2.0%) were significantly higher (P < 0.001) than TCI (86.3 ± 5.6%). Segmentation overlap of super-resolution with the original-resolution (DC = 97.6 ± 0.7%) was significantly higher (P < 0.0001) than TCI overlap (DC = 95.0 ± 1.1%). Cartilage image quality for sharpness and contrast levels, and the through-plane quantitative blur factor for super-resolution images, was significantly (P < 0.001) better than TCI. Super-resolution osteophyte detection sensitivity of 80% (76-82%), specificity of 93% (92-94%), and DOR of 32 (22-46) was significantly higher (P < 0.001) than TCI sensitivity of 73% (69-76%), specificity of 90% (89-91%), and DOR of 17 (13-22). DATA CONCLUSION: Super-resolution appears to consistently outperform naïve interpolation and may improve image quality without biasing quantitative biomarkers. LEVEL OF EVIDENCE: 2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2020;51:768-779.