Highly accurate differentiation of bone marrow cell morphologies using deep neural networks on a large image data set.
Ontology highlight
ABSTRACT:
SUBMITTER: Matek C
PROVIDER: S-EPMC8602932 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Accurate detection of somatic mutations is still a challenge in cancer analysis. Here we present NeuSomatic, the first convolutional neural network approach for somatic mutation detection, which significantly outperforms previous methods on different sequencing platforms, sequencing strategies, and tumor purities. NeuSomatic summarizes sequence alignments into small matrices and incorporates more than a hundred features to capture mutation signals effectively. It can be used universally as a stand-alone somatic mutation detection method or with an ensemble of existing methods to achieve the highest accuracy.
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Project description:Predicting the stability of crystals is one of the central problems in materials science. Today, density functional theory (DFT) calculations remain comparatively expensive and scale poorly with system size. Here we show that deep neural networks utilizing just two descriptors-the Pauling electronegativity and ionic radii-can predict the DFT formation energies of C3A2D3O12 garnets and ABO3 perovskites with low mean absolute errors (MAEs) of 7-10 meV atom-1 and 20-34 meV atom-1, respectively, well within the limits of DFT accuracy. Further extension to mixed garnets and perovskites with little loss in accuracy can be achieved using a binary encoding scheme, addressing a critical gap in the extension of machine-learning models from fixed stoichiometry crystals to infinite universe of mixed-species crystals. Finally, we demonstrate the potential of these models to rapidly transverse vast chemical spaces to accurately identify stable compositions, accelerating the discovery of novel materials with potentially superior properties.
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Project description:Introduction:Deep learning neural networks are especially potent at dealing with structured data, such as images and volumes. Both modified LiviaNET and HyperDense-Net performed well at a prior competition segmenting 6-month-old infant magnetic resonance images, but neonatal cerebral tissue type identification is challenging given its uniquely inverted tissue contrasts. The current study aims to evaluate the two architectures to segment neonatal brain tissue types at term equivalent age. Methods:Both networks were retrained over 24 pairs of neonatal T1 and T2 data from the Developing Human Connectome Project public data set and validated on another eight pairs against ground truth. We then reported the best-performing model from training and its performance by computing the Dice similarity coefficient (DSC) for each tissue type against eight test subjects. Results:During the testing phase, among the segmentation approaches tested, the dual-modality HyperDense-Net achieved the best statistically significantly test mean DSC values, obtaining 0.94/0.95/0.92 for the tissue types and took 80 h to train and 10 min to segment, including preprocessing. The single-modality LiviaNET was better at processing T2-weighted images than processing T1-weighted images across all tissue types, achieving mean DSC values of 0.90/0.90/0.88 for gray matter, white matter, and cerebrospinal fluid, respectively, while requiring 30 h to train and 8 min to segment each brain, including preprocessing. Discussion:Our evaluation demonstrates that both neural networks can segment neonatal brains, achieving previously reported performance. Both networks will be continuously retrained over an increasingly larger repertoire of neonatal brain data and be made available through the Canadian Neonatal Brain Platform to better serve the neonatal brain imaging research community.
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Project description:This paper studies the problem of detection of dental diseases. Dental problems affect the vast majority of the world's population. Caries, RCT (Root Canal Treatment), Abscess, Bone Loss, and missing teeth are some of the most common dental conditions that affect people of all ages all over the world. Delayed or incorrect diagnosis may result in mistreatment, affecting not only an individual's oral health but also his or her overall health, thereby making it an important research area in medicine and engineering. We propose a pipelined Deep Neural Network (DNN) approach to detect healthy and non-healthy periapical dental X-ray images. Even a minor enhancement or improvement in existing techniques can go a long way in providing significant health benefits in the medical field. This paper has made a successful attempt to contribute a different type of pipelined approach using AlexNet in this regard. The approach is trained on a large dataset of 16,000 dental X-ray images, correctly identifying healthy and non-healthy X-ray images. We use an optimized Convolutional Neural Networks and three state-of-the-art DNN models, namely Res-Net-18, ResNet-34, and AlexNet for disease classification. In our study, the AlexNet model outperforms the other models with an accuracy of 0.852. The precision, recall and F1 scores of AlexNet also surpass the other models with a score of 0.850 across all metrics. The area under ROC curve also signifies that both the false-positive rate and false-negative rate are low. We conclude that even with a big data set and raw X-ray pictures, the AlexNet model generalizes effectively to previously unseen data and can aid in the diagnosis of a variety of dental diseases.
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Project description:Wheat blast is a threat to global wheat production, and limited blast-resistant cultivars are available. The current estimations of wheat spike blast severity rely on human assessments, but this technique could have limitations. Reliable visual disease estimations paired with Red Green Blue (RGB) images of wheat spike blast can be used to train deep convolutional neural networks (CNN) for disease severity (DS) classification. Inter-rater agreement analysis was used to measure the reliability of who collected and classified data obtained under controlled conditions. We then trained CNN models to classify wheat spike blast severity. Inter-rater agreement analysis showed high accuracy and low bias before model training. Results showed that the CNN models trained provide a promising approach to classify images in the three wheat blast severity categories. However, the models trained on non-matured and matured spikes images showing the highest precision, recall, and F1 score when classifying the images. The high classification accuracy could serve as a basis to facilitate wheat spike blast phenotyping in the future.
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Project description:Celiac disease (CD) is a gluten-sensitive immune-mediated enteropathy. This proof-of-concept study used a convolutional neural network (CNN) to classify hematoxylin and eosin (H&E) CD histological images, normal small intestine control, and non-specified duodenal inflammation (7294, 11,642, and 5966 images, respectively). The trained network classified CD with high performance (accuracy 99.7%, precision 99.6%, recall 99.3%, F1-score 99.5%, and specificity 99.8%). Interestingly, when the same network (already trained for the 3 class images), analyzed duodenal adenocarcinoma (3723 images), the new images were classified as duodenal inflammation in 63.65%, small intestine control in 34.73%, and CD in 1.61% of the cases; and when the network was retrained using the 4 histological subtypes, the performance was above 99% for CD and 97% for adenocarcinoma. Finally, the model added 13,043 images of Crohn's disease to include other inflammatory bowel diseases; a comparison between different CNN architectures was performed, and the gradient-weighted class activation mapping (Grad-CAM) technique was used to understand why the deep learning network made its classification decisions. In conclusion, the CNN-based deep neural system classified 5 diagnoses with high performance. Narrow artificial intelligence (AI) is designed to perform tasks that typically require human intelligence, but it operates within limited constraints and is task-specific.
| S-EPMC11355344 | biostudies-literature
Project description:Acoustic signals serve communication within and across species throughout the animal kingdom. Studying the genetics, evolution, and neurobiology of acoustic communication requires annotating acoustic signals: segmenting and identifying individual acoustic elements like syllables or sound pulses. To be useful, annotations need to be accurate, robust to noise, and fast. We here introduce DeepAudioSegmenter (DAS), a method that annotates acoustic signals across species based on a deep-learning derived hierarchical presentation of sound. We demonstrate the accuracy, robustness, and speed of DAS using acoustic signals with diverse characteristics from insects, birds, and mammals. DAS comes with a graphical user interface for annotating song, training the network, and for generating and proofreading annotations. The method can be trained to annotate signals from new species with little manual annotation and can be combined with unsupervised methods to discover novel signal types. DAS annotates song with high throughput and low latency for experimental interventions in realtime. Overall, DAS is a universal, versatile, and accessible tool for annotating acoustic communication signals.
| S-EPMC8560090 | biostudies-literature
Project description:BackgroundDeep neural networks (DNNs) are widely investigated in medical image classification to achieve automated support for clinical diagnosis. It is necessary to evaluate the robustness of medical DNN tasks against adversarial attacks, as high-stake decision-making will be made based on the diagnosis. Several previous studies have considered simple adversarial attacks. However, the vulnerability of DNNs to more realistic and higher risk attacks, such as universal adversarial perturbation (UAP), which is a single perturbation that can induce DNN failure in most classification tasks has not been evaluated yet.MethodsWe focus on three representative DNN-based medical image classification tasks (i.e., skin cancer, referable diabetic retinopathy, and pneumonia classifications) and investigate their vulnerability to the seven model architectures of UAPs.ResultsWe demonstrate that DNNs are vulnerable to both nontargeted UAPs, which cause a task failure resulting in an input being assigned an incorrect class, and to targeted UAPs, which cause the DNN to classify an input into a specific class. The almost imperceptible UAPs achieved?>?80% success rates for nontargeted and targeted attacks. The vulnerability to UAPs depended very little on the model architecture. Moreover, we discovered that adversarial retraining, which is known to be an effective method for adversarial defenses, increased DNNs' robustness against UAPs in only very few cases.ConclusionUnlike previous assumptions, the results indicate that DNN-based clinical diagnosis is easier to deceive because of adversarial attacks. Adversaries can cause failed diagnoses at lower costs (e.g., without consideration of data distribution); moreover, they can affect the diagnosis. The effects of adversarial defenses may not be limited. Our findings emphasize that more careful consideration is required in developing DNNs for medical imaging and their practical applications.
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Project description:Although short tandem repeat (STR) analysis is available as a reliable method for the determination of the genetic origin of cell lines, the occurrence of misauthenticated cell lines remains an important issue. Reasons include the cost, effort and time associated with STR analysis. Moreover, there are currently no methods for the discrimination between isogenic cell lines (cell lines of the same genetic origin, e.g. different cell lines derived from the same organism, clonal sublines, sublines adapted to grow under certain conditions). Hence, additional complementary, ideally low-cost and low-effort methods are required that enable (1) the monitoring of cell line identity as part of the daily laboratory routine and 2) the authentication of isogenic cell lines. In this research, we automate the process of cell line identification by image-based analysis using deep convolutional neural networks. Two different convolutional neural networks models (MobileNet and InceptionResNet V2) were trained to automatically identify four parental cancer cell line (COLO 704, EFO-21, EFO-27 and UKF-NB-3) and their sublines adapted to the anti-cancer drugs cisplatin (COLO-704rCDDP1000, EFO-21rCDDP2000, EFO-27rCDDP2000) or oxaliplatin (UKF-NB-3rOXALI2000), hence resulting in an eight-class problem. Our best performing model, InceptionResNet V2, achieved an average of 0.91 F1-score on tenfold cross validation with an average area under the curve (AUC) of 0.95, for the 8-class problem. Our best model also achieved an average F1-score of 0.94 and 0.96 on the authentication through a classification process of the four parental cell lines and the respective drug-adapted cells, respectively, on a four-class problem separately. These findings provide the basis for further development of the application of deep learning for the automation of cell line authentication into a readily available easy-to-use methodology that enables routine monitoring of the identity of cell lines including isogenic cell lines. It should be noted that, this is just a proof of principal that, images can also be used as a method for authentication of cancer cell lines and not a replacement for the STR method.
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Project description:Phase recovery from intensity-only measurements forms the heart of coherent imaging techniques and holography. In this study, we demonstrate that a neural network can learn to perform phase recovery and holographic image reconstruction after appropriate training. This deep learning-based approach provides an entirely new framework to conduct holographic imaging by rapidly eliminating twin-image and self-interference-related spatial artifacts. This neural network-based method is fast to compute and reconstructs phase and amplitude images of the objects using only one hologram, requiring fewer measurements in addition to being computationally faster. We validated this method by reconstructing the phase and amplitude images of various samples, including blood and Pap smears and tissue sections. These results highlight that challenging problems in imaging science can be overcome through machine learning, providing new avenues to design powerful computational imaging systems.
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