Deep learning
Optimisation and Calibration of Bayesian Neural Network for Probabilistic Prediction of Biogas Performance in an Anaerobic Lagoon
Sensors (Basel). 2024 Apr 15;24(8):2537. doi: 10.3390/s24082537.
ABSTRACT
This study aims to enhance diagnostic capabilities for optimising the performance of the anaerobic sewage treatment lagoon at Melbourne Water's Western Treatment Plant (WTP) through a novel machine learning (ML)-based monitoring strategy. This strategy employs ML to make accurate probabilistic predictions of biogas performance by leveraging diverse real-life operational and inspection sensor and other measurement data for asset management, decision making, and structural health monitoring (SHM). The paper commences with data analysis and preprocessing of complex irregular datasets to facilitate efficient learning in an artificial neural network. Subsequently, a Bayesian mixture density neural network model incorporating an attention-based mechanism in bidirectional long short-term memory (BiLSTM) was developed. This probabilistic approach uses a distribution output layer based on the Gaussian mixture model and Monte Carlo (MC) dropout technique in estimating data and model uncertainties, respectively. Furthermore, systematic hyperparameter optimisation revealed that the optimised model achieved a negative log-likelihood (NLL) of 0.074, significantly outperforming other configurations. It achieved an accuracy approximately 9 times greater than the average model performance (NLL = 0.753) and 22 times greater than the worst performing model (NLL = 1.677). Key factors influencing the model's accuracy, such as the input window size and the number of hidden units in the BiLSTM layer, were identified, while the number of neurons in the fully connected layer was found to have no significant impact on accuracy. Moreover, model calibration using the expected calibration error was performed to correct the model's predictive uncertainty. The findings suggest that the inherent data significantly contribute to the overall uncertainty of the model, highlighting the need for more high-quality data to enhance learning. This study lays the groundwork for applying ML in transforming high-value assets into intelligent structures and has broader implications for ML in asset management, SHM applications, and renewable energy sectors.
PMID:38676155 | DOI:10.3390/s24082537
Deep learning for low-data drug discovery: Hurdles and opportunities
Curr Opin Struct Biol. 2024 Apr 25;86:102818. doi: 10.1016/j.sbi.2024.102818. Online ahead of print.
ABSTRACT
Deep learning is becoming increasingly relevant in drug discovery, from de novo design to protein structure prediction and synthesis planning. However, it is often challenged by the small data regimes typical of certain drug discovery tasks. In such scenarios, deep learning approaches-which are notoriously 'data-hungry'-might fail to live up to their promise. Developing novel approaches to leverage the power of deep learning in low-data scenarios is sparking great attention, and future developments are expected to propel the field further. This mini-review provides an overview of recent low-data-learning approaches in drug discovery, analyzing their hurdles and advantages. Finally, we venture to provide a forecast of future research directions in low-data learning for drug discovery.
PMID:38669740 | DOI:10.1016/j.sbi.2024.102818
Brain tumor detection using proper orthogonal decomposition integrated with deep learning networks
Comput Methods Programs Biomed. 2024 Apr 15;250:108167. doi: 10.1016/j.cmpb.2024.108167. Online ahead of print.
ABSTRACT
BACKGROUND AND OBJECTIVE: The central organ of the human nervous system is the brain, which receives and sends stimuli to the various parts of the body to engage in daily activities. Uncontrolled growth of brain cells can result in tumors which affect the normal functions of healthy brain cells. An automatic reliable technique for detecting tumors is imperative to assist medical practitioners in the timely diagnosis of patients. Although machine learning models are being used, with minimal data availability to train, development of low-order based models integrated with machine learning are a tool for reliable detection.
METHODS: In this study, we focus on comparing a low-order model such as proper orthogonal decomposition (POD) coupled with convolutional neural network (CNN) on 2D images from magnetic resonance imaging (MRI) scans to effectively identify brain tumors. The explainability of the coupled POD-CNN prediction output as well as the state-of-the-art pre-trained transfer learning models such as MobileNetV2, Inception-v3, ResNet101, and VGG-19 were explored.
RESULTS: The results showed that CNN predicted tumors with an accuracy of 99.21% whereas POD-CNN performed better with about 1/3rd of computational time at an accuracy of 95.88%. Explainable AI with SHAP showed MobileNetV2 has better prediction in identifying the tumor boundaries.
CONCLUSIONS: Integration of POD with CNN is carried for the first time to detect brain tumor detection with minimal MRI scan data. This study facilitates low-model approaches in machine learning to improve the accuracy and performance of tumor detection.
PMID:38669717 | DOI:10.1016/j.cmpb.2024.108167
Dense Sample Deep Learning
Neural Comput. 2024 Apr 17:1-17. doi: 10.1162/neco_a_01666. Online ahead of print.
ABSTRACT
Deep learning (DL), a variant of the neural network algorithms originally proposed in the 1980s (Rumelhart et al., 1986), has made surprising progress in artificial intelligence (AI), ranging from language translation, protein folding (Jumper et al, 2021), autonomous cars, and, more recently, human-like language models (chatbots). All that seemed intractable until very recently. Despite the growing use of DL networks, little is understood about the learning mechanisms and representations that make these networks effective across such a diverse range of applications. Part of the answer must be the huge scale of the architecture and, of course, the large scale of the data, since not much has changed since 1986. But the nature of deep learned representations remains largely unknown. Unfortunately, training sets with millions or billions of tokens have unknown combinatorics, and networks with millions or billions of hidden units can't easily be visualized and their mechanisms can't be easily revealed. In this letter, we explore these challenges with a large (1.24 million weights; VGG) DL in a novel high-density sample task (five unique tokens with more than 500 exemplars per token), which allows us to more carefully follow the emergence of category structure and feature construction. We use various visualization methods for following the emergence of the classification and the development of the coupling of feature detectors and structures that provide a type of graphical bootstrapping. From these results, we harvest some basic observations of the learning dynamics of DL and propose a new theory of complex feature construction based on our results.
PMID:38669696 | DOI:10.1162/neco_a_01666
Feature shared multi-decoder network using complementary learning for Photon counting CT ring artifact suppression
J Xray Sci Technol. 2024 Apr 25. doi: 10.3233/XST-230396. Online ahead of print.
ABSTRACT
BACKGROUND: Photon-counting computed tomography (Photon counting CT) utilizes photon-counting detectors to precisely count incident photons and measure their energy. These detectors, compared to traditional energy integration detectors, provide better image contrast and material differentiation. However, Photon counting CT tends to show more noticeable ring artifacts due to limited photon counts and detector response variations, unlike conventional spiral CT.
OBJECTIVE: To comprehensively address this issue, we propose a novel feature shared multi-decoder network (FSMDN) that utilizes complementary learning to suppress ring artifacts in Photon counting CT images.
METHODS: Specifically, we employ a feature-sharing encoder to extract context and ring artifact features, facilitating effective feature sharing. These shared features are also independently processed by separate decoders dedicated to the context and ring artifact channels, working in parallel. Through complementary learning, this approach achieves superior performance in terms of artifact suppression while preserving tissue details.
RESULTS: We conducted numerous experiments on Photon counting CT images with three-intensity ring artifacts. Both qualitative and quantitative results demonstrate that our network model performs exceptionally well in correcting ring artifacts at different levels while exhibiting superior stability and robustness compared to the comparison methods.
CONCLUSIONS: In this paper, we have introduced a novel deep learning network designed to mitigate ring artifacts in Photon counting CT images. The results illustrate the viability and efficacy of our proposed network model as a new deep learning-based method for suppressing ring artifacts.
PMID:38669511 | DOI:10.3233/XST-230396
Deep learning-based anatomical position recognition for gastroscopic examination
Technol Health Care. 2024 Apr 18. doi: 10.3233/THC-248004. Online ahead of print.
ABSTRACT
BACKGROUND: The gastroscopic examination is a preferred method for the detection of upper gastrointestinal lesions. However, gastroscopic examination has high requirements for doctors, especially for the strict position and quantity of the archived images. These requirements are challenging for the education and training of junior doctors.
OBJECTIVE: The purpose of this study is to use deep learning to develop automatic position recognition technology for gastroscopic examination.
METHODS: A total of 17182 gastroscopic images in eight anatomical position categories are collected. Convolutional neural network model MogaNet is used to identify all the anatomical positions of the stomach for gastroscopic examination The performance of four models is evaluated by sensitivity, precision, and F1 score.
RESULTS: The average sensitivity of the method proposed is 0.963, which is 0.074, 0.066 and 0.065 higher than ResNet, GoogleNet and SqueezeNet, respectively. The average precision of the method proposed is 0.964, which is 0.072, 0.067 and 0.068 higher than ResNet, GoogleNet, and SqueezeNet, respectively. And the average F1-Score of the method proposed is 0.964, which is 0.074, 0.067 and 0.067 higher than ResNet, GoogleNet, and SqueezeNet, respectively. The results of the t-test show that the method proposed is significantly different from other methods (p< 0.05).
CONCLUSION: The method proposed exhibits the best performance for anatomical positions recognition. And the method proposed can help junior doctors meet the requirements of completeness of gastroscopic examination and the number and position of archived images quickly.
PMID:38669495 | DOI:10.3233/THC-248004
Clinical VMAT machine parameter optimization for localized prostate cancer using deep reinforcement learning
Med Phys. 2024 Apr 26. doi: 10.1002/mp.17100. Online ahead of print.
ABSTRACT
BACKGROUND: Volumetric modulated arc therapy (VMAT) machine parameter optimization (MPO) remains computationally expensive and sensitive to input dose objectives creating challenges for manual and automatic planning. Reinforcement learning (RL) involves machine learning through extensive trial-and-error, demonstrating performance exceeding humans, and existing algorithms in several domains.
PURPOSE: To develop and evaluate an RL approach for VMAT MPO for localized prostate cancer to rapidly and automatically generate deliverable VMAT plans for a clinical linear accelerator (linac) and compare resultant dosimetry to clinical plans.
METHODS: We extended our previous RL approach to enable VMAT MPO of a 3D beam model for a clinical linac through a policy network. It accepts an input state describing the current control point and predicts continuous machine parameters for the next control point, which are used to update the input state, repeating until plan termination. RL training was conducted to minimize a dose-based cost function for prescription of 60 Gy in 20 fractions using CT scans and contours from 136 retrospective localized prostate cancer patients, 20 of which had existing plans used to initialize training. Data augmentation was employed to mitigate over-fitting, and parameter exploration was achieved using Gaussian perturbations. Following training, RL VMAT was applied to an independent cohort of 15 patients, and the resultant dosimetry was compared to clinical plans. We also combined the RL approach with our clinical treatment planning system (TPS) to automate final plan refinement, and creating the potential for manual review and edits as required for clinical use.
RESULTS: RL training was conducted for 5000 iterations, producing 40 000 plans during exploration. Mean ± SD execution time to produce deliverable VMAT plans in the test cohort was 3.3 ± 0.5 s which were automatically refined in the TPS taking an additional 77.4 ± 5.8 s. When normalized to provide equivalent target coverage, the RL+TPS plans provided a similar mean ± SD overall maximum dose of 63.2 ± 0.6 Gy and a lower mean rectum dose of 17.4 ± 7.4 compared to 63.9 ± 1.5 Gy (p = 0.061) and 21.0 ± 6.0 (p = 0.024) for the clinical plans.
CONCLUSIONS: An approach for VMAT MPO using RL for a clinical linac model was developed and applied to automatically generate deliverable plans for localized prostate cancer patients, and when combined with the clinical TPS shows potential to rapidly generate high-quality plans. The RL VMAT approach shows promise to discover advanced linac control policies through trial-and-error, and algorithm limitations and future directions are identified and discussed.
PMID:38669457 | DOI:10.1002/mp.17100
Real-time 3D tracking of swimming microbes using digital holographic microscopy and deep learning
PLoS One. 2024 Apr 26;19(4):e0301182. doi: 10.1371/journal.pone.0301182. eCollection 2024.
ABSTRACT
The three-dimensional swimming tracks of motile microorganisms can be used to identify their species, which holds promise for the rapid identification of bacterial pathogens. The tracks also provide detailed information on the cells' responses to external stimuli such as chemical gradients and physical objects. Digital holographic microscopy (DHM) is a well-established, but computationally intensive method for obtaining three-dimensional cell tracks from video microscopy data. We demonstrate that a common neural network (NN) accelerates the analysis of holographic data by an order of magnitude, enabling its use on single-board computers and in real time. We establish a heuristic relationship between the distance of a cell from the focal plane and the size of the bounding box assigned to it by the NN, allowing us to rapidly localise cells in three dimensions as they swim. This technique opens the possibility of providing real-time feedback in experiments, for example by monitoring and adapting the supply of nutrients to a microbial bioreactor in response to changes in the swimming phenotype of microbes, or for rapid identification of bacterial pathogens in drinking water or clinical samples.
PMID:38669245 | DOI:10.1371/journal.pone.0301182
Understanding Double Descent Using VC-Theoretical Framework
IEEE Trans Neural Netw Learn Syst. 2024 Apr 26;PP. doi: 10.1109/TNNLS.2024.3388873. Online ahead of print.
ABSTRACT
In spite of many successful applications of deep learning (DL) networks, theoretical understanding of their generalization capabilities and limitations remains limited. We present analysis of generalization performance of DL networks for classification under VC-theoretical framework. In particular, we analyze the so-called "double descent" phenomenon, when large overparameterized networks can generalize well, even when they perfectly memorize all available training data. This appears to contradict conventional statistical view that optimal model complexity should reflect an optimal balance between underfitting and overfitting, i.e., the bias-variance trade-off. We present VC-theoretical explanation of double descent phenomenon, under classification setting. Our theoretical explanation is supported by empirical modeling of double descent curves, using analytic VC-bounds, for several learning methods, such as support vector machine (SVM), least squares (LS), and multilayer perceptron classifiers. The proposed VC-theoretical approach enables better understanding of overparameterized estimators during second descent.
PMID:38669171 | DOI:10.1109/TNNLS.2024.3388873
Classification of the quality of canine and feline ventrodorsal and dorsoventral thoracic radiographs through machine learning
Vet Radiol Ultrasound. 2024 Apr 26. doi: 10.1111/vru.13373. Online ahead of print.
ABSTRACT
Thoracic radiographs are an essential diagnostic tool in companion animal medicine and are frequently used as a part of routine workups in patients presenting for coughing, respiratory distress, cardiovascular diseases, and for staging of neoplasia. Quality control is a critical aspect of radiology practice in preventing misdiagnosis and ensuring consistent, accurate, and reliable diagnostic imaging. Implementing an effective quality control procedure in radiology can impact patient outcomes, facilitate clinical decision-making, and decrease healthcare costs. In this study, a machine learning-based quality classification model is suggested for canine and feline thoracic radiographs captured in both ventrodorsal and dorsoventral positions. The problem of quality classification was divided into collimation, positioning, and exposure, and then an automatic classification method was proposed for each based on deep learning and machine learning. We utilized a dataset of 899 radiographs of dogs and cats. Evaluations using fivefold cross-validation resulted in an F1 score and AUC score of 91.33 (95% CI: 88.37-94.29) and 91.10 (95% CI: 88.16-94.03), respectively. Results indicated that the proposed automatic quality classification has the potential to be implemented in radiology clinics to improve radiograph quality and reduce nondiagnostic images.
PMID:38668682 | DOI:10.1111/vru.13373
3D auto-segmentation of biliary structure of living liver donors using magnetic resonance cholangiopancreatography for enhanced preoperative planning
Int J Surg. 2024 Apr 1;110(4):1975-1982. doi: 10.1097/JS9.0000000000001067.
ABSTRACT
BACKGROUND: This study aimed to develop an automated segmentation system for biliary structures using a deep learning model, based on data from magnetic resonance cholangiopancreatography (MRCP).
MATERIALS AND METHODS: Living liver donors who underwent MRCP using the gradient and spin echo technique followed by three-dimensional modeling were eligible for this study. A three-dimensional residual U-Net model was implemented for the deep learning process. Data were divided into training and test sets at a 9:1 ratio. Performance was assessed using the dice similarity coefficient to compare the model's segmentation with the manually labeled ground truth.
RESULTS: The study incorporated 250 cases. There was no difference in the baseline characteristics between the train set (n=225) and test set (n=25). The overall mean Dice Similarity Coefficient was 0.80±0.20 between the ground truth and inference result. The qualitative assessment of the model showed relatively high accuracy especially for the common bile duct (88%), common hepatic duct (92%), hilum (96%), right hepatic duct (100%), and left hepatic duct (96%), while the third-order branch of the right hepatic duct (18.2%) showed low accuracy.
CONCLUSION: The developed automated segmentation model for biliary structures, utilizing MRCP data and deep learning techniques, demonstrated robust performance and holds potential for further advancements in automation.
PMID:38668656 | DOI:10.1097/JS9.0000000000001067
Impact of Deep Learning Denoising Algorithm on Diffusion Tensor Imaging of the Growth Plate on Different Spatial Resolutions
Tomography. 2024 Apr 2;10(4):504-519. doi: 10.3390/tomography10040039.
ABSTRACT
To assess the impact of a deep learning (DL) denoising reconstruction algorithm applied to identical patient scans acquired with two different voxel dimensions, representing distinct spatial resolutions, this IRB-approved prospective study was conducted at a tertiary pediatric center in compliance with the Health Insurance Portability and Accountability Act. A General Electric Signa Premier unit (GE Medical Systems, Milwaukee, WI) was employed to acquire two DTI (diffusion tensor imaging) sequences of the left knee on each child at 3T: an in-plane 2.0 × 2.0 mm2 with section thickness of 3.0 mm and a 2 mm3 isovolumetric voxel; neither had an intersection gap. For image acquisition, a multi-band DTI with a fat-suppressed single-shot spin-echo echo-planar sequence (20 non-collinear directions; b-values of 0 and 600 s/mm2) was utilized. The MR vendor-provided a commercially available DL model which was applied with 75% noise reduction settings to the same subject DTI sequences at different spatial resolutions. We compared DTI tract metrics from both DL-reconstructed scans and non-denoised scans for the femur and tibia at each spatial resolution. Differences were evaluated using Wilcoxon-signed ranked test and Bland-Altman plots. When comparing DL versus non-denoised diffusion metrics in femur and tibia using the 2 mm × 2 mm × 3 mm voxel dimension, there were no significant differences between tract count (p = 0.1, p = 0.14) tract volume (p = 0.1, p = 0.29) or tibial tract length (p = 0.16); femur tract length exhibited a significant difference (p < 0.01). All diffusion metrics (tract count, volume, length, and fractional anisotropy (FA)) derived from the DL-reconstructed scans, were significantly different from the non-denoised scan DTI metrics in both the femur and tibial physes using the 2 mm3 voxel size (p < 0.001). DL reconstruction resulted in a significant decrease in femorotibial FA for both voxel dimensions (p < 0.01). Leveraging denoising algorithms could address the drawbacks of lower signal-to-noise ratios (SNRs) associated with smaller voxel volumes and capitalize on their better spatial resolutions, allowing for more accurate quantification of diffusion metrics.
PMID:38668397 | DOI:10.3390/tomography10040039
Deep Learning Prediction of Axillary Lymph Node Metastasis in Breast Cancer Patients Using Clinical Implication-Applied Preprocessed CT Images
Curr Oncol. 2024 Apr 18;31(4):2278-2288. doi: 10.3390/curroncol31040169.
ABSTRACT
Background: Accurate detection of axillary lymph node (ALN) metastases in breast cancer is crucial for clinical staging and treatment planning. This study aims to develop a deep learning model using clinical implication-applied preprocessed computed tomography (CT) images to enhance the prediction of ALN metastasis in breast cancer patients. Methods: A total of 1128 axial CT images of ALN (538 malignant and 590 benign lymph nodes) were collected from 523 breast cancer patients who underwent preoperative CT scans between January 2012 and July 2022 at Hallym University Medical Center. To develop an optimal deep learning model for distinguishing metastatic ALN from benign ALN, a CT image preprocessing protocol with clinical implications and two different cropping methods (fixed size crop [FSC] method and adjustable square crop [ASC] method) were employed. The images were analyzed using three different convolutional neural network (CNN) architectures (ResNet, DenseNet, and EfficientNet). Ensemble methods involving and combining the selection of the two best-performing CNN architectures from each cropping method were applied to generate the final result. Results: For the two different cropping methods, DenseNet consistently outperformed ResNet and EfficientNet. The area under the receiver operating characteristic curve (AUROC) for DenseNet, using the FSC and ASC methods, was 0.934 and 0.939, respectively. The ensemble model, which combines the performance of the DenseNet121 architecture for both cropping methods, delivered outstanding results with an AUROC of 0.968, an accuracy of 0.938, a sensitivity of 0.980, and a specificity of 0.903. Furthermore, distinct trends observed in gradient-weighted class activation mapping images with the two cropping methods suggest that our deep learning model not only evaluates the lymph node itself, but also distinguishes subtler changes in lymph node margin and adjacent soft tissue, which often elude human interpretation. Conclusions: This research demonstrates the promising performance of a deep learning model in accurately detecting malignant ALNs in breast cancer patients using CT images. The integration of clinical considerations into image processing and the utilization of ensemble methods further improved diagnostic precision.
PMID:38668072 | DOI:10.3390/curroncol31040169
Large Language Models in Oncology: Revolution or Cause for Concern?
Curr Oncol. 2024 Mar 29;31(4):1817-1830. doi: 10.3390/curroncol31040137.
ABSTRACT
The technological capability of artificial intelligence (AI) continues to advance with great strength. Recently, the release of large language models has taken the world by storm with concurrent excitement and concern. As a consequence of their impressive ability and versatility, their provide a potential opportunity for implementation in oncology. Areas of possible application include supporting clinical decision making, education, and contributing to cancer research. Despite the promises that these novel systems can offer, several limitations and barriers challenge their implementation. It is imperative that concerns, such as accountability, data inaccuracy, and data protection, are addressed prior to their integration in oncology. As the progression of artificial intelligence systems continues, new ethical and practical dilemmas will also be approached; thus, the evaluation of these limitations and concerns will be dynamic in nature. This review offers a comprehensive overview of the potential application of large language models in oncology, as well as concerns surrounding their implementation in cancer care.
PMID:38668040 | DOI:10.3390/curroncol31040137
Development and Implementation of an Innovative Framework for Automated Radiomics Analysis in Neuroimaging
J Imaging. 2024 Apr 22;10(4):96. doi: 10.3390/jimaging10040096.
ABSTRACT
Radiomics represents an innovative approach to medical image analysis, enabling comprehensive quantitative evaluation of radiological images through advanced image processing and Machine or Deep Learning algorithms. This technique uncovers intricate data patterns beyond human visual detection. Traditionally, executing a radiomic pipeline involves multiple standardized phases across several software platforms. This could represent a limit that was overcome thanks to the development of the matRadiomics application. MatRadiomics, a freely available, IBSI-compliant tool, features its intuitive Graphical User Interface (GUI), facilitating the entire radiomics workflow from DICOM image importation to segmentation, feature selection and extraction, and Machine Learning model construction. In this project, an extension of matRadiomics was developed to support the importation of brain MRI images and segmentations in NIfTI format, thus extending its applicability to neuroimaging. This enhancement allows for the seamless execution of radiomic pipelines within matRadiomics, offering substantial advantages to the realm of neuroimaging.
PMID:38667994 | DOI:10.3390/jimaging10040096
Enhancing Apple Cultivar Classification Using Multiview Images
J Imaging. 2024 Apr 17;10(4):94. doi: 10.3390/jimaging10040094.
ABSTRACT
Apple cultivar classification is challenging due to the inter-class similarity and high intra-class variations. Human experts do not rely on single-view features but rather study each viewpoint of the apple to identify a cultivar, paying close attention to various details. Following our previous work, we try to establish a similar multiview approach for machine-learning (ML)-based apple classification in this paper. In our previous work, we studied apple classification using one single view. While these results were promising, it also became clear that one view alone might not contain enough information in the case of many classes or cultivars. Therefore, exploring multiview classification for this task is the next logical step. Multiview classification is nothing new, and we use state-of-the-art approaches as a base. Our goal is to find the best approach for the specific apple classification task and study what is achievable with the given methods towards our future goal of applying this on a mobile device without the need for internet connectivity. In this study, we compare an ensemble model with two cases where we use single networks: one without view specialization trained on all available images without view assignment and one where we combine the separate views into a single image of one specific instance. The two latter options reflect dataset organization and preprocessing to allow the use of smaller models in terms of stored weights and number of operations than an ensemble model. We compare the different approaches based on our custom apple cultivar dataset. The results show that the state-of-the-art ensemble provides the best result. However, using images with combined views shows a decrease in accuracy by 3% while requiring only 60% of the memory for weights. Thus, simpler approaches with enhanced preprocessing can open a trade-off for classification tasks on mobile devices.
PMID:38667992 | DOI:10.3390/jimaging10040094
Denoising of Optical Coherence Tomography Images in Ophthalmology Using Deep Learning: A Systematic Review
J Imaging. 2024 Apr 1;10(4):86. doi: 10.3390/jimaging10040086.
ABSTRACT
Imaging from optical coherence tomography (OCT) is widely used for detecting retinal diseases, localization of intra-retinal boundaries, etc. It is, however, degraded by speckle noise. Deep learning models can aid with denoising, allowing clinicians to clearly diagnose retinal diseases. Deep learning models can be considered as an end-to-end framework. We selected denoising studies that used deep learning models with retinal OCT imagery. Each study was quality-assessed through image quality metrics (including the peak signal-to-noise ratio-PSNR, contrast-to-noise ratio-CNR, and structural similarity index metric-SSIM). Meta-analysis could not be performed due to heterogeneity in the methods of the studies and measurements of their performance. Multiple databases (including Medline via PubMed, Google Scholar, Scopus, Embase) and a repository (ArXiv) were screened for publications published after 2010, without any limitation on language. From the 95 potential studies identified, a total of 41 were evaluated thoroughly. Fifty-four of these studies were excluded after full text assessment depending on whether deep learning (DL) was utilized or the dataset and results were not effectively explained. Numerous types of OCT images are mentioned in this review consisting of public retinal image datasets utilized purposefully for denoising OCT images (n = 37) and the Optic Nerve Head (ONH) (n = 4). A wide range of image quality metrics was used; PSNR and SNR that ranged between 8 and 156 dB. The minority of studies (n = 8) showed a low risk of bias in all domains. Studies utilizing ONH images produced either a PSNR or SNR value varying from 8.1 to 25.7 dB, and that of public retinal datasets was 26.4 to 158.6 dB. Further analysis on denoising models was not possible due to discrepancies in reporting that did not allow useful pooling. An increasing number of studies have investigated denoising retinal OCT images using deep learning, with a range of architectures being implemented. The reported increase in image quality metrics seems promising, while study and reporting quality are currently low.
PMID:38667984 | DOI:10.3390/jimaging10040086
Real-Time Dynamic Intelligent Image Recognition and Tracking System for Rockfall Disasters
J Imaging. 2024 Mar 26;10(4):78. doi: 10.3390/jimaging10040078.
ABSTRACT
Taiwan, frequently affected by extreme weather causing phenomena such as earthquakes and typhoons, faces a high incidence of rockfall disasters due to its largely mountainous terrain. These disasters have led to numerous casualties, government compensation cases, and significant transportation safety impacts. According to the National Science and Technology Center for Disaster Reduction records from 2010 to 2022, 421 out of 866 soil and rock disasters occurred in eastern Taiwan, causing traffic disruptions due to rockfalls. Since traditional sensors of disaster detectors only record changes after a rockfall, there is no system in place to detect rockfalls as they occur. To combat this, a rockfall detection and tracking system using deep learning and image processing technology was developed. This system includes a real-time image tracking and recognition system that integrates YOLO and image processing technology. It was trained on a self-collected dataset of 2490 high-resolution RGB images. The system's performance was evaluated on 30 videos featuring various rockfall scenarios. It achieved a mean Average Precision (mAP50) of 0.845 and mAP50-95 of 0.41, with a processing time of 125 ms. Tested on advanced hardware, the system proves effective in quickly tracking and identifying hazardous rockfalls, offering a significant advancement in disaster management and prevention.
PMID:38667976 | DOI:10.3390/jimaging10040078
PyDTS: A Python Toolkit for Deep Learning Time Series Modelling
Entropy (Basel). 2024 Mar 31;26(4):311. doi: 10.3390/e26040311.
ABSTRACT
In this article, the topic of time series modelling is discussed. It highlights the criticality of analysing and forecasting time series data across various sectors, identifying five primary application areas: denoising, forecasting, nonlinear transient modelling, anomaly detection, and degradation modelling. It further outlines the mathematical frameworks employed in a time series modelling task, categorizing them into statistical, linear algebra, and machine- or deep-learning-based approaches, with each category serving distinct dimensions and complexities of time series problems. Additionally, the article reviews the extensive literature on time series modelling, covering statistical processes, state space representations, and machine and deep learning applications in various fields. The unique contribution of this work lies in its presentation of a Python-based toolkit for time series modelling (PyDTS) that integrates popular methodologies and offers practical examples and benchmarking across diverse datasets.
PMID:38667865 | DOI:10.3390/e26040311
Automated osteoporosis classification and T-score prediction using hip radiographs via deep learning algorithm
Ther Adv Musculoskelet Dis. 2024 Apr 24;16:1759720X241237872. doi: 10.1177/1759720X241237872. eCollection 2024.
ABSTRACT
BACKGROUND: Despite being the gold standard for diagnosing osteoporosis, dual-energy X-ray absorptiometry (DXA) is an underutilized screening tool for osteoporosis.
OBJECTIVES: This study proposed and validated a controllable feature layer of a convolutional neural network (CNN) model with a preprocessing image algorithm to classify osteoporosis and predict T-score on the proximal hip region via simple hip radiographs.
DESIGN: This was a single-center, retrospective study.
METHODS: An image dataset of 3460 unilateral hip images from 1730 patients (age ⩾50 years) was retrospectively collected with matched DXA assessment for T-score for the targeted proximal hip regions to train (2473 unilateral hip images from 1430 patients) and test (497 unilateral hip images from 300 patients) the proposed CNN model. All images were processed with a fully automated CNN model, X1AI-Osteo.
RESULTS: The proposed screening tool illustrated a better performance (sensitivity: 97.2%; specificity: 95.6%; positive predictive value: 95.7%; negative predictive value: 97.1%; area under the curve: 0.96) than the open-sourced CNN models in predicting osteoporosis. Moreover, when combining variables, including age, body mass index, and sex as features in the training metric, there was high consistency in the T-score on the targeted hip regions between the proposed CNN model and the DXA (r = 0.996, p < 0.001).
CONCLUSION: The proposed CNN model may identify osteoporosis and predict T-scores on the targeted hip regions from simple hip radiographs with high accuracy, highlighting the future application for population-based opportunistic osteoporosis screening with low cost and high adaptability for a broader population at risk.
TRIAL REGISTRATION: TMU-JIRB N201909036.
PMID:38665415 | PMC:PMC11044771 | DOI:10.1177/1759720X241237872