Využití umělé inteligence jako asistenční detekční metody v endoskopii se v uplynulých letech těší zvyšujícímu se zájmu. Algoritmy strojového učení slibují zefektivnění detekce polypů, a dokonce optickou lokalizaci nálezů, to vše s minimálním zaškolením endoskopisty. Praktickým cílem této studie je analýza CAD softwaru (computer-aided diagnosis) Carebot pro detekci kolorektálních polypů s využitím konvoluční neuronové sítě. Navržený binární klasifikátor pro detekci polypů dosahuje přesnosti až 98 %, specificity 0,99 a preciznosti 0,96. Současně je diskutována nezbytnost dostupnosti rozsáhlých klinických dat pro vývoj modelů na bázi umělé inteligence pro automatickou detekci adenomů a benigních neoplastických lézí.

The use of artificial intelligence as an assistive detection method in endoscopy has attracted increasing interest in recent years. Machine learning algorithms promise to improve the efficiency of polyp detection and even optical localization of findings, all with minimal training of the endoscopist. The practical goal of this study is to analyse the CAD software (computer-aided diagnosis) Carebot for colorectal polyp detection using a convolutional neural network. The proposed binary classifier for polyp detection achieves accuracy of up to 98%, specificity of 0.99 and precision of 0.96. At the same time, the need for the availability of large-scale clinical data for the development of artificial--intelligence-based models for the automatic detection of adenomas and benign neoplastic lesions is discussed.

• Klíčová slova
• prostorová lokalizace,
• MeSH
• diagnóza počítačová * MeSH
• lidé MeSH
• neuronové sítě MeSH
• polypy střeva * diagnóza   MeSH
• umělá inteligence MeSH
• Check Tag
• lidé MeSH

BACKGROUND AND OBJECTIVES: Cardiovascular diseases are critical diseases and need to be diagnosed as early as possible. There is a lack of medical professionals in remote areas to diagnose these diseases. Artificial intelligence-based automatic diagnostic tools can help to diagnose cardiac diseases. This work presents an automatic classification method using machine learning to diagnose multiple cardiac diseases from phonocardiogram signals. METHODS: The proposed system involves a convolutional neural network (CNN) model because of its high accuracy and robustness to automatically diagnose the cardiac disorders from the heart sounds. To improve the accuracy in a noisy environment and make the method robust, the proposed method has used data augmentation techniques for training and multi-classification of multiple cardiac diseases. RESULTS: The model has been validated both heart sound data and augmented data using n-fold cross-validation. Results of all fold have been shown reported in this work. The model has achieved accuracy on the test set up to 98.60% to diagnose multiple cardiac diseases. CONCLUSIONS: The proposed model can be ported to any computing devices like computers, single board computing processors, android handheld devices etc. To make a stand-alone diagnostic tool that may be of help in remote primary health care centres. The proposed method is non-invasive, efficient, robust, and has low time complexity making it suitable for real-time applications.

• MeSH
• lidé MeSH
• nemoci srdce * diagnostické zobrazování   MeSH
• neuronové sítě MeSH
• srdeční ozvy * MeSH
• strojové učení MeSH
• umělá inteligence MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Genomic regions that encode small RNA genes exhibit characteristic patterns in their sequence, secondary structure, and evolutionary conservation. Convolutional Neural Networks are a family of algorithms that can classify data based on learned patterns. Here we present MuStARD an application of Convolutional Neural Networks that can learn patterns associated with user-defined sets of genomic regions, and scan large genomic areas for novel regions exhibiting similar characteristics. We demonstrate that MuStARD is a generic method that can be trained on different classes of human small RNA genomic loci, without need for domain specific knowledge, due to the automated feature and background selection processes built into the model. We also demonstrate the ability of MuStARD for inter-species identification of functional elements by predicting mouse small RNAs (pre-miRNAs and snoRNAs) using models trained on the human genome. MuStARD can be used to filter small RNA-Seq datasets for identification of novel small RNA loci, intra- and inter- species, as demonstrated in three use cases of human, mouse, and fly pre-miRNA prediction. MuStARD is easy to deploy and extend to a variety of genomic classification questions. Code and trained models are freely available at gitlab.com/RBP_Bioinformatics/mustard.

• MeSH
• algoritmy MeSH
• genomika metody   MeSH
• lidé MeSH
• malá jadérková RNA genetika   MeSH
• mikro RNA genetika   MeSH
• myši MeSH
• nekódující RNA genetika   MeSH
• neuronové sítě MeSH
• software MeSH
• výpočetní biologie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Manual and semi-automatic identification of artifacts and unwanted physiological signals in large intracerebral electroencephalographic (iEEG) recordings is time consuming and inaccurate. To date, unsupervised methods to accurately detect iEEG artifacts are not available. This study introduces a novel machine-learning approach for detection of artifacts in iEEG signals in clinically controlled conditions using convolutional neural networks (CNN) and benchmarks the method's performance against expert annotations. The method was trained and tested on data obtained from St Anne's University Hospital (Brno, Czech Republic) and validated on data from Mayo Clinic (Rochester, Minnesota, U.S.A). We show that the proposed technique can be used as a generalized model for iEEG artifact detection. Moreover, a transfer learning process might be used for retraining of the generalized version to form a data-specific model. The generalized model can be efficiently retrained for use with different EEG acquisition systems and noise environments. The generalized and specialized model F1 scores on the testing dataset were 0.81 and 0.96, respectively. The CNN model provides faster, more objective, and more reproducible iEEG artifact detection compared to manual approaches.

• MeSH
• artefakty * MeSH
• elektroencefalografie metody   MeSH
• lidé MeSH
• mozek fyziologie   MeSH
• neuronové sítě * MeSH
• retrospektivní studie MeSH
• strojové učení * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

BACKGROUND: Estimation of the risk of malignancy in pulmonary nodules detected by CT is central in clinical management. The use of artificial intelligence (AI) offers an opportunity to improve risk prediction. Here we compare the performance of an AI algorithm, the lung cancer prediction convolutional neural network (LCP-CNN), with that of the Brock University model, recommended in UK guidelines. METHODS: A dataset of incidentally detected pulmonary nodules measuring 5-15 mm was collected retrospectively from three UK hospitals for use in a validation study. Ground truth diagnosis for each nodule was based on histology (required for any cancer), resolution, stability or (for pulmonary lymph nodes only) expert opinion. There were 1397 nodules in 1187 patients, of which 234 nodules in 229 (19.3%) patients were cancer. Model discrimination and performance statistics at predefined score thresholds were compared between the Brock model and the LCP-CNN. RESULTS: The area under the curve for LCP-CNN was 89.6% (95% CI 87.6 to 91.5), compared with 86.8% (95% CI 84.3 to 89.1) for the Brock model (p≤0.005). Using the LCP-CNN, we found that 24.5% of nodules scored below the lowest cancer nodule score, compared with 10.9% using the Brock score. Using the predefined thresholds, we found that the LCP-CNN gave one false negative (0.4% of cancers), whereas the Brock model gave six (2.5%), while specificity statistics were similar between the two models. CONCLUSION: The LCP-CNN score has better discrimination and allows a larger proportion of benign nodules to be identified without missing cancers than the Brock model. This has the potential to substantially reduce the proportion of surveillance CT scans required and thus save significant resources.

• MeSH
• algoritmy MeSH
• časná detekce nádoru metody   MeSH
• databáze faktografické MeSH
• dospělí MeSH
• hodnocení rizik MeSH
• incidence MeSH
• invazivní růst nádoru patologie   MeSH
• kohortové studie MeSH
• lidé středního věku MeSH
• lidé MeSH
• mnohočetné plicní uzly epidemiologie   patologie   patofyziologie   MeSH
• nádorová transformace buněk patologie   MeSH
• nádory plic epidemiologie   patologie   patofyziologie   MeSH
• neuronové sítě * MeSH
• plocha pod křivkou MeSH
• prediktivní hodnota testů MeSH
• prognóza MeSH
• retrospektivní studie MeSH
• ROC křivka MeSH
• senioři MeSH
• staging nádorů MeSH
• umělá inteligence * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• multicentrická studie MeSH
• práce podpořená grantem MeSH
• validační studie MeSH

This paper aims to address the segmentation and classification of lytic and sclerotic metastatic lesions that are difficult to define by using spinal 3D Computed Tomography (CT) images obtained from highly pathologically affected cases. As the lesions are ill-defined and consequently it is difficult to find relevant image features that would enable detection and classification of lesions by classical methods of texture and shape analysis, the problem is solved by automatic feature extraction provided by a deep Convolutional Neural Network (CNN). Our main contributions are: (i) individual CNN architecture, and pre-processing steps that are dependent on a patient data and a scan protocol - it enables work with different types of CT scans; (ii) medial axis transform (MAT) post-processing for shape simplification of segmented lesion candidates with Random Forest (RF) based meta-analysis; and (iii) usability of the proposed method on whole-spine CTs (cervical, thoracic, lumbar), which is not treated in other published methods (they work with thoracolumbar segments of spine only). Our proposed method has been tested on our own dataset annotated by two mutually independent radiologists and has been compared to other published methods. This work is part of the ongoing complex project dealing with spine analysis and spine lesion longitudinal studies.

• MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádory páteře diagnostické zobrazování   sekundární   MeSH
• neuronové sítě * MeSH
• počítačová rentgenová tomografie * MeSH
• rentgenový obraz - interpretace počítačová metody   MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• zobrazování trojrozměrné * MeSH
• Check Tag
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři nad 80 let MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Deep learning has recently been utilized with great success in a large number of diverse application domains, such as visual and face recognition, natural language processing, speech recognition, and handwriting identification. Convolutional neural networks, that belong to the deep learning models, are a subtype of artificial neural networks, which are inspired by the complex structure of the human brain and are often used for image classification tasks. One of the biggest challenges in all deep neural networks is the overfitting issue, which happens when the model performs well on the training data, but fails to make accurate predictions for the new data that is fed into the model. Several regularization methods have been introduced to prevent the overfitting problem. In the research presented in this manuscript, the overfitting challenge was tackled by selecting a proper value for the regularization parameter dropout by utilizing a swarm intelligence approach. Notwithstanding that the swarm algorithms have already been successfully applied to this domain, according to the available literature survey, their potential is still not fully investigated. Finding the optimal value of dropout is a challenging and time-consuming task if it is performed manually. Therefore, this research proposes an automated framework based on the hybridized sine cosine algorithm for tackling this major deep learning issue. The first experiment was conducted over four benchmark datasets: MNIST, CIFAR10, Semeion, and UPS, while the second experiment was performed on the brain tumor magnetic resonance imaging classification task. The obtained experimental results are compared to those generated by several similar approaches. The overall experimental results indicate that the proposed method outperforms other state-of-the-art methods included in the comparative analysis in terms of classification error and accuracy.

• MeSH
• algoritmy MeSH
• lidé MeSH
• magnetická rezonanční tomografie MeSH
• nádory mozku * MeSH
• neuronové sítě * MeSH
• psaní rukou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Liver volumetry is an important tool in clinical practice. The calculation of liver volume is primarily based on Computed Tomography. Unfortunately, automatic segmentation algorithms based on handcrafted features tend to leak segmented objects into surrounding tissues like the heart or the spleen. Currently, convolutional neural networks are widely used in various applications of computer vision including image segmentation, while providing very promising results. In our work, we utilize robustly segmentable structures like the spine, body surface, and sagittal plane. They are used as key points for position estimation inside the body. The signed distance fields derived from these structures are calculated and used as an additional channel on the input of our convolutional neural network, to be more specific U-Net, which is widely used in medical image segmentation tasks. Our work shows that this additional position information improves the results of the segmentation. We test our approach in two experiments on two public datasets of Computed Tomography images. To evaluate the results, we use the Accuracy, the Hausdorff distance, and the Dice coefficient. Code is publicly available at: https://gitlab.com/hachaf/liver-segmentation.git.

• Publikační typ
• časopisecké články MeSH

BACKGROUND: The recent big data revolution in Genomics, coupled with the emergence of Deep Learning as a set of powerful machine learning methods, has shifted the standard practices of machine learning for Genomics. Even though Deep Learning methods such as Convolutional Neural Networks (CNNs) and Recurrent Neural Networks (RNNs) are becoming widespread in Genomics, developing and training such models is outside the ability of most researchers in the field. RESULTS: Here we present ENNGene-Easy Neural Network model building tool for Genomics. This tool simplifies training of custom CNN or hybrid CNN-RNN models on genomic data via an easy-to-use Graphical User Interface. ENNGene allows multiple input branches, including sequence, evolutionary conservation, and secondary structure, and performs all the necessary preprocessing steps, allowing simple input such as genomic coordinates. The network architecture is selected and fully customized by the user, from the number and types of the layers to each layer's precise set-up. ENNGene then deals with all steps of training and evaluation of the model, exporting valuable metrics such as multi-class ROC and precision-recall curve plots or TensorBoard log files. To facilitate interpretation of the predicted results, we deploy Integrated Gradients, providing the user with a graphical representation of an attribution level of each input position. To showcase the usage of ENNGene, we train multiple models on the RBP24 dataset, quickly reaching the state of the art while improving the performance on more than half of the proteins by including the evolutionary conservation score and tuning the network per protein. CONCLUSIONS: As the role of DL in big data analysis in the near future is indisputable, it is important to make it available for a broader range of researchers. We believe that an easy-to-use tool such as ENNGene can allow Genomics researchers without a background in Computational Sciences to harness the power of DL to gain better insights into and extract important information from the large amounts of data available in the field.

• MeSH
• genomika MeSH
• neuronové sítě * MeSH
• sekundární struktura proteinů MeSH
• strojové učení * MeSH
• Publikační typ
• časopisecké články MeSH

This study aims to develop a fully automated imaging protocol independent system for pituitary adenoma segmentation from magnetic resonance imaging (MRI) scans that can work without user interaction and evaluate its accuracy and utility for clinical applications. We trained two independent artificial neural networks on MRI scans of 394 patients. The scans were acquired according to various imaging protocols over the course of 11 years on 1.5T and 3T MRI systems. The segmentation model assigned a class label to each input pixel (pituitary adenoma, internal carotid artery, normal pituitary gland, background). The slice segmentation model classified slices as clinically relevant (structures of interest in slice) or irrelevant (anterior or posterior to sella turcica). We used MRI data of another 99 patients to evaluate the performance of the model during training. We validated the model on a prospective cohort of 28 patients, Dice coefficients of 0.910, 0.719, and 0.240 for tumour, internal carotid artery, and normal gland labels, respectively, were achieved. The slice selection model achieved 82.5% accuracy, 88.7% sensitivity, 76.7% specificity, and an AUC of 0.904. A human expert rated 71.4% of the segmentation results as accurate, 21.4% as slightly inaccurate, and 7.1% as coarsely inaccurate. Our model achieved good results comparable with recent works of other authors on the largest dataset to date and generalized well for various imaging protocols. We discussed future clinical applications, and their considerations. Models and frameworks for clinical use have yet to be developed and evaluated.

• MeSH
• adenom * diagnostické zobrazování   chirurgie   MeSH
• lidé MeSH
• magnetická rezonanční tomografie MeSH
• nádory hypofýzy * diagnostické zobrazování   chirurgie   MeSH
• neuronové sítě MeSH
• počítačové zpracování obrazu metody   MeSH
• prospektivní studie MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH