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.

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.

A Fully Automated Deep Learning Network for Brain Tumor Segmentation.

We developed a fully automated method for brain tumor segmentation using deep learning; 285 brain tumor cases with multiparametric magnetic resonance images from the BraTS2018 data set were used. We designed 3 separate 3D-Dense-UNets to simplify the complex multiclass segmentation problem into individual binary-segmentation problems for each subcomponent. We implemented a 3-fold cross-validation to generalize the network's performance. The mean cross-validation Dice-scores for whole tumor (WT), tumor core (TC), and enhancing tumor (ET) segmentations were 0.92, 0.84, and 0.80, respectively. We then retrained the individual binary-segmentation networks using 265 of the 285 cases, with 20 cases held-out for testing. We also tested the network on 46 cases from the BraTS2017 validation data set, 66 cases from the BraTS2018 validation data set, and 52 cases from an independent clinical data set. The average Dice-scores for WT, TC, and ET were 0.90, 0.84, and 0.80, respectively, on the 20 held-out testing cases. The average Dice-scores for WT, TC, and ET on the BraTS2017 validation data set, the BraTS2018 validation data set, and the clinical data set were as follows: 0.90, 0.80, and 0.78; 0.90, 0.82, and 0.80; and 0.85, 0.80, and 0.77, respectively. A fully automated deep learning method was developed to segment brain tumors into their subcomponents, which achieved high prediction accuracy on the BraTS data set and on the independent clinical data set. This method is promising for implementation into a clinical workflow.

A novel fully automated MRI-based deep-learning method for classification of IDH mutation status in brain gliomas.

BACKGROUND: Isocitrate dehydrogenase (IDH) mutation status has emerged as an important prognostic marker in gliomas. Currently, reliable IDH mutation determination requires invasive surgical procedures. The purpose of this study was to develop a highly accurate, MRI-based, voxelwise deep-learning IDH classification network using T2-weighted (T2w) MR images and compare its performance to a multicontrast network. METHODS: Multiparametric brain MRI data and corresponding genomic information were obtained for 214 subjects (94 IDH-mutated, 120 IDH wild-type) from The Cancer Imaging Archive and The Cancer Genome Atlas. Two separate networks were developed, including a T2w image-only network (T2-net) and a multicontrast (T2w, fluid attenuated inversion recovery, and T1 postcontrast) network (TS-net) to perform IDH classification and simultaneous single label tumor segmentation. The networks were trained using 3D Dense-UNets. Three-fold cross-validation was performed to generalize the networks' performance. Receiver operating characteristic analysis was also performed. Dice scores were computed to determine tumor segmentation accuracy. RESULTS: T2-net demonstrated a mean cross-validation accuracy of 97.14% ± 0.04 in predicting IDH mutation status, with a sensitivity of 0.97 ± 0.03, specificity of 0.98 ± 0.01, and an area under the curve (AUC) of 0.98 ± 0.01. TS-net achieved a mean cross-validation accuracy of 97.12% ± 0.09, with a sensitivity of 0.98 ± 0.02, specificity of 0.97 ± 0.001, and an AUC of 0.99 ± 0.01. The mean whole tumor segmentation Dice scores were 0.85 ± 0.009 for T2-net and 0.89 ± 0.006 for TS-net. CONCLUSION: We demonstrate high IDH classification accuracy using only T2-weighted MR images. This represents an important milestone toward clinical translation.

Classification of brain tumor isocitrate dehydrogenase status using MRI and deep learning.

Isocitrate dehydrogenase (IDH) mutation status is an important marker in glioma diagnosis and therapy. We propose an automated pipeline for noninvasively predicting IDH status using deep learning and T2-weighted (T2w) magnetic resonance (MR) images with minimal preprocessing (N4 bias correction and normalization to zero mean and unit variance). T2w MR images and genomic data were obtained from The Cancer Imaging Archive dataset for 260 subjects (120 high-grade and 140 low-grade gliomas). A fully automated two-dimensional densely connected model was trained to classify IDH mutation status on 208 subjects and tested on another held-out set of 52 subjects using fivefold cross validation. Data leakage was avoided by ensuring subject separation during the slice-wise randomization. Mean classification accuracy of 90.5% was achieved for each axial slice in predicting the three classes of no tumor, IDH mutated, and IDH wild type. Test accuracy of 83.8% was achieved in predicting IDH mutation status for individual subjects on the test dataset of 52 subjects. We demonstrate a deep learning method to predict IDH mutation status using T2w MRI alone. Radiologic imaging studies using deep learning methods must address data leakage (subject duplication) in the randomization process to avoid upward bias in the reported classification accuracy.

A Comparison of Acoustic Radiation Force-Derived Indices of Cardiac Function in the Langendorff Perfused Rabbit Heart.

In the past decade, there has been an increased interest in characterizing cardiac tissue mechanics utilizing newly developed ultrasound-based elastography techniques. These methods excite the tissue mechanically and track the response. Two frequently used methods, acoustic radiation force impulse (ARFI) and shear-wave elasticity imaging (SWEI), have been considered qualitative and quantitative techniques providing relative and absolute measures of tissue stiffness, respectively. Depending on imaging conditions, it is desirable to identify indices of cardiac function that could be measured by ARFI and SWEI and to characterize the relationship between the measures. In this study, we have compared two indices (i.e., relaxation time constant used for diastolic dysfunction assessment and systolic/diastolic stiffness ratio) measured nearly simultaneously by M-mode ARFI and SWEI techniques. We additionally correlated ARFI-measured inverse displacements with SWEI-measured values of the shear modulus of stiffness. For the eight animals studied, the average relaxation time constant ( τ) measured by ARFI and SWEI were ([Formula: see text]) and ([Formula: see text]), respectively ([Formula: see text]). Average systolic/diastolic stiffness ratios for ARFI and SWEI measurements were 6.01±1.37 and 7.12±3.24, respectively ([Formula: see text]). Shear modulus of stiffness (SWEI) was linearly related to inverse displacement values (ARFI) with a 95% CI for the slope of 0.010-0.011 [Formula: see text] ( R(2)=0.73). In conclusion, the relaxation time constant and the systolic/diastolic stiffness ratio were calculated with good agreement between the ARFI- and SWEI-derived measurements. ARFI relative and SWEI absolute stiffness measurements were linearly related with varying slopes based on imaging conditions and subject tissue properties.