Multi-model Ensemble Learning Architecture Based on 3D CNN for Lung Nodule Malignancy Suspiciousness Classification.
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ABSTRACT:
SUBMITTER: Liu H
PROVIDER: S-EPMC7649841 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundChest Computed tomography (CT) scans detect lung nodules and assess pulmonary fibrosis. While pulmonary fibrosis indicates increased lung cancer risk, current clinical practice characterizes nodule risk of malignancy based on nodule size and smoking history; little consideration is given to the fibrotic microenvironment.PurposeTo evaluate the effect of incorporating fibrotic microenvironment into classifying malignancy of lung nodules in chest CT images using deep learning techniques.Materials and methodsWe developed a visualizable 3D classification model trained with in-house CT dataset for the nodule malignancy classification task. Three slightly-modified datasets were created: (1) nodule alone (microenvironment removed); (2) nodule with surrounding lung microenvironment; and (3) nodule in microenvironment with semantic fibrosis metadata. For each of the models, tenfold cross-validation was performed. Results were evaluated using quantitative measures, such as accuracy, sensitivity, specificity, and area-under-curve (AUC), as well as qualitative assessments, such as attention maps and class activation maps (CAM).ResultsThe classification model trained with nodule alone achieved 75.61% accuracy, 50.00% sensitivity, 88.46% specificity, and 0.78 AUC; the model trained with nodule and microenvironment achieved 79.03% accuracy, 65.46% sensitivity, 85.86% specificity, and 0.84 AUC. The model trained with additional semantic fibrosis metadata achieved 80.84% accuracy, 74.67% sensitivity, 84.95% specificity, and 0.89 AUC. Our visual evaluation of attention maps and CAM suggested that both the nodules and the microenvironment contributed to the task.ConclusionThe nodule malignancy classification performance was found to be improving with microenvironment data. Further improvement was found when incorporating semantic fibrosis information.
| S-EPMC10787502 | biostudies-literature
Project description:Dependence on the internet and computer programs demonstrates the significance of computer programs in our day-to-day lives. Such demands motivate malware developers to create more malware, both in terms of quantity and variety. Researchers are constantly faced with hurdles while attempting to protect themselves from potential hazards and risks due to malware authors' usage of code obfuscation techniques. Metamorphic and polymorphic variations are easily able to elude the widely utilized signature-based detection procedures. Researchers are more interested in deep learning approaches than machine learning techniques to analyze the behavior of such a vast number of virus variants. Researchers have been drawn to the categorization of malware within itself in addition to the classification of malware against benign programs to examine the behavioral differences between them. In order to investigate the relationship between the application programming interface (API) calls throughout API sequences and classify them, this work uses the one-dimensional convolutional neural network (1D-CNN) model to solve a multiclass classification problem. On API sequences, feature vectors for distinctive APIs are created using the Word2Vec word embedding approach and the skip-gram model. The one-vs.-rest approach is used to train 1D-CNN models to categorize malware, and all of them are then combined with a suggested ModifiedSoftVoting algorithm to improve classification. On the open benchmark dataset Mal-API-2019, the suggested ensembled 1D-CNN architecture captures improved evaluation scores with an accuracy of 0.90, a weighted average F1-score of 0.90, and an AUC score of more than 0.96 for all classes of malware.
| S-EPMC10702937 | biostudies-literature
Project description:The clinical management of patients with indeterminate pulmonary nodules is associated with unintended harm to patients and better methods are required to more precisely quantify lung cancer risk in this group. Here, we combine multiple noninvasive approaches to more accurately identify lung cancer in indeterminate pulmonary nodules. We analyzed 94 quantitative radiomic imaging features and 41 qualitative semantic imaging variables with molecular biomarkers from blood derived from an antibody-based microarray platform that determines protein, cancer-specific glycan, and autoantibody-antigen complex content with high sensitivity. From these datasets, we created a PSR (plasma, semantic, radiomic) risk prediction model comprising nine blood-based and imaging biomarkers with an area under the receiver operating curve (AUROC) of 0.964 that when tested in a second, independent cohort yielded an AUROC of 0.846. Incorporating known clinical risk factors (age, gender, and smoking pack years) for lung cancer into the PSR model improved the AUROC to 0.897 in the second cohort and was more accurate than a well-characterized clinical risk prediction model (AUROC = 0.802). Our findings support the use of a multi-omics approach to guide the clinical management of indeterminate pulmonary nodules.
| S-EPMC10341085 | biostudies-literature
Project description:This paper aims to identify uncommon cardiothoracic diseases and patterns on chest X-ray images. Training a machine learning model to classify rare diseases with multi-label indications is challenging without sufficient labeled training samples. Our model leverages the information from common diseases and adapts to perform on less common mentions. We propose to use multi-label few-shot learning (FSL) schemes including neighborhood component analysis loss, generating additional samples using distribution calibration and fine-tuning based on multi-label classification loss. We utilize the fact that the widely adopted nearest neighbor-based FSL schemes like ProtoNet are Voronoi diagrams in feature space. In our method, the Voronoi diagrams in the features space generated from multi-label schemes are combined into our geometric DeepVoro Multi-label ensemble. The improved performance in multi-label few-shot classification using the multi-label ensemble is demonstrated in our experiments (The code is publicly available at https://github.com/Saurabh7/Few-shot-learning-multilabel-cxray).
| S-EPMC9652771 | biostudies-literature
Project description:MotivationAnti-cancer drug sensitivity prediction using deep learning models for individual cell line is a significant challenge in personalized medicine. Recently developed REFINED (REpresentation of Features as Images with NEighborhood Dependencies) CNN (Convolutional Neural Network)-based models have shown promising results in improving drug sensitivity prediction. The primary idea behind REFINED-CNN is representing high dimensional vectors as compact images with spatial correlations that can benefit from CNN architectures. However, the mapping from a high dimensional vector to a compact 2D image depends on the a priori choice of the distance metric and projection scheme with limited empirical procedures guiding these choices.ResultsIn this article, we consider an ensemble of REFINED-CNN built under different choices of distance metrics and/or projection schemes that can improve upon a single projection based REFINED-CNN model. Results, illustrated using NCI60 and NCI-ALMANAC databases, demonstrate that the ensemble approaches can provide significant improvement in prediction performance as compared to individual models. We also develop the theoretical framework for combining different distance metrics to arrive at a single 2D mapping. Results demonstrated that distance-averaged REFINED-CNN produced comparable performance as obtained from stacking REFINED-CNN ensemble but with significantly lower computational cost.Availability and implementationThe source code, scripts, and data used in the paper have been deposited in GitHub (https://github.com/omidbazgirTTU/IntegratedREFINED).Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC8275339 | biostudies-literature
Project description:Convolutional neural network is widely used to perform the task of image classification, including pretraining, followed by fine-tuning whereby features are adapted to perform the target task, on ImageNet. ImageNet is a large database consisting of 15 million images belonging to 22,000 categories. Images collected from the Web are labeled using Amazon Mechanical Turk crowd-sourcing tool by human labelers. ImageNet is useful for transfer learning because of the sheer volume of its dataset and the number of object classes available. Transfer learning using pretrained models is useful because it helps to build computer vision models in an accurate and inexpensive manner. Models that have been pretrained on substantial datasets are used and repurposed for our requirements. Scene recognition is a widely used application of computer vision in many communities and industries, such as tourism. This study aims to show multilabel scene classification using five architectures, namely, VGG16, VGG19, ResNet50, InceptionV3, and Xception using ImageNet weights available in the Keras library. The performance of different architectures is comprehensively compared in the study. Finally, EnsemV3X is presented in this study. The proposed model with reduced number of parameters is superior to state-of-of-the-art models Inception and Xception because it demonstrates an accuracy of 91%.
| S-EPMC8176534 | biostudies-literature
Project description:BackgroundLow-dose CT screening can reduce lung cancer-related mortality. However, most screen-detected pulmonary abnormalities do not develop into cancer and it often remains challenging to identify malignant nodules, particularly among indeterminate nodules. We aimed to develop and assess prediction models based on radiological features to discriminate between benign and malignant pulmonary lesions detected on a baseline screen.MethodsUsing four international lung cancer screening studies, we extracted 2060 radiomic features for each of 16 797 nodules (513 malignant) among 6865 participants. After filtering out low-quality radiomic features, 642 radiomic and 9 epidemiological features remained for model development. We used cross-validation and grid search to assess three machine learning (ML) models (eXtreme Gradient Boosted Trees, random forest, least absolute shrinkage and selection operator (LASSO)) for their ability to accurately predict risk of malignancy for pulmonary nodules. We report model performance based on the area under the curve (AUC) and calibration metrics in the held-out test set.ResultsThe LASSO model yielded the best predictive performance in cross-validation and was fit in the full training set based on optimised hyperparameters. Our radiomics model had a test-set AUC of 0.93 (95% CI 0.90 to 0.96) and outperformed the established Pan-Canadian Early Detection of Lung Cancer model (AUC 0.87, 95% CI 0.85 to 0.89) for nodule assessment. Our model performed well among both solid (AUC 0.93, 95% CI 0.89 to 0.97) and subsolid nodules (AUC 0.91, 95% CI 0.85 to 0.95).ConclusionsWe developed highly accurate ML models based on radiomic and epidemiological features from four international lung cancer screening studies that may be suitable for assessing indeterminate screen-detected pulmonary nodules for risk of malignancy.
| S-EPMC10947877 | biostudies-literature
Project description:The current approach to diagnosing and classifying brain tumors relies on the histological evaluation of biopsy samples, which is invasive, time-consuming, and susceptible to manual errors. These limitations underscore the pressing need for a fully automated, deep-learning-based multi-classification system for brain malignancies. This article aims to leverage a deep convolutional neural network (CNN) to enhance early detection and presents three distinct CNN models designed for different types of classification tasks. The first CNN model achieves an impressive detection accuracy of 99.53% for brain tumors. The second CNN model, with an accuracy of 93.81%, proficiently categorizes brain tumors into five distinct types: normal, glioma, meningioma, pituitary, and metastatic. Furthermore, the third CNN model demonstrates an accuracy of 98.56% in accurately classifying brain tumors into their different grades. To ensure optimal performance, a grid search optimization approach is employed to automatically fine-tune all the relevant hyperparameters of the CNN models. The utilization of large, publicly accessible clinical datasets results in robust and reliable classification outcomes. This article conducts a comprehensive comparison of the proposed models against classical models, such as AlexNet, DenseNet121, ResNet-101, VGG-19, and GoogleNet, reaffirming the superiority of the deep CNN-based approach in advancing the field of brain tumor classification and early detection.
| S-EPMC10799524 | biostudies-literature
Project description:We investigate the predictive performance of two novel CNN-DNN machine learning ensemble models in predicting county-level corn yields across the US Corn Belt (12 states). The developed data set is a combination of management, environment, and historical corn yields from 1980 to 2019. Two scenarios for ensemble creation are considered: homogenous and heterogenous ensembles. In homogenous ensembles, the base CNN-DNN models are all the same, but they are generated with a bagging procedure to ensure they exhibit a certain level of diversity. Heterogenous ensembles are created from different base CNN-DNN models which share the same architecture but have different hyperparameters. Three types of ensemble creation methods were used to create several ensembles for either of the scenarios: Basic Ensemble Method (BEM), Generalized Ensemble Method (GEM), and stacked generalized ensembles. Results indicated that both designed ensemble types (heterogenous and homogenous) outperform the ensembles created from five individual ML models (linear regression, LASSO, random forest, XGBoost, and LightGBM). Furthermore, by introducing improvements over the heterogenous ensembles, the homogenous ensembles provide the most accurate yield predictions across US Corn Belt states. This model could make 2019 yield predictions with a root mean square error of 866 kg/ha, equivalent to 8.5% relative root mean square and could successfully explain about 77% of the spatio-temporal variation in the corn grain yields. The significant predictive power of this model can be leveraged for designing a reliable tool for corn yield prediction which will in turn assist agronomic decision makers.
| S-EPMC8364956 | biostudies-literature
Project description:The real cause of breast cancer is very challenging to determine and therefore early detection of the disease is necessary for reducing the death rate due to risks of breast cancer. Early detection of cancer boosts increasing the survival chance up to 8%. Primarily, breast images emanating from mammograms, X-Rays or MRI are analyzed by radiologists to detect abnormalities. However, even experienced radiologists face problems in identifying features like micro-calcifications, lumps and masses, leading to high false positive and high false negative. Recent advancement in image processing and deep learning create some hopes in devising more enhanced applications that can be used for the early detection of breast cancer. In this work, we have developed a Deep Convolutional Neural Network (CNN) to segment and classify the various types of breast abnormalities, such as calcifications, masses, asymmetry and carcinomas, unlike existing research work, which mainly classified the cancer into benign and malignant, leading to improved disease management. Firstly, a transfer learning was carried out on our dataset using the pre-trained model ResNet50. Along similar lines, we have developed an enhanced deep learning model, in which learning rate is considered as one of the most important attributes while training the neural network. The learning rate is set adaptively in our proposed model based on changes in error curves during the learning process involved. The proposed deep learning model has achieved a performance of 88% in the classification of these four types of breast cancer abnormalities such as, masses, calcifications, carcinomas and asymmetry mammograms.
| S-EPMC8389446 | biostudies-literature