matRadiomics: A Novel and Complete Radiomics Framework, from Image Visualization to Predictive Model

Development and Implementation of an Innovative Framework for Automated Radiomics Analysis in Neuroimaging

Radiomics represents an innovative approach to medical image analysis, enabling comprehensive quantitative evaluation of radiological images through advanced image processing and Machine or Deep Learning algorithms. This technique uncovers intricate data patterns beyond human visual detection. Traditionally, executing a radiomic pipeline involves multiple standardized phases across several software platforms. This could represent a limit that was overcome thanks to the development of the matRadiomics application. MatRadiomics, a freely available, IBSI-compliant tool, features its intuitive Graphical User Interface (GUI), facilitating the entire radiomics workflow from DICOM image importation to segmentation, feature selection and extraction, and Machine Learning model construction. In this project, an extension of matRadiomics was developed to support the importation of brain MRI images and segmentations in NIfTI format, thus extending its applicability to neuroimaging. This enhancement allows for the seamless execution of radiomic pipelines within matRadiomics, offering substantial advantages to the realm of neuroimaging.

Cancer Radiomic and Perfusion Imaging Automated Framework: Validation on Musculoskeletal Tumors

PURPOSE

Limitations from commercial software applications prevent the implementation of a robust and cost-efficient high-throughput cancer imaging radiomic feature extraction and perfusion analysis workflow. This study aimed to develop and validate a cancer research computational solution using open-source software for vendor- and sequence-neutral high-throughput image processing and feature extraction.

METHODS

The Cancer Radiomic and Perfusion Imaging (CARPI) automated framework is a Python-based software application that is vendor- and sequence-neutral. CARPI uses contour files generated using an application of the user's choice and performs automated radiomic feature extraction and perfusion analysis. This workflow solution was validated using two clinical data sets, one consisted of 40 pelvic chondrosarcomas and 42 sacral chordomas with a total of 82 patients, and a second data set consisted of 26 patients with undifferentiated pleomorphic sarcoma (UPS) imaged at multiple points during presurgical treatment.

RESULTS

Three hundred sixteen volumetric contour files were processed using CARPI. The application automatically extracted 107 radiomic features from multiple magnetic resonance imaging sequences and seven semiquantitative perfusion parameters from time-intensity curves. Statistically significant differences (P < .00047) were found in 18 of 107 radiomic features in chordoma versus chondrosarcoma, including six first-order and 12 high-order features. In UPS postradiation, the apparent diffusion coefficient mean increased 41% in good responders (P = .0017), while firstorder_10Percentile (P = .0312) was statistically significant between good and partial/nonresponders.

CONCLUSION

The CARPI processing of two clinical validation data sets confirmed the software application's ability to differentiate between different types of tumors and help predict patient response to treatment on the basis of radiomic features. Benchmark comparison with five similar open-source solutions demonstrated the advantages of CARPI in the automated perfusion feature extraction, relational database generation, and graphic report export features, although lacking a user-friendly graphical user interface and predictive model building.

A Critical Analysis of the Robustness of Radiomics to Variations in Segmentation Methods in 18F-PSMA-1007 PET Images of Patients Affected by Prostate Cancer

BACKGROUND

Radiomics shows promising results in supporting the clinical decision process, and much effort has been put into its standardization, thus leading to the Imaging Biomarker Standardization Initiative (IBSI), that established how radiomics features should be computed. However, radiomics still lacks standardization and many factors, such as segmentation methods, limit study reproducibility and robustness.

AIM

We investigated the impact that three different segmentation methods (manual, thresholding and region growing) have on radiomics features extracted from 18F-PSMA-1007 Positron Emission Tomography (PET) images of 78 patients (43 Low Risk, 35 High Risk). Segmentation was repeated for each patient, thus leading to three datasets of segmentations. Then, feature extraction was performed for each dataset, and 1781 features (107 original, 930 Laplacian of Gaussian (LoG) features, 744 wavelet features) were extracted. Feature robustness and reproducibility were assessed through the intra class correlation coefficient (ICC) to measure agreement between the three segmentation methods. To assess the impact that the three methods had on machine learning models, feature selection was performed through a hybrid descriptive-inferential method, and selected features were given as input to three classifiers, K-Nearest Neighbors (KNN), Support Vector Machines (SVM), Linear Discriminant Analysis (LDA), Random Forest (RF), AdaBoost and Neural Networks (NN), whose performance in discriminating between low-risk and high-risk patients have been validated through 30 times repeated five-fold cross validation.

CONCLUSIONS

Our study showed that segmentation methods influence radiomics features and that Shape features were the least reproducible (average ICC: 0.27), while GLCM features the most reproducible. Moreover, feature reproducibility changed depending on segmentation type, resulting in 51.18% of LoG features exhibiting excellent reproducibility (range average ICC: 0.68-0.87) and 47.85% of wavelet features exhibiting poor reproducibility that varied between wavelet sub-bands (range average ICC: 0.34-0.80) and resulted in the LLL band showing the highest average ICC (0.80). Finally, model performance showed that region growing led to the highest accuracy (74.49%), improved sensitivity (84.38%) and AUC (79.20%) in contrast with manual segmentation.

The Potential of Ultrasound Radiomics in Carpal Tunnel Syndrome Diagnosis: A Systematic Review and Meta-Analysis

Background: Carpal tunnel syndrome (CTS) is the most common entrapment neuropathy for which ultrasound imaging has recently emerged as a valuable diagnostic tool. This meta-analysis aims to investigate the role of ultrasound radiomics in the diagnosis of CTS and compare it with other diagnostic approaches. Methods: We conducted a comprehensive search of electronic databases from inception to September 2023. The included studies were assessed for quality using the Quality Assessment Tool for Diagnostic Accuracy Studies. The primary outcome was the diagnostic performance of ultrasound radiomics compared to radiologist evaluation for diagnosing CTS. Results: Our meta-analysis included five observational studies comprising 840 participants. In the context of radiologist evaluation, the combined statistics for sensitivity, specificity, and diagnostic odds ratio were 0.78 (95% confidence interval (CI), 0.71 to 0.83), 0.72 (95% CI, 0.59 to 0.81), and 9 (95% CI, 5 to 15), respectively. In contrast, the ultrasound radiomics training mode yielded a combined sensitivity of 0.88 (95% CI, 0.85 to 0.91), a specificity of 0.88 (95% CI, 0.84 to 0.92), and a diagnostic odds ratio of 58 (95% CI, 38 to 87). Similarly, the ultrasound radiomics testing mode demonstrated an aggregated sensitivity of 0.85 (95% CI, 0.78 to 0.89), a specificity of 0.80 (95% CI, 0.73 to 0.85), and a diagnostic odds ratio of 22 (95% CI, 12 to 41). Conclusions: In contrast to assessments by radiologists, ultrasound radiomics exhibited superior diagnostic performance in detecting CTS. Furthermore, there was minimal variability in the diagnostic accuracy between the training and testing sets of ultrasound radiomics, highlighting its potential as a robust diagnostic tool in CTS.

Analysis of Connectome Graphs Based on Boundary Scale

The purpose of this work is to advance in the computational study of connectome graphs from a topological point of view. Specifically, starting from a sequence of hypergraphs associated to a brain graph (obtained using the Boundary Scale model, BS2), we analyze the resulting scale-space representation using classical topological features, such as Betti numbers and average node and edge degrees. In this way, the topological information that can be extracted from the original graph is substantially enriched, thus providing an insightful description of the graph from a clinical perspective. To assess the qualitative and quantitative topological information gain of the BS2 model, we carried out an empirical analysis of neuroimaging data using a dataset that contains the connectomes of 96 healthy subjects, 52 women and 44 men, generated from MRI scans in the Human Connectome Project. The results obtained shed light on the differences between these two classes of subjects in terms of neural connectivity.

Machine learning for differentiation of lipid-poor adrenal adenoma and subclinical pheochromocytoma based on multiphase CT imaging radiomics

BACKGROUND

There is a paucity of research investigating the application of machine learning techniques for distinguishing between lipid-poor adrenal adenoma (LPA) and subclinical pheochromocytoma (sPHEO) based on radiomic features extracted from non-contrast and dynamic contrast-enhanced computed tomography (CT) scans of the abdomen.

METHODS

We conducted a retrospective analysis of multiphase spiral CT scans, including non-contrast, arterial, venous, and delayed phases, as well as thin- and thick-thickness images from 134 patients with surgically and pathologically confirmed. A total of 52 patients with LPA and 44 patients with sPHEO were randomly assigned to training/testing sets in a 7:3 ratio. Additionally, a validation set was comprised of 22 LPA cases and 16 sPHEO cases from two other hospitals. We used 3D Slicer and PyRadiomics to segment tumors and extract radiomic features, respectively. We then applied T-test and least absolute shrinkage and selection operator (LASSO) to select features. Six binary classifiers, including K-nearest neighbor (KNN), logistic regression (LR), decision tree (DT), random forest (RF), support vector machine (SVM), and multi-layer perceptron (MLP), were employed to differentiate LPA from sPHEO. Receiver operating characteristic (ROC) curves and area under the curve (AUC) values were compared using DeLong's method.

RESULTS

All six classifiers showed good diagnostic performance for each phase and slice thickness, as well as for the entire CT data, with AUC values ranging from 0.706 to 1. Non-contrast CT densities of LPA were significantly lower than those of sPHEO (P < 0.001). However, using the optimal threshold for non-contrast CT density, sensitivity was only 0.743, specificity 0.744, and AUC 0.828. Delayed phase CT density yielded a sensitivity of 0.971, specificity of 0.641, and AUC of 0.814. In radiomics, AUC values for the testing set using non-contrast CT images were: KNN 0.919, LR 0.979, DT 0.835, RF 0.967, SVM 0.979, and MLP 0.981. In the validation set, AUC values were: KNN 0.891, LR 0.974, DT 0.891, RF 0.964, SVM 0.949, and MLP 0.979.

CONCLUSIONS

The machine learning model based on CT radiomics can accurately differentiate LPA from sPHEO, even using non-contrast CT data alone, making contrast-enhanced CT unnecessary for diagnosing LPA and sPHEO.

Radiomics Analyses to Predict Histopathology in Patients with Metastatic Testicular Germ Cell Tumors before Post-Chemotherapy Retroperitoneal Lymph Node Dissection

BACKGROUND

The identification of histopathology in metastatic non-seminomatous testicular germ cell tumors (TGCT) before post-chemotherapy retroperitoneal lymph node dissection (PC-RPLND) holds significant potential to reduce treatment-related morbidity in young patients, addressing an important survivorship concern.

AIM

To explore this possibility, we conducted a study investigating the role of computed tomography (CT) radiomics models that integrate clinical predictors, enabling personalized prediction of histopathology in metastatic non-seminomatous TGCT patients prior to PC-RPLND. In this retrospective study, we included a cohort of 122 patients.

METHODS

Using dedicated radiomics software, we segmented the targets and extracted quantitative features from the CT images. Subsequently, we employed feature selection techniques and developed radiomics-based machine learning models to predict histological subtypes. To ensure the robustness of our procedure, we implemented a 5-fold cross-validation approach. When evaluating the models' performance, we measured metrics such as the area under the receiver operating characteristic curve (AUC), sensitivity, specificity, precision, and F-score.

RESULT

Our radiomics model based on the Support Vector Machine achieved an optimal average AUC of 0.945.

CONCLUSIONS

The presented CT-based radiomics model can potentially serve as a non-invasive tool to predict histopathological outcomes, differentiating among fibrosis/necrosis, teratoma, and viable tumor in metastatic non-seminomatous TGCT before PC-RPLND. It has the potential to be considered a promising tool to mitigate the risk of over- or under-treatment in young patients, although multi-center validation is critical to confirm the clinical utility of the proposed radiomics workflow.

A proposed methodology for detecting the malignant potential of pulmonary nodules in sarcoma using computed tomographic imaging and artificial intelligence-based models

The presence of lung metastases in patients with primary malignancies is an important criterion for treatment management and prognostication. Computed tomography (CT) of the chest is the preferred method to detect lung metastasis. However, CT has limited efficacy in differentiating metastatic nodules from benign nodules (e.g., granulomas due to tuberculosis) especially at early stages (<5 mm). There is also a significant subjectivity associated in making this distinction, leading to frequent CT follow-ups and additional radiation exposure along with financial and emotional burden to the patients and family. Even 18F-fluoro-deoxyglucose positron emission technology-computed tomography (18F-FDG PET-CT) is not always confirmatory for this clinical problem. While pathological biopsy is the gold standard to demonstrate malignancy, invasive sampling of small lung nodules is often not clinically feasible. Currently, there is no non-invasive imaging technique that can reliably characterize lung metastases. The lung is one of the favored sites of metastasis in sarcomas. Hence, patients with sarcomas, especially from tuberculosis prevalent developing countries, can provide an ideal platform to develop a model to differentiate lung metastases from benign nodules. To overcome the lack of optimal specificity of CT scan in detecting pulmonary metastasis, a novel artificial intelligence (AI)-based protocol is proposed utilizing a combination of radiological and clinical biomarkers to identify lung nodules and characterize it as benign or metastasis. This protocol includes a retrospective cohort of nearly 2,000-2,250 sample nodules (from at least 450 patients) for training and testing and an ambispective cohort of nearly 500 nodules (from 100 patients; 50 patients each from the retrospective and prospective cohort) for validation. Ground-truth annotation of lung nodules will be performed using an in-house-built segmentation tool. Ground-truth labeling of lung nodules (metastatic/benign) will be performed based on histopathological results or baseline and/or follow-up radiological findings along with clinical outcome of the patient. Optimal methods for data handling and statistical analysis are included to develop a robust protocol for early detection and classification of pulmonary metastasis at baseline and at follow-up and identification of associated potential clinical and radiological markers.

Comparison and fusion prediction model for lung adenocarcinoma with micropapillary and solid pattern using clinicoradiographic, radiomics and deep learning features

To investigate whether the combination scheme of deep learning score (DL-score) and radiomics can improve preoperative diagnosis in the presence of micropapillary/solid (MPP/SOL) patterns in lung adenocarcinoma (ADC). A retrospective cohort of 514 confirmed pathologically lung ADC in 512 patients after surgery was enrolled. The clinicoradiographic model (model 1) and radiomics model (model 2) were developed with logistic regression. The deep learning model (model 3) was constructed based on the deep learning score (DL-score). The combine model (model 4) was based on DL-score and R-score and clinicoradiographic variables. The performance of these models was evaluated with area under the receiver operating characteristic curve (AUC) and compared using DeLong's test internally and externally. The prediction nomogram was plotted, and clinical utility depicted with decision curve. The performance of model 1, model 2, model 3 and model 4 was supported by AUCs of 0.848, 0.896, 0.906, 0.921 in the Internal validation set, that of 0.700, 0.801, 0.730, 0.827 in external validation set, respectively. These models existed statistical significance in internal validation (model 4 vs model 3, P = 0.016; model 4 vs model 1, P = 0.009, respectively) and external validation (model 4 vs model 2, P = 0.036; model 4 vs model 3, P = 0.047; model 4 vs model 1, P = 0.016, respectively). The decision curve analysis (DCA) demonstrated that model 4 predicting the lung ADC with MPP/SOL structure would be more beneficial than the model 1and model 3 but comparable with the model 2. The combined model can improve preoperative diagnosis in the presence of MPP/SOL pattern in lung ADC in clinical practice.

CT based intratumor and peritumoral radiomics for differentiating complete from incomplete capsular characteristics of parotid pleomorphic adenoma: a two-center study

OBJECTIVE

Capsular characteristics of pleomorphic adenoma (PA) has various forms. Patients without complete capsule has a higher risk of recurrence than patients with complete capsule. We aimed to develop and validate CT-based intratumoral and peritumoral radiomics models to make a differential diagnosis between parotid PA with and without complete capsule.

METHODS

Data of 260 patients (166 patients with PA from institution 1 (training set) and 94 patients (test set) from institution 2) were retrospectively analyzed. Three Volume of interest (VOIs) were defined in the CT images of each patient: tumor volume of interest (VOI_tumor), VOI_peritumor, and VOI_{intra-plus peritumor}. Radiomics features were extracted from each VOI and used to train nine different machine learning algorithms. Model performance was evaluated using receiver operating characteristic (ROC) curves and the area under the curve (AUC).

RESULTS

The results showed that the radiomics models based on features from VOI_{intra-plus peritumor} achieved higher AUCs compared to models based on features from VOI_tumor. The best performing model was Linear discriminant analysis, which achieved an AUC of 0.86 in the tenfold cross-validation and 0.869 in the test set. The model was based on 15 features, including shape-based features and texture features.

CONCLUSIONS

We demonstrated the feasibility of combining artificial intelligence with CT-based peritumoral radiomics features can be used to accurately predict capsular characteristics of parotid PA. This may assist in clinical decision-making by preoperative identification of capsular characteristics of parotid PA.

Machine learning models combining computed tomography semantic features and selected clinical variables for accurate prediction of the pathological grade of bladder cancer

Objective

The purpose of this research was to develop a radiomics model that combines several clinical features for preoperative prediction of the pathological grade of bladder cancer (BCa) using non-enhanced computed tomography (NE-CT) scanning images.

Materials and methods

The computed tomography (CT), clinical, and pathological data of 105 BCa patients attending our hospital between January 2017 and August 2022 were retrospectively evaluated. The study cohort comprised 44 low-grade BCa and 61 high-grade BCa patients. The subjects were randomly divided into training (n = 73) and validation (n = 32) cohorts at a ratio of 7:3. Radiomic features were extracted from NE-CT images. A total of 15 representative features were screened using the least absolute shrinkage and selection operator (LASSO) algorithm. Based on these characteristics, six models for predicting BCa pathological grade, including support vector machine (SVM), k-nearest neighbor (KNN), gradient boosting decision tree (GBDT), logical regression (LR), random forest (RF), and extreme gradient boosting (XGBOOST) were constructed. The model combining radiomics score and clinical factors was further constructed. The predictive performance of the models was evaluated based on the area under the receiver operating characteristic (ROC) curve, DeLong test, and decision curve analysis (DCA).

Results

The selected clinical factors for the model included age and tumor size. LASSO regression analysis identified 15 features most linked to BCa grade, which were included in the machine learning model. The SVM analysis revealed that the highest AUC of the model was 0.842. A nomogram combining the radiomics signature and selected clinical variables showed accurate prediction of the pathological grade of BCa preoperatively. The AUC of the training cohort was 0.919, whereas that of the validation cohort was 0.854. The clinical value of the combined radiomics nomogram was validated using calibration curve and DCA.

Conclusion

Machine learning models combining CT semantic features and the selected clinical variables can accurately predict the pathological grade of BCa, offering a non-invasive and accurate approach for predicting the pathological grade of BCa preoperatively.

QuantImage v2: a comprehensive and integrated physician-centered cloud platform for radiomics and machine learning research

BACKGROUND

Radiomics, the field of image-based computational medical biomarker research, has experienced rapid growth over the past decade due to its potential to revolutionize the development of personalized decision support models. However, despite its research momentum and important advances toward methodological standardization, the translation of radiomics prediction models into clinical practice only progresses slowly. The lack of physicians leading the development of radiomics models and insufficient integration of radiomics tools in the clinical workflow contributes to this slow uptake.

METHODS

We propose a physician-centered vision of radiomics research and derive minimal functional requirements for radiomics research software to support this vision. Free-to-access radiomics tools and frameworks were reviewed to identify best practices and reveal the shortcomings of existing software solutions to optimally support physician-driven radiomics research in a clinical environment.

RESULTS

Support for user-friendly development and evaluation of radiomics prediction models via machine learning was found to be missing in most tools. QuantImage v2 (QI2) was designed and implemented to address these shortcomings. QI2 relies on well-established existing tools and open-source libraries to realize and concretely demonstrate the potential of a one-stop tool for physician-driven radiomics research. It provides web-based access to cohort management, feature extraction, and visualization and supports "no-code" development and evaluation of machine learning models against patient-specific outcome data.

CONCLUSIONS

QI2 fills a gap in the radiomics software landscape by enabling "no-code" radiomics research, including model validation, in a clinical environment. Further information about QI2, a public instance of the system, and its source code is available at https://medgift.github.io/quantimage-v2-info/ . Key points As domain experts, physicians play a key role in the development of radiomics models. Existing software solutions do not support physician-driven research optimally. QuantImage v2 implements a physician-centered vision for radiomics research. QuantImage v2 is a web-based, "no-code" radiomics research platform.

Phenotyping the Histopathological Subtypes of Non-Small-Cell Lung Carcinoma: How Beneficial Is Radiomics?

The aim of this study was to investigate the usefulness of radiomics in the absence of well-defined standard guidelines. Specifically, we extracted radiomics features from multicenter computed tomography (CT) images to differentiate between the four histopathological subtypes of non-small-cell lung carcinoma (NSCLC). In addition, the results that varied with the radiomics model were compared. We investigated the presence of the batch effects and the impact of feature harmonization on the models' performance. Moreover, the question on how the training dataset composition influenced the selected feature subsets and, consequently, the model's performance was also investigated. Therefore, through combining data from the two publicly available datasets, this study involves a total of 152 squamous cell carcinoma (SCC), 106 large cell carcinoma (LCC), 150 adenocarcinoma (ADC), and 58 no other specified (NOS). Through the matRadiomics tool, which is an example of Image Biomarker Standardization Initiative (IBSI) compliant software, 1781 radiomics features were extracted from each of the malignant lesions that were identified in CT images. After batch analysis and feature harmonization, which were based on the ComBat tool and were integrated in matRadiomics, the datasets (the harmonized and the non-harmonized) were given as an input to a machine learning modeling pipeline. The following steps were articulated: (i) training-set/test-set splitting (80/20); (ii) a Kruskal-Wallis analysis and LASSO linear regression for the feature selection; (iii) model training; (iv) a model validation and hyperparameter optimization; and (v) model testing. Model optimization consisted of a 5-fold cross-validated Bayesian optimization, repeated ten times (inner loop). The whole pipeline was repeated 10 times (outer loop) with six different machine learning classification algorithms. Moreover, the stability of the feature selection was evaluated. Results showed that the batch effects were present even if the voxels were resampled to an isotropic form and whether feature harmonization correctly removed them, even though the models' performances decreased. Moreover, the results showed that a low accuracy (61.41%) was reached when differentiating between the four subtypes, even though a high average area under curve (AUC) was reached (0.831). Further, a NOS subtype was classified as almost completely correct (true positive rate ~90%). The accuracy increased (77.25%) when only the SCC and ADC subtypes were considered, as well as when a high AUC (0.821) was obtained-although harmonization decreased the accuracy to 58%. Moreover, the features that contributed the most to models' performance were those extracted from wavelet decomposed and Laplacian of Gaussian (LoG) filtered images and they belonged to the texture feature class.. In conclusion, we showed that our multicenter data were affected by batch effects, that they could significantly alter the models' performance, and that feature harmonization correctly removed them. Although wavelet features seemed to be the most informative features, an absolute subset could not be identified since it changed depending on the training/testing splitting. Moreover, performance was influenced by the chosen dataset and by the machine learning methods, which could reach a high accuracy in binary classification tasks, but could underperform in multiclass problems. It is, therefore, essential that the scientific community propose a more systematic radiomics approach, focusing on multicenter studies, with clear and solid guidelines to facilitate the translation of radiomics to clinical practice.

CT Rendering and Radiomic Analysis in Post-Chemotherapy Retroperitoneal Lymph Node Dissection for Testicular Cancer to Anticipate Difficulties for Young Surgeons

Post-chemotherapy retroperitoneal lymph node dissection (PC-RPLND) in non-seminomatous germ-cell tumor (NSTGCTs) is a complex procedure. We evaluated whether 3D computed tomography (CT) rendering and their radiomic analysis help predict resectability by junior surgeons. The ambispective analysis was performed between 2016-2021. A prospective group (A) of 30 patients undergoing CT was segmented using the 3D Slicer software while a retrospective group (B) of 30 patients was evaluated with conventional CT (without 3D reconstruction). CatFisher's exact test showed a p-value of 0.13 for group A and 1.0 for Group B. The difference between the proportion test showed a p-value of 0.009149 (IC 0.1-0.63). The proportion of the correct classification showed a p-value of 0.645 (IC 0.55-0.87) for A, and 0.275 (IC 0.11-0.43) for Group B. Furthermore, 13 shape features were extracted: elongation, flatness, volume, sphericity, and surface area, among others. Performing a logistic regression with the entire dataset, n = 60, the results were: Accuracy: 0.7 and Precision: 0.65. Using n = 30 randomly chosen, the best result obtained was Accuracy: 0.73 and Precision: 0.83, with a p-value: 0.025 for Fisher's exact test. In conclusion, the results showed a significant difference in the prediction of resectability with conventional CT versus 3D reconstruction by junior surgeons versus experienced surgeons. Radiomic features used to elaborate an artificial intelligence model improve the prediction of resectability. The proposed model could be of great support in a university hospital, allowing it to plan the surgery and to anticipate complications.

Dynamic radiomics for predicting the efficacy of antiangiogenic therapy in colorectal liver metastases

Background and objective

For patients with advanced colorectal liver metastases (CRLMs) receiving first-line anti-angiogenic therapy, an accurate, rapid and noninvasive indicator is urgently needed to predict its efficacy. In previous studies, dynamic radiomics predicted more accurately than conventional radiomics. Therefore, it is necessary to establish a dynamic radiomics efficacy prediction model for antiangiogenic therapy to provide more accurate guidance for clinical diagnosis and treatment decisions.

Methods

In this study, we use dynamic radiomics feature extraction method that extracts static features using tomographic images of different sequences of the same patient and then quantifies them into new dynamic features for the prediction of treatmentefficacy. In this retrospective study, we collected 76 patients who were diagnosed with unresectable CRLM between June 2016 and June 2021 in the First Hospital of China Medical University. All patients received standard treatment regimen of bevacizumab combined with chemotherapy in the first-line treatment, and contrast-enhanced abdominal CT (CECT) scans were performed before treatment. Patients with multiple primary lesions as well as missing clinical or imaging information were excluded. Area Under Curve (AUC) and accuracy were used to evaluate model performance. Regions of interest (ROIs) were independently delineated by two radiologists to extract radiomics features. Three machine learning algorithms were used to construct two scores based on the best response and progression-free survival (PFS).

Results

For the task that predict the best response patients will achieve after treatment, by using ROC curve analysis, it can be seen that the relative change rate (RCR) feature performed best among all features and best in linear discriminantanalysis (AUC: 0.945 and accuracy: 0.855). In terms of predicting PFS, the Kaplan-Meier plots suggested that the score constructed using the RCR features could significantly distinguish patients with good response from those with poor response (Two-sided P<0.0001 for survival analysis).

Conclusions

This study demonstrates that the application of dynamic radiomics features can better predict the efficacy of CRLM patients receiving antiangiogenic therapy compared with conventional radiomics features. It allows patients to have a more accurate assessment of the effect of medical treatment before receiving treatment, and this assessment method is noninvasive, rapid, and less expensive. Dynamic radiomics model provides stronger guidance for the selection of treatment options and precision medicine.

Risk stratification and prognostic value of multi-modal MRI-based radiomics for extranodal nasal-type NK/T-cell lymphoma

BACKGROUND

Magnetic resonance imaging (MRI) performs well in the locoregional assessment of extranodal nasal-type NK/T-cell lymphoma (ENKTCL). It's important to assess the value of multi-modal MRI-based radiomics for estimating overall survival (OS) in patients with ENKTCL.

METHODS

Patients with ENKTCL in a prospectively cohort were systemically reviewed and all the pretreatment MRI were acquisitioned. An unsupervised spectral clustering method was used to identify risk groups of patients and radiomic features. A nomogram-revised risk index (NRI) plus MRI radiomics signature (NRI-M) was developed, and compared with the NRI.

RESULTS

The 2 distinct type I and II groups of the MRI radiomics signatures were identified. The 5-year OS rates between the type I and type II groups were 87.2% versus 67.3% (P = 0.002) in all patients, and 88.8% versus 69.2% (P = 0.003) in early-stage patients. The discrimination and calibration of the NRI-M for OS prediction demonstrated a better performance than that of either MRI radiomics or NRI, with a mean area under curve (AUC) of 0.748 and 0.717 for predicting the 5-year OS in all-stages and early-stage patients.

CONCLUSIONS

The NRI-M model has good performance for predicting the prognosis of ENKTCL and may help design clinical trials and improve clinical decision making.

CT-based machine learning radiomics predicts CCR5 expression level and survival in ovarian cancer

OBJECTIVE

We aimed to evaluate the prognostic value of C-C motif chemokine receptor type 5 (CCR5) expression level for patients with ovarian cancer and to establish a radiomics model that can predict CCR5 expression level using The Cancer Imaging Archive (TCIA) and The Cancer Genome Atlas (TCGA) database.

METHODS

A total of 343 cases of ovarian cancer from the TCGA were used for the gene-based prognostic analysis. Fifty seven cases had preoperative computed tomography (CT) images stored in TCIA with genomic data in TCGA were used for radiomics feature extraction and model construction. 89 cases with both TCGA and TCIA clinical data were used for radiomics model evaluation. After feature extraction, a radiomics signature was constructed using the least absolute shrinkage and selection operator (LASSO) regression analysis. A prognostic scoring system incorporating radiomics signature based on CCR5 expression level and clinicopathologic risk factors was proposed for survival prediction.

RESULTS

CCR5 was identified as a differentially expressed prognosis-related gene in tumor and normal sample, which were involved in the regulation of immune response and tumor invasion and metastasis. Four optimal radiomics features were selected to predict overall survival. The performance of the radiomics model for predicting the CCR5 expression level with 10-fold cross- validation achieved Area Under Curve (AUCs) of 0.770 and of 0.726, respectively, in the training and validation sets. A predictive nomogram was generated based on the total risk score of each patient, the AUCs of the time-dependent receiver operating characteristic (ROC) curve of the model was 0.8, 0.673 and 0.792 for 1-year, 3-year and 5-year, respectively. Along with clinical features, important imaging biomarkers could improve the overall survival accuracy of the prediction model.

CONCLUSION

The expression levels of CCR5 can affect the prognosis of patients with ovarian cancer. CT-based radiomics could serve as a new tool for prognosis prediction.

An exploratory study of CT radiomics using differential network feature selection for WHO/ISUP grading and progression-free survival prediction of clear cell renal cell carcinoma

Objectives

To explore the feasibility of predicting the World Health Organization/International Society of Urological Pathology (WHO/ISUP) grade and progression-free survival (PFS) of clear cell renal cell cancer (ccRCC) using the radiomics features (RFs) based on the differential network feature selection (FS) method using the maximum-entropy probability model (MEPM).

Methods

175 ccRCC patients were divided into a training set (125) and a test set (50). The non-contrast phase (NCP), cortico-medullary phase, nephrographic phase, excretory phase phases, and all-phase WHO/ISUP grade prediction models were constructed based on a new differential network FS method using the MEPM. The diagnostic performance of the best phase model was compared with the other state-of-the-art machine learning models and the clinical models. The RFs of the best phase model were used for survival analysis and visualized using risk scores and nomograms. The performance of the above models was tested in both cross-validated and independent validation and checked by the Hosmer-Lemeshow test.

Results

The NCP RFs model was the best phase model, with an AUC of 0.89 in the test set, and performed superior to other machine learning models and the clinical models (all p &lt;0.05). Kaplan-Meier survival analysis, univariate and multivariate cox regression results, and risk score analyses showed the NCP RFs could predict PFS well (almost all p &lt; 0.05). The nomogram model incorporated the best two RFs and showed good discrimination, a C-index of 0.71 and 0.69 in the training and test set, and good calibration.

Conclusion

The NCP CT-based RFs selected by differential network FS could predict the WHO/ISUP grade and PFS of RCC.

Fusing hand-crafted and deep-learning features in a convolutional neural network model to identify prostate cancer in pathology images

Prostate cancer can be diagnosed by prostate biopsy using transectal ultrasound guidance. The high number of pathology images from biopsy tissues is a burden on pathologists, and analysis is subjective and susceptible to inter-rater variability. The use of machine learning techniques could make prostate histopathology diagnostics more precise, consistent, and efficient overall. This paper presents a new classification fusion network model that was created by fusing eight advanced image features: seven hand-crafted features and one deep-learning feature. These features are the scale-invariant feature transform (SIFT), speeded up robust feature (SURF), oriented features from accelerated segment test (FAST) and rotated binary robust independent elementary features (BRIEF) (ORB) of local features, shape and texture features of the cell nuclei, the histogram of oriented gradients (HOG) feature of the cavities, a color feature, and a convolution deep-learning feature. Matching, integrated, and fusion networks are the three essential components of the proposed deep-learning network. The integrated network consists of both a backbone and an additional network. When classifying 1100 prostate pathology images using this fusion network with different backbones (ResNet-18/50, VGG-11/16, and DenseNet-121/201), we discovered that the proposed model with the ResNet-18 backbone achieved the best performance in terms of the accuracy (95.54%), specificity (93.64%), and sensitivity (97.27%) as well as the area under the receiver operating characteristic curve (98.34%). However, each of the assessment criteria for these separate features had a value lower than 90%, which demonstrates that the suggested model combines differently derived characteristics in an effective manner. Moreover, a Grad-CAM++ heatmap was used to observe the differences between the proposed model and ResNet-18 in terms of the regions of interest. This map showed that the proposed model was better at focusing on cancerous cells than ResNet-18. Hence, the proposed classification fusion network, which combines hand-crafted features and a deep-learning feature, is useful for computer-aided diagnoses based on pathology images of prostate cancer. Because of the similarities in the feature engineering and deep learning for different types of pathology images, the proposed method could be used for other pathology images, such as those of breast, thyroid cancer.