Development and validation of a deep learning model to assess tumor progression to immunotherapy.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. e20601-e20601 ◽  
Author(s):  
Yi Yang ◽  
Jiancheng Yang ◽  
Yuxiang Ye ◽  
Tian Xia ◽  
Shun Lu
Keyword(s):  
Deep Learning ◽  
Tumor Progression ◽  
Tumor Volume ◽  
Tumor Response ◽  
Learning Model ◽  
Ct Scans ◽  
Tumor Diameter ◽  
Data Set ◽  
Senior Clinician ◽  
Deep Learning Model

e20601 Background: Manual application of length-based tumor response criteria is the standard-of-care for assessing metastatic tumor response. It is technically challenging, time-consuming and associated with low reproducibility. In this study, we presented a novel automatic Deep Neural Networks (DNNs) based segmentation method for assessing tumor progression to immunotherapy. Next stage, AI will assist Physicians assessing pseudo-progression. Methods: A data set of 39 lung cancer patients with 156 computed tomography (CT) scans was used for model training and validation. A 3D segmentation DNN DenseSharp, was trained with an input size of on CT scans of tumor with manual delineated volume of interest (VOI) as ground truth. The trained model was subsequently used to estimate the volumes of target lesions via 16 sliding windows. We referred the progression-free survival (PFS) only considering tumor size as PFS-T. PFS-Ts assessed by longest tumor diameter (PFS-Tdiam), by tumor volume (PFS-Tvol), and by predicted tumor volume (PFS-Tpred-vol) were compared with standard PFS (as assessed by one junior and one senior clinician). Tumor progression was defined as > 20% increase in the longest tumor diameter or > 50% increase in tumor volume. Effective treatment was defined as a PFS of > 60 days after immunotherapy. Results: In a 4-fold cross-validation test, the DenseSharp segmentation neural network achieved a mean per-class intersection over union (mIoU) of 80.1%. The effectiveness rates of immunotherapy assessed using PFS-Tdiam (32 / 39, 82.1%), PFS-Tvol (33/39, 84.6%) and PFS-T pred-vol (32/39, 82.1%) were the same as standard PFS. The agreement between PFS-Tvol, and PFS-Tpred-vol was 97.4% (38/39). Evaluation time with deep learning model implemented with PyTorch 0.4.1 on GTX 1080 GPU was hundred-fold faster than manual evaluation (1.42s vs. 5-10 min per patient). Conclusions: In this study, DNN based model demonstrated fast and stable performance for tumor progression evaluation. Automatic volumetric measurement of tumor lesion enabled by deep learning provides the potential for a more efficient, objective and sensitive measurement than linear measurement by clinicians.

Pure and Hybrid Deep Learning Models can Predict Pathologic Tumor Response to Neoadjuvant Therapy in Pancreatic Adenocarcinoma: A Pilot Study

2020 ◽  
pp. 000313482098255
Author(s):  
Michael D. Watson ◽  
Maria R. Baimas-George ◽  
Keith J. Murphy ◽  
Ryan C. Pickens ◽  
David A. Iannitti ◽  
...  
Keyword(s):  
Deep Learning ◽  
Neoadjuvant Therapy ◽  
Pancreatic Adenocarcinoma ◽  
Hybrid Model ◽  
Tumor Response ◽  
Tumor Regression ◽  
Area Under The Curve ◽  
Learning Model ◽  
Response To Therapy ◽  
Deep Learning Model

Background Neoadjuvant therapy may improve survival of patients with pancreatic adenocarcinoma; however, determining response to therapy is difficult. Artificial intelligence allows for novel analysis of images. We hypothesized that a deep learning model can predict tumor response to NAC. Methods Patients with pancreatic cancer receiving neoadjuvant therapy prior to pancreatoduodenectomy were identified between November 2009 and January 2018. The College of American Pathologists Tumor Regression Grades 0-2 were defined as pathologic response (PR) and grade 3 as no response (NR). Axial images from preoperative computed tomography scans were used to create a 5-layer convolutional neural network and LeNet deep learning model to predict PRs. The hybrid model incorporated decrease in carbohydrate antigen 19-9 (CA19-9) of 10%. Accuracy was determined by area under the curve. Results A total of 81 patients were included in the study. Patients were divided between PR (333 images) and NR (443 images). The pure model had an area under the curve (AUC) of .738 ( P < .001), whereas the hybrid model had an AUC of .785 ( P < .001). CA19-9 decrease alone was a poor predictor of response with an AUC of .564 ( P = .096). Conclusions A deep learning model can predict pathologic tumor response to neoadjuvant therapy for patients with pancreatic adenocarcinoma and the model is improved with the incorporation of decreases in serum CA19-9. Further model development is needed before clinical application.

scholarly journals Classification of Clinically Significant Prostate Cancer on Multi-Parametric MRI: A Validation Study Comparing Deep Learning and Radiomics

Cancers ◽  
2021 ◽  
Vol 14 (1) ◽  
pp. 12
Author(s):  
Jose M. Castillo T. ◽  
Muhammad Arif ◽  
Martijn P. A. Starmans ◽  
Wiro J. Niessen ◽  
Chris H. Bangma ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Deep Learning ◽  
Characteristic Curve ◽  
Model Development ◽  
Learning Model ◽  
Multiparametric Mri ◽  
Data Sets ◽  
Data Set ◽  
Test Sets ◽  
Deep Learning Model

The computer-aided analysis of prostate multiparametric MRI (mpMRI) could improve significant-prostate-cancer (PCa) detection. Various deep-learning- and radiomics-based methods for significant-PCa segmentation or classification have been reported in the literature. To be able to assess the generalizability of the performance of these methods, using various external data sets is crucial. While both deep-learning and radiomics approaches have been compared based on the same data set of one center, the comparison of the performances of both approaches on various data sets from different centers and different scanners is lacking. The goal of this study was to compare the performance of a deep-learning model with the performance of a radiomics model for the significant-PCa diagnosis of the cohorts of various patients. We included the data from two consecutive patient cohorts from our own center (n = 371 patients), and two external sets of which one was a publicly available patient cohort (n = 195 patients) and the other contained data from patients from two hospitals (n = 79 patients). Using multiparametric MRI (mpMRI), the radiologist tumor delineations and pathology reports were collected for all patients. During training, one of our patient cohorts (n = 271 patients) was used for both the deep-learning- and radiomics-model development, and the three remaining cohorts (n = 374 patients) were kept as unseen test sets. The performances of the models were assessed in terms of their area under the receiver-operating-characteristic curve (AUC). Whereas the internal cross-validation showed a higher AUC for the deep-learning approach, the radiomics model obtained AUCs of 0.88, 0.91 and 0.65 on the independent test sets compared to AUCs of 0.70, 0.73 and 0.44 for the deep-learning model. Our radiomics model that was based on delineated regions resulted in a more accurate tool for significant-PCa classification in the three unseen test sets when compared to a fully automated deep-learning model.

Ground-truth uncertainty-aware metrics for machine learning applications on seismic image interpretation: Application to faults and horizon extraction

2020 ◽  
Vol 39 (10) ◽  
pp. 734-741
Author(s):  
Sébastien Guillon ◽  
Frédéric Joncour ◽  
Pierre-Emmanuel Barrallon ◽  
Laurent Castanié
Keyword(s):  
Deep Learning ◽  
Image Interpretation ◽  
Ground Truth ◽  
Learning Model ◽  
Seismic Interpretation ◽  
Data Set ◽  
Seismic Image ◽  
Machine Learning Applications ◽  
Deep Learning Model

We propose new metrics to measure the performance of a deep learning model applied to seismic interpretation tasks such as fault and horizon extraction. Faults and horizons are thin geologic boundaries (1 pixel thick on the image) for which a small prediction error could lead to inappropriately large variations in common metrics (precision, recall, and intersection over union). Through two examples, we show how classical metrics could fail to indicate the true quality of fault or horizon extraction. Measuring the accuracy of reconstruction of thin objects or boundaries requires introducing a tolerance distance between ground truth and prediction images to manage the uncertainties inherent in their delineation. We therefore adapt our metrics by introducing a tolerance function and illustrate their ability to manage uncertainties in seismic interpretation. We compare classical and new metrics through different examples and demonstrate the robustness of our metrics. Finally, we show on a 3D West African data set how our metrics are used to tune an optimal deep learning model.

Supporting risk management in the Caribbean by application of Deep Learning for object classification of aerial imagery with MATLAB

2020 ◽  
Author(s):  
Sebastian Bomberg ◽  
Neha Goel
Keyword(s):  
Risk Management ◽  
Deep Learning ◽  
Gpu Computing ◽  
Learning Model ◽  
Aerial Imagery ◽  
Validation Data ◽  
Data Set ◽  
Roof Material ◽  
Caribbean Islands ◽  
Deep Learning Model

&lt;p&gt;The presented work focuses on disaster risk management of cities which are prone to natural hazards. Based on aerial imagery captured by drones of regions in Caribbean islands, we show how to process and automatically identify roof material of individual structures using a deep learning model. Deep learning refers to a machine learning technique using deep artificial neural networks. Unlike other techniques, deep learning does not necessarily require feature engineering but may process raw data directly. The outcome of this assessment can be used for steering risk mitigations measures, creating risk hazard maps or advising municipal bodies or help organizations on investing their resources in rebuilding reinforcements. Data at hand consists of images in BigTIFF format and GeoJSON files including the building footprint, unique building ID and roof material labels. We demonstrate how to use MATLAB and its toolboxes for processing large image files that do not fit in computer memory. Based on this, we perform the training of a deep learning model to classify roof material present in the images. We achieve this by subjecting a pretrained ResNet-18 neural network to transfer learning. Training is further accelerated by means of GPU computing. The accuracy computed from a validation data set achieved by this baseline model is 74%. Further tuning of hyperparameters is expected to improve accuracy significantly.&lt;/p&gt;

scholarly journals Predicting the Mortality and Readmission of In-Hospital Cardiac Arrest Patients With Electronic Health Records: A Machine Learning Approach (Preprint)

2021 ◽  
Author(s):  
Chien-Yu Chi ◽  
Shuang Ao ◽  
Adrian Winkler ◽  
Kuan-Chun Fu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Cardiac Arrest ◽  
Deep Learning ◽  
Operating Characteristic ◽  
Outcome Prediction ◽  
Learning Model ◽  
Data Set ◽  
Clinical Records ◽  
Care Costs ◽  
Deep Learning Model ◽  
Hospital Cardiac Arrest

BACKGROUND In-hospital cardiac arrest (IHCA) is associated with high mortality and health care costs in the recovery phase. Predicting adverse outcome events, including readmission, improves the chance for appropriate interventions and reduces health care costs. However, studies related to the early prediction of adverse events of IHCA survivors are rare. Therefore, we used a deep learning model for prediction in this study. OBJECTIVE This study aimed to demonstrate that with the proper data set and learning strategies, we can predict the 30-day mortality and readmission of IHCA survivors based on their historical claims. METHODS National Health Insurance Research Database claims data, including 168,693 patients who had experienced IHCA at least once and 1,569,478 clinical records, were obtained to generate a data set for outcome prediction. We predicted the 30-day mortality/readmission after each current record (ALL-mortality/ALL-readmission) and 30-day mortality/readmission after IHCA (cardiac arrest [CA]-mortality/CA-readmission). We developed a hierarchical vectorizer (HVec) deep learning model to extract patients’ information and predict mortality and readmission. To embed the textual medical concepts of the clinical records into our deep learning model, we used Text2Node to compute the distributed representations of all medical concept codes as a 128-dimensional vector. Along with the patient’s demographic information, our novel HVec model generated embedding vectors to hierarchically describe the health status at the record-level and patient-level. Multitask learning involving two main tasks and auxiliary tasks was proposed. As CA-mortality and CA-readmission were rare, person upsampling of patients with CA and weighting of CA records were used to improve prediction performance. RESULTS With the multitask learning setting in the model learning process, we achieved an area under the receiver operating characteristic of 0.752 for CA-mortality, 0.711 for ALL-mortality, 0.852 for CA-readmission, and 0.889 for ALL-readmission. The area under the receiver operating characteristic was improved to 0.808 for CA-mortality and 0.862 for CA-readmission after solving the extremely imbalanced issue for CA-mortality/CA-readmission by upsampling and weighting. CONCLUSIONS This study demonstrated the potential of predicting future outcomes for IHCA survivors by machine learning. The results showed that our proposed approach could effectively alleviate data imbalance problems and train a better model for outcome prediction.

scholarly journals Transfer learning with chest X-rays for ER patient classification

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jonathan Stubblefield ◽  
Mitchell Hervert ◽  
Jason L. Causey ◽  
Jake A. Qualls ◽  
Wei Dong ◽  
...  
Keyword(s):  
Deep Learning ◽  
Current Model ◽  
Image Data ◽  
Learning Model ◽  
Image Features ◽  
Clinical Feature ◽  
Patient Classification ◽  
X Rays ◽  
Data Set ◽  
Deep Learning Model

AbstractOne of the challenges with urgent evaluation of patients with acute respiratory distress syndrome (ARDS) in the emergency room (ER) is distinguishing between cardiac vs infectious etiologies for their pulmonary findings. We conducted a retrospective study with the collected data of 171 ER patients. ER patient classification for cardiac and infection causes was evaluated with clinical data and chest X-ray image data. We show that a deep-learning model trained with an external image data set can be used to extract image features and improve the classification accuracy of a data set that does not contain enough image data to train a deep-learning model. An analysis of clinical feature importance was performed to identify the most important clinical features for ER patient classification. The current model is publicly available with an interface at the web link: http://nbttranslationalresearch.org/.

scholarly journals Mobile Deep Learning System That Calculates UVI Using Illuminance Value of User’s Location

Sensors ◽  
2021 ◽  
Vol 21 (4) ◽  
pp. 1227
Author(s):  
Seung-Taek Oh ◽  
Deog-Hyeon Ga ◽  
Jae-Hyun Lim
Keyword(s):  
Deep Learning ◽  
Mobile Devices ◽  
Mobile Device ◽  
Local Level ◽  
Learning Model ◽  
Learning System ◽  
Ultraviolet Rays ◽  
Optimum Number ◽  
Data Set ◽  
Deep Learning Model

Ultraviolet rays are closely related with human health and, recently, optimum exposure to the UV rays has been recommended, with growing importance being placed on correct UV information. However, many countries provide UV information services at a local level, which makes it impossible for individuals to acquire user-based, accurate UV information unless individuals operate UV measurement devices with expertise on the relevant field for interpretation of the measurement results. There is a limit in measuring ultraviolet rays’ information by the users at their respective locations. Research about how to utilize mobile devices such as smartphones to overcome such limitation is also lacking. This paper proposes a mobile deep learning system that calculates UVI based on the illuminance values at the user’s location obtained with mobile devices’ help. The proposed method analyzed the correlation between illuminance and UVI based on the natural light DB collected through the actual measurements, and the deep learning model’s data set was extracted. After the selection of the input variables to calculate the correct UVI, the deep learning model based on the TensorFlow set with the optimum number of layers and number of nodes was designed and implemented, and learning was executed via the data set. After the data set was converted to the mobile deep learning model to operate under the mobile environment, the converted data were loaded on the mobile device. The proposed method enabled providing UV information at the user’s location through a mobile device on which the illuminance sensors were loaded even in the environment without UVI measuring equipment. The comparison of the experiment results with the reference device (spectrometer) proved that the proposed method could provide UV information with an accuracy of 90–95% in the summers, as well as in winters.

A Multi-attention Collaborative Deep Learning Approach for Blood Pressure Prediction

2022 ◽  
Vol 13 (2) ◽  
pp. 1-20
Author(s):  
Luo He ◽  
Hongyan Liu ◽  
Yinghui Yang ◽  
Bei Wang
Keyword(s):  
Blood Pressure ◽  
Deep Learning ◽  
Physical Examination ◽  
Short Term Memory ◽  
Learning Model ◽  
Natural Setting ◽  
Data Set ◽  
Health Related ◽  
Common Items ◽  
Deep Learning Model

We develop a deep learning model based on Long Short-term Memory (LSTM) to predict blood pressure based on a unique data set collected from physical examination centers capturing comprehensive multi-year physical examination and lab results. In the Multi-attention Collaborative Deep Learning model (MAC-LSTM) we developed for this type of data, we incorporate three types of attention to generate more explainable and accurate results. In addition, we leverage information from similar users to enhance the predictive power of the model due to the challenges with short examination history. Our model significantly reduces predictive errors compared to several state-of-the-art baseline models. Experimental results not only demonstrate our model’s superiority but also provide us with new insights about factors influencing blood pressure. Our data is collected in a natural setting instead of a setting designed specifically to study blood pressure, and the physical examination items used to predict blood pressure are common items included in regular physical examinations for all the users. Therefore, our blood pressure prediction results can be easily used in an alert system for patients and doctors to plan prevention or intervention. The same approach can be used to predict other health-related indexes such as BMI.

Hybrid Deep Learning Model For Diagnosis Of Covid-19 Using Ct Scans And Clinical/Demographic Data

2021 ◽  
Author(s):  
Parnian Afshar ◽  
Shahin Heidarian ◽  
Farnoosh Naderkhani ◽  
Moezedin Javad Rafiee ◽  
Anastasia Oikonomou ◽  
...  
Keyword(s):  
Deep Learning ◽  
Demographic Data ◽  
Learning Model ◽  
Ct Scans ◽  
Deep Learning Model

scholarly journals Detection of invisible cracks in ceramic materials using by pre-trained deep convolutional neural network

2021 ◽  
Author(s):  
Hidir Selcuk Nogay ◽  
Tahir Cetin Akinci ◽  
Musa Yilmaz
Keyword(s):  
Deep Learning ◽  
Crack Detection ◽  
Acoustic Noise ◽  
Ceramic Materials ◽  
Learning Model ◽  
Ceramic Plate ◽  
Data Set ◽  
Model Based ◽  
Noise Data ◽  
Deep Learning Model

AbstractCeramic materials are an indispensable part of our lives. Today, ceramic materials are mainly used in construction and kitchenware production. The fact that some deformations cannot be seen with the naked eye in the ceramic industry leads to a loss of time in the detection of deformations in the products. Delays that may occur in the elimination of deformations and in the planning of the production process cause the products with deformation to be excessive, which adversely affects the quality. In this study, a deep learning model based on acoustic noise data and transfer learning techniques was designed to detect cracks in ceramic plates. In order to create a data set, noise curves were obtained by applying the same magnitude impact to the ceramic experiment plates by impact pendulum. For experimental application, ceramic plates with three invisible cracks and one undamaged ceramic plate were used. The deep learning model was trained and tested for crack detection in ceramic plates by the data set obtained from the noise graphs. As a result, 99.50% accuracy was achieved with the deep learning model based on acoustic noise.

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