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Radiomics and deep learning characterisation of liver malignancies in CT images - A systematic review.

Yahaya BS, Osman ND, Karim NKA, Appalanaido GK, Isa IS

pubmed logopapersJun 3 2025
Computed tomography (CT) has been widely used as an effective tool for liver imaging due to its high spatial resolution, and ability to differentiate tissue densities, which contributing to comprehensive image analysis. Recent advancements in artificial intelligence (AI) promoted the role of Machine Learning (ML) in managing liver cancers by predicting or classifying tumours using mathematical algorithms. Deep learning (DL), a subset of ML, expanded these capabilities through convolutional neural networks (CNN) that analyse large data automatically. This review examines methods, achievements, limitations, and performance outcomes of ML-based radiomics and DL models for liver malignancies from CT imaging. A systematic search for full-text articles in English on CT radiomics and DL in liver cancer analysis was conducted in PubMed, Scopus, Science Citation Index, and Cochrane Library databases between 2020 and 2024 using the keywords; machine learning, radiomics, deep learning, computed tomography, liver cancer and associated MESH terms. PRISMA guidelines were used to identify and screen studies for inclusion. A total of 49 studies were included consisting of 17 Radiomics, 24 DL, and 8 combined DL/Radiomics studies. Radiomics has been predominantly utilised for predictive analysis, while DL has been extensively applied to automatic liver and tumour segmentation with a surge of a recent increase in studies integrating both techniques. Despite the growing popularity of DL methods, classical radiomics models are still relevant and often preferred over DL methods when performance is similar, due to lower computational and data needs. Performance of models keep improving, but challenges like data scarcity and lack of standardised protocols persists.

Deep Learning-Based Opportunistic CT Osteoporosis Screening and Establishment of Normative Values

Westerhoff, M., Gyftopoulos, S., Dane, B., Vega, E., Murdock, D., Lindow, N., Herter, F., Bousabarah, K., Recht, M. P., Bredella, M. A.

medrxiv logopreprintJun 3 2025
BackgroundOsteoporosis is underdiagnosed and undertreated prompting the exploration of opportunistic screening using CT and artificial intelligence (AI). PurposeTo develop a reproducible deep learning-based convolutional neural network to automatically place a 3D region of interest (ROI) in trabecular bone, develop a correction method to normalize attenuation across different CT protocols or and scanner models, and to establish thresholds for osteoporosis in a large diverse population. MethodsA deep learning-based method was developed to automatically quantify trabecular attenuation using a 3D ROI of the thoracic and lumbar spine on chest, abdomen, or spine CTs, adjusted for different tube voltages and scanner models. Normative values, thresholds for osteoporosis of trabecular attenuation of the spine were established across a diverse population, stratified by age, sex, race, and ethnicity using reported prevalence of osteoporosis by the WHO. Results538,946 CT examinations from 283,499 patients (mean age 65 years{+/-}15, 51.2% women and 55.5% White), performed on 50 scanner models using six different tube voltages were analyzed. Hounsfield Units at 80 kVp versus 120 kVp differed by 23%, and different scanner models resulted in differences of values by < 10%. Automated ROI placement of 1496 vertebra was validated by manual radiologist review, demonstrating >99% agreement. Mean trabecular attenuation was higher in young women (<50 years) than young men (p<.001) and decreased with age, with a steeper decline in postmenopausal women. In patients older than 50 years, trabecular attention was higher in males than females (p<.001). Trabecular attenuation was highest in Blacks, followed by Asians and lowest in Whites (p<.001). The threshold for L1 in diagnosing osteoporosis was 80 HU. ConclusionDeep learning-based automated opportunistic osteoporosis screening can identify patients with low bone mineral density that undergo CT scans for clinical purposes on different scanners and protocols. Key Results 3 main results/conclusionsO_LIIn a study of 538,946 CT examinations performed in 283,499 patients using different scanner models and imaging protocols, an automated deep learning-based convolutional neural network was able to accurately place a three-dimensional regions of interest within thoracic and lumbar vertebra to measure trabecular attenuation. C_LIO_LITube voltage had a larger influence on attenuation values (23%) than scanner model (<10%). C_LIO_LIA threshold of 80 HU was identified for L1 to diagnose osteoporosis using an automated three-dimensional region of interest. C_LI

Exploring <i>SLC25A42</i> as a Radiogenomic Marker from the Perioperative Stage to Chemotherapy in Hepatitis-Related Hepatocellular Carcinoma.

Dou L, Jiang J, Yao H, Zhang B, Wang X

pubmed logopapersJun 2 2025
<b><i>Background:</i></b> The molecular mechanisms driving hepatocellular carcinoma (HCC) and predict the chemotherapy sensitive remain unclear; therefore, identification of these key biomarkers is essential for early diagnosis and treatment of HCC. <b><i>Method:</i></b> We collected and processed Computed Tomography (CT) and clinical data from 116 patients with autoimmune hepatitis (AIH) and HCC who came to our hospital's Liver Cancer Center. We then identified and extracted important characteristic features of significant patient images and correlated them with mitochondria-related genes using machine learning techniques such as multihead attention networks, lasso regression, principal component analysis (PCA), and support vector machines (SVM). These genes were integrated into radiomics signature models to explore their role in disease progression. We further correlated these results with clinical variables to screen for driver genes and evaluate the predict ability of chemotherapy sensitive of key genes in liver cancer (LC) patients. Finally, qPCR was used to validate the expression of this gene in patient samples. <b><i>Results:</i></b> Our study utilized attention networks to identify disease regions in medical images with 97% accuracy and an AUC of 94%. We extracted 942 imaging features, identifying five key features through lasso regression that accurately differentiate AIH from HCC. Transcriptome analysis revealed 132 upregulated and 101 downregulated genes in AIH, with 45 significant genes identified by XGBOOST. In HCC analysis, PCA and random forest highlighted 11 key features. Among mitochondrial genes, <i>SLC25A42</i> correlated positively with normal tissue imaging features but negatively with cancerous tissues and was identified as a driver gene. Low expression of <i>SLC25A42</i> was associated with chemotherapy sensitive in HCC patients. <b><i>Conclusions:</i></b> In conclusion, machine learning modeling combined with genomic profiling provides a promising approach to identify the driver gene <i>SLC25A42</i> in LC, which may help improve diagnostic accuracy and chemotherapy sensitivity for this disease.

SPCF-YOLO: An Efficient Feature Optimization Model for Real-Time Lung Nodule Detection.

Ren Y, Shi C, Zhu D, Zhou C

pubmed logopapersJun 2 2025
Accurate pulmonary nodule detection in CT imaging remains challenging due to fragmented feature integration in conventional deep learning models. This paper proposes SPCF-YOLO, a real-time detection framework that synergizes hierarchical feature fusion with anatomical context modeling. First, the space-to-depth convolution (SPDConv) module preserves fine-grained features in low-resolution images through spatial dimension reorganization. Second, the shared feature pyramid convolution (SFPConv) module is designed to dynamically extract multi-scale contextual information using multi-dilation-rate convolutional layers. Incorporating a small object detection layer aims to improve sensitivity to small nodules. This is achieved in combination with the improved pyramid squeeze attention (PSA) module and the improved contextual transformer (CoTB) module, which enhance global channel dependencies and reduce feature loss. The model achieves 82.8% mean average precision (mAP) and 82.9% F1 score on LUNA16 at 151 frames per second (representing improvements of 17.5% and 82.9% over YOLOv8 respectively), demonstrating real-time clinical viability. Cross-modality validation on SIIM-COVID-19 shows 1.5% improvement, confirming robust generalization.

Harnessing Artificial Intelligence to Predict Spontaneous Stone Passage: Development and Testing of a Machine Learning-Based Calculator.

Gupta K, Ricapito A, Lundon D, Khargi R, Connors C, Yaghoubian AJ, Gallante B, Atallah WM, Gupta M

pubmed logopapersJun 2 2025
<b><i>Objective:</i></b> We sought to use artificial intelligence (AI) to develop and test calculators to predict spontaneous stone passage (SSP) using radiographical and clinical data. <b><i>Methods:</i></b> Consecutive patients with solitary ureteral stones ≤10 mm on CT were prospectively enrolled and managed according to American Urological Association guidelines. The first 70% of patients were placed in the "training group" and used to develop the calculators. The latter 30% were enrolled in the "testing group" to externally validate the calculators. Exclusion criteria included contraindication to trial of SSP, ureteral stent, and anatomical anomaly. Demographic, clinical, and radiographical data were obtained and fed into machine learning (ML) platforms. SSP was defined as passage of stone without intervention. Calculators were derived from data using multivariate logistic regression. Discrimination, calibration, and clinical utility/net benefit of the developed models were assessed in the validation cohort. Receiver operating characteristic curves were constructed to measure their discriminative ability. <b><i>Results:</i></b> Fifty-one percent of 131 "training" patients spontaneously passed their stones. Passed stones were significantly closer to the bladder (8.6 <i>vs</i> 11.8 cm, p = 0.01) and smaller in length, width, and height. Two ML calculators were developed, one supervised machine learning (SML) and the other unsupervised machine learning (USML), and compared to an existing tool Multi-centre Cohort Study Evaluating the role of Inflammatory Markers In Patients Presenting with Acute Ureteric Colic (MIMIC). The SML calculator included maximum stone width (MSW), ureteral diameter above the stone (UDA), and distance from ureterovesical junction to bottom of stone and had an area under the curve (AUC) of 0.737 upon external validation of 58 "test" patients. Parameters selected by USML included MSW, UDA, and use of an anticholinergic, and it had an AUC of 0.706. The MIMIC calculator's AUC was 0.588 (0.489-0.686). <b><i>Conclusion:</i></b> We used AI to develop calculators that outperformed an existing tool and can help providers and patients make a better-informed decision for the treatment of ureteral stones.

Decision support using machine learning for predicting adequate bladder filling in prostate radiotherapy: a feasibility study.

Saiyo N, Assawanuwat K, Janthawanno P, Paduka S, Prempetch K, Chanphol T, Sakchatchawan B, Thongsawad S

pubmed logopapersJun 2 2025
This study aimed to develop a model for predicting the bladder volume ratio between daily CBCT and CT to determine adequate bladder filling in patients undergoing treatment for prostate cancer with external beam radiation therapy (EBRT). The model was trained using 465 datasets obtained from 34 prostate cancer patients. A total of 16 features were collected as input data, which included basic patient information, patient health status, blood examination laboratory results, and specific radiation therapy information. The ratio of the bladder volume between daily CBCT (dCBCT) and planning CT (pCT) was used as the model response. The model was trained using a bootstrap aggregation (bagging) algorithm with two machine learning (ML) approaches: classification and regression. The model accuracy was validated using other 93 datasets. For the regression approach, the accuracy of the model was evaluated based on the root mean square error (RMSE) and mean absolute error (MAE). By contrast, the model performance of the classification approach was assessed using sensitivity, specificity, and accuracy scores. The ML model showed promising results in the prediction of the bladder volume ratio between dCBCT and pCT, with an RMSE of 0.244 and MAE of 0.172 for the regression approach, sensitivity of 95.24%, specificity of 92.16%, and accuracy of 93.55% for the classification approach. The prediction model could potentially help the radiological technologist determine whether the bladder is full before treatment, thereby reducing the requirement for re-scan CBCT. HIGHLIGHTS: The bagging model demonstrates strong performance in predicting optimal bladder filling. The model achieves promising results with 95.24% sensitivity and 92.16% specificity. It supports therapists in assessing bladder fullness prior to treatment. It helps reduce the risk of requiring repeat CBCT scans.

Performance Comparison of Machine Learning Using Radiomic Features and CNN-Based Deep Learning in Benign and Malignant Classification of Vertebral Compression Fractures Using CT Scans.

Yeom JC, Park SH, Kim YJ, Ahn TR, Kim KG

pubmed logopapersJun 2 2025
Distinguishing benign from malignant vertebral compression fractures is critical for clinical management but remains challenging on contrast-enhanced abdominal CT, which lacks the soft tissue contrast of MRI. This study evaluates and compares radiomic feature-based machine learning and convolutional neural network-based deep learning models for classifying VCFs using abdominal CT. A retrospective cohort of 447 vertebral compression fractures (196 benign, 251 malignant) from 286 patients was analyzed. Radiomic features were extracted using PyRadiomics, with Recursive Feature Elimination selecting six key texture-based features (e.g., Run Variance, Dependence Non-Uniformity Normalized), highlighting textural heterogeneity as a malignancy marker. Machine learning models (XGBoost, SVM, KNN, Random Forest) and a 3D CNN were trained on CT data, with performance assessed via precision, recall, F1 score, accuracy, and AUC. The deep learning model achieved marginally superior overall performance, with a statistically significant higher AUC (77.66% vs. 75.91%, p < 0.05) and better precision, F1 score, and accuracy compared to the top-performing machine learning model (XGBoost). Deep learning's attention maps localized diagnostically relevant regions, mimicking radiologists' focus, whereas radiomics lacked spatial interpretability despite offering quantifiable biomarkers. This study underscores the complementary strengths of machine learning and deep learning: radiomics provides interpretable features tied to tumor heterogeneity, while DL autonomously extracts high-dimensional patterns with spatial explainability. Integrating both approaches could enhance diagnostic accuracy and clinician trust in abdominal CT-based VCF assessment. Limitations include retrospective single-center data and potential selection bias. Future multi-center studies with diverse protocols and histopathological validation are warranted to generalize these findings.

Tomographic Foundation Model -- FORCE: Flow-Oriented Reconstruction Conditioning Engine

Wenjun Xia, Chuang Niu, Ge Wang

arxiv logopreprintJun 2 2025
Computed tomography (CT) is a major medical imaging modality. Clinical CT scenarios, such as low-dose screening, sparse-view scanning, and metal implants, often lead to severe noise and artifacts in reconstructed images, requiring improved reconstruction techniques. The introduction of deep learning has significantly advanced CT image reconstruction. However, obtaining paired training data remains rather challenging due to patient motion and other constraints. Although deep learning methods can still perform well with approximately paired data, they inherently carry the risk of hallucination due to data inconsistencies and model instability. In this paper, we integrate the data fidelity with the state-of-the-art generative AI model, referred to as the Poisson flow generative model (PFGM) with a generalized version PFGM++, and propose a novel CT framework: Flow-Oriented Reconstruction Conditioning Engine (FORCE). In our experiments, the proposed method shows superior performance in various CT imaging tasks, outperforming existing unsupervised reconstruction approaches.

Medical World Model: Generative Simulation of Tumor Evolution for Treatment Planning

Yijun Yang, Zhao-Yang Wang, Qiuping Liu, Shuwen Sun, Kang Wang, Rama Chellappa, Zongwei Zhou, Alan Yuille, Lei Zhu, Yu-Dong Zhang, Jieneng Chen

arxiv logopreprintJun 2 2025
Providing effective treatment and making informed clinical decisions are essential goals of modern medicine and clinical care. We are interested in simulating disease dynamics for clinical decision-making, leveraging recent advances in large generative models. To this end, we introduce the Medical World Model (MeWM), the first world model in medicine that visually predicts future disease states based on clinical decisions. MeWM comprises (i) vision-language models to serve as policy models, and (ii) tumor generative models as dynamics models. The policy model generates action plans, such as clinical treatments, while the dynamics model simulates tumor progression or regression under given treatment conditions. Building on this, we propose the inverse dynamics model that applies survival analysis to the simulated post-treatment tumor, enabling the evaluation of treatment efficacy and the selection of the optimal clinical action plan. As a result, the proposed MeWM simulates disease dynamics by synthesizing post-treatment tumors, with state-of-the-art specificity in Turing tests evaluated by radiologists. Simultaneously, its inverse dynamics model outperforms medical-specialized GPTs in optimizing individualized treatment protocols across all metrics. Notably, MeWM improves clinical decision-making for interventional physicians, boosting F1-score in selecting the optimal TACE protocol by 13%, paving the way for future integration of medical world models as the second readers.

Machine Learning Methods Based on Chest CT for Predicting the Risk of COVID-19-Associated Pulmonary Aspergillosis.

Liu J, Zhang J, Wang H, Fang C, Wei L, Chen J, Li M, Wu S, Zeng Q

pubmed logopapersJun 1 2025
To develop and validate a machine learning model based on chest CT and clinical risk factors to predict secondary aspergillus infection in hospitalized COVID-19 patients. This retrospective study included 291 COVID-19 patients with complete clinical data between December 2022 and March 2024, and some (n=82) of them developed secondary aspergillus infection after admission. Patients were divided into training (n=162), internal validation (n=69) and external validation (n=60) cohorts. The least absolute shrinkage and selection operator regression was applied to select the most significant image features extracted from chest CT. Univariate and multivariate logistic regression analyses were performed to develop a multifactorial model, which integrated chest CT with clinical risk factors, to predict secondary aspergillus infection in hospitalized COVID-19 patients. The performance of the constructed models was assessed with the receiver operating characteristic curve and the area under the curve (AUC). The clinical application value of the models was comprehensively evaluated using decision curve analysis (DCA). Eleven radiomics features and seven clinical risk factors were selected to develop prediction models. The multifactorial model demonstrated a favorable predictive performance with the highest AUC values of 0.98 (95% CI, 0.96-1.00) in the training cohort, 0.98 (95% CI, 0.96-1.00) in the internal validation cohort, and 0.87 (95% CI, 0.75-0.99) in the external validation cohort, which was significantly superior to the models relied solely on chest CT or clinical risk factors. The calibration curves from Hosmer-Lemeshow tests showed that there were no significant differences in the training cohort (p=0.359) and internal validation cohort (p=0.941), suggesting the good performance of the multifactorial model. DCA indicated that the multifactorial model exhibited better performance than others. The multifactorial model can serve as a reliable tool for predicting the risk of COVID-19-associated pulmonary aspergillosis.
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