What can artificial intelligence teach us about the molecular mechanisms underlying disease?

Dallal Bashi O, Nik Ali N, Mahmood Al Kubaisi Y. Lung disease recognition methods using audio-based analysis with machine learning

The use of computer-based automated approaches and improvements in lung sound recording techniques have made lung sound-based diagnostics even better and devoid of subjectivity errors. Using a computer to evaluate lung sound features more thoroughly with the use of analyzing changes in lung sound behavior, recording measurements, suppressing the presence of noise contaminations, and graphical representations are all made possible by computer-based lung sound analysis. This paper starts with a discussion of the need for this research area, providing an overview of the field and the motivations behind it. Following that, it details the survey methodology used in this work. It presents a discussion on the elements of sound-based lung disease classification using machine learning algorithms. This includes commonly prior considered datasets, feature extraction techniques, pre-processing methods, artifact removal methods, lung-heart sound separation, deep learning algorithms, and wavelet transform of lung audio signals. The study introduces studies that review lung screening including a summary table of these references and discusses the literature gaps in the existing studies. It is concluded that the use of sound-based machine learning in the classification of respiratory diseases has promising results. While we believe this material will prove valuable to physicians and researchers exploring sound-signal-based machine learning, large-scale investigations remain essential to solidify the findings and foster wider adoption within the medical community.

Implications of Activating the ANT2/mTOR/PGC-1α Feedback Loop: Insights into Mitochondria-Mediated Injury in Hypoxic Myocardial Cells

Mitochondrial dysfunction is known to play a critical role in the development of cardiomyocyte death during acute myocardial infarction (AMI). However, the exact mechanisms underlying this dysfunction are still under investigation. Adenine nucleotide translocase 2 (ANT2) is a key functional protein in mitochondria. We aimed at exploring the potential benefits of ANT2 inhibition against AMI. We utilized an oxygen-glucose deprivation (OGD) cell model and an AMI mice model to detect cardiomyocyte injury. We observed elevated levels of reactive oxygen species (ROS), disrupted mitochondrial membrane potential (MMP), and increased apoptosis due to the overexpression of ANT2. Additionally, we discovered that ANT2 is involved in myocardial apoptosis by activating the mTOR (mechanistic target of rapamycin kinase)-dependent PGC-1α (PPARG coactivator 1 alpha) pathway, establishing a novel feedback loop during AMI. In our experiments with AC16 cells under OGD conditions, we observed protective effects when transfected with ANT2 siRNA and miR-1203. Importantly, the overexpression of ANT2 counteracted the protective effect resulting from miR-1203 upregulation in OGD-induced AC16 cells. All these results supported that the inhibition of ANT2 could alleviate myocardial cell injury under OGD conditions. Based on these findings, we propose that RNA interference (RNAi) technology, specifically miRNA and siRNA, holds therapeutic potential by activating the ANT2/mTOR/PGC-1α feedback loop. This activation could help mitigate mitochondria-mediated injury in the context of AMI. These insights may contribute to the development of future clinical strategies for AMI.

A review on lung disease recognition by acoustic signal analysis with deep learning networks

Recently, assistive explanations for difficulties in the health check area have been made viable thanks in considerable portion to technologies like deep learning and machine learning. Using auditory analysis and medical imaging, they also increase the predictive accuracy for prompt and early disease detection. Medical professionals are thankful for such technological support since it helps them manage further patients because of the shortage of skilled human resources. In addition to serious illnesses like lung cancer and respiratory diseases, the plurality of breathing difficulties is gradually rising and endangering society. Because early prediction and immediate treatment are crucial for respiratory disorders, chest X-rays and respiratory sound audio are proving to be quite helpful together. Compared to related review studies on lung disease classification/detection using deep learning algorithms, only two review studies based on signal analysis for lung disease diagnosis have been conducted in 2011 and 2018. This work provides a review of lung disease recognition with acoustic signal analysis with deep learning networks. We anticipate that physicians and researchers working with sound-signal-based machine learning will find this material beneficial.

Deep Neural Networks and Machine Learning Radiomics Modelling for Prediction of Relapse in Mantle Cell Lymphoma

Simple Summary

Mantle cell lymphoma (MCL) is an aggressive lymphoid tumour with a poor prognosis. There exist no routine biomarkers for the early prediction of relapse. Our study compared the potential of radiomics-based machine learning and 3D deep learning models as non-invasive biomarkers to risk-stratify MCL patients, thus promoting precision imaging in clinical oncology.

Abstract

Mantle cell lymphoma (MCL) is a rare lymphoid malignancy with a poor prognosis characterised by frequent relapse and short durations of treatment response. Most patients present with aggressive disease, but there exist indolent subtypes without the need for immediate intervention. The very heterogeneous behaviour of MCL is genetically characterised by the translocation t(11;14)(q13;q32), leading to Cyclin D1 overexpression with distinct clinical and biological characteristics and outcomes. There is still an unfulfilled need for precise MCL prognostication in real-time. Machine learning and deep learning neural networks are rapidly advancing technologies with promising results in numerous fields of application. This study develops and compares the performance of deep learning (DL) algorithms and radiomics-based machine learning (ML) models to predict MCL relapse on baseline CT scans. Five classification algorithms were used, including three deep learning models (3D SEResNet50, 3D DenseNet, and an optimised 3D CNN) and two machine learning models based on K-nearest Neighbor (KNN) and Random Forest (RF). The best performing method, our optimised 3D CNN, predicted MCL relapse with a 70% accuracy, better than the 3D SEResNet50 (62%) and the 3D DenseNet (59%). The second-best performing method was the KNN-based machine learning model (64%) after principal component analysis for improved accuracy. Our optimised CNN developed by ourselves correctly predicted MCL relapse in 70% of the patients on baseline CT imaging. Once prospectively tested in clinical trials with a larger sample size, our proposed 3D deep learning model could facilitate clinical management by precision imaging in MCL.

Longitudinal CT Imaging to Explore the Predictive Power of 3D Radiomic Tumour Heterogeneity in Precise Imaging of Mantle Cell Lymphoma (MCL)

The study's primary aim is to evaluate the predictive performance of CT-derived 3D radiomics for MCL risk stratification. The secondary objective is to search for radiomic features associated with sustained remission. Included were 70 patients: 31 MCL patients and 39 control subjects with normal axillary lymph nodes followed over five years. Radiomic analysis of all targets (n = 745) was performed and features selected using the Mann Whitney U test; the discriminative power of identifying "high-risk MCL" was evaluated by receiver operating characteristics (ROC). The four radiomic features, "Uniformity", "Entropy", "Skewness" and "Difference Entropy" showed predictive significance for relapse (p < 0.05)-in contrast to the routine size measurements, which showed no relevant difference. The best prognostication for relapse achieved the feature "Uniformity" (AUC-ROC-curve 0.87; optimal cut-off ≤0.0159 to predict relapse with 87% sensitivity, 65% specificity, 69% accuracy). Several radiomic features, including the parameter "Short Axis," were associated with sustained remission. CT-derived 3D radiomics improves the predictive estimation of MCL patients; in combination with the ability to identify potential radiomic features that are characteristic for sustained remission, it may assist physicians in the clinical management of MCL.

Medical imaging and nuclear medicine: a Lancet Oncology Commission

The diagnosis and treatment of patients with cancer requires access to imaging to ensure accurate management decisions and optimal outcomes. Our global assessment of imaging and nuclear medicine resources identified substantial shortages in equipment and workforce, particularly in low-income and middle-income countries (LMICs). A microsimulation model of 11 cancers showed that the scale-up of imaging would avert 3·2% (2·46 million) of all 76·0 million deaths caused by the modelled cancers worldwide between 2020 and 2030, saving 54·92 million life-years. A comprehensive scale-up of imaging, treatment, and care quality would avert 9·55 million (12·5%) of all cancer deaths caused by the modelled cancers worldwide, saving 232·30 million life-years. Scale-up of imaging would cost US$6·84 billion in 2020-30 but yield lifetime productivity gains of $1·23 trillion worldwide, a net return of $179·19 per $1 invested. Combining the scale-up of imaging, treatment, and quality of care would provide a net benefit of $2·66 trillion and a net return of $12·43 per $1 invested. With the use of a conservative approach regarding human capital, the scale-up of imaging alone would provide a net benefit of $209·46 billion and net return of $31·61 per $1 invested. With comprehensive scale-up, the worldwide net benefit using the human capital approach is $340·42 billion and the return per dollar invested is $2·46. These improved health and economic outcomes hold true across all geographical regions. We propose actions and investments that would enhance access to imaging equipment, workforce capacity, digital technology, radiopharmaceuticals, and research and training programmes in LMICs, to produce massive health and economic benefits and reduce the burden of cancer globally.

Artificial intelligence applications for oncological positron emission tomography imaging

Positron emission tomography (PET), a functional and dynamic molecular imaging technique, is generally used to reveal tumors' biological behavior. Radiomics allows a high-throughput extraction of multiple features from images with artificial intelligence (AI) approaches and develops rapidly worldwide. Quantitative and objective features of medical images have been explored to recognize reliable biomarkers, with the development of PET radiomics. This paper will review the current clinical exploration of PET-based classical machine learning and deep learning methods, including disease diagnosis, the prediction of histological subtype, gene mutation status, tumor metastasis, tumor relapse, therapeutic side effects, therapeutic intervention and evaluation of prognosis. The applications of AI in oncology will be mainly discussed. The image-guided biopsy or surgery assisted by PET-based AI will be introduced as well. This paper aims to present the applications and methods of AI for PET imaging, which may offer important details for further clinical studies. Relevant precautions are put forward and future research directions are suggested.

A bird's-eye view of deep learning in bioimage analysis

Deep learning of artificial neural networks has become the de facto standard approach to solving data analysis problems in virtually all fields of science and engineering. Also in biology and medicine, deep learning technologies are fundamentally transforming how we acquire, process, analyze, and interpret data, with potentially far-reaching consequences for healthcare. In this mini-review, we take a bird's-eye view at the past, present, and future developments of deep learning, starting from science at large, to biomedical imaging, and bioimage analysis in particular.

[18F]FDG-PET/CT Radiomics for Prediction of Bone Marrow Involvement in Mantle Cell Lymphoma: A Retrospective Study in 97 Patients

Biopsy is the standard for assessment of bone marrow involvement in mantle cell lymphoma (MCL). We investigated whether [18F]FDG-PET radiomic texture features can improve prediction of bone marrow involvement in MCL, compared to standardized uptake values (SUV), and whether combination with laboratory data improves results. Ninety-seven MCL patients were retrospectively included. SUVmax, SUVmean, SUVpeak and 16 co-occurrence matrix texture features were extracted from pelvic bones on [18F]FDG-PET/CT. A multi-layer perceptron neural network was used to compare three combinations for prediction of bone marrow involvement—the SUVs, a radiomic signature based on SUVs and texture features, and the radiomic signature combined with laboratory parameters. This step was repeated using two cut-off values for relative bone marrow involvement: REL > 5% (>5% of red/cellular bone marrow); and REL > 10%. Biopsy demonstrated bone marrow involvement in 67/97 patients (69.1%). SUVs, the radiomic signature, and the radiomic signature with laboratory data showed AUCs of up to 0.66, 0.73, and 0.81 for involved vs. uninvolved bone marrow; 0.68, 0.84, and 0.84 for REL ≤ 5% vs. REL > 5%; and 0.69, 0.85, and 0.87 for REL ≤ 10% vs. REL > 10%. In conclusion, [18F]FDG-PET texture features improve SUV-based prediction of bone marrow involvement in MCL. The results may be further improved by combination with laboratory parameters.

Introduction to Radiomics

Radiomics is a rapidly evolving field of research concerned with the extraction of quantitative metrics-the so-called radiomic features-within medical images. Radiomic features capture tissue and lesion characteristics such as heterogeneity and shape and may, alone or in combination with demographic, histologic, genomic, or proteomic data, be used for clinical problem solving. The goal of this continuing education article is to provide an introduction to the field, covering the basic radiomics workflow: feature calculation and selection, dimensionality reduction, and data processing. Potential clinical applications in nuclear medicine that include PET radiomics-based prediction of treatment response and survival will be discussed. Current limitations of radiomics, such as sensitivity to acquisition parameter variations, and common pitfalls will also be covered.