A Low-Dose CT-Based Radiomic Model to Improve Characterization and Screening Recall Intervals of Indeterminate Prevalent Pulmonary Nodules

CT-Based Radiomics Predicts the Malignancy of Pulmonary Nodules: A Systematic Review and Meta-Analysis

RATIONALE AND OBJECTIVES

More pulmonary nodules (PNs) have been detected with the wide application of computed tomography (CT) in lung cancer screening. Radiomics is a noninvasive approach to predict the malignancy of PNs. We aimed to systematically evaluate the methodological quality of the eligible studies regarding CT-based radiomics models in predicting the malignancy of PNs and evaluate the model performance of the available studies.

MATERIALS AND METHODS

PubMed, Embase, and Web of Science were searched to retrieve relevant studies. The methodological quality of the included studies was assessed using the Radiomics Quality Score (RQS) and Prediction model Risk of Bias Assessment Tool. A meta-analysis was conducted to evaluate the performance of CT-based radiomics model. Meta-regression and subgroup analyses were employed to investigate the source of heterogeneity.

RESULTS

In total, 49 studies were eligible for qualitative analysis and 27 studies were included in quantitative synthesis. The median RQS of 49 studies was 13 (range -2 to 20). The overall risk of bias was found to be high, and the overall applicability was of low concern in all included studies. The pooled sensitivity, specificity, and diagnostic odds ratio were 0.86 95% confidence interval (CI): 0.79-0.91, 0.84 95% CI: 0.78-0.88, and 31.55 95% CI: 21.31-46.70, respectively. The overall area under the curve was 0.91 95% CI: 0.89-0.94. Meta-regression showed the type of PNs on heterogeneity. CT-based radiomics models performed better in studies including only solid PNs.

CONCLUSION

CT-based radiomics models exhibited excellent diagnostic performance in predicting the malignancy of PNs. Prospective, large sample size, and well-devised studies are desired to verify the prediction capabilities of CT-based radiomics model.

Harmonization of supervised machine learning practices for efficient source attribution of Listeria monocytogenes based on genomic data

BACKGROUND

Genomic data-based machine learning tools are promising for real-time surveillance activities performing source attribution of foodborne bacteria such as Listeria monocytogenes. Given the heterogeneity of machine learning practices, our aim was to identify those influencing the source prediction performance of the usual holdout method combined with the repeated k-fold cross-validation method.

METHODS

A large collection of 1 100 L. monocytogenes genomes with known sources was built according to several genomic metrics to ensure authenticity and completeness of genomic profiles. Based on these genomic profiles (i.e. 7-locus alleles, core alleles, accessory genes, core SNPs and pan kmers), we developed a versatile workflow assessing prediction performance of different combinations of training dataset splitting (i.e. 50, 60, 70, 80 and 90%), data preprocessing (i.e. with or without near-zero variance removal), and learning models (i.e. BLR, ERT, RF, SGB, SVM and XGB). The performance metrics included accuracy, Cohen's kappa, F1-score, area under the curves from receiver operating characteristic curve, precision recall curve or precision recall gain curve, and execution time.

RESULTS

The testing average accuracies from accessory genes and pan kmers were significantly higher than accuracies from core alleles or SNPs. While the accuracies from 70 and 80% of training dataset splitting were not significantly different, those from 80% were significantly higher than the other tested proportions. The near-zero variance removal did not allow to produce results for 7-locus alleles, did not impact significantly the accuracy for core alleles, accessory genes and pan kmers, and decreased significantly accuracy for core SNPs. The SVM and XGB models did not present significant differences in accuracy between each other and reached significantly higher accuracies than BLR, SGB, ERT and RF, in this order of magnitude. However, the SVM model required more computing power than the XGB model, especially for high amount of descriptors such like core SNPs and pan kmers.

CONCLUSIONS

In addition to recommendations about machine learning practices for L. monocytogenes source attribution based on genomic data, the present study also provides a freely available workflow to solve other balanced or unbalanced multiclass phenotypes from binary and categorical genomic profiles of other microorganisms without source code modifications.

Software-based quantitative CT analysis to predict the growth trend of persistent nonsolid pulmonary nodules: a retrospective study

PURPOSE

Persistent nonsolid nodules (NSNs) usually exhibit an indolent course and may remain stable for several years; however, some NSNs grow quickly and require surgical excision. Therefore, identifying quantitative features capable of early discrimination between growing and nongrowing NSNs is becoming a crucial aspect of radiological analysis. The main purpose of this study was to evaluate the performance of an open-source software (ImageJ) to predict the future growth of NSNs detected in a Caucasian (Italian) population.

MATERIAL AND METHODS

We retrospectively selected 60 NSNs with an axial diameter of 6-30 mm scanned with the same acquisition-reconstruction parameters and the same computed tomography (CT) scanner. Software-based analysis was performed on thin-section CT images using ImageJ. For each NSNs, several quantitative features were extracted from the baseline CT images. The relationships of NSN growth with quantitative CT features and other categorical variables were analyzed using univariate and multivariable logistic regression analyses.

RESULTS

In multivariable analysis, only the skewness and linear mass density (LMD) were significantly associated with NSN growth, and the skewness was the strongest predictor of growth. In receiver operating characteristic curve analyses, the optimal cutoff values of skewness and LMD were 0.90 and 19.16 mg/mm, respectively. The two predictive models that included the skewness, with or without LMD, exhibited an excellent power for predicting NSN growth.

CONCLUSION

According to our results, NSNs with a skewness value > 0.90, specifically those with a LMD > 19.16 mg/mm, should require closer follow-up due to their higher growth potential, and higher risk of becoming an active cancer.

Secondary prevention and treatment innovation of early stage non-small cell lung cancer: Impact on diagnostic-therapeutic pathway from a multidisciplinary perspective

Lung cancer (LC) is the leading cause of cancer-related death worldwide, mostly because the lack of a screening program so far. Although smoking cessation has a central role in LC primary prevention, several trials on LC screening through low-dose computed tomography (LDCT) in a high risk population showed a significant reduction of LC related mortality. Most trials showed heterogeneity in terms of selection criteria, comparator arm, detection nodule method, timing and intervals of screening and duration of the follow-up. LC screening programs currently active in Europe as well as around the world will lead to a higher number of early-stage Non Small Cell Lung Cancer (NSCLC) at the diagnosis. Innovative drugs have been recently transposed from the metastatic to the perioperative setting, leading to improvements in terms of resection rates and pathological responses after induction chemoimmunotherapy, and disease free survival with targeted agents and immune checkpoint inhibitors. The present review summarizes available evidence about LC screening, highlighting potential pitfalls and benefits and underlining the impact on the diagnostic therapeutic pathway of NSCLC from a multidisciplinary perspective. Future perspectives in terms of circulating biomarkers under evaluation for patients' risk stratification as well as a focus on recent clinical trials results and ongoing studies in the perioperative setting will be also presented.

Radiomics in Oncology III

In recent years, radiomics has been among the most impactful topics in the research field of quantitative imaging [...].

Evaluating Histological Subtypes Classification of Primary Lung Cancers on Unenhanced Computed Tomography Based on Random Forest Model

Lung cancer is the leading cause of cancer-related death in many countries, and an accurate histopathological diagnosis is of great importance in subsequent treatment. The aim of this study was to establish the random forest (RF) model based on radiomic features to automatically classify and predict lung adenocarcinoma (ADC), lung squamous cell carcinoma (SCC), and small cell lung cancer (SCLC) on unenhanced computed tomography (CT) images. Eight hundred and fifty-two patients (mean age: 61.4, range: 29-87, male/female: 536/316) with preoperative unenhanced CT and postoperative histopathologically confirmed primary lung cancers, including 525 patients with ADC, 161 patients with SCC, and 166 patients with SCLC, were included in this retrospective study. Radiomic features were extracted, selected, and then used to establish the RF classification model to analyse and classify primary lung cancers into three subtypes, including ADC, SCC, and SCLC according to histopathological results. The training (446 ADC, 137 SCC, and 141 SCLC) and testing cohorts (79 ADC, 24 SCC, and 25 SCLC) accounted for 85% and 15% of the whole datasets, respectively. The prediction performance of the RF classification model was evaluated by F1 scores and the receiver operating characteristic (ROC) curve. On the testing cohort, the areas under the ROC curve (AUC) of the RF model in classifying ADC, SCC, and SCLC were 0.74, 0.77, and 0.88, respectively. The F1 scores achieved 0.80, 0.40, and 0.73 in ADC, SCC, and SCLC, respectively, and the weighted average F1 score was 0.71. In addition, for the RF classification model, the precisions were 0.72, 0.64, and 0.70; the recalls were 0.86, 0.29, and 0.76; and the specificities were 0.55, 0.96, and 0.92 in ADC, SCC, and SCLC. The primary lung cancers were feasibly and effectively classified into ADC, SCC, and SCLC based on the combination of RF classification model and radiomic features, which has the potential for noninvasive predicting histological subtypes of primary lung cancers.

Neural-Symbolic Ensemble Learning for early-stage prediction of critical state of Covid-19 patients

Recently, Artificial Intelligence (AI) and Machine Learning (ML) have been successfully applied to many domains of interest including medical diagnosis. Due to the availability of a large quantity of data, it is possible to build reliable AI systems that assist humans in making decisions. The recent Covid-19 pandemic quickly spread over the world causing serious health problems and severe economic and social damage. Computer scientists are actively working together with doctors on different ML models to diagnose Covid-19 patients using Computed Tomography (CT) scans and clinical data. In this work, we propose a neural-symbolic system that predicts if a Covid-19 patient arriving at the hospital will end in a critical condition. The proposed system relies on Deep 3D Convolutional Neural Networks (3D-CNNs) for analyzing lung CT scans of Covid-19 patients, Decision Trees (DTs) for predicting if a Covid-19 patient will eventually pass away by analyzing its clinical data, and a neural system that integrates the previous ones using Hierarchical Probabilistic Logic Programs (HPLPs). Predicting if a Covid-19 patient will end in a critical condition is useful for managing the limited number of intensive care at the hospital. Moreover, knowing early that a Covid-19 patient could end in serious conditions allows doctors to gain early knowledge on patients and provide special treatment to those predicted to finish in critical conditions. The proposed system, entitled Neural HPLP, obtains good performance in terms of area under the receiver operating characteristic and precision curves with values of about 0.96 for both metrics. Therefore, with Neural HPLP, it is possible not only to efficiently predict if Covid-19 patients will end in severe conditions but also possible to provide an explanation of the prediction. This makes Neural HPLP explainable, interpretable, and reliable.

Graphical abstract

Form Factors as Potential Imaging Biomarkers to Differentiate Benign vs. Malignant Lung Lesions on CT Scans

Indeterminate lung nodules detected on CT scans are common findings in clinical practice. Their correct assessment is critical, as early diagnosis of malignancy is crucial to maximise the treatment outcome. In this work, we evaluated the role of form factors as imaging biomarkers to differentiate benign vs. malignant lung lesions on CT scans. We tested a total of three conventional imaging features, six form factors, and two shape features for significant differences between benign and malignant lung lesions on CT scans. The study population consisted of 192 lung nodules from two independent datasets, containing 109 (38 benign, 71 malignant) and 83 (42 benign, 41 malignant) lung lesions, respectively. The standard of reference was either histological evaluation or stability on radiological followup. The statistical significance was determined via the Mann-Whitney U nonparametric test, and the ability of the form factors to discriminate a benign vs. a malignant lesion was assessed through multivariate prediction models based on Support Vector Machines. The univariate analysis returned four form factors (Angelidakis compactness and flatness, Kong flatness, and maximum projection sphericity) that were significantly different between the benign and malignant group in both datasets. In particular, we found that the benign lesions were on average flatter than the malignant ones; conversely, the malignant ones were on average more compact (isotropic) than the benign ones. The multivariate prediction models showed that adding form factors to conventional imaging features improved the prediction accuracy by up to 14.5 pp. We conclude that form factors evaluated on lung nodules on CT scans can improve the differential diagnosis between benign and malignant lesions.