Reproducible and Interpretable Spiculation Quantification for Lung Cancer Screening

Novel Functional Radiomics for Prediction of Cardiac Positron Emission Tomography Avidity in Lung Cancer Radiotherapy

PURPOSE

Traditional methods of evaluating cardiotoxicity focus on radiation doses to the heart. Functional imaging has the potential to provide improved prediction for cardiotoxicity for patients with lung cancer. Fluorine-18 (18F) fluorodeoxyglucose (FDG)-positron emission tomography (PET)/computed tomography (CT) imaging is routinely obtained in a standard cancer staging workup. This work aimed to develop a radiomics model predicting clinical cardiac assessment using 18F-FDG PET/CT scans before thoracic radiation therapy.

METHODS

Pretreatment 18F-FDG PET/CT scans from three study populations (N = 100, N = 39, N = 70) were used, comprising two single-institutional protocols and one publicly available data set. A clinician (V.J.) classified the PET/CT scans per clinical cardiac guidelines as no uptake, diffuse uptake, or focal uptake. The heart was delineated, and 210 novel functional radiomics features were selected to classify cardiac FDG uptake patterns. Training data were divided into training (80%)/validation (20%) sets. Feature reduction was performed using the Wilcoxon test, hierarchical clustering, and recursive feature elimination. Ten-fold cross-validation was carried out for training, and the accuracy of the models to predict clinical cardiac assessment was reported.

RESULTS

From 202 of 209 scans, cardiac FDG uptake was scored as no uptake (39.6%), diffuse uptake (25.3%), and focal uptake (35.1%), respectively. Sixty-two independent radiomics features were reduced to nine clinically pertinent features. The best model showed 93% predictive accuracy in the training data set and 80% and 92% predictive accuracy in two external validation data sets.

CONCLUSION

This work used an extensive patient data set to develop a functional cardiac radiomic model from standard-of-care 18F-FDG PET/CT scans, showing good predictive accuracy. The radiomics model has the potential to provide an automated method to predict existing cardiac conditions and provide an early functional biomarker to identify patients at risk of developing cardiac complications after radiotherapy.

Exploring published and novel pre-treatment CT and PET radiomics to stratify risk of progression among early-stage non-small cell lung cancer patients treated with stereotactic radiation

PURPOSE

Disease progression after definitive stereotactic body radiation therapy (SBRT) for early-stage non-small cell lung cancer (NSCLC) occurs in 20-40% of patients. Here, we explored published and novel pre-treatment CT and PET radiomics features to identify patients at risk of progression.

MATERIALS/METHODS

Published CT and PET features were identified and explored along with 15 other CT and PET features in 408 consecutively treated early-stage NSCLC patients having CT and PET < 3 months pre-SBRT (training/set-aside validation subsets: n = 286/122). Features were associated with progression-free survival (PFS) using bootstrapped Cox regression (Bonferroni-corrected univariate predictor: p ≤ 0.002) and only non-strongly correlated predictors were retained (|Rs|<0.70) in forward-stepwise multivariate analysis.

RESULTS

Tumor diameter and SUVmax were the two most frequently reported features associated with progression/survival (in 6/20 and 10/20 identified studies). These two features and 12 of the 15 additional features (CT: 6; PET: 6) were candidate PFS predictors. A re-fitted model including diameter and SUVmax presented with the best performance (c-index: 0.78; log-rank p-value < 0.0001). A model built with the two best additional features (CTspiculation1 and SUVentropy) had a c-index of 0.75 (log-rank p-value < 0.0001).

CONCLUSIONS

A re-fitted pre-treatment model using the two most frequently published features - tumor diameter and SUVmax - successfully stratified early-stage NSCLC patients by PFS after receiving SBRT.

Preoperative 18F-FDG PET/CT and CT radiomics for identifying aggressive histopathological subtypes in early stage lung adenocarcinoma

Lung adenocarcinoma (ADC) is the most common non-small cell lung cancer. Surgical resection is the primary treatment for early-stage lung ADC while lung-sparing surgery is an alternative for non-aggressive cases. Identifying histopathologic subtypes before surgery helps determine the optimal surgical approach. Predominantly solid or micropapillary (MIP) subtypes are aggressive and associated with a higher likelihood of recurrence and metastasis and lower survival rates. This study aims to non-invasively identify these aggressive subtypes using preoperative 18F-FDG PET/CT and diagnostic CT radiomics analysis. We retrospectively studied 119 patients with stage I lung ADC and tumors ≤ 2 cm, where 23 had aggressive subtypes (18 solid and 5 MIPs). Out of 214 radiomic features from the PET/CT and CT scans and 14 clinical parameters, 78 significant features (3 CT and 75 PET features) were identified through univariate analysis and hierarchical clustering with minimized feature collinearity. A combination of Support Vector Machine classifier and Least Absolute Shrinkage and Selection Operator built predictive models. Ten iterations of 10-fold cross-validation (10 ×10-fold CV) evaluated the model. A pair of texture feature (PET GLCM Correlation) and shape feature (CT Sphericity) emerged as the best predictor. The radiomics model significantly outperformed the conventional predictor SUVmax (accuracy: 83.5% vs. 74.7%, p = 9e-9) and identified aggressive subtypes by evaluating FDG uptake in the tumor and tumor shape. It also demonstrated a high negative predictive value of 95.6% compared to SUVmax (88.2%, p = 2e-10). The proposed radiomics approach could reduce unnecessary extensive surgeries for non-aggressive subtype patients, improving surgical decision-making for early-stage lung ADC patients.

Semantic characteristic grading of pulmonary nodules based on deep neural networks

BACKGROUND

Accurate grading of semantic characteristics is helpful for radiologists to determine the probabilities of the likelihood of malignancy of a pulmonary nodule. Nevertheless, because of the complex and varied properties of pulmonary nodules, assessing semantic characteristics (SC) is a difficult task.

METHOD

In this paper, we first analyze a set of important semantic characteristics of pulmonary nodules and extract the important SCs relating to pulmonary nodule malignancy by Pearson's correlation approach. Then, we propose three automatic SC grading models based on deep belief network (DBN) and a multi-branch convolutional neural network (CNN) classifier, MBCNN. The first DBN model takes grayscale and binary nodule images as the input, and the second DBN model takes grayscale nodule images and 72 features extracted from pulmonary nodules as the input.

RESULTS

Experimental results indicate that our algorithms can achieve satisfying results on semantic characteristic grading. Especially, the MBCNN can obtain higher semantic characteristic grading results with an average accuracy of 89.37%.

CONCLUSIONS

Quantitative and automatic grading of semantic characteristics proposed in this paper can assist radiologists effectively assess the likelihood of pulmonary nodules being malignant and further promote the early expectant treatment of malignant nodules.

Artificial intelligence-driven radiomics study in cancer: the role of feature engineering and modeling

Modern medicine is reliant on various medical imaging technologies for non-invasively observing patients' anatomy. However, the interpretation of medical images can be highly subjective and dependent on the expertise of clinicians. Moreover, some potentially useful quantitative information in medical images, especially that which is not visible to the naked eye, is often ignored during clinical practice. In contrast, radiomics performs high-throughput feature extraction from medical images, which enables quantitative analysis of medical images and prediction of various clinical endpoints. Studies have reported that radiomics exhibits promising performance in diagnosis and predicting treatment responses and prognosis, demonstrating its potential to be a non-invasive auxiliary tool for personalized medicine. However, radiomics remains in a developmental phase as numerous technical challenges have yet to be solved, especially in feature engineering and statistical modeling. In this review, we introduce the current utility of radiomics by summarizing research on its application in the diagnosis, prognosis, and prediction of treatment responses in patients with cancer. We focus on machine learning approaches, for feature extraction and selection during feature engineering and for imbalanced datasets and multi-modality fusion during statistical modeling. Furthermore, we introduce the stability, reproducibility, and interpretability of features, and the generalizability and interpretability of models. Finally, we offer possible solutions to current challenges in radiomics research.

A generic model-free feature screening procedure for ultra-high dimensional data with categorical response

BACKGROUND AND OBJECTIVE

Identifying active features from ultra-high dimensional data is one of the primary and vital tasks in statistical learning and biological discovery.

METHODS

In this paper, we develop a generic concordance index screening (CI-SIS) procedure to wrestle with ultra-high dimensional data with categorical response. The proposed procedure is model-free and nonparametric based on the concordance index measure. It enjoys both sure screening and ranking consistency properties under some relatively weak assumptions. We investigate the flexibility of this procedure by considering some commonly-encountered challenging settings in biomedical studies, such as category-adaptive data and extremely unbalanced response distributions. A data-driven threshold selection procedure via knockoff features is also presented.

RESULTS

On the real lung dataset, our method achieves a lower prediction error with a mean error of 0.107 with linear discriminant analysis (LDA) and 0.117 with random forest (RF), respectively. In addition, we obtain an accuracy improvement of 3% with LDA and 5% with RF compared to the runner-up method. In a more challenging real data of SRBCT (Small round blue cell tumours), CI-SIS brings about a amazing performance improvement, which is at least 8% higher than all other competing methods.

CONCLUSION

Experimental results show that the proposed method can efficiently identify genes that are associated with certain types of diseases. Therefore, survived features (filtering out irrelevant features) selected by our procedure can help doctors make precision diagnoses and refined treatments of patients.

CIRDataset: A large-scale Dataset for Clinically-Interpretable lung nodule Radiomics and malignancy prediction

Spiculations/lobulations, sharp/curved spikes on the surface of lung nodules, are good predictors of lung cancer malignancy and hence, are routinely assessed and reported by radiologists as part of the standardized Lung-RADS clinical scoring criteria. Given the 3D geometry of the nodule and 2D slice-by-slice assessment by radiologists, manual spiculation/lobulation annotation is a tedious task and thus no public datasets exist to date for probing the importance of these clinically-reported features in the SOTA malignancy prediction algorithms. As part of this paper, we release a large-scale Clinically-Interpretable Radiomics Dataset, CIRDataset, containing 956 radiologist QA/QC'ed spiculation/lobulation annotations on segmented lung nodules from two public datasets, LIDC-IDRI (N=883) and LUNGx (N=73). We also present an end-to-end deep learning model based on multi-class Voxel2Mesh extension to segment nodules (while preserving spikes), classify spikes (sharp/spiculation and curved/lobulation), and perform malignancy prediction. Previous methods have performed malignancy prediction for LIDC and LUNGx datasets but without robust attribution to any clinically reported/actionable features (due to known hyperparameter sensitivity issues with general attribution schemes). With the release of this comprehensively-annotated CIRDataset and end-to-end deep learning baseline, we hope that malignancy prediction methods can validate their explanations, benchmark against our baseline, and provide clinically-actionable insights. Dataset, code, pretrained models, and docker containers are available at https://github.com/nadeemlab/CIR.

A predictive nomogram for lymph node metastasis in part-solid invasive lung adenocarcinoma: A complement to the IASLC novel grading system

Background

The International Association for the Study of Lung Cancer (IASLC) proposed a novel grading system for invasive lung adenocarcinoma, but lymphatic invasion was not evaluated. Meanwhile, the scope of lymph node dissection in part-solid invasive lung adenocarcinoma (PSILA) is still controversial. Therefore, this study aims to explore preoperative risk factors for lymph node metastasis in PSILA, to provide reference for intraoperative dissection of lymph nodes.

Methods

From 2018 to 2020, clinical data of patients (stage cN0) consecutively diagnosed as PSILA were retrospectively analyzed and classified according to the novel grading system. Logistic regression was conducted to screen the clinicopathological factors of lymph node metastasis in PSILA.

Results

A large cohort of 960 patients with PSILA who underwent lobectomy or sub-lobectomy were enrolled. By logistic regression analyses, solid part size, bronchial cutoff sign, spiculation, and carbohydrate antigen 199 (CA199) were eventually identified as independent risk factors for lymph node metastasis, based on which a nomogram was built to preoperatively predict the risk of lymph node metastasis [area under the receiver operating characteristic curve (AUC)=0.858; concordance index = 0.857; best cutoff, 0.027]. This suggests that intraoperative systematic lymph node dissection is recommended when the predicted risk value exceeds 0.027. Reproducibility of the novel grading system was verified.

Conclusions

The novel IASLC grading system was applicative in real world. The nomogram for preoperative prediction of lymph node metastasis may provide reference for the lymph node dissection strategy during PSILA surgeries.

Malignancy risk stratification for solitary pulmonary nodule: A clinical practice guideline

CLINICAL QUESTION

The detection rate of the solitary pulmonary nodule (SPN) is increasing with the popularization of CT scanning. Malignancy risk stratification for SPN is a major clinical difficulty.

CURRENT PRACTICE

There have been several guidelines for SPN assessment. Inconsistency of these guidelines makes the clinical application difficult and confusing.

RECOMMENDATIONS

In this Rapid Recommendation, solid and subsolid SPNs are recommended to be evaluated respectively. Six factors, namely the combination of age with sex, smoking history, history of malignancy, family history of malignancy, and nodule size, are recommended for malignancy risk stratification for both kinds of SPNs; the border of nodules (spiculation and lobulation) is recommended for evaluating solid SPNs and the density of nodules (pure or mixed ground-glass nodule) is recommended for subsolid nodules. Among them, smoking history and radiologic features (nodule diameter, border, and density) are of relatively higher importance. A scoring system was proposed to assist malignancy risk stratification of SPNs, with a total score ranging from six points to 15 points (if solid) or 17 points (if subsolid). For each SPN, regardless of solid or subsolid in nature, a total score of ≤ 7 points suggested a low risk of being malignant, while 7 to 9 points suggested medium risk, and ≥ 9 points suggested high risk.

HOW THIS GUIDELINE WAS CREATED

This rapid recommendation was developed using the MAGIC (Making GRADE the Irresistible Choice) methodological framework. First, a clinical subcommittee identified the topic of recommendation and requested evidence. Then, an independent evidence synthesis subcommittee performed a comprehensive literature review and evaluated the evidence. Finally, based on findings from the systematic review and use of real-world data, the clinical subcommittee formulated recommendations, including the scoring system, through a consensus procedure.

THE EVIDENCE

A total of 13857 patients with SPNs were included in the meta-analysis and the association between 12 candidate factors and the risk of SPNs being malignant was studied. Eventually, seven factors were recommended for SPNs evaluation, and a scoring system was proposed.

UNDERSTANDING THE RECOMMENDATION

The parameters included are objective. Therefore, this recommendation is feasible in clinical practice. However, there are several uncertainties, such as a lack of further verification. It might be misclassified by the scoring system. Clinicians could choose the most suitable scheme according to the recommendation, along with their own experience in specific situations.