scholarly journals Discriminating pseudoprogression and true progression in diffuse infiltrating glioma using multi-parametric MRI data through deep learning

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Joonsang Lee ◽  
Nicholas Wang ◽  
Sevcan Turk ◽  
Shariq Mohammed ◽  
Remy Lobo ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Tumor Progression ◽  
Sequence Data ◽  
Training Dataset ◽  
Post Contrast ◽  
Glioma Recurrence ◽  
Mri Sequences ◽  
The Mean ◽  
Pass Through

AbstractDifferentiating pseudoprogression from true tumor progression has become a significant challenge in follow-up of diffuse infiltrating gliomas, particularly high grade, which leads to a potential treatment delay for patients with early glioma recurrence. In this study, we proposed to use a multiparametric MRI data as a sequence input for the convolutional neural network with the recurrent neural network based deep learning structure to discriminate between pseudoprogression and true tumor progression. In this study, 43 biopsy-proven patient data identified as diffuse infiltrating glioma patients whose disease progressed/recurred were used. The dataset consists of five original MRI sequences; pre-contrast T1-weighted, post-contrast T1-weighted, T2-weighted, FLAIR, and ADC images as well as two engineered sequences; T1post–T1pre and T2–FLAIR. Next, we used three CNN-LSTM models with a different set of sequences as input sequences to pass through CNN-LSTM layers. We performed threefold cross-validation in the training dataset and generated the boxplot, accuracy, and ROC curve, AUC from each trained model with the test dataset to evaluate models. The mean accuracy for VGG16 models ranged from 0.44 to 0.60 and the mean AUC ranged from 0.47 to 0.59. For CNN-LSTM model, the mean accuracy ranged from 0.62 to 0.75 and the mean AUC ranged from 0.64 to 0.81. The performance of the proposed CNN-LSTM with multiparametric sequence data was found to outperform the popular convolutional CNN with a single MRI sequence. In conclusion, incorporating all available MRI sequences into a sequence input for a CNN-LSTM model improved diagnostic performance for discriminating between pseudoprogression and true tumor progression.

scholarly journals Effectiveness of transfer learning for enhancing tumor classification with a convolutional neural network on frozen sections

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Young-Gon Kim ◽  
Sungchul Kim ◽  
Cristina Eunbee Cho ◽  
In Hye Song ◽  
Hee Jin Lee ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Transfer Learning ◽  
Frozen Section ◽  
Medical Center ◽  
External Validation ◽  
Model Performance ◽  
Classification Model ◽  
Training Dataset

AbstractFast and accurate confirmation of metastasis on the frozen tissue section of intraoperative sentinel lymph node biopsy is an essential tool for critical surgical decisions. However, accurate diagnosis by pathologists is difficult within the time limitations. Training a robust and accurate deep learning model is also difficult owing to the limited number of frozen datasets with high quality labels. To overcome these issues, we validated the effectiveness of transfer learning from CAMELYON16 to improve performance of the convolutional neural network (CNN)-based classification model on our frozen dataset (N = 297) from Asan Medical Center (AMC). Among the 297 whole slide images (WSIs), 157 and 40 WSIs were used to train deep learning models with different dataset ratios at 2, 4, 8, 20, 40, and 100%. The remaining, i.e., 100 WSIs, were used to validate model performance in terms of patch- and slide-level classification. An additional 228 WSIs from Seoul National University Bundang Hospital (SNUBH) were used as an external validation. Three initial weights, i.e., scratch-based (random initialization), ImageNet-based, and CAMELYON16-based models were used to validate their effectiveness in external validation. In the patch-level classification results on the AMC dataset, CAMELYON16-based models trained with a small dataset (up to 40%, i.e., 62 WSIs) showed a significantly higher area under the curve (AUC) of 0.929 than those of the scratch- and ImageNet-based models at 0.897 and 0.919, respectively, while CAMELYON16-based and ImageNet-based models trained with 100% of the training dataset showed comparable AUCs at 0.944 and 0.943, respectively. For the external validation, CAMELYON16-based models showed higher AUCs than those of the scratch- and ImageNet-based models. Model performance for slide feasibility of the transfer learning to enhance model performance was validated in the case of frozen section datasets with limited numbers.

scholarly journals Orchard Mapping with Deep Learning Semantic Segmentation

Sensors ◽  
2021 ◽  
Vol 21 (11) ◽  
pp. 3813
Author(s):  
Athanasios Anagnostis ◽  
Aristotelis C. Tagarakis ◽  
Dimitrios Kateris ◽  
Vasileios Moysiadis ◽  
Claus Grøn Sørensen ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Semantic Segmentation ◽  
Automated Detection ◽  
Aerial Images ◽  
Training Dataset ◽  
Field Boundary ◽  
Different Seasons ◽  
Detection And Localization ◽  
Different Levels

This study aimed to propose an approach for orchard trees segmentation using aerial images based on a deep learning convolutional neural network variant, namely the U-net network. The purpose was the automated detection and localization of the canopy of orchard trees under various conditions (i.e., different seasons, different tree ages, different levels of weed coverage). The implemented dataset was composed of images from three different walnut orchards. The achieved variability of the dataset resulted in obtaining images that fell under seven different use cases. The best-trained model achieved 91%, 90%, and 87% accuracy for training, validation, and testing, respectively. The trained model was also tested on never-before-seen orthomosaic images or orchards based on two methods (oversampling and undersampling) in order to tackle issues with out-of-the-field boundary transparent pixels from the image. Even though the training dataset did not contain orthomosaic images, it achieved performance levels that reached up to 99%, demonstrating the robustness of the proposed approach.

scholarly journals Automatic Handgun Detection with Deep Learning in Video Surveillance Images

2021 ◽  
Vol 11 (13) ◽  
pp. 6085
Author(s):  
Jesus Salido ◽  
Vanesa Lomas ◽  
Jesus Ruiz-Santaquiteria ◽  
Oscar Deniz
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Video Surveillance ◽  
Automatic Detection ◽  
Public Spaces ◽  
Detection Methods ◽  
Training Dataset ◽  
Average Precision ◽  
Terrorist Acts

There is a great need to implement preventive mechanisms against shootings and terrorist acts in public spaces with a large influx of people. While surveillance cameras have become common, the need for monitoring 24/7 and real-time response requires automatic detection methods. This paper presents a study based on three convolutional neural network (CNN) models applied to the automatic detection of handguns in video surveillance images. It aims to investigate the reduction of false positives by including pose information associated with the way the handguns are held in the images belonging to the training dataset. The results highlighted the best average precision (96.36%) and recall (97.23%) obtained by RetinaNet fine-tuned with the unfrozen ResNet-50 backbone and the best precision (96.23%) and F1 score values (93.36%) obtained by YOLOv3 when it was trained on the dataset including pose information. This last architecture was the only one that showed a consistent improvement—around 2%—when pose information was expressly considered during training.

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Encoding Health Records into Pathway Representations for Deep Learning

2021 ◽  
Author(s):  
Marco Luca Sbodio ◽  
Natasha Mulligan ◽  
Stefanie Speichert ◽  
Vanessa Lopez ◽  
Joao Bettencourt-Silva
Keyword(s):  
Neural Network ◽  
Machine Learning ◽  
Deep Learning ◽  
Source Code ◽  
Training Dataset ◽  
Health Records ◽  
Learning Tasks ◽  
Patient Pathways ◽  
Computational Resources ◽  
The Impact

There is a growing trend in building deep learning patient representations from health records to obtain a comprehensive view of a patient’s data for machine learning tasks. This paper proposes a reproducible approach to generate patient pathways from health records and to transform them into a machine-processable image-like structure useful for deep learning tasks. Based on this approach, we generated over a million pathways from FAIR synthetic health records and used them to train a convolutional neural network. Our initial experiments show the accuracy of the CNN on a prediction task is comparable or better than other autoencoders trained on the same data, while requiring significantly less computational resources for training. We also assess the impact of the size of the training dataset on autoencoders performances. The source code for generating pathways from health records is provided as open source.

scholarly journals A Deep Learning-Based Approach for the Detection of Early Signs of Gingivitis in Orthodontic Patients Using Faster Region-Based Convolutional Neural Networks

2020 ◽  
Vol 17 (22) ◽  
pp. 8447
Author(s):  
Dima M. Alalharith ◽  
Hajar M. Alharthi ◽  
Wejdan M. Alghamdi ◽  
Yasmine M. Alsenbel ◽  
Nida Aslam ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Periodontal Disease ◽  
Convolutional Neural Network ◽  
Region Of Interest ◽  
Training Dataset ◽  
Detection Accuracy ◽  
Detection Model ◽  
Art Object ◽  
Orthodontic Patients

Computer-based technologies play a central role in the dentistry field, as they present many methods for diagnosing and detecting various diseases, such as periodontitis. The current study aimed to develop and evaluate the state-of-the-art object detection and recognition techniques and deep learning algorithms for the automatic detection of periodontal disease in orthodontic patients using intraoral images. In this study, a total of 134 intraoral images were divided into a training dataset (n = 107 [80%]) and a test dataset (n = 27 [20%]). Two Faster Region-based Convolutional Neural Network (R-CNN) models using ResNet-50 Convolutional Neural Network (CNN) were developed. The first model detects the teeth to locate the region of interest (ROI), while the second model detects gingival inflammation. The detection accuracy, precision, recall, and mean average precision (mAP) were calculated to verify the significance of the proposed model. The teeth detection model achieved an accuracy, precision, recall, and mAP of 100 %, 100%, 51.85%, and 100%, respectively. The inflammation detection model achieved an accuracy, precision, recall, and mAP of 77.12%, 88.02%, 41.75%, and 68.19%, respectively. This study proved the viability of deep learning models for the detection and diagnosis of gingivitis in intraoral images. Hence, this highlights its potential usability in the field of dentistry and aiding in reducing the severity of periodontal disease globally through preemptive non-invasive diagnosis.

scholarly journals A Fortran-Keras Deep Learning Bridge for Scientific Computing

2020 ◽  
Vol 2020 ◽  
pp. 1-13 ◽  
Author(s):  
Jordan Ott ◽  
Mike Pritchard ◽  
Natalie Best ◽  
Erik Linstead ◽  
Milan Curcic ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Large Scale ◽  
Climate Model ◽  
Emergent Behavior ◽  
Training Dataset ◽  
Climate Simulation ◽  
Network Architectures ◽  
Efficient Computation ◽  
Radiation Physics

Implementing artificial neural networks is commonly achieved via high-level programming languages such as Python and easy-to-use deep learning libraries such as Keras. These software libraries come preloaded with a variety of network architectures, provide autodifferentiation, and support GPUs for fast and efficient computation. As a result, a deep learning practitioner will favor training a neural network model in Python, where these tools are readily available. However, many large-scale scientific computation projects are written in Fortran, making it difficult to integrate with modern deep learning methods. To alleviate this problem, we introduce a software library, the Fortran-Keras Bridge (FKB). This two-way bridge connects environments where deep learning resources are plentiful with those where they are scarce. The paper describes several unique features offered by FKB, such as customizable layers, loss functions, and network ensembles. The paper concludes with a case study that applies FKB to address open questions about the robustness of an experimental approach to global climate simulation, in which subgrid physics are outsourced to deep neural network emulators. In this context, FKB enables a hyperparameter search of one hundred plus candidate models of subgrid cloud and radiation physics, initially implemented in Keras, to be transferred and used in Fortran. Such a process allows the model’s emergent behavior to be assessed, i.e., when fit imperfections are coupled to explicit planetary-scale fluid dynamics. The results reveal a previously unrecognized strong relationship between offline validation error and online performance, in which the choice of the optimizer proves unexpectedly critical. This in turn reveals many new neural network architectures that produce considerable improvements in climate model stability including some with reduced error, for an especially challenging training dataset.

Development and external validation of a deep learning model for predicting response to HER2-targeted neoadjuvant therapy from pretreatment breast MRI.

2019 ◽  
Vol 37 (15_suppl) ◽  
pp. 593-593 ◽  
Author(s):  
Manasa Vulchi ◽  
Mohammed El Adoui ◽  
Nathaniel Braman ◽  
Paulette Turk ◽  
Maryam Etesami ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Validation Cohort ◽  
Superior Performance ◽  
Receptor Subtype ◽  
Post Contrast ◽  
Internal Validation ◽  
Her2 Breast Cancer ◽  
Contrast Enhanced ◽  
Pre Treatment

593 Background: HER2-targeted neoadjuvant chemotherapy (NAC) possesses heterogeneous outcomes and currently lacks clinically-accepted markers of response. A means of predicting which patients will benefit prior to the treatment could reduce toxicity and the delay to effective intervention. Computational analysis of MRI via a deep neural network has shown promise in identifying NAC responders among mixed receptor subtype and treatment regimen cohorts, but faces challenges due to reproducibility across institutions and has not yet been explored in the context of HER2-targeted therapy. Here we present a deep learning approach for predicting response to HER2-targeted NAC from pre-treatment MRI. Methods: 100 HER2+ breast cancer patients who received NAC with docetaxel, carboplatin, trastuzumab, and pertuzumab at Cleveland Clinic (CCF) and had pre-treatment contrast-enhanced MRI’s were included in this analysis. 49 patients achieved pathological complete response (pCR, ypT0/is), while 51 patients retained presence of residual disease following NAC (non-pCR). 85 patients were used to train a convolutional neural network to predict pCR based on pre- and post-contrast MRI images, and the model design was optimized based on performance within a 15 patient internal validation cohort. An external, held-out testing dataset consisting of 28 patients (16 pCR, 12 non-pCR) imaged and treated at University Hospitals (UH) Cleveland Medical Center was used to validate the performance of the model. Performance was assessed by area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity. A multivariable model incorporating age, hormone receptor status, stage, and tumor size was developed and similarly evaluated. Results: The neural network was able to predict the response to HER2-targeted NAC in the internal validation cohort (AUC = 0.93) as well as in an independent cohort from a separate institution (AUC = 0.85). This model offered superior performance compared to a multivariate clinical model, which achieved AUC = 0.67 and AUC = 0.52, in internal validation and external held-out testing cohorts, respectively. Conclusions: Deep learning analysis of contrast-enhanced MRI could be used to better target anti-HER2 therapy by pre-treatment prediction of response.[Table: see text]

scholarly journals Covid-19 detection via deep neural network and occlusion sensitivity maps

2021 ◽  
Author(s):  
Noor Ahmad ◽  
Muhammad Aminu ◽  
Mohd Halim Mohd Noor
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Deep Neural Network ◽  
State Of The Art ◽  
Color Images ◽  
Fine Tuning ◽  
Training Dataset ◽  
Learning Approaches ◽  
Learning Models ◽  
Sensitivity Maps

Deep learning approaches have attracted a lot of attention in the automatic detection of Covid-19 and transfer learning is the most common approach. However, majority of the pre-trained models are trained on color images, which can cause inefficiencies when fine-tuning the models on Covid-19 images which are often grayscale. To address this issue, we propose a deep learning architecture called CovidNet which requires a relatively smaller number of parameters. CovidNet accepts grayscale images as inputs and is suitable for training with limited training dataset. Experimental results show that CovidNet outperforms other state-of-the-art deep learning models for Covid-19 detection.

scholarly journals Development of a generative adversarial neural network for identification of potential HIV-1 inhibitors by deep learning methods

Informatics ◽  
2020 ◽  
Vol 17 (1) ◽  
pp. 7-17
Author(s):  
G. I. Nikolaev ◽  
N. A. Shuldov ◽  
A. I. Anishenko, ◽  
A. V. Tuzikov ◽  
A. M. Andrianov
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Rational Design ◽  
Binding Free Energy ◽  
Viral Envelope ◽  
Training Dataset ◽  
Learning Methods ◽  
The Neural Network ◽  
Wide Range ◽  
Hiv 1

A generative adversarial autoencoder for the rational design of potential HIV-1 entry inhibitors able to block the region of the viral envelope protein gp120 critical for the virus binding to cellular receptor CD4 was developed using deep learning methods. The research were carried out to create the  architecture of the neural network, to form  virtual compound library of potential anti-HIV-1 agents for training the neural network, to make  molecular docking of all compounds from this library with gp120, to  calculate the values of binding free energy, to generate molecular fingerprints for chemical compounds from the training dataset. The training the neural network was implemented followed by estimation of the learning outcomes and work of the autoencoder.  The validation of the neural network on a wide range of compounds from the ZINC database was carried out. The use of the neural network in combination with virtual screening of chemical databases was shown to form a productive platform for identifying the basic structures promising for the design of novel antiviral drugs that inhibit the early stages of HIV infection.

Sign in / Sign up

Export Citation Format

Share Document