Sci Rep. 2024 Mar 9;14(1):5791. doi: 10.1038/s41598-024-56389-4.

ABSTRACT

Diabetic retinopathy (DR) is a serious ocular complication that can pose a serious risk to a patient's vision and overall health. Currently, the automatic grading of DR is mainly using deep learning techniques. However, the lesion information in DR images is complex, variable in shape and size, and randomly distributed in the images, which leads to some shortcomings of the current research methods, i.e., it is difficult to effectively extract the information of these various features, and it is difficult to establish the connection between the lesion information in different regions. To address these shortcomings, we design a multi-scale dynamic fusion (MSDF) module and combine it with graph convolution operations to propose a multi-scale dynamic graph convolutional network (MDGNet) in this paper. MDGNet firstly uses convolution kernels with different sizes to extract features with different shapes and sizes in the lesion regions, and then automatically learns the corresponding weights for feature fusion according to the contribution of different features to model grading. Finally, the graph convolution operation is used to link the lesion features in different regions. As a result, our proposed method can effectively combine local and global features, which is beneficial for the correct DR grading. We evaluate the effectiveness of method on two publicly available datasets, namely APTOS and DDR. Extensive experiments demonstrate that our proposed MDGNet achieves the best grading results on APTOS and DDR, and is more accurate and diverse for the extraction of lesion information.

PMID:38461342 | DOI:10.1038/s41598-024-56389-4

Ultrasound Med Biol. 2024 Mar 8:S0301-5629(24)00030-9. doi: 10.1016/j.ultrasmedbio.2024.01.016. Online ahead of print.

ABSTRACT

OBJECTIVE: Spontaneous echo contrast (SEC) is a vascular ultrasound finding associated with increased thromboembolism risk. However, identification requires expert determination and clinician time to report. We developed a deep learning model that can automatically identify SEC. Our model can be applied retrospectively without deviating from routine clinical practice. The retrospective nature of our model means future works could scan archival data to opportunistically correlate SEC findings with documented clinical outcomes.

METHODS: We curated a data set of 801 archival acquisitions along the femoral vein from 201 patients. We used a multisequence convolutional neural network (CNN) with ResNetv2 backbone and visualized keyframe importance using soft attention. We evaluated SEC prediction performance using an 80/20 train/test split. We report receiver operating characteristic area under the curve (ROC-AUC), along with the Youden threshold-associated sensitivity, specificity, F1 score, true negative, false negative, false positive and true positive.

RESULTS: Using soft attention, we can identify SEC with an AUC of 0.74, sensitivity of 0.73 and specificity of 0.68. Without soft attention, our model achieves an AUC of 0.69, sensitivity of 0.71 and specificity of 0.60. Additionally, we provide attention visualizations and note that our model assigns higher attention score to ultrasound frames containing more vessel lumen.

CONCLUSION: Our multisequence CNN model can identify the presence of SEC from ultrasound keyframes with an AUC of 0.74, which could enable screening applications and enable more SEC data discovery. The model does not require the expert intervention or additional clinician reporting time that are currently significant barriers to SEC adoption. Model and processed data sets are publicly available at https://github.com/Ouwen/automatic-spontaneous-echo-contrast.

PMID:38461036 | DOI:10.1016/j.ultrasmedbio.2024.01.016

BMJ Open Respir Res. 2024 Mar 9;11(1):e002226. doi: 10.1136/bmjresp-2023-002226.

ABSTRACT

PURPOSE: Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is the primary cause of death in patients with IPF, characterised by diffuse, bilateral ground-glass opacification on high-resolution CT (HRCT). This study proposes a three-dimensional (3D)-based deep learning algorithm for classifying AE-IPF using HRCT images.

MATERIALS AND METHODS: A novel 3D-based deep learning algorithm, SlowFast, was developed by applying a database of 306 HRCT scans obtained from two centres. The scans were divided into four separate subsets (training set, n=105; internal validation set, n=26; temporal test set 1, n=79; and geographical test set 2, n=96). The final training data set consisted of 1050 samples with 33 600 images for algorithm training. Algorithm performance was evaluated using accuracy, sensitivity, specificity, positive predictive value, negative predictive value, receiver operating characteristic (ROC) curve and weighted κ coefficient.

RESULTS: The accuracy of the algorithm in classifying AE-IPF on the test sets 1 and 2 was 93.9% and 86.5%, respectively. Interobserver agreements between the algorithm and the majority opinion of the radiologists were good (κw=0.90 for test set 1 and κw=0.73 for test set 2, respectively). The ROC accuracy of the algorithm for classifying AE-IPF on the test sets 1 and 2 was 0.96 and 0.92, respectively. The algorithm performance was superior to visual analysis in accurately diagnosing radiological findings. Furthermore, the algorithm's categorisation was a significant predictor of IPF progression.

CONCLUSIONS: The deep learning algorithm provides high auxiliary diagnostic efficiency in patients with AE-IPF and may serve as a useful clinical aid for diagnosis.

PMID:38460976 | DOI:10.1136/bmjresp-2023-002226

Comput Biol Med. 2024 Feb 28;172:108235. doi: 10.1016/j.compbiomed.2024.108235. Online ahead of print.

ABSTRACT

Cardiovascular diseases (CVD) are a leading cause of death globally, and result in significant morbidity and reduced quality of life. The electrocardiogram (ECG) plays a crucial role in CVD diagnosis, prognosis, and prevention; however, different challenges still remain, such as an increasing unmet demand for skilled cardiologists capable of accurately interpreting ECG. This leads to higher workload and potential diagnostic inaccuracies. Data-driven approaches, such as machine learning (ML) and deep learning (DL) have emerged to improve existing computer-assisted solutions and enhance physicians' ECG interpretation of the complex mechanisms underlying CVD. However, many ML and DL models used to detect ECG-based CVD suffer from a lack of explainability, bias, as well as ethical, legal, and societal implications (ELSI). Despite the critical importance of these Trustworthy Artificial Intelligence (AI) aspects, there is a lack of comprehensive literature reviews that examine the current trends in ECG-based solutions for CVD diagnosis or prognosis that use ML and DL models and address the Trustworthy AI requirements. This review aims to bridge this knowledge gap by providing a systematic review to undertake a holistic analysis across multiple dimensions of these data-driven models such as type of CVD addressed, dataset characteristics, data input modalities, ML and DL algorithms (with a focus on DL), and aspects of Trustworthy AI like explainability, bias and ethical considerations. Additionally, within the analyzed dimensions, various challenges are identified. To these, we provide concrete recommendations, equipping other researchers with valuable insights to understand the current state of the field comprehensively.

PMID:38460311 | DOI:10.1016/j.compbiomed.2024.108235

Comput Biol Med. 2024 Mar 2;172:108239. doi: 10.1016/j.compbiomed.2024.108239. Online ahead of print.

ABSTRACT

The identification of compound-protein interactions (CPIs) plays a vital role in drug discovery. However, the huge cost and labor-intensive nature in vitro and vivo experiments make it urgent for researchers to develop novel CPI prediction methods. Despite emerging deep learning methods have achieved promising performance in CPI prediction, they also face ongoing challenges: (i) providing bidirectional interpretability from both the chemical and biological perspective for the prediction results; (ii) comprehensively evaluating model generalization performance; (iii) demonstrating the practical applicability of these models. To overcome the challenges posed by current deep learning methods, we propose a cross multi-head attention oriented bidirectional interpretable CPI prediction model (CmhAttCPI). First, CmhAttCPI takes molecular graphs and protein sequences as inputs, utilizing the GCW module to learn atom features and the CNN module to learn residue features, respectively. Second, the model applies cross multi-head attention module to compute attention weights for atoms and residues. Finally, CmhAttCPI employs a fully connected neural network to predict scores for CPIs. We evaluated the performance of CmhAttCPI on balanced datasets and imbalanced datasets. The results consistently show that CmhAttCPI outperforms multiple state-of-the-art methods. We constructed three scenarios based on compound and protein clustering and comprehensively evaluated the model generalization ability within these scenarios. The results demonstrate that the generalization ability of CmhAttCPI surpasses that of other models. Besides, the visualizations of attention weights reveal that CmhAttCPI provides chemical and biological interpretation for CPI prediction. Moreover, case studies confirm the practical applicability of CmhAttCPI in discovering anticancer candidates.

PMID:38460309 | DOI:10.1016/j.compbiomed.2024.108239

Sci Rep. 2024 Mar 9;14(1):5809. doi: 10.1038/s41598-024-56476-6.

ABSTRACT

This study aimed to develop a deep learning model to assess the quality of fetal echocardiography and to perform prospective clinical validation. The model was trained on data from the 18-22-week anomaly scan conducted in seven hospitals from 2008 to 2018. Prospective validation involved 100 patients from two hospitals. A total of 5363 images from 2551 pregnancies were used for training and validation. The model's segmentation accuracy depended on image quality measured by a quality score (QS). It achieved an overall average accuracy of 0.91 (SD 0.09) across the test set, with images having above-average QS scoring 0.97 (SD 0.03). During prospective validation of 192 images, clinicians rated 44.8% (SD 9.8) of images as equal in quality, 18.69% (SD 5.7) favoring auto-captured images and 36.51% (SD 9.0) preferring manually captured ones. Images with above average QS showed better agreement on segmentations (p < 0.001) and QS (p < 0.001) with fetal medicine experts. Auto-capture saved additional planes beyond protocol requirements, resulting in more comprehensive echocardiographies. Low QS had adverse effect on both model performance and clinician's agreement with model feedback. The findings highlight the importance of developing and evaluating AI models based on 'noisy' real-life data rather than pursuing the highest accuracy possible with retrospective academic-grade data.

PMID:38461322 | DOI:10.1038/s41598-024-56476-6

BMC Bioinformatics. 2024 Mar 9;25(1):105. doi: 10.1186/s12859-024-05723-8.

ABSTRACT

MOTIVATION: The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the characteristics of the drug itself and the genomic characteristics of the patient can greatly influence the results of cancer drug response. Therefore, accurate, efficient, and comprehensive methods for drug feature extraction and genomics integration are crucial to improve the prediction accuracy.

RESULTS: Accurate prediction of cancer drug response is vital for guiding the design of anticancer drugs. In this study, we propose an end-to-end deep learning model named DeepAEG which is based on a complete-graph update mode to predict IC50. Specifically, we integrate an edge update mechanism on the basis of a hybrid graph convolutional network to comprehensively learn the potential high-dimensional representation of topological structures in drugs, including atomic characteristics and chemical bond information. Additionally, we present a novel approach for enhancing simplified molecular input line entry specification data by employing sequence recombination to eliminate the defect of single sequence representation of drug molecules. Our extensive experiments show that DeepAEG outperforms other existing methods across multiple evaluation parameters in multiple test sets. Furthermore, we identify several potential anticancer agents, including bortezomib, which has proven to be an effective clinical treatment option. Our results highlight the potential value of DeepAEG in guiding the design of specific cancer treatment regimens.

PMID:38461284 | DOI:10.1186/s12859-024-05723-8

Sci Rep. 2024 Mar 9;14(1):5787. doi: 10.1038/s41598-024-56522-3.

ABSTRACT

All-optical plasmonic switches (AOPSs) utilizing surface plasmon polaritons are well-suited for integration into photonic integrated circuits (PICs) and play a crucial role in advancing all-optical signal processing. The current AOPS design methods still rely on trial-and-error or empirical approaches. In contrast, recent deep learning (DL) advances have proven highly effective as computational tools, offering an alternative means to accelerate nanophotonics simulations. This paper proposes an innovative approach utilizing DL for spectrum prediction and inverse design of AOPS. The switches employ circular nonlinear plasmonic ring resonators (NPRRs) composed of interconnected metal-insulator-metal waveguides with a ring resonator. The NPRR switching performance is shown using the nonlinear Kerr effect. The forward model presented in this study demonstrates superior computational efficiency when compared to the finite-difference time-domain method. The model analyzes various structural parameters to predict transmission spectra with a distinctive dip. Inverse modeling enables the prediction of design parameters for desired transmission spectra. This model provides a rapid estimation of design parameters, offering a clear advantage over time-intensive conventional optimization approaches. The loss of prediction for both the forward and inverse models, when compared to simulations, is exceedingly low and on the order of 10-4. The results confirm the suitability of employing DL for forward and inverse design of AOPSs in PICs.

PMID:38461205 | DOI:10.1038/s41598-024-56522-3

Chest. 2024 Mar;165(3):e87-e89. doi: 10.1016/j.chest.2023.10.039.

NO ABSTRACT

PMID:38461027 | DOI:10.1016/j.chest.2023.10.039

Anal Biochem. 2024 Mar 7:115491. doi: 10.1016/j.ab.2024.115491. Online ahead of print.

ABSTRACT

Bioactive peptides can hinder oxidative processes and microbial spoilage in foodstuffs and play important roles in treating diverse diseases and disorders. While most of the methods focus on single-functional bioactive peptides and have obtained promising prediction performance, it is still a significant challenge to accurately detect complex and diverse functions simultaneously with the quick increase of multi-functional bioactive peptides. In contrast to previous research on multi-functional bioactive peptide prediction based solely on sequence, we propose a novel multimodal dual-branch (MMDB) lightweight deep learning model that designs two different branches to effectively capture the complementary information of peptide sequence and structural properties. Specifically, a multi-scale dilated convolution with Bi-LSTM branch is presented to effectively model the different scales sequence properties of peptides while a multi-layer convolution branch is proposed to capture structural information. To the best of our knowledge, this is the first effective extraction of peptide sequence features using multi-scale dilated convolution without parameter increase. Multimodal features from both branches are integrated via a fully connected layer for multi-label classification. Compared to state-of-the-art methods, our MMDB model exhibits competitive results across metrics, with a 9.1% Coverage increase and 5.3% and 3.5% improvements in Precision and Accuracy, respectively.

PMID:38460901 | DOI:10.1016/j.ab.2024.115491

Mol Divers. 2024 Mar 9. doi: 10.1007/s11030-024-10811-1. Online ahead of print.

ABSTRACT

Contemporary research has convincingly demonstrated that upregulation of G protein-coupled receptor 183 (GPR183), orchestrated by its endogenous agonist, 7α,25-dihydroxyxcholesterol (7α,25-OHC), leads to the development of cancer, diabetes, multiple sclerosis, infectious, and inflammatory diseases. A recent study unveiled the cryo-EM structure of 7α,25-OHC bound GPR183 complex, presenting an untapped opportunity for computational exploration of potential GPR183 inhibitors, which served as our inspiration for the current work. A predictive and validated two-dimensional QSAR model using genetic algorithm (GA) and multiple linear regression (MLR) on experimental GPR183 inhibition data was developed. QSAR study highlighted that structural features like dissimilar electronegative atoms, quaternary carbon atoms, and CH2RX fragment (X: heteroatoms) influence positively, while the existence of oxygen atoms with a topological separation of 3, negatively affects GPR183 inhibitory activity. Post assessment of true external set prediction capability, the MLR model was deployed to screen 12,449 DrugBank compounds, followed by a screening pipeline involving molecular docking, druglikeness, ADMET, protein-ligand stability assessment using deep learning algorithm, molecular dynamics, and molecular mechanics. The current findings strongly evidenced DB05790 as a potential lead for prospective interference of oxysterol-mediated GPR183 overexpression, warranting further in vitro and in vivo validation.

PMID:38460065 | DOI:10.1007/s11030-024-10811-1

J Stomatol Oral Maxillofac Surg. 2024 Mar 6:101817. doi: 10.1016/j.jormas.2024.101817. Online ahead of print.

ABSTRACT

OBJECTIVE: The aim of this study is to determine if a deep learning (DL) model can predict the surgical difficulty for impacted maxillary third molar tooth using panoramic images before surgery.

MATERIALS AND METHODS: The dataset consists of 708 panoramic radiographs of the patients who applied to the Oral and Maxillofacial Surgery Clinic for various reasons. Each maxillary third molar difficulty was scored based on dept (V), angulation (H), relation with maxillary sinus (S), and relation with ramus (R) on panoramic images. The YoloV5x architecture was used to perform automatic segmentation and classification. To prevent re-testing of images, participate in the training, the data set was subdivided as: 80 % training, 10 % validation, and 10 % test group.

RESULTS: Impacted Upper Third Molar Segmentation model showed best success on sensitivity, precision and F1 score with 0,9705, 0,9428 and 0,9565, respectively. S-model had a lesser sensitivity, precision and F1 score than the other models with 0,8974, 0,6194, 0,7329, respectively.

CONCLUSION: The results showed that the proposed DL model could be effective for predicting the surgical difficulty of an impacted maxillary third molar tooth using panoramic radiographs and this approach might help as a decision support mechanism for the clinicians in peri-surgical period.

PMID:38458545 | DOI:10.1016/j.jormas.2024.101817

Anal Biochem. 2024 Mar 6:115492. doi: 10.1016/j.ab.2024.115492. Online ahead of print.

ABSTRACT

DNA 4 mC plays a crucial role in the genetic expression process of organisms. However, existing deep learning algorithms have shortcomings in the ability to represent DNA sequence features. In this paper, we propose a 4 mC site identification algorithm, DNABert-4mC, based on a fusion of the pruned pre-training DNABert-Pruning model and artificial feature encoding to identify 4 mC sites. The algorithm prunes and compresses the DNABert model, resulting in the pruned pre-training model DNABert-Pruning. This model reduces the number of parameters and removes redundancy from output features, yielding more precise feature representations while upholding accuracy.Simultaneously, the algorithm constructs an artificial feature encoding module to assist the DNABert-Pruning model in feature representation, effectively supplementing the information that is missing from the pre-trained features. The algorithm also introduces the AFF-4mC fusion strategy, which combines artificial feature encoding with the DNABert-Pruning model, to improve the feature representation capability of DNA sequences in multi-semantic spaces and better extract 4 mC sites and the distribution of nucleotide importance within the sequence. In experiments on six independent test sets, the DNABert-4mC algorithm achieved an average AUC value of 93.81%, outperforming seven other advanced algorithms with improvements of 2.05%, 5.02%, 11.32%, 5.90%, 12.02%, 2.42% and 2.34%, respectively.

PMID:38458307 | DOI:10.1016/j.ab.2024.115492

J Neurosci Methods. 2024 Mar 6:110108. doi: 10.1016/j.jneumeth.2024.110108. Online ahead of print.

ABSTRACT

BACKGROUND: Motor-Imagery-based Brain-Computer Interface (MI-BCI) is a promising technology to assist communication, movement, and neurological rehabilitation for motor-impaired individuals. Electroencephalography (EEG) decoding techniques using deep learning (DL) possess noteworthy advantages due to automatic feature extraction and end-to-end learning. However, the DL-based EEG decoding models tend to show large variations due to intersubject variability of EEG, which results from inconsistencies of different subjects' optimal hyperparameters.

NEW METHODS: This study proposes a multi-branch multi-attention mechanism EEGNet model (MBMANet) for robust decoding. It applies the multi-branch EEGNet structure to achieve various feature extractions. Further, the different attention mechanisms introduced in each branch attain diverse adaptive weight adjustments. This combination of multi-branch and multi-attention mechanisms allows for multi-level feature fusion to provide robust decoding for different subjects.

RESULTS: The MBMANet model has a four-classification accuracy of 83.18% and kappa of 0.776 on the BCI Competition IV-2a dataset, which outperforms other eight CNN-based decoding models. This consistently satisfactory performance across all nine subjects indicates that the proposed model is robust.

CONCLUSIONS: The combine of multi-branch and multi-attention mechanisms empowers the DL-based models to adaptively learn different EEG features, which provides a feasible solution for dealing with data variability. It also gives the MBMANet model more accurate decoding of motion intentions and lower training costs, thus improving the MI-BCI's utility and robustness.

PMID:38458260 | DOI:10.1016/j.jneumeth.2024.110108

Talanta. 2024 Mar 7;273:125868. doi: 10.1016/j.talanta.2024.125868. Online ahead of print.

ABSTRACT

Magnetic nanoparticle (MNP)-based immunochromatographic tests (ICTs) display long-term stability and an enhanced capability for multiplex biomarker detection, surpassing conventional gold nanoparticles (AuNPs) and fluorescence-based ICTs. In this study, we innovatively developed zwitterionic silica-coated MNPs (MNP@Si-Zwit/COOH) with outstanding antifouling capabilities and effectively utilised them for the simultaneous identification of the nucleocapsid protein (N protein) of the severe acute respiratory syndrome coronavirus (SARS-CoV-2) and influenza A/B. The carboxyl-functionalised MNPs with 10% zwitterionic ligands (MNP@Si-Zwit 10/COOH) exhibited a wide linear dynamic detection range and the most pronounced signal-to-noise ratio when used as probes in the ICT. The relative limit of detection (LOD) values were achieved in 12 min by using a magnetic assay reader (MAR), with values of 0.0062 ng/mL for SARS-CoV-2 and 0.0051 and 0.0147 ng/mL, respectively, for the N protein of influenza A and influenza B. By integrating computer vision and deep learning to enhance the image processing of immunoassay results for multiplex detection, a classification accuracy in the range of 0.9672-0.9936 was achieved for evaluating the three proteins at concentrations of 0, 0.1, 1, and 10 ng/mL. The proposed MNP-based ICT for the multiplex diagnosis of biomarkers holds substantial promise for applications in both medical institutions and self-administered diagnostic settings.

PMID:38458085 | DOI:10.1016/j.talanta.2024.125868

Comput Methods Programs Biomed. 2024 Feb 29;248:108104. doi: 10.1016/j.cmpb.2024.108104. Online ahead of print.

ABSTRACT

BACKGROUND AND OBJECTIVE: Survival analysis plays an essential role in the medical field for optimal treatment decision-making. Recently, survival analysis based on the deep learning (DL) approach has been proposed and is demonstrating promising results. However, developing an ideal prediction model requires integrating large datasets across multiple institutions, which poses challenges concerning medical data privacy.

METHODS: In this paper, we propose FedSurv, an asynchronous federated learning (FL) framework designed to predict survival time using clinical information and positron emission tomography (PET)-based features. This study used two datasets: a public radiogenic dataset of non-small cell lung cancer (NSCLC) from the Cancer Imaging Archive (RNSCLC), and an in-house dataset from the Chonnam National University Hwasun Hospital (CNUHH) in South Korea, consisting of clinical risk factors and F-18 fluorodeoxyglucose (FDG) PET images in NSCLC patients. Initially, each dataset was divided into multiple clients according to histological attributes, and each client was trained using the proposed DL model to predict individual survival time. The FL framework collected weights and parameters from the clients, which were then incorporated into the global model. Finally, the global model aggregated all weights and parameters and redistributed the updated model weights to each client. We evaluated different frameworks including single-client-based approach, centralized learning and FL.

RESULTS: We evaluated our method on two independent datasets. First, on the RNSCLC dataset, the mean absolute error (MAE) was 490.80±22.95 d and the C-Index was 0.69±0.01. Second, on the CNUHH dataset, the MAE was 494.25±40.16 d and the C-Index was 0.71±0.01. The FL approach achieved centralized method performance in PET-based survival time prediction and outperformed single-client-based approaches.

CONCLUSIONS: Our results demonstrated the feasibility and effectiveness of employing FL for individual survival prediction in NSCLC patients, using clinical information and PET-based features.

PMID:38457959 | DOI:10.1016/j.cmpb.2024.108104

Radiat Oncol. 2024 Mar 8;19(1):33. doi: 10.1186/s13014-024-02428-3.

ABSTRACT

BACKGROUND: Radiotherapy (RT) is an important treatment modality for patients with brain malignancies. Traditionally, computed tomography (CT) images are used for RT treatment planning whereas magnetic resonance imaging (MRI) images are used for tumor delineation. Therefore, MRI and CT need to be registered, which is an error prone process. The purpose of this clinical study is to investigate the clinical feasibility of a deep learning-based MRI-only workflow for brain radiotherapy, that eliminates the registration uncertainty through calculation of a synthetic CT (sCT) from MRI data.

METHODS: A total of 54 patients with an indication for radiation treatment of the brain and stereotactic mask immobilization will be recruited. All study patients will receive standard therapy and imaging including both CT and MRI. All patients will receive dedicated RT-MRI scans in treatment position. An sCT will be reconstructed from an acquired MRI DIXON-sequence using a commercially available deep learning solution on which subsequent radiotherapy planning will be performed. Through multiple quality assurance (QA) measures and reviews during the course of the study, the feasibility of an MRI-only workflow and comparative parameters between sCT and standard CT workflow will be investigated holistically. These QA measures include feasibility and quality of image guidance (IGRT) at the linear accelerator using sCT derived digitally reconstructed radiographs in addition to potential dosimetric deviations between the CT and sCT plan. The aim of this clinical study is to establish a brain MRI-only workflow as well as to identify risks and QA mechanisms to ensure a safe integration of deep learning-based sCT into radiotherapy planning and delivery.

DISCUSSION: Compared to CT, MRI offers a superior soft tissue contrast without additional radiation dose to the patients. However, up to now, even though the dosimetrical equivalence of CT and sCT has been shown in several retrospective studies, MRI-only workflows have still not been widely adopted. The present study aims to determine feasibility and safety of deep learning-based MRI-only radiotherapy in a holistic manner incorporating the whole radiotherapy workflow.

TRIAL REGISTRATION: NCT06106997.

PMID:38459584 | DOI:10.1186/s13014-024-02428-3

J Imaging Inform Med. 2024 Mar 8. doi: 10.1007/s10278-024-01057-2. Online ahead of print.

ABSTRACT

Magnetic resonance imaging (MRI) occupies a pivotal position within contemporary diagnostic imaging modalities, offering non-invasive and radiation-free scanning. Despite its significance, MRI's principal limitation is the protracted data acquisition time, which hampers broader practical application. Promising deep learning (DL) methods for undersampled magnetic resonance (MR) image reconstruction outperform the traditional approaches in terms of speed and image quality. However, the intricate inter-coil correlations have been insufficiently addressed, leading to an underexploitation of the rich information inherent in multi-coil acquisitions. In this article, we proposed a method called "Multi-coil Feature Fusion Variation Network" (MFFVN), which introduces an encoder to extract the feature from multi-coil MR image directly and explicitly, followed by a feature fusion operation. Coil reshaping enables the 2D network to achieve satisfactory reconstruction results, while avoiding the introduction of a significant number of parameters and preserving inter-coil information. Compared with VN, MFFVN yields an improvement in the average PSNR and SSIM of the test set, registering enhancements of 0.2622 dB and 0.0021 dB respectively. This uplift can be attributed to the integration of feature extraction and fusion stages into the network's architecture, thereby effectively leveraging and combining the multi-coil information for enhanced image reconstruction quality. The proposed method outperforms the state-of-the-art methods on fastMRI dataset of multi-coil brains under a fourfold acceleration factor without incurring substantial computation overhead.

PMID:38459398 | DOI:10.1007/s10278-024-01057-2

Nat Methods. 2024 Mar 8. doi: 10.1038/s41592-024-02210-z. Online ahead of print.

ABSTRACT

Cryo-electron tomography (cryo-ET) enables observation of macromolecular complexes in their native, spatially contextualized cellular environment. Cryo-ET processing software to visualize such complexes at nanometer resolution via iterative alignment and averaging are well developed but rely upon assumptions of structural homogeneity among the complexes of interest. Recently developed tools allow for some assessment of structural diversity but have limited capacity to represent highly heterogeneous structures, including those undergoing continuous conformational changes. Here we extend the highly expressive cryoDRGN (Deep Reconstructing Generative Networks) deep learning architecture, originally created for single-particle cryo-electron microscopy analysis, to cryo-ET. Our new tool, tomoDRGN, learns a continuous low-dimensional representation of structural heterogeneity in cryo-ET datasets while also learning to reconstruct heterogeneous structural ensembles supported by the underlying data. Using simulated and experimental data, we describe and benchmark architectural choices within tomoDRGN that are uniquely necessitated and enabled by cryo-ET. We additionally illustrate tomoDRGN's efficacy in analyzing diverse datasets, using it to reveal high-level organization of human immunodeficiency virus (HIV) capsid complexes assembled in virus-like particles and to resolve extensive structural heterogeneity among ribosomes imaged in situ.

PMID:38459385 | DOI:10.1038/s41592-024-02210-z

Sci Rep. 2024 Mar 8;14(1):5745. doi: 10.1038/s41598-024-56211-1.

ABSTRACT

Semantic segmentation of remote sensing images (RSI) is an important research direction in remote sensing technology. This paper proposes a multi-feature fusion and channel attention network, MFCA-Net, aiming to improve the segmentation accuracy of remote sensing images and the recognition performance of small target objects. The architecture is built on an encoding-decoding structure. The encoding structure includes the improved MobileNet V2 (IMV2) and multi-feature dense fusion (MFDF). In IMV2, the attention mechanism is introduced twice to enhance the feature extraction capability, and the design of MFDF can obtain more dense feature sampling points and larger receptive fields. In the decoding section, three branches of shallow features of the backbone network are fused with deep features, and upsampling is performed to achieve the pixel-level classification. Comparative experimental results of the six most advanced methods effectively prove that the segmentation accuracy of the proposed network has been significantly improved. Furthermore, the recognition degree of small target objects is higher. For example, the proposed MFCA-Net achieves about 3.65-23.55% MIoU improvement on the dataset Vaihingen.

PMID:38459115 | DOI:10.1038/s41598-024-56211-1