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Convolutional neural network using magnetic resonance brain imaging to predict outcome from tuberculosis meningitis.

Dong THK, Canas LS, Donovan J, Beasley D, Thuong-Thuong NT, Phu NH, Ha NT, Ourselin S, Razavi R, Thwaites GE, Modat M

pubmed logopapersJan 1 2025
Tuberculous meningitis (TBM) leads to high mortality, especially amongst individuals with HIV. Predicting the incidence of disease-related complications is challenging, for which purpose the value of brain magnetic resonance imaging (MRI) has not been well investigated. We used a convolutional neural network (CNN) to explore the complementary contribution of brain MRI to the conventional prognostic determinants. We pooled data from two randomised control trials of HIV-positive and HIV-negative adults with clinical TBM in Vietnam to predict the occurrence of death or new neurological complications in the first two months after the subject's first MRI session. We developed and compared three models: a logistic regression with clinical, demographic and laboratory data as reference, a CNN that utilised only T1-weighted MRI volumes, and a model that fused all available information. All models were fine-tuned using two repetitions of 5-fold cross-validation. The final evaluation was based on a random 70/30 training/test split, stratified by the outcome and HIV status. Based on the selected model, we explored the interpretability maps derived from the models. 215 patients were included, with an event prevalence of 22.3%. On the test set our non-imaging model had higher AUC (71.2% [Formula: see text] 1.1%) than the imaging-only model (67.3% [Formula: see text] 2.6%). The fused model was superior to both, with an average AUC = 77.3% [Formula: see text] 4.0% in the test set. The non-imaging variables were more informative in the HIV-positive group, while the imaging features were more predictive in the HIV-negative group. All three models performed better in the HIV-negative cohort. The interpretability maps show the model's focus on the lateral fissures, the corpus callosum, the midbrain, and peri-ventricular tissues. Imaging information can provide added value to predict unwanted outcomes of TBM. However, to confirm this finding, a larger dataset is needed.

Auxiliary Diagnosis of Pulmonary Nodules' Benignancy and Malignancy Based on Machine Learning: A Retrospective Study.

Wang W, Yang B, Wu H, Che H, Tong Y, Zhang B, Liu H, Chen Y

pubmed logopapersJan 1 2025
Lung cancer, one of the most lethal malignancies globally, often presents insidiously as pulmonary nodules. Its nonspecific clinical presentation and heterogeneous imaging characteristics hinder accurate differentiation between benign and malignant lesions, while biopsy's invasiveness and procedural constraints underscore the critical need for non-invasive early diagnostic approaches. In this retrospective study, we analyzed outpatient and inpatient records from the First Medical Center of Chinese PLA General Hospital between 2011 and 2021, focusing on pulmonary nodules measuring 5-30mm on CT scans without overt signs of malignancy. Pathological examination served as the reference standard. Comparative experiments evaluated SVM, RF, XGBoost, FNN, and Atten_FNN using five-fold cross-validation to assess AUC, sensitivity, and specificity. The dataset was split 70%/30%, and stratified five-fold cross-validation was applied to the training set. The optimal model was interpreted with SHAP to identify the most influential predictive features. This study enrolled 3355 patients, including 1156 with benign and 2199 with malignant pulmonary nodules. The Atten_FNN model demonstrated superior performance in five-fold cross-validation, achieving an AUC of 0.82, accuracy of 0.75, sensitivity of 0.77, and F1 score of 0.80. SHAP analysis revealed key predictive factors: demographic variables (age, sex, BMI), CT-derived features (maximum nodule diameter, morphology, density, calcification, ground-glass opacity), and laboratory biomarkers (neuroendocrine markers, carcinoembryonic antigen). This study integrates electronic medical records and pathology data to predict pulmonary nodule malignancy using machine/deep learning models. SHAP-based interpretability analysis uncovered key clinical determinants. Acknowledging limitations in cross-center generalizability, we propose the development of a multimodal diagnostic systems that combines CT imaging and radiomics, to be validated in multi-center prospective cohorts to facilitate clinical translation. This framework establishes a novel paradigm for early precision diagnosis of lung cancer.

Radiomics of Dynamic Contrast-Enhanced MRI for Predicting Radiation-Induced Hepatic Toxicity After Intensity Modulated Radiotherapy for Hepatocellular Carcinoma: A Machine Learning Predictive Model Based on the SHAP Methodology.

Liu F, Chen L, Wu Q, Li L, Li J, Su T, Li J, Liang S, Qing L

pubmed logopapersJan 1 2025
To develop an interpretable machine learning (ML) model using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) radiomic data, dosimetric parameters, and clinical data for predicting radiation-induced hepatic toxicity (RIHT) in patients with hepatocellular carcinoma (HCC) following intensity-modulated radiation therapy (IMRT). A retrospective analysis of 150 HCC patients was performed, with a 7:3 ratio used to divide the data into training and validation cohorts. Radiomic features from the original MRI sequences and Delta-radiomic features were extracted. Seven ML models based on radiomics were developed: logistic regression (LR), random forest (RF), support vector machine (SVM), eXtreme Gradient Boosting (XGBoost), adaptive boosting (AdaBoost), decision tree (DT), and artificial neural network (ANN). The predictive performance of the models was evaluated using receiver operating characteristic (ROC) curve analysis and calibration curves. Shapley additive explanations (SHAP) were employed to interpret the contribution of each variable and its risk threshold. Original radiomic features and Delta-radiomic features were extracted from DCE-MRI images and filtered to generate Radiomics-scores and Delta-Radiomics-scores. These were then combined with independent risk factors (Body Mass Index (BMI), V5, and pre-Child-Pugh score(pre-CP)) identified through univariate and multivariate logistic regression and Spearman correlation analysis to construct the ML models. In the training cohort, the AUC values were 0.8651 for LR, 0.7004 for RF, 0.6349 for SVM, 0.6706 for XGBoost, 0.7341 for AdaBoost, 0.6806 for Decision Tree, and 0.6786 for ANN. The corresponding accuracies were 84.4%, 65.6%, 75.0%, 65.6%, 71.9%, 68.8%, and 71.9%, respectively. The validation cohort further confirmed the superiority of the LR model, which was selected as the optimal model. SHAP analysis revealed that Delta-radiomics made a substantial positive contribution to the model. The interpretable ML model based on radiomics provides a non-invasive tool for predicting RIHT in patients with HCC, demonstrating satisfactory discriminative performance.

Improved swin transformer-based thorax disease classification with optimal feature selection using chest X-ray.

Rana N, Coulibaly Y, Noor A, Noor TH, Alam MI, Khan Z, Tahir A, Khan MZ

pubmed logopapersJan 1 2025
Thoracic diseases, including pneumonia, tuberculosis, lung cancer, and others, pose significant health risks and require timely and accurate diagnosis to ensure proper treatment. Thus, in this research, a model for thorax disease classification using Chest X-rays is proposed by considering deep learning model. The input is pre-processed by resizing, normalizing pixel values, and applying data augmentation to address the issue of imbalanced datasets and improve model generalization. Significant features are extracted from the images using an Enhanced Auto-Encoder (EnAE) model, which combines a stacked auto-encoder architecture with an attention module to enhance feature representation and classification accuracy. To further improve feature selection, we utilize the Chaotic Whale Optimization (ChWO) Algorithm, which optimally selects the most relevant attributes from the extracted features. Finally, the disease classification is performed using the novel Improved Swin Transformer (IMSTrans) model, which is designed to efficiently process high-dimensional medical image data and achieve superior classification performance. The proposed EnAE + ChWO+IMSTrans model for thorax disease classification was evaluated using extensive Chest X-ray datasets and the Lung Disease Dataset. The proposed method demonstrates enhanced Accuracy, Precision, Recall, F-Score, MCC and MAE of 0.964, 0.977, 0.9845, 0.964, 0.9647, and 0.184 respectively indicating the reliable and efficient solution for thorax disease classification.

Radiomic Model Associated with Tumor Microenvironment Predicts Immunotherapy Response and Prognosis in Patients with Locoregionally Advanced Nasopharyngeal Carcinoma.

Sun J, Wu X, Zhang X, Huang W, Zhong X, Li X, Xue K, Liu S, Chen X, Li W, Liu X, Shen H, You J, He W, Jin Z, Yu L, Li Y, Zhang S, Zhang B

pubmed logopapersJan 1 2025
<b>Background:</b> No robust biomarkers have been identified to predict the efficacy of programmed cell death protein 1 (PD-1) inhibitors in patients with locoregionally advanced nasopharyngeal carcinoma (LANPC). We aimed to develop radiomic models using pre-immunotherapy MRI to predict the response to PD-1 inhibitors and the patient prognosis. <b>Methods:</b> This study included 246 LANPC patients (training cohort, <i>n</i> = 117; external test cohort, <i>n</i> = 129) from 10 centers. The best-performing machine learning classifier was employed to create the radiomic models. A combined model was constructed by integrating clinical and radiomic data. A radiomic interpretability study was performed with whole slide images (WSIs) stained with hematoxylin and eosin (H&E) and immunohistochemistry (IHC). A total of 150 patient-level nuclear morphological features (NMFs) and 12 cell spatial distribution features (CSDFs) were extracted from WSIs. The correlation between the radiomic and pathological features was assessed using Spearman correlation analysis. <b>Results:</b> The radiomic model outperformed the clinical and combined models in predicting treatment response (area under the curve: 0.760 vs. 0.559 vs. 0.652). For overall survival estimation, the combined model performed comparably to the radiomic model but outperformed the clinical model (concordance index: 0.858 vs. 0.812 vs. 0.664). Six treatment response-related radiomic features correlated with 50 H&E-derived (146 pairs, |<i>r</i>|= 0.31 to 0.46) and 2 to 26 IHC-derived NMF, particularly for CD45RO (69 pairs, |<i>r</i>|= 0.31 to 0.48), CD8 (84, |<i>r</i>|= 0.30 to 0.59), PD-L1 (73, |<i>r</i>|= 0.32 to 0.48), and CD163 (53, |<i>r</i>| = 0.32 to 0.59). Eight prognostic radiomic features correlated with 11 H&E-derived (16 pairs, |<i>r</i>|= 0.48 to 0.61) and 2 to 31 IHC-derived NMF, particularly for PD-L1 (80 pairs, |<i>r</i>|= 0.44 to 0.64), CD45RO (65, |<i>r</i>|= 0.42 to 0.67), CD19 (35, |<i>r</i>|= 0.44 to 0.58), CD66b (61, |<i>r</i>| = 0.42 to 0.67), and FOXP3 (21, |<i>r</i>| = 0.41 to 0.71). In contrast, fewer CSDFs exhibited correlations with specific radiomic features. <b>Conclusion:</b> The radiomic model and combined model are feasible in predicting immunotherapy response and outcomes in LANPC patients. The radiology-pathology correlation suggests a potential biological basis for the predictive models.

A novel spectral transformation technique based on special functions for improved chest X-ray image classification.

Aljohani A

pubmed logopapersJan 1 2025
Chest X-ray image classification plays an important role in medical diagnostics. Machine learning algorithms enhanced the performance of these classification algorithms by introducing advance techniques. These classification algorithms often requires conversion of a medical data to another space in which the original data is reduced to important values or moments. We developed a mechanism which converts a given medical image to a spectral space which have a base set composed of special functions. In this study, we propose a chest X-ray image classification method based on spectral coefficients. The spectral coefficients are based on an orthogonal system of Legendre type smooth polynomials. We developed the mathematical theory to calculate spectral moment in Legendre polynomails space and use these moments to train traditional classifier like SVM and random forest for a classification task. The procedure is applied to a latest data set of X-Ray images. The data set is composed of X-Ray images of three different classes of patients, normal, Covid infected and pneumonia. The moments designed in this study, when used in SVM or random forest improves its ability to classify a given X-Ray image at a high accuracy. A parametric study of the proposed approach is presented. The performance of these spectral moments is checked in Support vector machine and Random forest algorithm. The efficiency and accuracy of the proposed method is presented in details. All our simulation is performed in computation softwares, Matlab and Python. The image pre processing and spectral moments generation is performed in Matlab and the implementation of the classifiers is performed with python. It is observed that the proposed approach works well and provides satisfactory results (0.975 accuracy), however further studies are required to establish a more accurate and fast version of this approach.

Deep learning-based fine-grained assessment of aneurysm wall characteristics using 4D-CT angiography.

Kumrai T, Maekawa T, Chen Y, Sugiyama Y, Takagaki M, Yamashiro S, Takizawa K, Ichinose T, Ishida F, Kishima H

pubmed logopapersJan 1 2025
This study proposes a novel deep learning-based approach for aneurysm wall characteristics, including thin-walled (TW) and hyperplastic-remodeling (HR) regions. We analyzed fifty-two unruptured cerebral aneurysms employing 4D-computed tomography angiography (4D-CTA) and intraoperative recordings. The TW and HR regions were identified in intraoperative images. The 3D trajectories of observation points on aneurysm walls were processed to compute a time series of 3D speed, acceleration, and smoothness of motion, aiming to evaluate the aneurysm wall characteristics. To facilitate point-level risk evaluation using the time-series data, we developed a convolutional neural network (CNN)-long- short-term memory (LSTM)-based regression model enriched with attention layers. In order to accommodate patient heterogeneity, a patient-independent feature extraction mechanism was introduced. Furthermore, unlabeled data were incorporated to enhance the data-intensive deep model. The proposed method achieved an average diagnostic accuracy of 92%, significantly outperforming a simpler model lacking attention. These results underscore the significance of patient-independent feature extraction and the use of unlabeled data. This study demonstrates the efficacy of a fine-grained deep learning approach in predicting aneurysm wall characteristics using 4D-CTA. Notably, incorporating an attention-based network structure proved to be particularly effective, contributing to enhanced performance.

Integrating multimodal imaging and peritumoral features for enhanced prostate cancer diagnosis: A machine learning approach.

Zhou H, Xie M, Shi H, Shou C, Tang M, Zhang Y, Hu Y, Liu X

pubmed logopapersJan 1 2025
Prostate cancer is a common malignancy in men, and accurately distinguishing between benign and malignant nodules at an early stage is crucial for optimizing treatment. Multimodal imaging (such as ADC and T2) plays an important role in the diagnosis of prostate cancer, but effectively combining these imaging features for accurate classification remains a challenge. This retrospective study included MRI data from 199 prostate cancer patients. Radiomic features from both the tumor and peritumoral regions were extracted, and a random forest model was used to select the most contributive features for classification. Three machine learning models-Random Forest, XGBoost, and Extra Trees-were then constructed and trained on four different feature combinations (tumor ADC, tumor T2, tumor ADC+T2, and tumor + peritumoral ADC+T2). The model incorporating multimodal imaging features and peritumoral characteristics showed superior classification performance. The Extra Trees model outperformed the others across all feature combinations, particularly in the tumor + peritumoral ADC+T2 group, where the AUC reached 0.729. The AUC values for the other combinations also exceeded 0.65. While the Random Forest and XGBoost models performed slightly lower, they still demonstrated strong classification abilities, with AUCs ranging from 0.63 to 0.72. SHAP analysis revealed that key features, such as tumor texture and peritumoral gray-level features, significantly contributed to the model's classification decisions. The combination of multimodal imaging data with peritumoral features moderately improved the accuracy of prostate cancer classification. This model provides a non-invasive and effective diagnostic tool for clinical use and supports future personalized treatment decisions.

Patients', clinicians' and developers' perspectives and experiences of artificial intelligence in cardiac healthcare: A qualitative study.

Baillie L, Stewart-Lord A, Thomas N, Frings D

pubmed logopapersJan 1 2025
This study investigated perspectives and experiences of artificial intelligence (AI) developers, clinicians and patients about the use of AI-based software in cardiac healthcare. A qualitative study took place at two hospitals in England that had trialled AI-based software use in stress echocardiography, a scan that uses ultrasound to assess heart function. Semi-structured interviews were conducted with: patients (<i>n = </i>9), clinicians (<i>n = </i>16) and AI software developers (<i>n = </i>5). Data were analysed using thematic analysis. Potential benefits identified were increasing consistency and reliability through reducing human error, and greater efficiency. Concerns included over-reliance on the AI technology, and data security. Participants discussed the need for human input and empathy within healthcare, transparency about AI use, and issues around trusting AI. Participants considered AI's role as assisting diagnosis but not replacing clinician involvement. Clinicians and patients emphasised holistic diagnosis that involves more than the scan. Clinicians considered their diagnostic ability as superior and discrepancies were managed in line with clinicians' diagnoses rather than AI reports. The practicalities of using the AI software concerned image acquisition to meet AI processing requirements and workflow integration. There was positivity towards AI use, but the AI software was considered an adjunct to clinicians rather than replacing their input. Clinicians' experiences were that their diagnostic ability remained superior to the AI, and acquiring images acceptable to AI was sometimes problematic. Despite hopes for increased efficiency through AI use, clinicians struggled to identify fit with clinical workflow to bring benefit.

Ensuring Fairness in Detecting Mild Cognitive Impairment with MRI.

Tong B, Edwards T, Yang S, Hou B, Tarzanagh DA, Urbanowicz RJ, Moore JH, Ritchie MD, Davatzikos C, Shen L

pubmed logopapersJan 1 2024
Machine learning (ML) algorithms play a crucial role in the early and accurate diagnosis of Alzheimer's Disease (AD), which is essential for effective treatment planning. However, existing methods are not well-suited for identifying Mild Cognitive Impairment (MCI), a critical transitional stage between normal aging and AD. This inadequacy is primarily due to label imbalance and bias from different sensitve attributes in MCI classification. To overcome these challenges, we have designed an end-to-end fairness-aware approach for label-imbalanced classification, tailored specifically for neuroimaging data. This method, built on the recently developed FACIMS framework, integrates into STREAMLINE, an automated ML environment. We evaluated our approach against nine other ML algorithms and found that it achieves comparable balanced accuracy to other methods while prioritizing fairness in classifications with five different sensitive attributes. This analysis contributes to the development of equitable and reliable ML diagnostics for MCI detection.
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