Deep learning-based image classification of turtles imported into Korea
Ontology highlight
ABSTRACT:
SUBMITTER: Baek J
PROVIDER: S-EPMC10709346 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:Accurate cancer type classification based on genetic mutation can significantly facilitate cancer-related diagnosis. However, existing methods usually use feature selection combined with simple classifiers to quantify key mutated genes, resulting in poor classification performance. To circumvent this problem, a novel image-based deep learning strategy is employed to distinguish different types of cancer. Unlike conventional methods, we first convert gene mutation data containing single nucleotide polymorphisms, insertions and deletions into a genetic mutation map, and then apply the deep learning networks to classify different cancer types based on the mutation map. We outline these methods and present results obtained in training VGG-16, Inception-v3, ResNet-50 and Inception-ResNet-v2 neural networks to classify 36 types of cancer from 9047 patient samples. Our approach achieves overall higher accuracy (over 95%) compared with other widely adopted classification methods. Furthermore, we demonstrate the application of a Guided Grad-CAM visualization to generate heatmaps and identify the top-ranked tumor-type-specific genes and pathways. Experimental results on prostate and breast cancer demonstrate our method can be applied to various types of cancer. Powered by the deep learning, this approach can potentially provide a new solution for pan-cancer classification and cancer driver gene discovery. The source code and datasets supporting the study is available at https://github.com/yetaoyu/Genomic-pan-cancer-classification.
| S-EPMC7848437 | biostudies-literature
Project description:While convolutional operation effectively extracts local features, their limited receptive fields make it challenging to capture global dependencies. Transformer, on the other hand, excels at global modeling and effectively captures global dependencies. However, the self-attention mechanism used in Transformers lacks a local mechanism for information exchange within specific regions. This article attempts to leverage the strengths of both Transformers and convolutional neural networks (CNNs) to enhance the Swin Transformer V2 model. By incorporating both convolutional operation and self-attention mechanism, the enhanced model combines the local information-capturing capability of CNNs and the long-range dependency-capturing ability of Transformers. The improved model enhances the extraction of local information through the introduction of the Swin Transformer Stem, inverted residual feed-forward network, and Dual-Branch Downsampling structure. Subsequently, it models global dependencies using the improved self-attention mechanism. Additionally, downsampling is applied to the attention mechanism's Q and K to reduce computational and memory overhead. Under identical training conditions, the proposed method significantly improves classification accuracy on multiple image classification datasets, showcasing more robust generalization capabilities.
| S-EPMC10703013 | biostudies-literature
Project description:PurposeVision impairment affects 2.2 billion people worldwide, half of which is preventable with early detection and treatment. Currently, automatic screening of ocular pathologies using convolutional neural networks (CNNs) on retinal fundus photographs is limited to a few pathologies. Simultaneous detection of multiple ophthalmic pathologies would increase clinical usability and uptake.MethodsTwo thousand five hundred sixty images were used from the Retinal Fundus Multi-Disease Image Dataset (RFMiD). Models were trained (n = 1920) and validated (n = 640). Five selected CNN architectures were trained to predict the presence of any pathology and categorize the 28 pathologies. All models were trained to minimize asymmetric loss, a modified form of binary cross-entropy. Individual model predictions were averaged to obtain a final ensembled model and assessed for mean area under the receiver-operator characteristic curve (AUROC) for disease screening (healthy versus pathologic image) and classification (AUROC for each class).ResultsThe ensemble network achieved a disease screening (healthy versus pathologic) AUROC score of 0.9613. The highest single network score was 0.9586 using the SE-ResNeXt architecture. For individual disease classification, the average AUROC score for each class was 0.9295.ConclusionsRetinal fundus images analyzed by an ensemble of CNNs trained to minimize asymmetric loss were effective in detection and classification of ocular pathologies than individual models. External validation is needed to translate machine learning models to diverse clinical contexts.Translational relevanceThis study demonstrates the potential benefit of ensemble-based deep learning methods on improving automatic screening and diagnosis of multiple ocular pathologies from fundoscopy imaging.
| S-EPMC9624270 | biostudies-literature
Project description:Medical image classification is a novel technology that presents a new challenge. It is essential that pathological images are automatically and correctly classified to enable doctors to provide precise treatment. Convolutional neural networks have demonstrated their effectiveness in classifying images in deep learning, which may have dozens or hundreds of layers, to illustrate the relationship between them in terms of their different neural network features. Convolutional layers consisting of small kernels take weights as input and guide them through an activation function as output. The main advantage of using convolutional neural networks (CNNs) instead of traditional neural networks is that they reduce the model parameters for greater accuracy. However, many studies have simply been focused on finding the best CNN model and classification results from a single medical image classification. Therefore, we applied a common deep learning network model in an attempt to identify the best model framework by training and validating different model parameters to classify medical images. After conducting experiments on six publicly available databases of pathological images, including colorectal cancer tissue, chest X-rays, common skin lesions, diabetic retinopathy, pediatric chest X-ray, and breast ultrasound image datasets, we were able to confirm that the recognition accuracy of the Inception V3 method was significantly better than that of other existing deep learning models.
| S-EPMC9600639 | biostudies-literature
Project description:PurposeRecently, a large number of patients with acute ischemic stroke benefited from the use of thrombectomy, a minimally invasive intervention technique for mechanically removing thrombi from the cerebrovasculature. During thrombectomy, 2D digital subtraction angiography (DSA) image sequences are acquired simultaneously from the posterior-anterior and the lateral view to control whether thrombus removal was successful, and to possibly detect newly occluded areas caused by thrombus fragments split from the main thrombus. However, such new occlusions, which would be treatable by thrombectomy, may be overlooked during the intervention. To prevent this, we developed a deep learning-based approach to automatic classification of DSA sequences into thrombus-free and non-thrombus-free sequences.MethodsWe performed a retrospective study based on the single-center DSA data of thrombectomy patients. For classifying the DSA sequences, we applied Long Short-Term Memory or Gated Recurrent Unit networks and combined them with different Convolutional Neural Networks used as feature extractor. These network variants were trained on the DSA data by using five-fold cross-validation. The classification performance was determined on a test data set with respect to the Matthews correlation coefficient (MCC) and the area under the curve (AUC). Finally, we evaluated our models on patient cases, in which overlooking thrombi during thrombectomy had happened.ResultsDepending on the specific model configuration used, we obtained a performance of up to 0.77[Formula: see text]0.94 for the MCC[Formula: see text]AUC, respectively. Additionally, overlooking thrombi could have been prevented in the reported patient cases, as our models would have classified the corresponding DSA sequences correctly.ConclusionOur deep learning-based approach to thrombus identification in DSA sequences yielded high accuracy on our single-center test data set. External validation is now required to investigate the generalizability of our method. As demonstrated, using this new approach may help reduce the incident risk of overlooking thrombi during thrombectomy in the future.
| S-EPMC9463240 | biostudies-literature
Project description:Sleep-stage classification is essential for sleep research. Various automatic judgment programs, including deep learning algorithms using artificial intelligence (AI), have been developed, but have limitations with regard to data format compatibility, human interpretability, cost, and technical requirements. We developed a novel program called GI-SleepNet, generative adversarial network (GAN)-assisted image-based sleep staging for mice that is accurate, versatile, compact, and easy to use. In this program, electroencephalogram and electromyography data are first visualized as images, and then classified into three stages (wake, NREM, and REM) by a supervised image learning algorithm. To increase its accuracy, we adopted GAN and artificially generated fake REM sleep data to equalize the number of stages. This resulted in improved accuracy, and as little as one mouse's data yielded significant accuracy. Due to its image-based nature, the program is easy to apply to data of different formats, different species of animals, and even outside sleep research. Image data can be easily understood; thus, confirmation by experts is easily obtained, even when there are prediction anomalies. As deep learning in image processing is one of the leading fields in AI, numerous algorithms are also available.
| S-EPMC8628800 | biostudies-literature
Project description:This study aimed to develop a deep learning-based image classification model that can differentiate tufted astrocytes (TA), astrocytic plaques (AP), and neuritic plaques (NP) based on images of tissue sections stained with phospho-tau immunohistochemistry. Phospho-tau-immunostained slides from the motor cortex were scanned at 20× magnification. An automated deep learning platform, Google AutoML, was used to create a model for distinguishing TA in progressive supranuclear palsy (PSP) from AP in corticobasal degeneration (CBD) and NP in Alzheimer disease (AD). A total of 1500 images of representative tau lesions were captured from 35 PSP, 27 CBD, and 33 AD patients. Of those, 1332 images were used for training, and 168 images for cross-validation. We tested the model using 100 additional test images taken from 20 patients of each disease. In cross-validation, precision and recall for each individual lesion type were 100% and 98.0% for TA, 98.5% and 98.5% for AP, and 98.0% and 100% for NP, respectively. In a test set, all images of TA and NP were correctly predicted. Only eleven images of AP were predicted to be TA or NP. Our data indicate the potential usefulness of deep learning-based image classification methods to assist in differential diagnosis of tauopathies.
| S-EPMC7985829 | biostudies-literature
Project description:Background and aimMelasma (ML), naevus fusco-caeruleus zygomaticus (NZ), freckles (FC), cafe-au-lait spots (CS), nevus of ota (NO), and lentigo simplex (LS), are common skin diseases causing hyperpigmentation. Deep learning algorithms learn the inherent laws and representation levels of sample data and can analyze the internal details of the image and classify it objectively to be used for image diagnosis. However, deep learning algorithms that can assist clinicians in diagnosing skin hyperpigmentation conditions are lacking.MethodsThe optimal deep-learning image recognition algorithm was explored for the auxiliary diagnosis of hyperpigmented skin disease. Pretrained models, such as VGG-19, GoogLeNet, InceptionV3, ResNet50V2, ResNet101V2, ResNet152V2, InceptionResNetV2, DesseNet201, MobileNet, and NASNetMobile were used to classify images of six common hyperpigmented skin diseases. The best deep learning algorithm for developing an online clinical diagnosis system was selected by using accuracy and area under curve (AUC) as evaluation indicators.ResultsIn this research, the parameters of the above-mentioned ten deep learning algorithms were 18333510, 5979702, 21815078, 23577094, 42638854, 58343942, 54345958, 18333510, 3235014, and 4276058, respectively, and their training time was 380, 162, 199, 188, 315, 511, 471, 697, 101, and 144 min respectively. The respective accuracies of the training set were 85.94%, 99.72%, 99.61%, 99.52%, 99.52%, 98.84%, 99.61%, 99.13%, 99.52%, and 99.61%. The accuracy rates of the test set data were 73.28%, 57.40%, 70.04%, 71.48%, 68.23%, 71.11%, 71.84%, 73.28%, 70.39%, and 43.68%, respectively. Finally, the areas of AUC curves were 0.93, 0.86, 0.93, 0.91, 0.91, 0.92, 0.93, 0.92, 0.93, and 0.82, respectively.ConclusionsThe experimental parameters, training time, accuracy, and AUC of the above models suggest that MobileNet provides a good clinical application prospect in the auxiliary diagnosis of hyperpigmented skin.
| S-EPMC10559947 | biostudies-literature
Project description:Cell shape reflects the spatial configuration resulting from the equilibrium of cellular and environmental signals and is considered a highly relevant indicator of its function and biological properties. For cancer cells, various physiological and environmental challenges, including chemotherapy, cause a cell state transition, which is accompanied by a continuous morphological alteration that is often extremely difficult to recognize even by direct microscopic inspection. To determine whether deep learning-based image analysis enables the detection of cell shape reflecting a crucial cell state alteration, we used the oral cancer cell line resistant to chemotherapy but having cell morphology nearly indiscernible from its non-resistant parental cells. We then implemented the automatic approach via deep learning methods based on EfficienNet-B3 models, along with over- and down-sampling techniques to determine whether image analysis of the Convolutional Neural Network (CNN) can accomplish three-class classification of non-cancer cells vs. cancer cells with and without chemoresistance. We also examine the capability of CNN-based image analysis to approximate the composition of chemoresistant cancer cells within a population. We show that the classification model achieves at least 98.33% accuracy by the CNN model trained with over- and down-sampling techniques. For heterogeneous populations, the best model can approximate the true proportions of non-chemoresistant and chemoresistant cancer cells with Root Mean Square Error (RMSE) reduced to 0.16 by Ensemble Learning (EL). In conclusion, our study demonstrates the potential of CNN models to identify altered cell shapes that are visually challenging to recognize, thus supporting future applications with this automatic approach to image analysis.
| S-EPMC11530068 | biostudies-literature
Project description:Artificial intelligence (AI)-based image analysis has increased drastically in recent years. However, all applications use individual solutions, highly specialized for a particular task. Here, an easy-to-use, adaptable, and open source software, called AIDeveloper (AID) to train neural nets (NN) for image classification without the need for programming is presented. AID provides a variety of NN-architectures, allowing to apply trained models on new data, obtain performance metrics, and export final models to different formats. AID is benchmarked on large image datasets (CIFAR-10 and Fashion-MNIST). Furthermore, models are trained to distinguish areas of differentiated stem cells in images of cell culture. A conventional blood cell count and a blood count obtained using an NN are compared, trained on >1.2 million images, and demonstrated how AID can be used for label-free classification of B- and T-cells. All models are generated by non-programmers on generic computers, allowing for an interdisciplinary use.
| S-EPMC8188199 | biostudies-literature