Search

Background: Glaucoma, the second leading cause of global blindness, demands timely detection due to its asymptomatic progression. This paper introduces an advanced computerized system, integrates Machine Learning (ML), convolutional neural networks (CNNs), and image processing for accurate glaucoma detection using medical imaging data, surpassing prior research efforts. Method: Developing a hybrid glaucoma detection framework using CNNs (ResNet50, VGG-16) and Random Forest. Models analyze pre-processed retinal images independently, and post-processing rules combine predictions for an overall glaucoma impact assessment. Result: The hybrid framework achieves a significant 95.41% accuracy, with precision and recall at 99.37% and 88.37%, respectively. The F1 score, balancing precision and recall, reaches a commendable 93.52%. These results highlight the robustness and effectiveness of the hybrid framework in accurate glaucoma diagnosis. Conclusion: In summary, our research presents an innovative hybrid framework combining CNNs and traditional ML models for glaucoma detection. Using ResNet50, VGG-16, and Random Forest in an ensemble approach yields remarkable accuracy, precision, recall, and F1 score. These results showcase the methodology's potential to enhance glaucoma diagnosis, emphasizing its promising role in early detection and preventing irreversible vision loss. The integration of ML and DNNs in medical imaging analysis suggests a valuable path for future advancements in ophthalmic healthcare. [ABSTRACT FROM AUTHOR]

Background: MicroRNAs play a critical role in regulating gene expression by binding to specific target sites within gene transcripts, making the identification of microRNA targets a prominent focus of research. Conventional experimental methods for identifying microRNA targets are both time-consuming and expensive, prompting the development of computational tools for target prediction. However, the existing computational tools exhibit limited performance in meeting the demands of practical applications, highlighting the need to improve the performance of microRNA target prediction models. Results: In this paper, we utilize the most popular natural language processing and computer vision technologies to propose a novel approach, called TEC-miTarget, for microRNA target prediction based on transformer encoder and convolutional neural networks. TEC-miTarget treats RNA sequences as a natural language and encodes them using a transformer encoder, a widely used encoder in natural language processing. It then combines the representations of a pair of microRNA and its candidate target site sequences into a contact map, which is a three-dimensional array similar to a multi-channel image. Therefore, the contact map's features are extracted using a four-layer convolutional neural network, enabling the prediction of interactions between microRNA and its candidate target sites. We applied a series of comparative experiments to demonstrate that TEC-miTarget significantly improves microRNA target prediction, compared with existing state-of-the-art models. Our approach is the first approach to perform comparisons with other approaches at both sequence and transcript levels. Furthermore, it is the first approach compared with both deep learning-based and seed-match-based methods. We first compared TEC-miTarget's performance with approaches at the sequence level, and our approach delivers substantial improvements in performance using the same datasets and evaluation metrics. Moreover, we utilized TEC-miTarget to predict microRNA targets in long mRNA sequences, which involves two steps: selecting candidate target site sequences and applying sequence-level predictions. We finally showed that TEC-miTarget outperforms other approaches at the transcript level, including the popular seed match methods widely used in previous years. Conclusions: We propose a novel approach for predicting microRNA targets at both sequence and transcript levels, and demonstrate that our approach outperforms other methods based on deep learning or seed match. We also provide our approach as an easy-to-use software, TEC-miTarget, at https://github.com/tingpeng17/TEC-miTarget. Our results provide new perspectives for microRNA target prediction. [ABSTRACT FROM AUTHOR]

Background: With the rapid development of the medical industry and the gradual increase in people's awareness of their health, the use of the Internet for medical question and answer, to obtain more accurate medical answers. It is necessary to first calculate the similarity of the questions asked by users, which further matches professional medical answers. Improving the efficiency of online medical question and answer sessions will not only reduce the burden on doctors, but also enhance the patient's experience of online medical diagnosis. Method: This paper focuses on building a bidirectional gated recurrent unit(BiGRU) deep learning model based on Siamese network for medical interrogative similarity matching, using Word2Vec word embedding tool for word vector processing of ethnic-medical corpus, and introducing an attention mechanism and convolutional neural network. Bidirectional gated recurrent unit extracts contextual semantic information and long-distance dependency features of interrogative sentences; Similar ethnic medicine interrogatives vary in length and structure, and the key information in the interrogative is crucial to similarity identification. By introducing an attention mechanism higher weight can be given to the keywords in the question, further improving the recognition of similar words in the question. Convolutional neural network takes into account the local information of interrogative sentences and can capture local position invariance, allowing feature extraction for words of different granularity through convolutional operations; By comparing the Euclidean distance, cosine distance and Manhattan distance to calculate the spatial distance of medical interrogatives, the Manhattan distance produced the best similarity result. Result: Based on the ethnic medical question dataset constructed in this paper, the accuracy and F1-score reached 97.24% and 97.98%, which is a significant improvement compared to several other models. Conclusion: By comparing with other models, the model proposed in this paper has better performance and achieve accurate matching of similar semantic question data of ethnic medicine. [ABSTRACT FROM AUTHOR]

Background: Locomotion behaviors of Caenorhabditis elegans play an important role in drug activity screening, anti-aging research, and toxicological assessment. Previous studies have provided important insights into drug activity screening, anti-aging, and toxicological research by manually counting the number of body bends. However, manual counting is often low-throughput and takes a lot of time and manpower. And it is easy to cause artificial bias and error in counting results. Results: In this paper, an algorithm is proposed for automatic counting and analysis of the body bending behavior of nematodes. First of all, the numerical coordinate regression method with convolutional neural network is used to obtain the head and tail coordinates. Next, curvature-based feature point extraction algorithm is used to calculate the feature points of the nematode centerline. Then the maximum distance between the peak point and the straight line between the pharynx and the tail is calculated. The number of body bends is counted according to the change in the maximum distance per frame. Conclusion: Experiments are performed to prove the effectiveness of the proposed algorithm. The accuracy of head coordinate prediction is 0.993, and the accuracy of tail coordinate prediction is 0.990. The Pearson correlation coefficient between the results of the automatic count and manual count of the number of body bends is 0.998 and the mean absolute error is 1.931. Different strains of nematodes are selected to analyze differences in body bending behavior, demonstrating a relationship between nematode vitality and lifespan. The code is freely available at https://github.com/hthana/Body-Bend-Count. [ABSTRACT FROM AUTHOR]

Background: The electroencephalography (EEG) signal carries important information about the electrical activity of the brain, which may reveal many pathologies. This information is carried in certain waveforms and events, one of which is the K-complex. It is used by neurologists to diagnose neurophysiologic and cognitive disorders as well as sleep studies. Existing detection methods largely depend on tedious, time-consuming, and error-prone manual inspection of the EEG waveform.Methods: In this paper, a highly accurate K-complex detection system is developed. Based on multiple convolutional neural network (CNN) feature extraction backbones and EEG waveform images, a regions with faster regions with convolutional neural networks (Faster R-CNN) detector was designed, trained, and tested. Extensive performance evaluation was performed using four deep transfer learning feature extraction models (AlexNet, ResNet-101, VGG19 and Inceptionv3). The dataset was comprised of 10948 images of EEG waveforms, with the location of the K-complexes included as separate text files containing the bounding boxes information.Results: The Inceptionv3 and VGG19-based detectors performed consistently high (i.e., up to 99.8% precision and 0.2% miss rate) over different testing scenarios, in which the number of training images was varied from 60% to 80% and the positive overlap threshold was increased from 60% to 90%.Conclusions: Our automated method appears to be a highly accurate automatic K-complex detection in real-time that can aid practitioners in speedy EEG inspection. [ABSTRACT FROM AUTHOR]

Background: To effectively detect and investigate various cell-related diseases, it is essential to understand cell behaviour. The ability to detection mitotic cells is a fundamental step in diagnosing cell-related diseases. Convolutional neural networks (CNNs) have been successfully applied to object detection tasks, however, when applied to mitotic cell detection, most existing methods generate high false-positive rates due to the complex characteristics that differentiate normal cells from mitotic cells. Cell size and orientation variations in each stage make detecting mitotic cells difficult in 2D approaches. Therefore, effective extraction of the spatial and temporal features from mitotic data is an important and challenging task. The computational time required for detection is another major concern for mitotic detection in 4D microscopic images. Results: In this paper, we propose a backbone feature extraction network named full scale connected recurrent deep layer aggregation (RDLA++) for anchor-free mitotic detection. We utilize a 2.5D method that includes 3D spatial information extracted from several 2D images from neighbouring slices that form a multi-stream input. Conclusions: Our proposed technique addresses the scale variation problem and can efficiently extract spatial and temporal features from 4D microscopic images, resulting in improved detection accuracy and reduced computation time compared with those of other state-of-the-art methods. [ABSTRACT FROM AUTHOR]

Objective: In this paper, we propose to evaluate the use of pre-trained convolutional neural networks (CNNs) as a features extractor followed by the Principal Component Analysis (PCA) to find the best discriminant features to perform classification using support vector machine (SVM) algorithm for neonatal sleep and wake states using Fluke® facial video frames. Using pre-trained CNNs as a feature extractor would hugely reduce the effort of collecting new neonatal data for training a neural network which could be computationally expensive. The features are extracted after fully connected layers (FCL's), where we compare several pre-trained CNNs, e.g., VGG16, VGG19, InceptionV3, GoogLeNet, ResNet, and AlexNet. Results: From around 2-h Fluke® video recording of seven neonates, we achieved a modest classification performance with an accuracy, sensitivity, and specificity of 65.3%, 69.8%, 61.0%, respectively with AlexNet using Fluke® (RGB) video frames. This indicates that using a pre-trained model as a feature extractor could not fully suffice for highly reliable sleep and wake classification in neonates. Therefore, in future work a dedicated neural network trained on neonatal data or a transfer learning approach is required. [ABSTRACT FROM AUTHOR]