Automatic Fungi Recognition: Deep Learning Meets Mycology.
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ABSTRACT:
SUBMITTER: Picek L
PROVIDER: S-EPMC8779018 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundTraining deep learning (DL) models to automatically recognize diseases in nasopharyngeal MRI is a challenging task, and optimizing the performance of DL models is difficult.PurposeTo develop a method of training anatomical partition-based DL model which integrates knowledge of clinical anatomical regions in otorhinolaryngology to automatically recognize diseases in nasopharyngeal MRI.Study typeSingle-center retrospective study.PopulationA total of 2485 patients with nasopharyngeal diseases (age range 14-82 years, female, 779[31.3%]) and 600 people with normal nasopharynx (age range 18-78 years, female, 281[46.8%]) were included.Sequence3.0 T; T2WI fast spin-echo sequence.AssessmentFull images (512 × 512) of 3085 patients constituted 100% of the dataset, 50% and 25% of which were randomly retained as two new datasets. Two new series of images (seg112 image [112 × 112] and seg224 image [224 × 224]) were automatically generated by a segmentation model. Four pretrained neural networks for nasopharyngeal diseases classification were trained under the nine datasets (full image, seg112 image, and seg224 image, each with 100% dataset, 50% dataset, and 25% dataset).Statistical testsThe receiver operating characteristic curve was used to evaluate the performance of the models. Analysis of variance was used to compare the performance of the models built with different datasets. Statistical significance was set at P < 0.05.ResultsWhen the 100% dataset was used for training, the performances of the models trained with the seg112 images (average area under the curve [aAUC] 0.949 ± 0.052), seg224 images (aAUC 0.948 ± 0.053), and full images (aAUC 0.935 ± 0.053) were similar (P = 0.611). When the 25% dataset was used for training, the mean aAUC of the models that were trained with seg112 images (0.823 ± 0.116) and seg224 images (0.765 ± 0.155) was significantly higher than the models that were trained with full images (0.640 ± 0.154).Data conclusionThe proposed method can potentially improve the performance of the DL model for automatic recognition of diseases in nasopharyngeal MRI.Level of evidence4 TECHNICAL EFFICACY STAGE: 1.
| S-EPMC9541866 | biostudies-literature
Project description:The aim of this study was to develop and evaluate a machine vision algorithm to assess the pain level in horses, using an automatic computational classifier based on the Horse Grimace Scale (HGS) and trained by machine learning method. The use of the Horse Grimace Scale is dependent on a human observer, who most of the time does not have availability to evaluate the animal for long periods and must also be well trained in order to apply the evaluation system correctly. In addition, even with adequate training, the presence of an unknown person near an animal in pain can result in behavioral changes, making the evaluation more complex. As a possible solution, the automatic video-imaging system will be able to monitor pain responses in horses more accurately and in real-time, and thus allow an earlier diagnosis and more efficient treatment for the affected animals. This study is based on assessment of facial expressions of 7 horses that underwent castration, collected through a video system positioned on the top of the feeder station, capturing images at 4 distinct timepoints daily for two days before and four days after surgical castration. A labeling process was applied to build a pain facial image database and machine learning methods were used to train the computational pain classifier. The machine vision algorithm was developed through the training of a Convolutional Neural Network (CNN) that resulted in an overall accuracy of 75.8% while classifying pain on three levels: not present, moderately present, and obviously present. While classifying between two categories (pain not present and pain present) the overall accuracy reached 88.3%. Although there are some improvements to be made in order to use the system in a daily routine, the model appears promising and capable of measuring pain on images of horses automatically through facial expressions, collected from video images.
| S-EPMC8525760 | biostudies-literature
Project description:BackgroundDividing a surgical procedure into a sequence of identifiable and meaningful steps facilitates intraoperative video data acquisition and storage. These efforts are especially valuable for technically challenging procedures that require intraoperative video analysis, such as transanal total mesorectal excision (TaTME); however, manual video indexing is time-consuming. Thus, in this study, we constructed an annotated video dataset for TaTME with surgical step information and evaluated the performance of a deep learning model in recognizing the surgical steps in TaTME.MethodsThis was a single-institutional retrospective feasibility study. All TaTME intraoperative videos were divided into frames. Each frame was manually annotated as one of the following major steps: (1) purse-string closure; (2) full thickness transection of the rectal wall; (3) down-to-up dissection; (4) dissection after rendezvous; and (5) purse-string suture for stapled anastomosis. Steps 3 and 4 were each further classified into four sub-steps, specifically, for dissection of the anterior, posterior, right, and left planes. A convolutional neural network-based deep learning model, Xception, was utilized for the surgical step classification task.ResultsOur dataset containing 50 TaTME videos was randomly divided into two subsets for training and testing with 40 and 10 videos, respectively. The overall accuracy obtained for all classification steps was 93.2%. By contrast, when sub-step classification was included in the performance analysis, a mean accuracy (± standard deviation) of 78% (± 5%), with a maximum accuracy of 85%, was obtained.ConclusionsTo the best of our knowledge, this is the first study based on automatic surgical step classification for TaTME. Our deep learning model self-learned and recognized the classification steps in TaTME videos with high accuracy after training. Thus, our model can be applied to a system for intraoperative guidance or for postoperative video indexing and analysis in TaTME procedures.
| S-EPMC8758657 | biostudies-literature
Project description:Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes COVID-19 and is responsible for the ongoing pandemic. Screening of potential antiviral drugs against SARS-CoV-2 depend on in vitro experiments, which are based on the quantification of the virus titer. Here, we used virus-induced cytopathic effects (CPE) in brightfield microscopy of SARS-CoV-2-infected monolayers to quantify the virus titer. Images were classified using deep transfer learning (DTL) that fine-tune the last layers of a pre-trained Resnet18 (ImageNet). To exclude toxic concentrations of potential drugs, the network was expanded to include a toxic score (TOX) that detected cell death (CPETOXnet). With this analytic tool, the inhibitory effects of chloroquine, hydroxychloroquine, remdesivir, and emetine were validated. Taken together we developed a simple method and provided open access implementation to quantify SARS-CoV-2 titers and drug toxicity in experimental settings, which may be adaptable to assays with other viruses. The quantification of virus titers from brightfield images could accelerate the experimental approach for antiviral testing.
| S-EPMC8066066 | biostudies-literature
Project description:Video fluoroscopic swallowing study (VFSS) is considered as the gold standard diagnostic tool for evaluating dysphagia. However, it is time consuming and labor intensive for the clinician to manually search the recorded long video image frame by frame to identify the instantaneous swallowing abnormality in VFSS images. Therefore, this study aims to present a deep leaning-based approach using transfer learning with a convolutional neural network (CNN) that automatically annotates pharyngeal phase frames in untrimmed VFSS videos such that frames need not be searched manually. To determine whether the image frame in the VFSS video is in the pharyngeal phase, a single-frame baseline architecture based the deep CNN framework is used and a transfer learning technique with fine-tuning is applied. Compared with all experimental CNN models, that fine-tuned with two blocks of the VGG-16 (VGG16-FT5) model achieved the highest performance in terms of recognizing the frame of pharyngeal phase, that is, the accuracy of 93.20 (±1.25)%, sensitivity of 84.57 (±5.19)%, specificity of 94.36 (±1.21)%, AUC of 0.8947 (±0.0269) and Kappa of 0.7093 (±0.0488). Using appropriate and fine-tuning techniques and explainable deep learning techniques such as grad CAM, this study shows that the proposed single-frame-baseline-architecture-based deep CNN framework can yield high performances in the full automation of VFSS video analysis.
| S-EPMC7918932 | biostudies-literature
Project description:The emergence of deep-learning methods in different computer vision tasks has proved to offer increased detection, recognition or segmentation accuracy when large annotated image datasets are available. In the case of medical image processing and computer-aided diagnosis within ultrasound images, where the amount of available annotated data is smaller, a natural question arises: are deep-learning methods better than conventional machine-learning methods? How do the conventional machine-learning methods behave in comparison with deep-learning methods on the same dataset? Based on the study of various deep-learning architectures, a lightweight multi-resolution Convolutional Neural Network (CNN) architecture is proposed. It is suitable for differentiating, within ultrasound images, between the Hepatocellular Carcinoma (HCC), respectively the cirrhotic parenchyma (PAR) on which HCC had evolved. The proposed deep-learning model is compared with other CNN architectures that have been adapted by transfer learning for the ultrasound binary classification task, but also with conventional machine-learning (ML) solutions trained on textural features. The achieved results show that the deep-learning approach overcomes classical machine-learning solutions, by providing a higher classification performance.
| S-EPMC7309124 | biostudies-literature
Project description:Rice disease has serious negative effects on crop yield, and the correct diagnosis of rice diseases is the key to avoid these effects. However, the existing disease diagnosis methods for rice are neither accurate nor efficient, and special equipment is often required. In this study, an automatic diagnosis method was developed and implemented in a smartphone app. The method was developed using deep learning based on a large dataset that contained 33,026 images of six types of rice diseases: leaf blast, false smut, neck blast, sheath blight, bacterial stripe disease, and brown spot. The core of the method was the Ensemble Model in which submodels were integrated. Finally, the Ensemble Model was validated using a separate set of images. Results showed that the three best submodels were DenseNet-121, SE-ResNet-50, and ResNeSt-50, in terms of several attributes, such as, learning rate, precision, recall, and disease recognition accuracy. Therefore, these three submodels were selected and integrated in the Ensemble Model. The Ensemble Model minimized confusion among the different types of disease, reducing misdiagnosis of the disease. Using the Ensemble Model to diagnose six types of rice diseases, an overall accuracy of 91% was achieved, which is considered to be reasonably good, considering the appearance similarities in some types of rice disease. The smartphone app allowed the client to use the Ensemble Model on the web server through a network, which was convenient and efficient for the field diagnosis of rice leaf blast, false smut, neck blast, sheath blight, bacterial stripe disease, and brown spot.
| S-EPMC8416767 | biostudies-literature
Project description:Brief fragments of sleep shorter than 15 s are defined as microsleep episodes (MSEs), often subjectively perceived as sleepiness. Their main characteristic is a slowing in frequency in the electroencephalogram (EEG), similar to stage N1 sleep according to standard criteria. The maintenance of wakefulness test (MWT) is often used in a clinical setting to assess vigilance. Scoring of the MWT in most sleep-wake centers is limited to classical definition of sleep (30 s epochs), and MSEs are mostly not considered in the absence of established scoring criteria defining MSEs but also because of the laborious work. We aimed for automatic detection of MSEs with machine learning, i.e., with deep learning based on raw EEG and EOG data as input. We analyzed MWT data of 76 patients. Experts visually scored wakefulness, and according to recently developed scoring criteria MSEs, microsleep episode candidates (MSEc), and episodes of drowsiness (ED). We implemented segmentation algorithms based on convolutional neural networks (CNNs) and a combination of a CNN with a long-short term memory (LSTM) network. A LSTM network is a type of a recurrent neural network which has a memory for past events and takes them into account. Data of 53 patients were used for training of the classifiers, 12 for validation and 11 for testing. Our algorithms showed a good performance close to human experts. The detection was very good for wakefulness and MSEs and poor for MSEc and ED, similar to the low inter-expert reliability for these borderline segments. We performed a visualization of the internal representation of the data by the artificial neuronal network performing best using t-distributed stochastic neighbor embedding (t-SNE). Visualization revealed that MSEs and wakefulness were mostly separable, though not entirely, and MSEc and ED largely intersected with the two main classes. We provide a proof of principle that it is feasible to reliably detect MSEs with deep neuronal networks based on raw EEG and EOG data with a performance close to that of human experts. The code of the algorithms (https://github.com/alexander-malafeev/microsleep-detection) and data (https://zenodo.org/record/3251716) are available.
| S-EPMC8024556 | biostudies-literature
Project description:Artificial neural networks (ANN) have become the mainstream acoustic modeling technique for large vocabulary automatic speech recognition (ASR). A conventional ANN features a multi-layer architecture that requires massive amounts of computation. The brain-inspired spiking neural networks (SNN) closely mimic the biological neural networks and can operate on low-power neuromorphic hardware with spike-based computation. Motivated by their unprecedented energy-efficiency and rapid information processing capability, we explore the use of SNNs for speech recognition. In this work, we use SNNs for acoustic modeling and evaluate their performance on several large vocabulary recognition scenarios. The experimental results demonstrate competitive ASR accuracies to their ANN counterparts, while require only 10 algorithmic time steps and as low as 0.68 times total synaptic operations to classify each audio frame. Integrating the algorithmic power of deep SNNs with energy-efficient neuromorphic hardware, therefore, offer an attractive solution for ASR applications running locally on mobile and embedded devices.
| S-EPMC7090229 | biostudies-literature
Project description:BACKGROUND:The quality of health care is continuously improving and is expected to improve further because of the advancement of machine learning and knowledge-based techniques along with innovation and availability of wearable sensors. With these advancements, health care professionals are now becoming more interested and involved in seeking scientific research evidence from external sources for decision making relevant to medical diagnosis, treatments, and prognosis. Not much work has been done to develop methods for unobtrusive and seamless curation of data from the biomedical literature. OBJECTIVE:This study aimed to design a framework that can enable bringing quality publications intelligently to the users' desk to assist medical practitioners in answering clinical questions and fulfilling their informational needs. METHODS:The proposed framework consists of methods for efficient biomedical literature curation, including the automatic construction of a well-built question, the recognition of evidence quality by proposing extended quality recognition model (E-QRM), and the ranking and summarization of the extracted evidence. RESULTS:Unlike previous works, the proposed framework systematically integrates the echelons of biomedical literature curation by including methods for searching queries, content quality assessments, and ranking and summarization. Using an ensemble approach, our high-impact classifier E-QRM obtained significantly improved accuracy than the existing quality recognition model (1723/1894, 90.97% vs 1462/1894, 77.21%). CONCLUSIONS:Our proposed methods and evaluation demonstrate the validity and rigorousness of the results, which can be used in different applications, including evidence-based medicine, precision medicine, and medical education.
| S-EPMC6928703 | biostudies-literature