Development of a Fully Cross-Validated Bayesian Network Approach for Local Control Prediction in Lung Cancer

Prediction of early recurrence of adult-type diffuse gliomas following radiotherapy using multi-modal magnetic resonance images

BACKGROUND

Adult-type diffuse gliomas are among the central nervous system's most aggressive malignant primary neoplasms. Despite advancements in systemic therapies and technological improvements in radiation oncology treatment delivery, the survival outcome for these patients remains poor. Fast and accurate assessment of tumor response to oncologic treatments is crucial, as it can enable the early detection of recurrent or refractory gliomas, thereby allowing timely intervention with life-prolonging salvage therapies.

PURPOSE

Radiomics is a developing field with great potential to improve medical image interpretation. This study aims to apply a radiomics-based predictive model for classifying response to radiotherapy within the first 3 months post-treatment.

METHODS

Ninety-five patients were selected from the Burdenko Glioblastoma Progression Dataset. Tumor regions were delineated in the axial plane on contrast-enhanced T1(CE T1W) and T2 fluid-attenuated inversion recovery (T2_FLAIR) magnetic resonance imaging (MRI). Hand-crafted radiomic (HCR) features, including first- and second-order features, were extracted using PyRadiomics (3.7.6) in Python (3.10). Then, recursive feature elimination with a random forest (RF) classifier was applied for feature dimensionality reduction. RF and support vector machine (SVM) classifiers were built to predict treatment outcomes using the selected features. Leave-one-out cross-validation was employed to tune hyperparameters and evaluate the models.

RESULTS

For each segmented target, 186 HCR features were extracted from the MRI sequence. Using the top-ranked radiomic features from a combination of CE T1W and T2_FLAIR, an optimized classifier achieved the highest averaged area under the curve (AUC) of 0.829 ± 0.075 using the RF classifier. The HCR features of CE T1W produced the worst outcomes among all models (0.603 ± 0.024 and 0.615 ± 0.075 for RF and SVM classifiers, respectively).

CONCLUSIONS

We developed and evaluated a radiomics-based predictive model for early tumor response to radiotherapy, demonstrating excellent performance supported by high AUC values. This model, harnessing radiomic features from multi-modal MRI, showed superior predictive performance compared to single-modal MRI approaches. These results underscore the potential of radiomics in clinical decision support for this disease process.

Deep Learning-Guided Dosimetry for Mitigating Local Failure of Patients With Non-Small Cell Lung Cancer Receiving Stereotactic Body Radiation Therapy

PURPOSE

Non-small cell lung cancer (NSCLC) stereotactic body radiation therapy with 50 Gy/5 fractions is sometimes considered controversial, as the nominal biologically effective dose (BED) of 100 Gy is felt by some to be insufficient for long-term local control of some lesions. In this study, we analyzed such patients using explainable deep learning techniques and consequently proposed appropriate treatment planning criteria. These novel criteria could help planners achieve optimized treatment plans for maximal local control.

METHODS AND MATERIALS

A total of 535 patients treated with 50 Gy/5 fractions were used to develop a novel deep learning local response model. A multimodality approach, incorporating computed tomography images, 3-dimensional dose distribution, and patient demographics, combined with a discrete-time survival model, was applied to predict time to failure and the probability of local control. Subsequently, an integrated gradient-weighted class activation mapping method was used to identify the most significant dose-volume metrics predictive of local failure and their optimal cut-points.

RESULTS

The model was cross-validated, showing an acceptable performance (c-index: 0.72, 95% CI, 0.68-0.75); the testing c-index was 0.69. The model's spatial attention was concentrated mostly in the tumors' periphery (planning target volume [PTV] - internal gross target volume [IGTV]) region. Statistically significant dose-volume metrics in improved local control were BED Dnear-min ≥ 103.8 Gy in IGTV (hazard ratio [HR], 0.31; 95% CI, 015-0.63), V104 ≥ 98% in IGTV (HR, 0.30; 95% CI, 0.15-0.60), gEUD ≥ 103.8 Gy in PTV-IGTV (HR, 0.25; 95% CI, 0.12-0.50), and Dmean ≥ 104.5 Gy in PTV-IGTV (HR, 0.25; 95% CI, 0.12-0.51).

CONCLUSIONS

Deep learning-identified dose-volume metrics have shown significant prognostic power (log-rank, P = .003) and could be used as additional actionable criteria for treatment planning in NSCLC stereotactic body radiation therapy patients receiving 50 Gy in 5 fractions. Although our data do not confirm or refute that a significantly higher BED for the prescription dose is necessary for tumor control in NSCLC, it might be clinically effective to escalate the nominal prescribed dose from BED 100 to 105 Gy.

Predicting postoperative rehemorrhage in hypertensive intracerebral hemorrhage using noncontrast CT radiomics and clinical data with an interpretable machine learning approach

In hypertensive intracerebral hemorrhage (HICH) patients, while emergency surgeries effectively reduce intracranial pressure and hematoma volume, their significant risk of causing postoperative rehemorrhage necessitates early detection and management to improve patient prognosis. This study sought to develop and validate machine learning (ML) models leveraging clinical data and noncontrast CT radiomics to pinpoint patients at risk of postoperative rehemorrhage, equipping clinicians with an early detection tool for prompt intervention. The study conducted a retrospective analysis on 609 HICH patients, dividing them into training and external verification cohorts. These patients were categorized into groups with and without postoperative rehemorrhage. Radiomics features from noncontrast CT images were extracted, standardized, and employed to create several ML models. These models underwent internal validation using both radiomics and clinical data, with the best model's feature significance assessed via the Shapley additive explanations (SHAP) method, then externally validated. In the study of 609 patients, postoperative rehemorrhage rates were similar in the training (18.8%, 80/426) and external verification (17.5%, 32/183) cohorts. Six significant noncontrast CT radiomics features were identified, with the support vector machine (SVM) model outperforming others in both internal and external validations. SHAP analysis highlighted five critical predictors of postoperative rehemorrhage risk, encompassing three radiomics features from noncontrast CT and two clinical data indicators. This study highlights the effectiveness of an SVM model combining radiomics features from noncontrast CT and clinical parameters in predicting postoperative rehemorrhage among HICH patients. This approach enables timely and effective interventions, thereby improving patient outcomes.

AI-Driven Models for Diagnosing and Predicting Outcomes in Lung Cancer: A Systematic Review and Meta-Analysis

(1) Background: Lung cancer's high mortality due to late diagnosis highlights a need for early detection strategies. Artificial intelligence (AI) in healthcare, particularly for lung cancer, offers promise by analyzing medical data for early identification and personalized treatment. This systematic review evaluates AI's performance in early lung cancer detection, analyzing its techniques, strengths, limitations, and comparative edge over traditional methods. (2) Methods: This systematic review and meta-analysis followed the PRISMA guidelines rigorously, outlining a comprehensive protocol and employing tailored search strategies across diverse databases. Two reviewers independently screened studies based on predefined criteria, ensuring the selection of high-quality data relevant to AI's role in lung cancer detection. The extraction of key study details and performance metrics, followed by quality assessment, facilitated a robust analysis using R software (Version 4.3.0). The process, depicted via a PRISMA flow diagram, allowed for the meticulous evaluation and synthesis of the findings in this review. (3) Results: From 1024 records, 39 studies met the inclusion criteria, showcasing diverse AI model applications for lung cancer detection, emphasizing varying strengths among the studies. These findings underscore AI's potential for early lung cancer diagnosis but highlight the need for standardization amidst study variations. The results demonstrate promising pooled sensitivity and specificity of 0.87, signifying AI's accuracy in identifying true positives and negatives, despite the observed heterogeneity attributed to diverse study parameters. (4) Conclusions: AI demonstrates promise in early lung cancer detection, showing high accuracy levels in this systematic review. However, study variations underline the need for standardized protocols to fully leverage AI's potential in revolutionizing early diagnosis, ultimately benefiting patients and healthcare professionals. As the field progresses, validated AI models from large-scale perspective studies will greatly benefit clinical practice and patient care in the future.

Predictors on outcomes of cardiovascular disease of male patients in Malaysia using Bayesian network analysis

OBJECTIVES

Despite extensive advances in medical and surgical treatment, cardiovascular disease (CVD) remains the leading cause of mortality worldwide. Identifying the significant predictors will help clinicians with the prognosis of the disease and patient management. This study aims to identify and interpret the dependence structure between the predictors and health outcomes of ST-elevation myocardial infarction (STEMI) male patients in Malaysian setting.

DESIGN

Retrospective study.

SETTING

Malaysian National Cardiovascular Disease Database-Acute Coronary Syndrome (NCVD-ACS) registry years 2006-2013, which consists of 18 hospitals across the country.

PARTICIPANTS

7180 male patients diagnosed with STEMI from the NCVD-ACS registry.

PRIMARY AND SECONDARY OUTCOME MEASURES

A graphical model based on the Bayesian network (BN) approach has been considered. A bootstrap resampling approach was integrated into the structural learning algorithm to estimate probabilistic relations between the studied features that have the strongest influence and support.

RESULTS

The relationships between 16 features in the domain of CVD were visualised. From the bootstrap resampling approach, out of 250, only 25 arcs are significant (strength value ≥0.85 and the direction value ≥0.50). Age group, Killip class and renal disease were classified as the key predictors in the BN model for male patients as they were the most influential variables directly connected to the outcome, which is the patient status. Widespread probabilistic associations between the key predictors and the remaining variables were observed in the network structure. High likelihood values are observed for patient status variable stated alive (93.8%), Killip class I on presentation (66.8%), patient younger than 65 (81.1%), smoker patient (77.2%) and ethnic Malay (59.2%). The BN model has been shown to have good predictive performance.

CONCLUSIONS

The data visualisation analysis can be a powerful tool to understand the relationships between the CVD prognostic variables and can be useful to clinicians.

Artificial intelligence (AI) and machine learning (ML) in precision oncology: a review on enhancing discoverability through multiomics integration

Multiomics data including imaging radiomics and various types of molecular biomarkers have been increasingly investigated for better diagnosis and therapy in the era of precision oncology. Artificial intelligence (AI) including machine learning (ML) and deep learning (DL) techniques combined with the exponential growth of multiomics data may have great potential to revolutionize cancer subtyping, risk stratification, prognostication, prediction and clinical decision-making. In this article, we first present different categories of multiomics data and their roles in diagnosis and therapy. Second, AI-based data fusion methods and modeling methods as well as different validation schemes are illustrated. Third, the applications and examples of multiomics research in oncology are demonstrated. Finally, the challenges regarding the heterogeneity data set, availability of omics data, and validation of the research are discussed. The transition of multiomics research to real clinics still requires consistent efforts in standardizing omics data collection and analysis, building computational infrastructure for data sharing and storing, developing advanced methods to improve data fusion and interpretability, and ultimately, conducting large-scale prospective clinical trials to fill the gap between study findings and clinical benefits.

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 human-in-the-loop based Bayesian network approach to improve imbalanced radiation outcomes prediction for hepatocellular cancer patients with stereotactic body radiotherapy

Background

Imbalanced outcome is one of common characteristics of oncology datasets. Current machine learning approaches have limitation in learning from such datasets. Here, we propose to resolve this problem by utilizing a human-in-the-loop (HITL) approach, which we hypothesize will also lead to more accurate and explainable outcome prediction models.

Methods

A total of 119 HCC patients with 163 tumors were used in the study. 81 patients with 104 tumors from the University of Michigan Hospital treated with SBRT were considered as a discovery dataset for radiation outcomes model building. The external testing dataset included 59 tumors from 38 patients with SBRT from Princess Margaret Hospital. In the discovery dataset, 100 tumors from 77 patients had local control (LC) (96% of 104 tumors) and 23 patients had at least one grade increment of ALBI (I-ALBI) during six-month follow up (28% of 81 patients). Each patient had a total of 110 features, where 15 or 20 features were identified by physicians as expert knowledge features (EKFs) for LC or I-ALBI prediction. We proposed a HITL based Bayesian network (HITL-BN) approach to enhance the capability of selecting important features from imbalanced data in terms of accuracy and explainability through humans' participation by integrating feature importance ranking and Markov blanket algorithms. A pure data-driven Bayesian network (PD-BN) method was applied to the same discovery dataset of HCC patients as a benchmark.

Results

In the training and testing phases, the areas under receiver operating characteristic curves of the HITL-BN models for LC or I-ALBI prediction during SBRT are 0.85 (95% confidence interval: 0.75-0.95) or 0.89 (0.81-0.95) and 0.77 or 0.78, respectively. They significantly outperformed the during-treatment PD-BN model in predicting LC or I-ALBI based on the discovery cross-validation and testing datasets from the Delong tests.

Conclusion

By allowing the human expert to be part of the model building process, the HITL-BN approach yielded significantly improved accuracy as well as better explainability when dealing with imbalanced outcomes in the prediction of post-SBRT treatment response of HCC patients when compared to the PD-BN method.

Current status and future developments in predicting outcomes in radiation oncology

Advancements in data-driven technologies and the inclusion of information-rich multiomics features have significantly improved the performance of outcomes modeling in radiation oncology. For this current trend to be sustainable, challenges related to robust data modeling such as small sample size, low size to feature ratio, noisy data, as well as issues related to algorithmic modeling such as complexity, uncertainty, and interpretability, need to be mitigated if not resolved. Emerging computational technologies and new paradigms such as federated learning, human-in-the-loop, quantum computing, and novel interpretability methods show great potential in overcoming these challenges and bridging the gap towards precision outcome modeling in radiotherapy. Examples of these promising technologies will be presented and their potential role in improving outcome modeling will be discussed.

Cluster model incorporating heterogeneous dose distribution of partial parotid irradiation for radiotherapy induced xerostomia prediction with machine learning methods

PURPOSE

A cluster model incorporating heterogeneous dose distribution within the parotid gland was developed and validated retrospectively for radiotherapy (RT) induced xerostomia prediction with machine learning (ML) techniques.

METHODS

Sixty clusters were obtained at 1 Gy step size with threshold doses ranging from 1 to 60 Gy, for each of the enrolled 155 patients with HNC from three institutions. Feature clusters were selected with the neighborhood component analysis (NCA) and subsequently fed into four supervised ML models for xerostomia prediction comparison: support vector machines (SVM), k-nearest neighbor (kNN), naïve Bayes (NB), and random forest (RF). The predictive performance of each model was evaluated using cross validation resampling with the area-under-the-curves (AUC) of the receiver-operating-characteristic (ROC). The xerostomia predicting capacity using testing data was assessed with accuracy, sensitivity, and specificity for these models and three cluster connectivity choices. Mean dose based logistic regression served as the benchmark for evaluation.

RESULTS

Feature clusters identified by NCA fell in three threshold dose ranges: 5-15Gy, 25-35Gy, and 45-50Gy. Mean dose predictive power was 15% lower than that of the cluster model using the logistic regression classifier. Model validation demonstrated that kNN model outperformed slightly other three models but no substantial difference was observed. Applying the fine-tuned models to testing data yielded that the mean accuracy from SVM, kNN and NB models were between 0.68 and 0.7 while that of RF was ∼0.6. SVM model yielded the best sensitivity (0.76) and kNN model delivered consistent sensitivity and specificity. This is consistent with cross validation. Clusters calculated with three connectivity choices exhibited minimally different predictions.

CONCLUSION

Compared to mean dose, the proposed cluster model has shown its improvement as the xerostomia predictor. When combining with ML techniques, it could provide a clinically useful tool for xerostomia prediction and facilitate decision making during radiotherapy planning for patients with HNC.

Simulation of Logistics Delay in Bayesian Network Control Based on Genetic EM Algorithm

With the continuous development of e-commerce, the logistics industry is thriving, and logistics delays have become an issue that deserves more and more attention. Genetic EM algorithm is a genetic EM algorithm that is an iterative optimization strategy algorithm that can be used to solve the high-quality algorithm of travel problems with many nodes. Bayesian network (BN) is a network model based on probabilistic uncertainty. This article aims to study the probability of many factors that cause logistics delays to construct an algorithm model to control or reduce logistics delays. This paper constructs an EY model (That is the abbreviation of BN model based on genetic EM algorithm) based on the genetic EM algorithm, and conducts related simulation experiments based on the model to verify the accuracy and feasibility of the model. The experimental results of this paper show that the calculation efficiency of the EY model is significantly improved, and the actuarial accuracy is as high as 98%, which can effectively control logistics delays.

Imaging response assessment for predicting outcomes after bioselection chemotherapy in larynx cancer: A secondary analysis of two prospective trials

BACKGROUND AND PURPOSE

Bioselection with induction chemotherapy in larynx cancer is associated with excellent larynx preservation and disease-specific survival but requires visual inspection of the primary tumor. We retrospectively compare clinical and imaging response in bioselected patients to develop predictive models of surgeon-assessed response (SR), laryngectomy-free survival (LFS), and overall survival (OS) in bioselected patients.

MATERIALS AND METHODS

In a secondary analysis of patients on two single-institution bioselection trials, model building used a regularized regression model (elastic-net) and applied nested cross-validation. Logistic regression-based model was used to predict SR and Cox proportional hazard-based models were used to predict LFS and OS.

RESULTS

In 115 patients with a median age of 57 years, most patients had supraglottic tumors (73.0%) and T3/T4 disease (94.8%). Definitive treatment was chemoradiation in 76.5% and laryngectomy in 23.5%. Change in primary tumor (OR = 5.78, p < 0.001) and N-classification (OR = 1.64, p = 0.003) predicted SR (AUC 0.847). Change in tumor volume (HR = 0.58, p < 0.001) predicted LFS (c-index 0.724). N-classification (HR = 1.48, p = 0.04) and pre-chemotherapy tumor volume (HR = 1.30, p = 0.174) predicted OS (c-index 0.552).

CONCLUSIONS

Imaging offers a non-invasive opportunity to evaluate response to induction chemotherapy, complementary to surgeon assessment. Further evaluation of approaches to bioselection that optimize generalizability of this paradigm are needed, and clinical trials utilizing imaging to predict outcomes including LFS are warranted.

Predictive Modeling of Survival and Toxicity in Patients With Hepatocellular Carcinoma After Radiotherapy

PURPOSE

To stratify patients and aid clinical decision making, we developed machine learning models to predict treatment failure and radiation-induced toxicities after radiotherapy (RT) in patients with hepatocellular carcinoma across institutions.

MATERIALS AND METHODS

The models were developed using linear and nonlinear algorithms, predicting survival, nonlocal failure, radiation-induced liver disease, and lymphopenia from baseline patient and treatment parameters. The models were trained on 207 patients from Massachusetts General Hospital. Performance was quantified using Harrell's c-index, area under the curve (AUC), and accuracy in high-risk populations. Models' structures were optimized in a nested cross-validation approach to prevent overfitting. A study analysis plan was registered before external validation using 143 patients from MD Anderson Cancer Center. Clinical utility was assessed using net-benefit analysis.

RESULTS

The survival model stratified high-risk versus low-risk patients well in the external validation cohort (c-index = 0.75), better than existing risk scores. Predictions of 1-year survival and nonlocal failure were excellent (external AUC = 0.74 and 0.80, respectively), especially in the high-risk group (accuracy > 90%). Cause-of-death analysis showed differential modes of treatment failure in these cohorts and indicated that these models could be used to stratify RT patients for liver-sparing treatment regimen or combination approaches with systemic agents. Predictions of liver disease and lymphopenia were good but less robust (external AUC = 0.68 and 0.7, respectively), suggesting the need for more comprehensive consideration of dosimetry and better predictive biomarkers. The liver disease model showed excellent accuracy in the high-risk group (92%) and revealed possible interactions of platelet count with initial liver function.

CONCLUSION

Machine learning approaches can provide reliable outcome predictions in patients with hepatocellular carcinoma after RT in diverse cohorts across institutions. The excellent performance, particularly in high-risk patients, suggests novel strategies for patient stratification and treatment selection.

Synergistic Effects of Different Levels of Genomic Data for the Staging of Lung Adenocarcinoma: An Illustrative Study

Lung adenocarcinoma (LUAD) is a common and very lethal cancer. Accurate staging is a prerequisite for its effective diagnosis and treatment. Therefore, improving the accuracy of the stage prediction of LUAD patients is of great clinical relevance. Previous works have mainly focused on single genomic data information or a small number of different omics data types concurrently for generating predictive models. A few of them have considered multi-omics data from genome to proteome. We used a publicly available dataset to illustrate the potential of multi-omics data for stage prediction in LUAD. In particular, we investigated the roles of the specific omics data types in the prediction process. We used a self-developed method, Omics-MKL, for stage prediction that combines an existing feature ranking technique Minimum Redundancy and Maximum Relevance (mRMR), which avoids redundancy among the selected features, and multiple kernel learning (MKL), applying different kernels for different omics data types. Each of the considered omics data types individually provided useful prediction results. Moreover, using multi-omics data delivered notably better results than using single-omics data. Gene expression and methylation information seem to play vital roles in the staging of LUAD. The Omics-MKL method retained 70 features after the selection process. Of these, 21 (30%) were methylation features and 34 (48.57%) were gene expression features. Moreover, 18 (25.71%) of the selected features are known to be related to LUAD, and 29 (41.43%) to lung cancer in general. Using multi-omics data from genome to proteome for predicting the stage of LUAD seems promising because each omics data type may improve the accuracy of the predictions. Here, methylation and gene expression data may play particularly important roles.

Machine learning for dose-volume histogram based clinical decision-making support system in radiation therapy plans for brain tumors

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Extraction, analysis, and interpretation of historical treatment planning data is valuable but very time-consuming.

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Proposed machine learning model classifies radiotherapy plans based on their treatment planning objectives and trade-offs.

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Application of double nested cross-validation enabled to build a robust model that achieved 94% accuracy on a testing data.

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Model reasoning investigated with SHAP values showed consistency with clinical observations.

Purpose

To create and investigate a novel, clinical decision-support system using machine learning (ML).

Methods and Materials

The ML model was developed based on 79 radiotherapy plans of brain tumor patients that were prescribed a total dose of 60 Gy delivered with volumetric-modulated arc therapy (VMAT). Structures considered for analysis included planning target volume (PTV), brainstem, cochleae, and optic chiasm. The model aimed to classify the target variable that included class-0 corresponding to plans for which the PTV treatment planning objective was met and class-1 that was associated with plans for which the PTV objective was not met due to the priority trade-off to meet one or more organs-at-risk constraints. Several models were evaluated using double-nested cross-validation and an area-under-the-curve (AUC) metric, with the highest performing one selected for further investigation. The model predictions were explained with Shapely additive explanation (SHAP) interaction values.

Results

The highest-performing model was Logistic Regression achieving an accuracy of 93.8 ± 4.1% and AUC of 0.98 ± 0.02 on the testing data. The SHAP analysis indicated that the ΔD_99% metric for PTV had the greatest influence on the model predictions. The least important feature was ΔD_MAX for the left and right cochleae.

Conclusions

The trained model achieved satisfactory accuracy and can be used by medical physicists in a data-driven quality assurance program as well as by radiation oncologists to support their decision-making process in terms of treatment plan approval and potential plan modifications. Model explanation analysis showed that the model relies on clinically valid logic when making predictions.

Radiation Response Prediction Model based on Integrated Clinical and Genomic Data Analysis

Purpose

The value of the genomic profiling by targeted gene-sequencing on radiation therapy response prediction was evaluated through integrated analysis including clinical information. Radiation response prediction model was constructed based on the analyzed findings.

Materials and Methods

Patients who had the tumor sequenced using institutional cancer panel after informed consent and received radiotherapy for the measurable disease served as the target cohort. Patients with irradiated tumor locally controlled for more than 6 months after radiotherapy were defined as the durable local control (DLC) group, otherwise, non-durable local control (NDLC) group. Significant genomic factors and domain knowledge were used to develop the Bayesian Network model to predict radiotherapy response.

Results

Altogether, 88 patients were collected for analysis. Of those, 41 (43.6%) and 47 (54.4%) patients were classified as the NDLC and DLC group, respectively. Somatic mutations of NOTCH2 and BCL were enriched in the NDLC group, whereas, mutations of CHEK2, MSH2, and NOTCH1 were more frequently found in the DLC group. Altered DNA repair pathway was associated with better local failure-free survival (HR 0.40, 95%CI 0.19-0.86, p=0.014). Smoking somatic signature was found more frequently in the DLC group. AUC of the Bayesian Network model predicting probability of 6-month local control was 0.83.

Conclusion

Durable radiation response was associated with alterations of DNA repair pathway and smoking somatic signature. Bayesian network model could provide helpful insights for high precision radiotherapy. However, these findings should be verified in prospective cohort for further individualization.

Value of PET imaging for radiation therapy

This comprehensive review written by experts in their field gives an overview on the current status of incorporating positron emission tomography (PET) into radiation treatment planning. Moreover, it highlights ongoing studies for treatment individualisation and per-treatment tumour response monitoring for various primary tumours. Novel tracers and image analysis methods are discussed. The authors believe this contribution to be of crucial value for experts in the field as well as for policy makers deciding on the reimbursement of this powerful imaging modality.

Value of PET imaging for radiation therapy

This comprehensive review written by experts in their field gives an overview on the current status of incorporating positron emission tomography (PET) into radiation treatment planning. Moreover, it highlights ongoing studies for treatment individualisation and per-treatment tumour response monitoring for various primary tumours. Novel tracers and image analysis methods are discussed. The authors believe this contribution to be of crucial value for experts in the field as well as for policy makers deciding on the reimbursement of this powerful imaging modality.

A situational awareness Bayesian network approach for accurate and credible personalized adaptive radiotherapy outcomes prediction in lung cancer patients

PURPOSE

A situational awareness Bayesian network (SA-BN) approach is developed to improve physicians' trust in the prediction of radiation outcomes and evaluate its performance for personalized adaptive radiotherapy (pART).

METHODS

118 non-small-cell lung cancer patients with their biophysical features were employed for discovery (n = 68) and validation (n = 50) of radiation outcomes prediction modeling. Patients' important characteristics identified by radiation experts to predict individual's tumor local control (LC) or radiation pneumonitis with grade ≥ 2 (RP2) were incorporated as expert knowledge (EK). Besides generating an EK-based naïve BN (EK-NBN), an SA-BN was developed by incorporating the EK features into pure data-driven BN (PD-BN) methods to improve the credibility of LC or / and RP2 prediction. After using area under the free-response receiver operating characteristics curve (AU-FROC) to assess the joint prediction of these outcomes, their prediction performances were compared with a regression approach based on the expert yielded estimates (EYE) penalty and its variants.

RESULTS

In addition to improving the credibility of radiation outcomes prediction, the SA-BN approach outperformed the EYE penalty and its variants in terms of the joint prediction of LC and RP2. The value of AU-FROC improves from 0.70 (95% CI: 0.54-0.76) using EK-NBN, to 0.75 (0.65-0.82) using a variant of EYE penalty, to 0.83 (0.75-0.93) using PD-BN and 0.83 (0.77-0.90) using SA-BN; with similar trends in the validation cohort.

CONCLUSIONS

The SA-BN approach can provide an accurate and credible human-machine interface to gain physicians' trust in clinical decision-making, which has the potential to be an important component of pART.

Artificial Intelligence for Response Evaluation With PET/CT

Positron emission tomography (PET)/computed tomography (CT) are nuclear diagnostic imaging modalities that are routinely deployed for cancer staging and monitoring. They hold the advantage of detecting disease related biochemical and physiologic abnormalities in advance of anatomical changes, thus widely used for staging of disease progression, identification of the treatment gross tumor volume, monitoring of disease, as well as prediction of outcomes and personalization of treatment regimens. Among the arsenal of different functional imaging modalities, nuclear imaging has benefited from early adoption of quantitative image analysis starting from simple standard uptake value normalization to more advanced extraction of complex imaging uptake patterns; thanks to application of sophisticated image processing and machine learning algorithms. In this review, we discuss the application of image processing and machine/deep learning techniques to PET/CT imaging with special focus on the oncological radiotherapy domain as a case study and draw examples from our work and others to highlight current status and future potentials.

Machine and deep learning methods for radiomics

Radiomics is an emerging area in quantitative image analysis that aims to relate large-scale extracted imaging information to clinical and biological endpoints. The development of quantitative imaging methods along with machine learning has enabled the opportunity to move data science research towards translation for more personalized cancer treatments. Accumulating evidence has indeed demonstrated that noninvasive advanced imaging analytics, that is, radiomics, can reveal key components of tumor phenotype for multiple three-dimensional lesions at multiple time points over and beyond the course of treatment. These developments in the use of CT, PET, US, and MR imaging could augment patient stratification and prognostication buttressing emerging targeted therapeutic approaches. In recent years, deep learning architectures have demonstrated their tremendous potential for image segmentation, reconstruction, recognition, and classification. Many powerful open-source and commercial platforms are currently available to embark in new research areas of radiomics. Quantitative imaging research, however, is complex and key statistical principles should be followed to realize its full potential. The field of radiomics, in particular, requires a renewed focus on optimal study design/reporting practices and standardization of image acquisition, feature calculation, and rigorous statistical analysis for the field to move forward. In this article, the role of machine and deep learning as a major computational vehicle for advanced model building of radiomics-based signatures or classifiers, and diverse clinical applications, working principles, research opportunities, and available computational platforms for radiomics will be reviewed with examples drawn primarily from oncology. We also address issues related to common applications in medical physics, such as standardization, feature extraction, model building, and validation.

Application and Construction of Deep Learning Networks in Medical Imaging

Deep learning (DL) approaches are part of the machine learning (ML) subfield concerned with the development of computational models to train artificial intelligence systems. DL models are characterized by automatically extracting high-level features from the input data to learn the relationship between matching datasets. Thus, its implementation offers an advantage over common ML methods that often require the practitioner to have some domain knowledge of the input data to select the best latent representation. As a result of this advantage, DL has been successfully applied within the medical imaging field to address problems, such as disease classification and tumor segmentation for which it is difficult or impossible to determine which image features are relevant. Therefore, taking into consideration the positive impact of DL on the medical imaging field, this article reviews the key concepts associated with its evolution and implementation. The sections of this review summarize the milestones related to the development of the DL field, followed by a description of the elements of deep neural network and an overview of its application within the medical imaging field. Subsequently, the key steps necessary to implement a supervised DL application are defined, and associated limitations are discussed.

Feature-based PET/MRI radiomics in patients with brain tumors

Radiomics allows the extraction of quantitative features from medical images such as CT, MRI, or PET, thereby providing additional, potentially relevant diagnostic information for clinical decision-making. Because the computation of these features is performed highly automated on medical images acquired during routine follow-up, radiomics offers this information at low cost. Further, the radiomics features can be used alone or combined with other clinical or histomolecular parameters to generate predictive or prognostic mathematical models. These models can then be applied for various important diagnostic indications in neuro-oncology, for example, to noninvasively predict relevant biomarkers in glioma patients, to differentiate between treatment-related changes and local brain tumor relapse, or to predict treatment response. In recent years, amino acid PET has become an important diagnostic tool in patients with brain tumors. Therefore, the number of studies in patients with brain tumors investigating the potential of PET radiomics or combined PET/MRI radiomics is steadily increasing. This review summarizes current research regarding feature-based PET as well as combined PET/MRI radiomics in neuro-oncology.

Lessons learned in transitioning to AI in the medical imaging of COVID-19

The coronavirus disease 2019 (COVID-19) pandemic has wreaked havoc across the world. It also created a need for the urgent development of efficacious predictive diagnostics, specifically, artificial intelligence (AI) methods applied to medical imaging. This has led to the convergence of experts from multiple disciplines to solve this global pandemic including clinicians, medical physicists, imaging scientists, computer scientists, and informatics experts to bring to bear the best of these fields for solving the challenges of the COVID-19 pandemic. However, such a convergence over a very brief period of time has had unintended consequences and created its own challenges. As part of Medical Imaging Data and Resource Center initiative, we discuss the lessons learned from career transitions across the three involved disciplines (radiology, medical imaging physics, and computer science) and draw recommendations based on these experiences by analyzing the challenges associated with each of the three associated transition types: (1) AI of non-imaging data to AI of medical imaging data, (2) medical imaging clinician to AI of medical imaging, and (3) AI of medical imaging to AI of COVID-19 imaging. The lessons learned from these career transitions and the diffusion of knowledge among them could be accomplished more effectively by recognizing their associated intricacies. These lessons learned in the transitioning to AI in the medical imaging of COVID-19 can inform and enhance future AI applications, making the whole of the transitions more than the sum of each discipline, for confronting an emergency like the COVID-19 pandemic or solving emerging problems in biomedicine.

Artificial Intelligence for the Characterization of Pulmonary Nodules, Lung Tumors and Mediastinal Nodes on PET/CT

Lung cancer is the leading cause of cancer related death around the world although early diagnosis remains vital to enabling access to curative treatment options. This article briefly describes the current role of imaging, in particular 2-deoxy-2-[¹⁸F]fluoro-D-glucose (FDG) PET/CT, in lung cancer and specifically the role of artificial intelligence with CT followed by a detailed review of the published studies applying artificial intelligence (ie, machine learning and deep learning), on FDG PET or combined PET/CT images with the purpose of early detection and diagnosis of pulmonary nodules, and characterization of lung tumors and mediastinal lymph nodes. A comprehensive search was performed on Pubmed, Embase, and clinical trial databases. The studies were analyzed with a modified version of the Transparent Reporting of a multivariable prediction model for Individual Prognosis or Diagnosis (TRIPOD) and Prediction model Risk Of Bias Assessment Tool (PROBAST) statement. The search resulted in 361 studies; of these 29 were included; all retrospective; none were clinical trials. Twenty-two records evaluated standard machine learning (ML) methods on imaging features (ie, support vector machine), and 7 studies evaluated new ML methods (ie, deep learning) applied directly on PET or PET/CT images. The studies mainly reported positive results regarding the use of ML methods for diagnosing pulmonary nodules, characterizing lung tumors and mediastinal lymph nodes. However, 22 of the 29 studies were lacking a relevant comparator and/or lacking independent testing of the model. Application of ML methods with feature and image input from PET/CT for diagnosing and characterizing lung cancer is a relatively young area of research with great promise. Nevertheless, current published studies are often under-powered and lacking a clinically relevant comparator and/or independent testing.

Radiomics in radiation oncology-basics, methods, and limitations

Over the past years, the quantity and complexity of imaging data available for the clinical management of patients with solid tumors has increased substantially. Without the support of methods from the field of artificial intelligence (AI) and machine learning, a complete evaluation of the available image information is hardly feasible in clinical routine. Especially in radiotherapy planning, manual detection and segmentation of lesions is laborious, time consuming, and shows significant variability among observers. Here, AI already offers techniques to support radiation oncologists, whereby ultimately, the productivity and the quality are increased, potentially leading to an improved patient outcome. Besides detection and segmentation of lesions, AI allows the extraction of a vast number of quantitative imaging features from structural or functional imaging data that are typically not accessible by means of human perception. These features can be used alone or in combination with other clinical parameters to generate mathematical models that allow, for example, prediction of the response to radiotherapy. Within the large field of AI, radiomics is the subdiscipline that deals with the extraction of quantitative image features as well as the generation of predictive or prognostic mathematical models. This review gives an overview of the basics, methods, and limitations of radiomics, with a focus on patients with brain tumors treated by radiation therapy.

Expression levels of lncRNAs are prognostic for hepatocellular carcinoma overall survival

Studies have demonstrated that long non-coding RNAs (lncRNAs) play important roles in cancer development and progression. However, associations between the expression patterns and prognostic roles of lncRNAs in hepatocellular carcinoma (HCC) have not been comprehensively described. In this study, we established a prognostic model of lncRNA expression using public datasets of HCC from The Cancer Genome Atlas (TCGA) and adopted the International Cancer Genome Consortium (ICGC) as an independent cohort to validate the stability of our model. Cox regression analysis was used to explore the independent prognostic factor in both training and validation cohorts. Additionally, we explored the functional roles of lncRNAs using bioinformatic analyses. According to lncRNA consensus clusters, we resolved the distribution of molecular and clinical data and observed that individual lncRNA could function as prognostic biomarkers in HCC. Furthermore, the novel lncRNA molecular subtypes were statistically significant for predicting HCC status, which was validated by nested cross-validation. We found that lncRNA subtypes were partially related to gender, histological grade, and mutations within TP53. The lncRNA subtypes were also consistent with mRNA-based subtypes, and pathway enrichment analysis identified the involvement of multiple signaling pathways. In addition, we observed that upregulated DANCR was significantly associated with poor prognosis in HCC patients. In conclusion, our model based on lncRNA expression is statistically significant as a diagnostic and prognostic indicator for patients with HCC.

Balancing accuracy and interpretability of machine learning approaches for radiation treatment outcomes modeling

Radiation outcomes prediction (ROP) plays an important role in personalized prescription and adaptive radiotherapy. A clinical decision may not only depend on an accurate radiation outcomes’ prediction, but also needs to be made based on an informed understanding of the relationship among patients’ characteristics, radiation response and treatment plans. As more patients’ biophysical information become available, machine learning (ML) techniques will have a great potential for improving ROP. Creating explainable ML methods is an ultimate task for clinical practice but remains a challenging one. Towards complete explainability, the interpretability of ML approaches needs to be first explored. Hence, this review focuses on the application of ML techniques for clinical adoption in radiation oncology by balancing accuracy with interpretability of the predictive model of interest. An ML algorithm can be generally classified into an interpretable (IP) or non-interpretable (NIP) (“black box”) technique. While the former may provide a clearer explanation to aid clinical decision-making, its prediction performance is generally outperformed by the latter. Therefore, great efforts and resources have been dedicated towards balancing the accuracy and the interpretability of ML approaches in ROP, but more still needs to be done. In this review, current progress to increase the accuracy for IP ML approaches is introduced, and major trends to improve the interpretability and alleviate the “black box” stigma of ML in radiation outcomes modeling are summarized. Efforts to integrate IP and NIP ML approaches to produce predictive models with higher accuracy and interpretability for ROP are also discussed.

Markerless Pancreatic Tumor Target Localization Enabled By Deep Learning

PURPOSE

Deep learning is an emerging technique that allows us to capture imaging information beyond the visually recognizable level of a human being. Because of the anatomic characteristics and location, on-board target verification for radiation delivery to pancreatic tumors is a challenging task. Our goal was to use a deep neural network to localize the pancreatic tumor target on kV x-ray images acquired using an on-board imager for image guided radiation therapy.

METHODS AND MATERIALS

The network is set up in such a way that the input is either a digitally reconstructed radiograph image or a monoscopic x-ray projection image acquired by the on-board imager from a given direction, and the output is the location of the planning target volume in the projection image. To produce a sufficient number of training x-ray images reflecting the vast number of possible clinical scenarios of anatomy distribution, a series of changes were introduced to the planning computed tomography images, including deformation, rotation, and translation, to simulate inter- and intrafractional variations. After model training, the accuracy of the model was evaluated by retrospectively studying patients who underwent pancreatic cancer radiation therapy. Statistical analysis using mean absolute differences (MADs) and Lin's concordance correlation coefficient were used to assess the accuracy of the predicted target positions.

RESULTS

MADs between the model-predicted and the actual positions were found to be less than 2.60 mm in anteroposterior, lateral, and oblique directions for both axes in the detector plane. For comparison studies with and without fiducials, MADs are less than 2.49 mm. For all cases, Lin's concordance correlation coefficients between the predicted and actual positions were found to be better than 93%, demonstrating the success of the proposed deep learning for image guided radiation therapy.

CONCLUSIONS

We demonstrated that markerless pancreatic tumor target localization is achievable with high accuracy by using a deep learning technique approach.

Radiation Therapy Outcomes Models in the Era of Radiomics and Radiogenomics: Uncertainties and Validation

Recent advances in imaging and biotechnology have tremendously improved the availability of quantitative imaging (radiomics) and molecular data (radiogenomics) for radiotherapy patients. This big data development with its comprehensive nature promises to transform outcome modeling in radiotherapy from few dose-volume metrics into utilizing more data-driven analytics. However, it also presents new profound challenges and creates new tasks for alleviating uncertainties arising from dealing with heterogeneous data and complex big data analytics. Therefore, more rigorous validation procedures need to be devised for these radiomics/radiogenomics models compared to traditional outcome modeling approaches previously utilized in radiation oncology, before they can be safely deployed for clinical trials or incorporated into daily practice. This editorial highlights current affairs, identifies some of the frequent sources of uncertainties, and presents some of the recommended practices for radiomics/radiogenomics models’ evaluation and validation.

The Role of Machine Learning in Knowledge-Based Response-Adapted Radiotherapy

With the continuous increase in radiotherapy patient-specific data from multimodality imaging and biotechnology molecular sources, knowledge-based response-adapted radiotherapy (KBR-ART) is emerging as a vital area for radiation oncology personalized treatment. In KBR-ART, planned dose distributions can be modified based on observed cues in patients' clinical, geometric, and physiological parameters. In this paper, we present current developments in the field of adaptive radiotherapy (ART), the progression toward KBR-ART, and examine several applications of static and dynamic machine learning approaches for realizing the KBR-ART framework potentials in maximizing tumor control and minimizing side effects with respect to individual radiotherapy patients. Specifically, three questions required for the realization of KBR-ART are addressed: (1) what knowledge is needed; (2) how to estimate RT outcomes accurately; and (3) how to adapt optimally. Different machine learning algorithms for KBR-ART application shall be discussed and contrasted. Representative examples of different KBR-ART stages are also visited.

A multiobjective Bayesian networks approach for joint prediction of tumor local control and radiation pneumonitis in nonsmall-cell lung cancer (NSCLC) for response-adapted radiotherapy

PURPOSE

Individualization of therapeutic outcomes in NSCLC radiotherapy is likely to be compromised by the lack of proper balance of biophysical factors affecting both tumor local control (LC) and side effects such as radiation pneumonitis (RP), which are likely to be intertwined. Here, we compare the performance of separate and joint outcomes predictions for response-adapted personalized treatment planning.

METHODS

A total of 118 NSCLC patients treated on prospective protocols with 32 cases of local progression and 20 cases of RP grade 2 or higher (RP2) were studied. Sixty-eight patients with 297 features before and during radiotherapy were used for discovery and 50 patients were reserved for independent testing. A multiobjective Bayesian network (MO-BN) approach was developed to identify important features for joint LC/RP2 prediction using extended Markov blankets as inputs to develop a BN predictive structure. Cross-validation (CV) was used to guide the MO-BN structure learning. Area under the free-response receiver operating characteristic (AU-FROC) curve was used to evaluate joint prediction performance.

RESULTS

Important features including single nucleotide polymorphisms (SNPs), micro RNAs, pretreatment cytokines, pretreatment PET radiomics together with lung and tumor gEUDs were selected and their biophysical inter-relationships with radiation outcomes (LC and RP2) were identified in a pretreatment MO-BN. The joint LC/RP2 prediction yielded an AU-FROC of 0.80 (95% CI: 0.70-0.86) upon internal CV. This improved to 0.85 (0.75-0.91) with additional two SNPs, changes in one cytokine and two radiomics PET image features through the course of radiotherapy in a during-treatment MO-BN. This MO-BN model outperformed combined single-objective Bayesian networks (SO-BNs) during-treatment [0.78 (0.67-0.84)]. AU-FROC values in the evaluation of the MO-BN and individual SO-BNs on the testing dataset were 0.77 and 0.68 for pretreatment, and 0.79 and 0.71 for during-treatment, respectively.

CONCLUSIONS

MO-BNs can reveal possible biophysical cross-talks between competing radiotherapy clinical endpoints. The prediction is improved by providing additional during-treatment information. The developed MO-BNs can be an important component of decision support systems for personalized response-adapted radiotherapy.