Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients

Role of Artificial Intelligence in Human Papillomavirus Status Prediction for Oropharyngeal Cancer: A Scoping Review

Human papillomavirus (HPV) infection is sexually transmitted and commonly widespread in the head and neck region; however, its role in tumor development and prognosis has only been demonstrated for oropharyngeal squamous cell carcinoma (HPV-OPSCC). The aim of this review is to analyze the results of the most recent literature that has investigated the use of artificial intelligence (AI) as a method for discerning HPV-positive from HPV-negative OPSCC tumors. A review of the literature was performed using PubMed/MEDLINE, EMBASE, and Cochrane Library databases, according to PRISMA for scoping review criteria (from 2017 to July 2024). A total of 15 articles and 4063 patients have been included. Eleven studies analyzed the role of radiomics, and four analyzed the role of AI in determining HPV histological positivity. The results of this scoping review indicate that AI has the potential to play a role in predicting HPV positivity or negativity in OPSCC. Further studies are required to confirm these results.

Radiomics-based prediction of local control in patients with brain metastases following postoperative stereotactic radiotherapy

BACKGROUND

Surgical resection is the standard of care for patients with large or symptomatic brain metastases (BMs). Despite improved local control after adjuvant stereotactic radiotherapy, the risk of local failure (LF) persists. Therefore, we aimed to develop and externally validate a pre-therapeutic radiomics-based prediction tool to identify patients at high LF risk.

METHODS

Data were collected from A Multicenter Analysis of Stereotactic Radiotherapy to the Resection Cavity of BMs (AURORA) retrospective study (training cohort: 253 patients from 2 centers; external test cohort: 99 patients from 5 centers). Radiomic features were extracted from the contrast-enhancing BM (T1-CE MRI sequence) and the surrounding edema (T2-FLAIR sequence). Different combinations of radiomic and clinical features were compared. The final models were trained on the entire training cohort with the best parameter set previously determined by internal 5-fold cross-validation and tested on the external test set.

RESULTS

The best performance in the external test was achieved by an elastic net regression model trained with a combination of radiomic and clinical features with a concordance index (CI) of 0.77, outperforming any clinical model (best CI: 0.70). The model effectively stratified patients by LF risk in a Kaplan-Meier analysis (P < .001) and demonstrated an incremental net clinical benefit. At 24 months, we found LF in 9% and 74% of the low and high-risk groups, respectively.

CONCLUSIONS

A combination of clinical and radiomic features predicted freedom from LF better than any clinical feature set alone. Patients at high risk for LF may benefit from stricter follow-up routines or intensified therapy.

Fully automated 3D machine learning model for HPV status characterization in oropharyngeal squamous cell carcinomas based on CT images

BACKGROUND

Human papillomavirus (HPV) status plays a major role in predicting oropharyngeal squamous cell carcinoma (OPSCC) survival. This study assesses the accuracy of a fully automated 3D convolutional neural network (CNN) in predicting HPV status using CT images.

METHODS

Pretreatment CT images from OPSCC patients were used to train a 3D DenseNet-121 model to predict HPV-p16 status. Performance was evaluated by the ROC Curve (AUC), sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and F1 score.

RESULTS

The network achieved a mean AUC of 0.80 ± 0.06. The best-preforming fold had a sensitivity of 0.86 and specificity of 0.92 at the Youden's index. The PPV, NPV, and F1 scores are 0.97, 0.71, and 0.82, respectively.

CONCLUSIONS

A fully automated CNN can characterize the HPV status of OPSCC patients with high sensitivity and specificity. Further refinement of this algorithm has the potential to provide a non-invasive tool to guide clinical management.

Explainable prediction model for the human papillomavirus status in patients with oropharyngeal squamous cell carcinoma using CNN on CT images

Several studies have emphasised how positive and negative human papillomavirus (HPV+  and HPV-, respectively) oropharyngeal squamous cell carcinoma (OPSCC) has distinct molecular profiles, tumor characteristics, and disease outcomes. Different radiomics-based prediction models have been proposed, by also using innovative techniques such as Convolutional Neural Networks (CNNs). Although some of these models reached encouraging predictive performances, there evidence explaining the role of radiomic features in achieving a specific outcome is scarce. In this paper, we propose some preliminary results related to an explainable CNN-based model to predict HPV status in OPSCC patients. We extracted the Gross Tumor Volume (GTV) of pre-treatment CT images related to 499 patients (356 HPV+ and 143 HPV-) included into the OPC-Radiomics public dataset to train an end-to-end Inception-V3 CNN architecture. We also collected a multicentric dataset consisting of 92 patients (43 HPV+ , 49 HPV-), which was employed as an independent test set. Finally, we applied Gradient-weighted Class Activation Mapping (Grad-CAM) technique to highlight the most informative areas with respect to the predicted outcome. The proposed model reached an AUC value of 73.50% on the independent test. As a result of the Grad-CAM algorithm, the most informative areas related to the correctly classified HPV+ patients were located into the intratumoral area. Conversely, the most important areas referred to the tumor edges. Finally, since the proposed model provided additional information with respect to the accuracy of the classification given by the visualization of the areas of greatest interest for predictive purposes for each case examined, it could contribute to increase confidence in using computer-based predictive models in the actual clinical practice.

Dosiomics and radiomics-based prediction of pneumonitis after radiotherapy and immune checkpoint inhibition: The relevance of fractionation

OBJECTIVES

Post-therapy pneumonitis (PTP) is a relevant side effect of thoracic radiotherapy and immunotherapy with checkpoint inhibitors (ICI). The influence of the combination of both, including dose fractionation schemes on PTP development is still unclear. This study aims to improve the PTP risk estimation after radio(chemo)therapy (R(C)T) for lung cancer with and without ICI by investigation of the impact of dose fractionation on machine learning (ML)-based prediction.

MATERIALS AND METHODS

Data from 100 patients who received fractionated R(C)T were collected. 39 patients received additional ICI therapy. Computed Tomography (CT), RT segmentation and dose data were extracted and physical doses were converted to 2-Gy equivalent doses (EQD2) to account for different fractionation schemes. Features were reduced using Pearson intercorrelation and the Boruta algorithm within 1000-fold bootstrapping. Six single (clinics, Dose Volume Histogram (DVH), ICI, chemotherapy, radiomics, dosiomics) and four combined models (radiomics + dosiomics, radiomics + DVH + Clinics, dosiomics + DVH + Clinics, radiomics + dosiomics + DVH + Clinics) were trained to predict PTP. Dose-based models were tested using physical dose and EQD2. Four ML-algorithms (random forest (rf), logistic elastic net regression, support vector machine, logitBoost) were trained and tested using 5-fold nested cross validation and Synthetic Minority Oversampling Technique (SMOTE) for resampling in R. Prediction was evaluated using the area under the receiver operating characteristic curve (AUC) on the test sets of the outer folds.

RESULTS

The combined model of all features using EQD2 surpassed all other models (AUC = 0.77, Confidence Interval CI 0.76-0.78). DVH, clinical data and ICI therapy had minor impact on PTP prediction with AUC values between 0.42 and 0.57. All EQD2-based models outperformed models based on physical dose.

CONCLUSIONS

Radiomics + dosiomics based ML models combined with clinical and dosimetric models were found to be suited best for PTP prediction after R(C)T and could improve pre-treatment decision making. Different RT dose fractionation schemes should be considered for dose-based ML approaches.

Comparing three-dimensional and two-dimensional deep-learning, radiomics, and fusion models for predicting occult lymph node metastasis in laryngeal squamous cell carcinoma based on CT imaging: a multicentre, retrospective, diagnostic study

Background

The occult lymph node metastasis (LNM) of laryngeal squamous cell carcinoma (LSCC) affects the treatment and prognosis of patients. This study aimed to comprehensively compare the performance of the three-dimensional and two-dimensional deep learning models, radiomics model, and the fusion models for predicting occult LNM in LSCC.

Methods

In this retrospective diagnostic study, a total of 553 patients with clinical N0 stage LSCC, who underwent surgical treatment without distant metastasis and multiple primary cancers, were consecutively enrolled from four Chinese medical centres between January 01, 2016 and December 30, 2020. The participant data were manually retrieved from medical records, imaging databases, and pathology reports. The study cohort was divided into a training set (n = 300), an internal test set (n = 89), and two external test sets (n = 120 and 44, respectively). The three-dimensional deep learning (3D DL), two-dimensional deep learning (2D DL), and radiomics model were developed using CT images of the primary tumor. The clinical model was constructed based on clinical and radiological features. Two fusion strategies were utilized to develop the fusion model: the feature-based DLRad_FB model and the decision-based DLRad_DB model. The discriminative ability and correlation of 3D DL, 2D DL and radiomics features were analysed comprehensively. The performances of the predictive models were evaluated based on the pathological diagnosis.

Findings

The 3D DL features had superior discriminative ability and lower internal redundancy compared to 2D DL and radiomics features. The DLRad_DB model achieved the highest AUC (0.89-0.90) among all the study sets, significantly outperforming the clinical model (AUC = 0.73-0.78, P = 0.0001-0.042, Delong test). Compared to the DLRad_DB model, the AUC values for the DLRad_FB, 3D DL, 2D DL, and radiomics models were 0.82-0.84 (P = 0.025-0.46), 0.86-0.89 (P = 0.75-0.97), 0.83-0.86 (P = 0.029-0.66), and 0.79-0.82 (P = 0.0072-0.10), respectively in the study sets. Additionally, the DLRad_DB model exhibited the best sensitivity (82-88%) and specificity (79-85%) in the test sets.

Interpretation

The decision-based fusion model DLRad_DB, which combines 3D DL, 2D DL, radiomics, and clinical data, can be utilized to predict occult LNM in LSCC. This has the potential to minimize unnecessary lymph node dissection and prophylactic radiotherapy in patients with cN0 disease.

Funding

National Natural Science Foundation of China, Natural Science Foundation of Shandong Province.

Multiparametric machine learning algorithm for human papillomavirus status and survival prediction in oropharyngeal cancer patients

BACKGROUND

Human papillomavirus (HPV) status influences prognosis in oropharyngeal cancer (OPC). Identifying high-risk patients are critical to improving treatment. We aim to provide a noninvasive opportunity for managing OPC patients by training multiple machine learning pipelines to determine the best model for characterizing HPV status and survival.

METHODS

Multi-parametric algorithms were designed using a 492 OPC patient database. HPV status incorporated age, sex, smoking/drinking habits, cancer subsite, TNM, and AJCC 7th edition staging. Survival considered HPV model inputs plus HPV status. Patients were split 4:1 training: testing. Algorithm efficacy was assessed through accuracy and area under the receiver operator characteristic curve (AUC).

RESULTS

From 31 HPV status models, ensemble yielded 0.83 AUC and 78.7% accuracy. From 38 survival models, ensemble yielded 0.91 AUC and 87.7% accuracy.

CONCLUSION

Results reinforce artificial intelligence's potential to use tumor imaging and patient characterizations for HPV status and outcome prediction. Utilizing these algorithms can optimize clinical guidance and patient care noninvasively.

The importance of planning CT-based imaging features for machine learning-based prediction of pain response

Patients suffering from painful spinal bone metastases (PSBMs) often undergo palliative radiation therapy (RT), with an efficacy of approximately two thirds of patients. In this exploratory investigation, we assessed the effectiveness of machine learning (ML) models trained on radiomics, semantic and clinical features to estimate complete pain response. Gross tumour volumes (GTV) and clinical target volumes (CTV) of 261 PSBMs were segmented on planning computed tomography (CT) scans. Radiomics, semantic and clinical features were collected for all patients. Random forest (RFC) and support vector machine (SVM) classifiers were compared using repeated nested cross-validation. The best radiomics classifier was trained on CTV with an area under the receiver-operator curve (AUROC) of 0.62 ± 0.01 (RFC; 95% confidence interval). The semantic model achieved a comparable AUROC of 0.63 ± 0.01 (RFC), significantly below the clinical model (SVM, AUROC: 0.80 ± 0.01); and slightly lower than the spinal instability neoplastic score (SINS; LR, AUROC: 0.65 ± 0.01). A combined model did not improve performance (AUROC: 0,74 ± 0,01). We could demonstrate that radiomics and semantic analyses of planning CTs allowed for limited prediction of therapy response to palliative RT. ML predictions based on established clinical parameters achieved the best results.

Artificial intelligence for HPV status prediction based on disease-specific images in head and neck cancer: A systematic review and meta-analysis

Accurate early detection of the human papillomavirus (HPV) status in head and neck cancer (HNC) is crucial to identify at-risk populations, stratify patients, personalized treatment options, and predict prognosis. Artificial intelligence (AI) is an emerging tool to dissect imaging features. This systematic review and meta-analysis aimed to evaluate the performance of AI to predict the HPV positivity through the HPV-associated diseased images in HNC patients. A systematic literature search was conducted in databases including Ovid-MEDLINE, Embase, and Web of Science Core Collection for studies continuously published from inception up to October 30, 2022. Search strategies included keywords such as "artificial intelligence," "head and neck cancer," "HPV," and "sensitivity & specificity." Duplicates, articles without HPV predictions, letters, scientific reports, conference abstracts, or reviews were excluded. Binary diagnostic data were then extracted to generate contingency tables and then used to calculate the pooled sensitivity (SE), specificity (SP), area under the curve (AUC), and their 95% confidence interval (CI). A random-effects model was used for meta-analysis, four subgroup analyses were further explored. Totally, 22 original studies were included in the systematic review, 15 of which were eligible to generate 33 contingency tables for meta-analysis. The pooled SE and SP for all studies were 79% (95% CI: 75-82%) and 74% (95% CI: 69-78%) respectively, with an AUC of 0.83 (95% CI: 0.79-0.86). When only selecting one contingency table with the highest accuracy from each study, our analysis revealed a pooled SE of 79% (95% CI: 75-83%), SP of 75% (95% CI: 69-79%), and an AUC of 0.84 (95% CI: 0.81-0.87). The respective heterogeneities were moderate (I2 for SE and SP were 51.70% and 51.01%) and only low (35.99% and 21.44%). This evidence-based study showed an acceptable and promising performance for AI algorithms to predict HPV status in HNC but was not comparable to the routine p16 immunohistochemistry. The exploitation and optimization of AI algorithms warrant further research. Compared with previous studies, future studies anticipate to make progress in the selection of databases, improvement of international reporting guidelines, and application of high-quality deep learning algorithms.

A comprehensive review for machine learning based human papillomavirus detection in forensic identification with multiple medical samples

Human papillomavirus (HPV) is a sexually transmitted virus. Cervical cancer is one of the highest incidences of cancer, almost all patients are accompanied by HPV infection. In addition, the occurrence of a variety of cancers is also associated with HPV infection. HPV vaccination has gained widespread popularity in recent years with the increase in public health awareness. In this context, HPV testing not only needs to be sensitive and specific but also needs to trace the source of HPV infection. Through machine learning and deep learning, information from medical examinations can be used more effectively. In this review, we discuss recent advances in HPV testing in combination with machine learning and deep learning.

Deep learning PET/CT-based radiomics integrates clinical data: A feasibility study to distinguish between tuberculosis nodules and lung cancer

BACKGROUND

Radiomic diagnosis models generally consider only a single dimension of information, leading to limitations in their diagnostic accuracy and reliability. The integration of multiple dimensions of information into the deep learning model have the potential to improve its diagnostic capabilities. The purpose of study was to evaluate the performance of deep learning model in distinguishing tuberculosis (TB) nodules and lung cancer (LC) based on deep learning features, radiomic features, and clinical information.

METHODS

Positron emission tomography (PET) and computed tomography (CT) image data from 97 patients with LC and 77 patients with TB nodules were collected. One hundred radiomic features were extracted from both PET and CT imaging using the pyradiomics platform, and 2048 deep learning features were obtained through a residual neural network approach. Four models included traditional machine learning model with radiomic features as input (traditional radiomics), a deep learning model with separate input of image features (deep convolutional neural networks [DCNN]), a deep learning model with two inputs of radiomic features and deep learning features (radiomics-DCNN) and a deep learning model with inputs of radiomic features and deep learning features and clinical information (integrated model). The models were evaluated using area under the curve (AUC), sensitivity, accuracy, specificity, and F1-score metrics.

RESULTS

The results of the classification of TB nodules and LC showed that the integrated model achieved an AUC of 0.84 (0.82-0.88), sensitivity of 0.85 (0.80-0.88), and specificity of 0.84 (0.83-0.87), performing better than the other models.

CONCLUSION

The integrated model was found to be the best classification model in the diagnosis of TB nodules and solid LC.

Application of artificial intelligence for overall survival risk stratification in oropharyngeal carcinoma: A validation of ProgTOOL

BACKGROUND

In recent years, there has been a surge in machine learning-based models for diagnosis and prognostication of outcomes in oncology. However, there are concerns relating to the model's reproducibility and generalizability to a separate patient cohort (i.e., external validation).

OBJECTIVES

This study primarily provides a validation study for a recently introduced and publicly available machine learning (ML) web-based prognostic tool (ProgTOOL) for overall survival risk stratification of oropharyngeal squamous cell carcinoma (OPSCC). Additionally, we reviewed the published studies that have utilized ML for outcome prognostication in OPSCC to examine how many of these models were externally validated, type of external validation, characteristics of the external dataset, and diagnostic performance characteristics on the internal validation (IV) and external validation (EV) datasets were extracted and compared.

METHODS

We used a total of 163 OPSCC patients obtained from the Helsinki University Hospital to externally validate the ProgTOOL for generalizability. In addition, PubMed, OvidMedline, Scopus, and Web of Science databases were systematically searched according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.

RESULTS

The ProgTOOL produced a predictive performance of 86.5% balanced accuracy, Mathew's correlation coefficient of 0.78, Net Benefit (0.7) and Brier score (0.06) for overall survival stratification of OPSCC patients as either low-chance or high-chance. In addition, out of a total of 31 studies found to have used ML for the prognostication of outcomes in OPSCC, only seven (22.6%) reported a form of EV. Three studies (42.9%) each used either temporal EV or geographical EV while only one study (14.2%) used expert as a form of EV. Most of the studies reported a reduction in performance when externally validated.

CONCLUSION

The performance of the model in this validation study indicates that it may be generalized, therefore, bringing recommendations of the model for clinical evaluation closer to reality. However, the number of externally validated ML-based models for OPSCC is still relatively small. This significantly limits the transfer of these models for clinical evaluation and subsequently reduces the likelihood of the use of these models in daily clinical practice. As a gold standard, we recommend the use of geographical EV and validation studies to reveal biases and overfitting of these models. These recommendations are poised to facilitate the implementation of these models in clinical practice.

Dosiomics and radiomics to predict pneumonitis after thoracic stereotactic body radiotherapy and immune checkpoint inhibition

Introduction

Pneumonitis is a relevant side effect after radiotherapy (RT) and immunotherapy with checkpoint inhibitors (ICIs). Since the effect is radiation dose dependent, the risk increases for high fractional doses as applied for stereotactic body radiation therapy (SBRT) and might even be enhanced for the combination of SBRT with ICI therapy. Hence, patient individual pre-treatment prediction of post-treatment pneumonitis (PTP) might be able to support clinical decision making. Dosimetric factors, however, use limited information and, thus, cannot exploit the full potential of pneumonitis prediction.

Methods

We investigated dosiomics and radiomics model based approaches for PTP prediction after thoracic SBRT with and without ICI therapy. To overcome potential influences of different fractionation schemes, we converted physical doses to 2 Gy equivalent doses (EQD2) and compared both results. In total, four single feature models (dosiomics, radiomics, dosimetric, clinical factors) were tested and five combinations of those (dosimetric+clinical factors, dosiomics+radiomics, dosiomics+dosimetric+clinical factors, radiomics+dosimetric+clinical factors, radiomics+dosiomics+dosimetric+clinical factors). After feature extraction, a feature reduction was performed using pearson intercorrelation coefficient and the Boruta algorithm within 1000-fold bootstrapping runs. Four different machine learning models and the combination of those were trained and tested within 100 iterations of 5-fold nested cross validation.

Results

Results were analysed using the area under the receiver operating characteristic curve (AUC). We found the combination of dosiomics and radiomics features to outperform all other models with AUCradiomics+dosiomics, D = 0.79 (95% confidence interval 0.78-0.80) and AUCradiomics+dosiomics, EQD2 = 0.77 (0.76-0.78) for physical dose and EQD2, respectively. ICI therapy did not impact the prediction result (AUC ≤ 0.5). Clinical and dosimetric features for the total lung did not improve the prediction outcome.

Conclusion

Our results suggest that combined dosiomics and radiomics analysis can improve PTP prediction in patients treated with lung SBRT. We conclude that pre-treatment prediction could support clinical decision making on an individual patient basis with or without ICI therapy.

Largest diameter delineations can substitute 3D tumor volume delineations for radiomics prediction of human papillomavirus status on MRI's of oropharyngeal cancer

PURPOSE

Laborious and time-consuming tumor segmentations are one of the factors that impede adoption of radiomics in the clinical routine. This study investigates model performance using alternative tumor delineation strategies in models predictive of human papillomavirus (HPV) in oropharyngeal squamous cell carcinoma (OPSCC).

METHODS

Of 153 OPSCC patients, HPV status was determined using p16/p53 immunohistochemistry. MR-based radiomic features were extracted within 3D delineations by an inexperienced observer, experienced radiologist or radiation oncologist, and within a 2D delineation of the largest axial tumor diameter and 3D spheres within the tumor. First, logistic regression prediction models were constructed and tested separately for each of these six delineation strategies. Secondly, the model trained on experienced delineations was tested using these delineation strategies. The latter methodology was repeated with the omission of shape features. Model performance was evaluated using area under the curve (AUC), sensitivity and specificity.

RESULTS

Models constructed and tested using single-slice delineations (AUC/Sensitivity/Specificity: 0.84/0.75/0.84) perform better compared to 3D experienced observer delineations (AUC/Sensitivity/Specificity: 0.76/0.76/0.71), where models based on 4 mm sphere delineations (AUC/Sensitivity/Specificity: 0.77/0.59/0.71) show similar performance. Similar performance was found when experienced and largest diameter delineations (AUC/Sens/Spec: 0.76/0.75/0.65 vs 0.76/0.69/0.69) was used to test the model constructed using experienced delineations without shape features.

CONCLUSION

Alternative delineations can substitute labor and time intensive full tumor delineations in a model that predicts HPV status in OPSCC. These faster delineations may improve adoption of radiomics in the clinical setting. Future research should evaluate whether these alternative delineations are valid in other radiomics models.

The impact of radiomics for human papillomavirus status prediction in oropharyngeal cancer: systematic review and radiomics quality score assessment

Purpose

Human papillomavirus (HPV) status assessment is crucial for decision making in oropharyngeal cancer patients. In last years, several articles have been published investigating the possible role of radiomics in distinguishing HPV-positive from HPV-negative neoplasms. Aim of this review was to perform a systematic quality assessment of radiomic studies published on this topic.

Methods

Radiomics studies on HPV status prediction in oropharyngeal cancer patients were selected. The Radiomic Quality Score (RQS) was assessed by three readers to evaluate their methodological quality. In addition, possible correlations between RQS% and journal type, year of publication, impact factor, and journal rank were investigated.

Results

After the literature search, 19 articles were selected whose RQS median was 33% (range 0–42%). Overall, 16/19 studies included a well-documented imaging protocol, 13/19 demonstrated phenotypic differences, and all were compared with the current gold standard. No study included a public protocol, phantom study, or imaging at multiple time points. More than half (13/19) included feature selection and only 2 were comprehensive of non-radiomic features. Mean RQS was significantly higher in clinical journals.

Conclusion

Radiomics has been proposed for oropharyngeal cancer HPV status assessment, with promising results. However, these are supported by low methodological quality investigations. Further studies with higher methodological quality, appropriate standardization, and greater attention to validation are necessary prior to clinical adoption.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00234-022-02959-0.

A 2.5D convolutional neural network for HPV prediction in advanced oropharyngeal cancer

BACKGROUND

Infection with human papilloma virus (HPV) is one of the most relevant prognostic factors in advanced oropharyngeal cancer (OPC) treatment. In this study we aimed to assess the diagnostic accuracy of a deep learning-based method for HPV status prediction in computed tomography (CT) images of advanced OPC.

METHOD

An internal dataset and three public collections were employed (internal: n = 151, HNC1: n = 451; HNC2: n = 80; HNC3: n = 110). Internal and HNC1 datasets were used for training, whereas HNC2 and HNC3 collections were used as external test cohorts. All CT scans were resampled to a 2 mm³ resolution and a sub-volume of 72x72x72 pixels was cropped on each scan, centered around the tumor. Then, a 2.5D input of size 72x72x3 pixels was assembled by selecting the 2D slice containing the largest tumor area along the axial, sagittal and coronal planes, respectively. The convolutional neural network employed consisted of the first 5 modules of the Xception model and a small classification network. Ten-fold cross-validation was applied to evaluate training performance. At test time, soft majority voting was used to predict HPV status.

RESULTS

A final training mean [range] area under the curve (AUC) of 0.84 [0.76-0.89], accuracy of 0.76 [0.64-0.83] and F1-score of 0.74 [0.62-0.83] were achieved. AUC/accuracy/F1-score values of 0.83/0.75/0.69 and 0.88/0.79/0.68 were achieved on the HNC2 and HNC3 test sets, respectively.

CONCLUSION

Deep learning was successfully applied and validated in two external cohorts to predict HPV status in CT images of advanced OPC, proving its potential as a support tool in cancer precision medicine.

Development and External Validation of Deep-Learning-Based Tumor Grading Models in Soft-Tissue Sarcoma Patients Using MR Imaging

BACKGROUND

In patients with soft-tissue sarcomas, tumor grading constitutes a decisive factor to determine the best treatment decision. Tumor grading is obtained by pathological work-up after focal biopsies. Deep learning (DL)-based imaging analysis may pose an alternative way to characterize STS tissue. In this work, we sought to non-invasively differentiate tumor grading into low-grade (G1) and high-grade (G2/G3) STS using DL techniques based on MR-imaging.

METHODS

Contrast-enhanced T1-weighted fat-saturated (T1FSGd) MRI sequences and fat-saturated T2-weighted (T2FS) sequences were collected from two independent retrospective cohorts (training: 148 patients, testing: 158 patients). Tumor grading was determined following the French Federation of Cancer Centers Sarcoma Group in pre-therapeutic biopsies. DL models were developed using transfer learning based on the DenseNet 161 architecture.

RESULTS

The T1FSGd and T2FS-based DL models achieved area under the receiver operator characteristic curve (AUC) values of 0.75 and 0.76 on the test cohort, respectively. T1FSGd achieved the best F1-score of all models (0.90). The T2FS-based DL model was able to significantly risk-stratify for overall survival. Attention maps revealed relevant features within the tumor volume and in border regions.

CONCLUSIONS

MRI-based DL models are capable of predicting tumor grading with good reproducibility in external validation.

Prediction of Human Papillomavirus (HPV) Association of Oropharyngeal Cancer (OPC) Using Radiomics: The Impact of the Variation of CT Scanner

Simple Summary

Recent studies exploring the application of radiomics features in medicine have shown promising results. However, variation in imaging parameters may impact the robustness of these features. Feature robustness may then in turn affect the prediction performance of the machine learning models built upon these features. While numerous studies have tested feature robustness against a variety of imaging parameters, the extent to which feature robustness affects predictions remains unclear. A particularly notable application of radiomics in clinical oncology is the prediction of Human Papillomavirus (HPV) association in Oropharyngeal cancer. In this study we explore how CT scanner type affects the performance of radiomics features for HPV association prediction and highlight the need to implement precautionary approaches so as to minimize this effect.

Abstract

Studies have shown that radiomic features are sensitive to the variability of imaging parameters (e.g., scanner models), and one of the major challenges in these studies lies in improving the robustness of quantitative features against the variations in imaging datasets from multi-center studies. Here, we assess the impact of scanner choice on computed tomography (CT)-derived radiomic features to predict the association of oropharyngeal squamous cell carcinoma with human papillomavirus (HPV). This experiment was performed on CT image datasets acquired from two different scanner manufacturers. We demonstrate strong scanner dependency by developing a machine learning model to classify HPV status from radiological images. These experiments reveal the effect of scanner manufacturer on the robustness of radiomic features, and the extent of this dependency is reflected in the performance of HPV prediction models. The results of this study highlight the importance of implementing an appropriate approach to reducing the impact of imaging parameters on radiomic features and consequently on the machine learning models, without removing features which are deemed non-robust but may contain learning information.