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1.
BMC Med Inform Decis Mak ; 23(1): 16, 2023 Jan 23.
Artículo en Inglés | MEDLINE | ID: mdl-36691030

RESUMEN

BACKGROUND: Detecting brain tumors in their early stages is crucial. Brain tumors are classified by biopsy, which can only be performed through definitive brain surgery. Computational intelligence-oriented techniques can help physicians identify and classify brain tumors. Herein, we proposed two deep learning methods and several machine learning approaches for diagnosing three types of tumor, i.e., glioma, meningioma, and pituitary gland tumors, as well as healthy brains without tumors, using magnetic resonance brain images to enable physicians to detect with high accuracy tumors in early stages. MATERIALS AND METHODS: A dataset containing 3264 Magnetic Resonance Imaging (MRI) brain images comprising images of glioma, meningioma, pituitary gland tumors, and healthy brains were used in this study. First, preprocessing and augmentation algorithms were applied to MRI brain images. Next, we developed a new 2D Convolutional Neural Network (CNN) and a convolutional auto-encoder network, both of which were already trained by our assigned hyperparameters. Then 2D CNN includes several convolution layers; all layers in this hierarchical network have a 2*2 kernel function. This network consists of eight convolutional and four pooling layers, and after all convolution layers, batch-normalization layers were applied. The modified auto-encoder network includes a convolutional auto-encoder network and a convolutional network for classification that uses the last output encoder layer of the first part. Furthermore, six machine-learning techniques that were applied to classify brain tumors were also compared in this study. RESULTS: The training accuracy of the proposed 2D CNN and that of the proposed auto-encoder network were found to be 96.47% and 95.63%, respectively. The average recall values for the 2D CNN and auto-encoder networks were 95% and 94%, respectively. The areas under the ROC curve for both networks were 0.99 or 1. Among applied machine learning methods, Multilayer Perceptron (MLP) (28%) and K-Nearest Neighbors (KNN) (86%) achieved the lowest and highest accuracy rates, respectively. Statistical tests showed a significant difference between the means of the two methods developed in this study and several machine learning methods (p-value < 0.05). CONCLUSION: The present study shows that the proposed 2D CNN has optimal accuracy in classifying brain tumors. Comparing the performance of various CNNs and machine learning methods in diagnosing three types of brain tumors revealed that the 2D CNN achieved exemplary performance and optimal execution time without latency. This proposed network is less complex than the auto-encoder network and can be employed by radiologists and physicians in clinical systems for brain tumor detection.


Asunto(s)
Neoplasias Encefálicas , Aprendizaje Profundo , Glioma , Neoplasias Meníngeas , Meningioma , Neoplasias Hipofisarias , Humanos , Neoplasias Encefálicas/diagnóstico por imagen , Aprendizaje Automático , Imagen por Resonancia Magnética/métodos , Meningioma/diagnóstico por imagen , Neoplasias Hipofisarias/diagnóstico por imagen
2.
Math Biosci Eng ; 20(1): 1037-1057, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36650801

RESUMEN

DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learning-based language model for predicting DHSs, named LangMoDHS. The LangMoDHS mainly comprised the convolutional neural network (CNN), the bi-directional long short-term memory (Bi-LSTM) and the feed-forward attention. The CNN and the Bi-LSTM were stacked in a parallel manner, which was helpful to accumulate multiple-view representations from primary DNA sequences. We conducted 5-fold cross-validations and independent tests over 14 tissues and 4 developmental stages. The empirical experiments showed that the LangMoDHS is competitive with or slightly better than the iDHS-Deep, which is the latest method for predicting DHSs. The empirical experiments also implied substantial contribution of the CNN, Bi-LSTM, and attention to DHSs prediction. We implemented the LangMoDHS as a user-friendly web server which is accessible at http:/www.biolscience.cn/LangMoDHS/. We used indices related to information entropy to explore the sequence motif of DHSs. The analysis provided a certain insight into the DHSs.


Asunto(s)
Aprendizaje Profundo , Animales , Ratones , Desoxirribonucleasa I/genética , Desoxirribonucleasa I/metabolismo , Genómica , Secuencias Reguladoras de Ácidos Nucleicos
3.
Sci Rep ; 13(1): 1171, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670144

RESUMEN

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer. Neoadjuvant systemic therapy (NAST) followed by surgery are currently standard of care for TNBC with 50-60% of patients achieving pathologic complete response (pCR). We investigated ability of deep learning (DL) on dynamic contrast enhanced (DCE) MRI and diffusion weighted imaging acquired early during NAST to predict TNBC patients' pCR status in the breast. During the development phase using the images of 130 TNBC patients, the DL model achieved areas under the receiver operating characteristic curves (AUCs) of 0.97 ± 0.04 and 0.82 ± 0.10 for the training and the validation, respectively. The model achieved an AUC of 0.86 ± 0.03 when evaluated in the independent testing group of 32 patients. In an additional prospective blinded testing group of 48 patients, the model achieved an AUC of 0.83 ± 0.02. These results demonstrated that DL based on multiparametric MRI can potentially differentiate TNBC patients with pCR or non-pCR in the breast early during NAST.


Asunto(s)
Neoplasias de la Mama , Aprendizaje Profundo , Imágenes de Resonancia Magnética Multiparamétrica , Neoplasias de la Mama Triple Negativas , Humanos , Femenino , Neoplasias de la Mama Triple Negativas/diagnóstico por imagen , Neoplasias de la Mama Triple Negativas/tratamiento farmacológico , Neoplasias de la Mama Triple Negativas/patología , Neoplasias de la Mama/patología , Terapia Neoadyuvante/métodos , Estudios Prospectivos , Imagen por Resonancia Magnética/métodos , Estudios Retrospectivos
4.
Biomed Eng Online ; 22(1): 3, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670469

RESUMEN

OBJECTIVES: This study aims to develop and evaluate the deep learning-based classification model for recognizing the pathology of renal tumor from macroscopic cross-section image. METHODS: A total of 467 pathology-confirmed patients who received radical nephrectomy or partial nephrectomy were retrospectively enrolled. The experiment of distinguishing malignant and benign renal tumor are conducted followed by performing the multi-subtypes classification models for recognizing four subtypes of benign tumor and four subtypes of malignant tumors, respectively. The classification models used the same backbone networks which are based on the convolutional neural network (CNN), including EfficientNet-B4, ResNet-18, and VGG-16. The performance of the classification models was evaluated by area under the receiver operating characteristic curve (AUC), sensitivity, specificity, and accuracy. Besides, we performed the quantitative comparison among these CNN models. RESULTS: For the model to differentiate the malignant tumor from the benign tumor, three CNN models all obtained relatively satisfactory performance and the highest AUC was achieved by the ResNet-18 model (AUC = 0.9226). There is not statistically significance between EfficientNet-B4 and ResNet-18 architectures and both of them are significantly statistically better than the VGG-16 model. The micro-averaged AUC, macro-averaged sensitivity, macro-averaged specificity, and micro-averaged accuracy for the VGG-16 model to distinguish the malignant tumor subtypes achieved 0.9398, 0.5774, 0.8660, and 0.7917, respectively. The performance of the EfficientNet-B4 is not better than that of VGG-16 in terms of micro-averaged AUC except for other metrics. For the models to recognize the benign tumor subtypes, the EfficientNet-B4 ranked the best performance, but had no significantly statistical difference with other two models with respect to micro-averaged AUC. CONCLUSIONS: The classification results were relatively satisfactory, which showed the potential for clinical application when analyzing the renal tumor macroscopic cross-section images. Automatically distinguishing the malignant tumor from benign tumor and identifying the subtypes pathology of renal tumor could make the patient-management process more efficient.


Asunto(s)
Aprendizaje Profundo , Neoplasias Renales , Humanos , Estudios Retrospectivos , Neoplasias Renales/diagnóstico por imagen , Redes Neurales de la Computación , Curva ROC
5.
Cancer Imaging ; 23(1): 9, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670497

RESUMEN

BACKGROUND: The epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) are a first-line therapy for non-small cell lung cancer (NSCLC) with EGFR mutations. Approximately half of the patients with EGFR-mutated NSCLC are treated with EGFR-TKIs and develop disease progression within 1 year. Therefore, the early prediction of tumor progression in patients who receive EGFR-TKIs can facilitate patient management and development of treatment strategies. We proposed a deep learning approach based on both quantitative computed tomography (CT) characteristics and clinical data to predict progression-free survival (PFS) in patients with advanced NSCLC after EGFR-TKI treatment. METHODS: A total of 593 radiomic features were extracted from pretreatment chest CT images. The DeepSurv models for the progression risk stratification of EGFR-TKI treatment were proposed based on CT radiomic and clinical features from 270 stage IIIB-IV EGFR-mutant NSCLC patients. Time-dependent PFS predictions at 3, 12, 18, and 24 months and estimated personalized PFS curves were calculated using the DeepSurv models. RESULTS: The model combining clinical and radiomic features demonstrated better prediction performance than the clinical model. The model achieving areas under the curve of 0.76, 0.77, 0.76, and 0.86 can predict PFS at 3, 12, 18, and 24 months, respectively. The personalized PFS curves showed significant differences (p < 0.003) between groups with good (PFS > median) and poor (PFS < median) tumor control. CONCLUSIONS: The DeepSurv models provided reliable multi-time-point PFS predictions for EGFR-TKI treatment. The personalized PFS curves can help make accurate and individualized predictions of tumor progression. The proposed deep learning approach holds promise for improving the pre-TKI personalized management of patients with EGFR-mutated NSCLC.


Asunto(s)
Carcinoma de Pulmón de Células no Pequeñas , Aprendizaje Profundo , Neoplasias Pulmonares , Humanos , Carcinoma de Pulmón de Células no Pequeñas/diagnóstico por imagen , Carcinoma de Pulmón de Células no Pequeñas/tratamiento farmacológico , Carcinoma de Pulmón de Células no Pequeñas/genética , Neoplasias Pulmonares/diagnóstico por imagen , Neoplasias Pulmonares/tratamiento farmacológico , Neoplasias Pulmonares/genética , Supervivencia sin Progresión , Supervivencia sin Enfermedad , Inhibidores de Proteínas Quinasas/uso terapéutico , Receptores ErbB/genética , Mutación
6.
Biomolecules ; 13(1)2023 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-36671518

RESUMEN

Elucidating protein-ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein-ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein-ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein-ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein-ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein-ligand interactions on cryo-EM data using prior structural information.


Asunto(s)
Aprendizaje Profundo , Simulación del Acoplamiento Molecular , Microscopía por Crioelectrón/métodos , Ligandos , Proteínas/química , Conformación Proteica
7.
Cells ; 12(2)2023 Jan 04.
Artículo en Inglés | MEDLINE | ID: mdl-36672144

RESUMEN

Induced pluripotent stem cells (iPSCs) can be differentiated into mesenchymal stem cells (iPSC-MSCs), retinal ganglion cells (iPSC-RGCs), and retinal pigmental epithelium cells (iPSC-RPEs) to meet the demand of regeneration medicine. Since the production of iPSCs and iPSC-derived cell lineages generally requires massive and time-consuming laboratory work, artificial intelligence (AI)-assisted approach that can facilitate the cell classification and recognize the cell differentiation degree is of critical demand. In this study, we propose the multi-slice tensor model, a modified convolutional neural network (CNN) designed to classify iPSC-derived cells and evaluate the differentiation efficiency of iPSC-RPEs. We removed the fully connected layers and projected the features using principle component analysis (PCA), and subsequently classified iPSC-RPEs according to various differentiation degree. With the assistance of the support vector machine (SVM), this model further showed capabilities to classify iPSCs, iPSC-MSCs, iPSC-RPEs, and iPSC-RGCs with an accuracy of 97.8%. In addition, the proposed model accurately recognized the differentiation of iPSC-RPEs and showed the potential to identify the candidate cells with ideal features and simultaneously exclude cells with immature/abnormal phenotypes. This rapid screening/classification system may facilitate the translation of iPSC-based technologies into clinical uses, such as cell transplantation therapy.


Asunto(s)
Aprendizaje Profundo , Células Madre Pluripotentes Inducidas , Humanos , Inteligencia Artificial , Epitelio Pigmentado de la Retina , Diferenciación Celular
8.
Cell Syst ; 14(1): 58-71.e5, 2023 Jan 18.
Artículo en Inglés | MEDLINE | ID: mdl-36657391

RESUMEN

Mitochondria are extremely pleomorphic organelles. Automatically annotating each one accurately and precisely in any 2D or volume electron microscopy (EM) image is an unsolved computational challenge. Current deep learning-based approaches train models on images that provide limited cellular contexts, precluding generality. To address this, we amassed a highly heterogeneous ∼1.5 × 106 image 2D unlabeled cellular EM dataset and segmented ∼135,000 mitochondrial instances therein. MitoNet, a model trained on these resources, performs well on challenging benchmarks and on previously unseen volume EM datasets containing tens of thousands of mitochondria. We release a Python package and napari plugin, empanada, to rapidly run inference, visualize, and proofread instance segmentations. A record of this paper's transparent peer review process is included in the supplemental information.


Asunto(s)
Aprendizaje Profundo , Microscopía Electrónica , Mitocondrias
9.
Comput Biol Med ; 153: 106487, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36603432

RESUMEN

Pre-processing is widely applied in medical image analysis to remove the interference information. However, the existing pre-processing solutions mainly encounter two problems: (i) it is heavily relied on the assistance of clinical experts, making it hard for intelligent CAD systems to deploy quickly; (ii) due to the personnel and information barriers, it is difficult for medical institutions to conduct the same pre-processing operations, making a deep model that performs well on a specific medical institution difficult to achieve similar performances on the same task in other medical institutions. To overcome these problems, we propose a deep-reinforcement-learning-based task-oriented homogenized automatic pre-processing (DRL-HAPre) framework to overcome these two problems. This framework utilizes deep reinforcement learning techniques to learn a policy network to automatically and adaptively select the optimal pre-processing operations for the input medical images according to different analysis tasks, thus helping the intelligent CAD system to achieve a rapid deployment (i.e., painless) and maintain a satisfactory performance (i.e., accurate) among different medical institutes. To verify the effectiveness and advantages of the proposed DRL-HAPre framework, we further develop a homogenized automatic pre-processing model based on the DRL-HAPre framework to realize the automatic pre-processing of key region selection (called HAPre-KRS) in the pneumonia image classification task. Extensive experimental studies are conducted on three pediatric pneumonia classification datasets with different image qualities, and the results show that: (i) There does exist a hard-to-reproduce problem in clinical practices and the fact that having different medical image qualities in different medical institutes is an important reason for the existing of hard-to-reproduce problem, so it is compelling to propose homogenized automatic pre-processing method. (ii) The proposed HAPre-KRS model and DRL-HAPre framework greatly outperform three kinds of state-of-the-art baselines (i.e., pre-processing, attention and pneumonia baseline), and the lower the medical image quality, the greater the improvements of using our HAPre-KRS model and DRL-HAPre framework. (iii) With the help of homogenized pre-processing, HAPre-KRS (and DRL-HAPre framework) can greatly avoid performance degradation in real-world cross-source applications (i.e., thus overcoming the hard-to-reproduce problem).


Asunto(s)
Aprendizaje Profundo , Humanos , Niño , Procesamiento de Imagen Asistido por Computador/métodos
10.
Eur J Radiol ; 159: 110685, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36603479

RESUMEN

PURPOSE: To compare the image quality and conspicuity of pancreatic ductal adenocarcinoma (PDAC) between the low-kVp and dual-energy pancreatic protocol CT reconstructed with deep-learning image reconstruction (DLIR). METHOD: A cohort of 111 consecutive patients (median age, 72 years; 56 men) undergoing a pancreatic protocol CT were retrospectively analyzed. Among them, 58 patients underwent 80-kVp CT (80-kVp group), and 53 patients underwent dual-energy CT and reconstructed at 40-keV (40-keV group). The medium-strength level of DLIR were used in both groups. Quantitative measurements, qualitative image quality, PDAC conspicuity, and dose-length product (DLP) were compared between the two groups using Mann-Whitney U test. RESULTS: A total of 20 and 16 PDACs were found in the 80-kVp and 40-keV groups, respectively. CT numbers of the vasculatures and parenchymal organs (P <.001 for all) and the background noise at both pancreatic and portal venous phases (P <.001) were higher in the 40-keV group than in the 80-kVp group. The signal-to-noise ratio (SNR) of all anatomical structures (P <.001-0.005), except for the liver in reviewer 2 (P =.47), and the tumor-to-pancreas contrast-to-noise ratio (CNR; P <.001-0.01) were higher in the 40-keV group than in the 80-kVp group. No difference was found in the image quality at both phases (P =.30-0.90). PDAC conspicuity was better in the 40-keV group than in the 80-kVp group (P =.007-0.03). DLP at pancreatic (275 vs. 313 mGy*cm; P =.05) and portal venous phases (743 vs. 766 mGy*cm; P =.20) was comparable between the two groups. CONCLUSION: Under the same DLP, virtual monoenergetic images at 40-keV demonstrated higher SNR and tumor-to-pancreas CNR and better PDAC conspicuity compared to the 80-kVp setting.


Asunto(s)
Carcinoma Ductal Pancreático , Aprendizaje Profundo , Neoplasias Pancreáticas , Masculino , Humanos , Anciano , Estudios Retrospectivos , Medios de Contraste , Neoplasias Pancreáticas/diagnóstico por imagen , Carcinoma Ductal Pancreático/diagnóstico por imagen , Tomografía Computarizada por Rayos X/métodos , Relación Señal-Ruido , Algoritmos , Procesamiento de Imagen Asistido por Computador , Interpretación de Imagen Radiográfica Asistida por Computador/métodos
11.
Comput Biol Med ; 153: 106492, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36621191

RESUMEN

BACKGROUND: The O6-methylguanine-DNA methyltransferase (MGMT) is a deoxyribonucleic acid (DNA) repairing enzyme that has been established as an essential clinical brain tumor biomarker for Glioblastoma Multiforme (GBM). Knowing the status of MGMT methylation biomarkers using multi-parametric MRI (mp-MRI) helps neuro-oncologists to analyze GBM and its treatment plan. METHOD: The hand-crafted radiomics feature extraction of GBM's subregions, such as edema(ED), tumor core (TC), and enhancing tumor (ET) in the machine learning (ML) framework, was investigated using support vector machine(SVM), K-Nearest Neighbours (KNN), random forest (RF), LightGBM, and extreme gradient boosting (XGB). For tissue-level analysis of the promotor genes in GBM, we used the deep residual neural network (ResNet-18) with 3D architecture, followed by EfficientNet-based investigation for variants as B0 and B1. Lastly, we analyzed the fused deep learning (FDL) framework that combines ML and DL frameworks. RESULT: Structural mp-MRI consisting of T1, T2, FLAIR, and T1GD having a size of 400 and 185 patients, respectively, for discovery and replication cohorts. Using the CV protocol in the ResNet-3D framework, MGMT methylation status prediction in mp-MRI gave the AUC of 0.753 (p < 0.0001) and 0.72 (p < 0.0001) for the discovery and replication cohort, respectively. We presented that the FDL is ∼7% superior to solo DL and ∼15% to solo ML. CONCLUSION: The proposed study aims to provide solutions for building an efficient predictive model of MGMT for GBM patients using deep radiomics features obtained from mp-MRI with the end-to-end ResNet-18 3D and FDL imaging signatures.


Asunto(s)
Neoplasias Encefálicas , Aprendizaje Profundo , Glioblastoma , Humanos , Glioblastoma/diagnóstico por imagen , Glioblastoma/genética , Glioblastoma/tratamiento farmacológico , Metiltransferasas/genética , Metiltransferasas/uso terapéutico , Metilación de ADN/genética , Metilasas de Modificación del ADN/genética , Metilasas de Modificación del ADN/metabolismo , Metilasas de Modificación del ADN/uso terapéutico , Imagen por Resonancia Magnética/métodos , Neoplasias Encefálicas/diagnóstico por imagen , Neoplasias Encefálicas/genética , ADN , Biomarcadores
12.
Sci Rep ; 13(1): 1392, 2023 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-36697482

RESUMEN

Diabetic retinopathy (DR) at risk of vision loss (referable DR) needs to be identified by retinal screening and referred to an ophthalmologist. Existing automated algorithms have mostly been developed from images acquired with high cost mydriatic retinal cameras and cannot be applied in the settings used in most low- and middle-income countries. In this prospective multicentre study, we developed a deep learning system (DLS) that detects referable DR from retinal images acquired using handheld non-mydriatic fundus camera by non-technical field workers in 20 sites across India. Macula-centred and optic-disc-centred images from 16,247 eyes (9778 participants) were used to train and cross-validate the DLS and risk factor based logistic regression models. The DLS achieved an AUROC of 0.99 (1000 times bootstrapped 95% CI 0.98-0.99) using two-field retinal images, with 93.86 (91.34-96.08) sensitivity and 96.00 (94.68-98.09) specificity at the Youden's index operational point. With single field inputs, the DLS reached AUROC of 0.98 (0.98-0.98) for the macula field and 0.96 (0.95-0.98) for the optic-disc field. Intergrader performance was 90.01 (88.95-91.01) sensitivity and 96.09 (95.72-96.42) specificity. The image based DLS outperformed all risk factor-based models. This DLS demonstrated a clinically acceptable performance for the identification of referable DR despite challenging image capture conditions.


Asunto(s)
Aprendizaje Profundo , Diabetes Mellitus , Retinopatía Diabética , Humanos , Retinopatía Diabética/diagnóstico por imagen , Midriáticos , Estudios Prospectivos , Sensibilidad y Especificidad , Fotograbar/métodos , Retina/diagnóstico por imagen , Tamizaje Masivo/métodos
13.
Crit Care ; 27(1): 40, 2023 01 25.
Artículo en Inglés | MEDLINE | ID: mdl-36698191

RESUMEN

BACKGROUND: Chest radiographs are routinely performed in intensive care unit (ICU) to confirm the correct position of an endotracheal tube (ETT) relative to the carina. However, their interpretation is often challenging and requires substantial time and expertise. The aim of this study was to propose an externally validated deep learning model with uncertainty quantification and image segmentation for the automated assessment of ETT placement on ICU chest radiographs. METHODS: The CarinaNet model was constructed by applying transfer learning to the RetinaNet model using an internal dataset of ICU chest radiographs. The accuracy of the model in predicting the position of the ETT tip and carina was externally validated using a dataset of 200 images extracted from the MIMIC-CXR database. Uncertainty quantification was performed using the level of confidence in the ETT-carina distance prediction. Segmentation of the ETT was carried out using edge detection and pixel clustering. RESULTS: The interrater agreement was 0.18 cm for the ETT tip position, 0.58 cm for the carina position, and 0.60 cm for the ETT-carina distance. The mean absolute error of the model on the external test set was 0.51 cm for the ETT tip position prediction, 0.61 cm for the carina position prediction, and 0.89 cm for the ETT-carina distance prediction. The assessment of ETT placement was improved by complementing the human interpretation of chest radiographs with the CarinaNet model. CONCLUSIONS: The CarinaNet model is an efficient and generalizable deep learning algorithm for the automated assessment of ETT placement on ICU chest radiographs. Uncertainty quantification can bring the attention of intensivists to chest radiographs that require an experienced human interpretation. Image segmentation provides intensivists with chest radiographs that are quickly interpretable and allows them to immediately assess the validity of model predictions. The CarinaNet model is ready to be evaluated in clinical studies.


Asunto(s)
Aprendizaje Profundo , Humanos , Tráquea , Intubación Intratraqueal/métodos , Radiografía , Unidades de Cuidados Intensivos
14.
J Transl Med ; 21(1): 48, 2023 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-36698208

RESUMEN

BACKGROUND: Drug-target interaction (DTI) prediction has become a crucial prerequisite in drug design and drug discovery. However, the traditional biological experiment is time-consuming and expensive, as there are abundant complex interactions present in the large size of genomic and chemical spaces. For alleviating this phenomenon, plenty of computational methods are conducted to effectively complement biological experiments and narrow the search spaces into a preferred candidate domain. Whereas, most of the previous approaches cannot fully consider association behavior semantic information based on several schemas to represent complex the structure of heterogeneous biological networks. Additionally, the prediction of DTI based on single modalities cannot satisfy the demand for prediction accuracy. METHODS: We propose a multi-modal representation framework of 'DeepMPF' based on meta-path semantic analysis, which effectively utilizes heterogeneous information to predict DTI. Specifically, we first construct protein-drug-disease heterogeneous networks composed of three entities. Then the feature information is obtained under three views, containing sequence modality, heterogeneous structure modality and similarity modality. We proposed six representative schemas of meta-path to preserve the high-order nonlinear structure and catch hidden structural information of the heterogeneous network. Finally, DeepMPF generates highly representative comprehensive feature descriptors and calculates the probability of interaction through joint learning. RESULTS: To evaluate the predictive performance of DeepMPF, comparison experiments are conducted on four gold datasets. Our method can obtain competitive performance in all datasets. We also explore the influence of the different feature embedding dimensions, learning strategies and classification methods. Meaningfully, the drug repositioning experiments on COVID-19 and HIV demonstrate DeepMPF can be applied to solve problems in reality and help drug discovery. The further analysis of molecular docking experiments enhances the credibility of the drug candidates predicted by DeepMPF. CONCLUSIONS: All the results demonstrate the effectively predictive capability of DeepMPF for drug-target interactions. It can be utilized as a useful tool to prescreen the most potential drug candidates for the protein. The web server of the DeepMPF predictor is freely available at http://120.77.11.78/DeepMPF/ , which can help relevant researchers to further study.


Asunto(s)
COVID-19 , Aprendizaje Profundo , Humanos , Simulación del Acoplamiento Molecular , Semántica , Descubrimiento de Drogas/métodos , Proteínas
15.
Cancer Imaging ; 23(1): 12, 2023 Jan 25.
Artículo en Inglés | MEDLINE | ID: mdl-36698217

RESUMEN

PURPOSE: Metastatic bone disease (MBD) is the most common form of metastases, most frequently deriving from prostate cancer. MBD is screened with bone scintigraphy (BS), which have high sensitivity but low specificity for the diagnosis of MBD, often requiring further investigations. Deep learning (DL) - a machine learning technique designed to mimic human neuronal interactions- has shown promise in the field of medical imaging analysis for different purposes, including segmentation and classification of lesions. In this study, we aim to develop a DL algorithm that can classify areas of increased uptake on bone scintigraphy scans. METHODS: We collected 2365 BS from three European medical centres. The model was trained and validated on 1203 and 164 BS scans respectively. Furthermore we evaluated its performance on an external testing set composed of 998 BS scans. We further aimed to enhance the explainability of our developed algorithm, using activation maps. We compared the performance of our algorithm to that of 6 nuclear medicine physicians. RESULTS: The developed DL based algorithm is able to detect MBD on BSs, with high specificity and sensitivity (0.80 and 0.82 respectively on the external test set), in a shorter time compared to the nuclear medicine physicians (2.5 min for AI and 30 min for nuclear medicine physicians to classify 134 BSs). Further prospective validation is required before the algorithm can be used in the clinic.


Asunto(s)
Neoplasias Óseas , Aprendizaje Profundo , Masculino , Humanos , Neoplasias Óseas/diagnóstico por imagen , Neoplasias Óseas/secundario , Cintigrafía , Aprendizaje Automático , Algoritmos
16.
Phys Rev Lett ; 130(1): 016101, 2023 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-36669218

RESUMEN

We report the development of deep-learning coherent electron diffractive imaging at subangstrom resolution using convolutional neural networks (CNNs) trained with only simulated data. We experimentally demonstrate this method by applying the trained CNNs to recover the phase images from electron diffraction patterns of twisted hexagonal boron nitride, monolayer graphene, and a gold nanoparticle with comparable quality to those reconstructed by a conventional ptychographic algorithm. Fourier ring correlation between the CNN and ptychographic images indicates the achievement of a resolution in the range of 0.70 and 0.55 Å. We further develop CNNs to recover the probe function from the experimental data. The ability to replace iterative algorithms with CNNs and perform real-time atomic imaging from coherent diffraction patterns is expected to find applications in the physical and biological sciences.


Asunto(s)
Aprendizaje Profundo , Nanopartículas del Metal , Electrones , Oro , Redes Neurales de la Computación , Algoritmos
17.
Nat Commun ; 14(1): 339, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670105

RESUMEN

The El Niño Southern Oscillation (ENSO) is a semi-periodic fluctuation in sea surface temperature (SST) over the tropical central and eastern Pacific Ocean that influences interannual variability in regional hydrology across the world through long-range dependence or teleconnections. Recent research has demonstrated the value of Deep Learning (DL) methods for improving ENSO prediction as well as Complex Networks (CN) for understanding teleconnections. However, gaps in predictive understanding of ENSO-driven river flows include the black box nature of DL, the use of simple ENSO indices to describe a complex phenomenon and translating DL-based ENSO predictions to river flow predictions. Here we show that eXplainable DL (XDL) methods, based on saliency maps, can extract interpretable predictive information contained in global SST and discover SST information regions and dependence structures relevant for river flows which, in tandem with climate network constructions, enable improved predictive understanding. Our results reveal additional information content in global SST beyond ENSO indices, develop understanding of how SSTs influence river flows, and generate improved river flow prediction, including uncertainty estimation. Observations, reanalysis data, and earth system model simulations are used to demonstrate the value of the XDL-CN based methods for future interannual and decadal scale climate projections.


Asunto(s)
Aprendizaje Profundo , El Niño Oscilación del Sur , Ríos , Temperatura , Océano Pacífico
18.
Sci Rep ; 13(1): 1129, 2023 Jan 20.
Artículo en Inglés | MEDLINE | ID: mdl-36670171

RESUMEN

Nanophotonics exploits the best of photonics and nanotechnology which has transformed optics in recent years by allowing subwavelength structures to enhance light-matter interactions. Despite these breakthroughs, design, fabrication, and characterization of such exotic devices have remained through iterative processes which are often computationally costly, memory-intensive, and time-consuming. In contrast, deep learning approaches have recently shown excellent performance as practical computational tools, providing an alternate avenue for speeding up such nanophotonics simulations. This study presents a DNN framework for transmission, reflection, and absorption spectra predictions by grasping the hidden correlation between the independent nanostructure properties and their corresponding optical responses. The proposed DNN framework is shown to require a sufficient amount of training data to achieve an accurate approximation of the optical performance derived from computational models. The fully trained framework can outperform a traditional EM solution using on the COMSOL Multiphysics approach in terms of computational cost by three orders of magnitude. Furthermore, employing deep learning methodologies, the proposed DNN framework makes an effort to optimise design elements that influence the geometrical dimensions of the nanostructure, offering insight into the universal transmission, reflection, and absorption spectra predictions at the nanoscale. This paradigm improves the viability of complicated nanostructure design and analysis, and it has a lot of potential applications involving exotic light-matter interactions between nanostructures and electromagnetic fields. In terms of computational times, the designed algorithm is more than 700 times faster as compared to conventional FEM method (when manual meshing is used). Hence, this approach paves the way for fast yet universal methods for the characterization and analysis of the optical response of nanophotonic systems.


Asunto(s)
Aprendizaje Profundo , Nanoestructuras , Nanoestructuras/química , Nanotecnología/métodos , Óptica y Fotónica , Campos Electromagnéticos
19.
Molecules ; 28(2)2023 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-36677867

RESUMEN

Confusing low-molecular-weight hyaluronic acid (LMWHA) from acid degradation and enzymatic hydrolysis (named LMWHA-A and LMWHA-E, respectively) will lead to health hazards and commercial risks. The purpose of this work is to analyze the structural differences between LMWHA-A and LMWHA-E, and then achieve a fast and accurate classification based on near-infrared (NIR) spectroscopy and machine learning. First, we combined nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) spectroscopy, two-dimensional correlated NIR spectroscopy (2DCOS), and aquaphotomics to analyze the structural differences between LMWHA-A and LMWHA-E. Second, we compared the dimensionality reduction methods including principal component analysis (PCA), kernel PCA (KPCA), and t-distributed stochastic neighbor embedding (t-SNE). Finally, the differences in classification effect of traditional machine learning methods including partial least squares-discriminant analysis (PLS-DA), support vector classification (SVC), and random forest (RF) as well as deep learning methods including one-dimensional convolutional neural network (1D-CNN) and long short-term memory (LSTM) were compared. The results showed that genetic algorithm (GA)-SVC and RF were the best performers in traditional machine learning, but their highest accuracy in the test dataset was 90%, while the accuracy of 1D-CNN and LSTM models in the training dataset and test dataset classification was 100%. The results of this study show that compared with traditional machine learning, the deep learning models were better for the classification of LMWHA-A and LMWHA-E. Our research provides a new methodological reference for the rapid and accurate classification of biological macromolecules.


Asunto(s)
Aprendizaje Profundo , Espectroscopía Infrarroja Corta/métodos , Ácido Hialurónico , Redes Neurales de la Computación , Análisis Discriminante , Máquina de Vectores de Soporte
20.
Parasit Vectors ; 16(1): 29, 2023 Jan 24.
Artículo en Inglés | MEDLINE | ID: mdl-36694210

RESUMEN

BACKGROUND: The histological diagnosis of alveolar echinococcosis can be challenging. Decision support models based on deep learning (DL) are increasingly used to aid pathologists, but data on the histology of tissue-invasive parasitic infections are missing. The aim of this study was to implement DL methods to classify Echinococcus multilocularis liver lesions and normal liver tissue and assess which regions and structures play the most important role in classification decisions. METHODS: We extracted 15,756 echinococcus tiles from 28 patients using 59 whole slide images (WSI); 11,602 tiles of normal liver parenchyma from 18 patients using 33 WSI served as a control group. Different pretrained model architectures were used with a 60-20-20% random splitting. We visualized the predictions using probability-thresholded heat maps of WSI. The area-under-the-curve (AUC) value and other performance metrics were calculated. The GradCAM method was used to calculate and visualize important spatial features. RESULTS: The models achieved a high validation and test set accuracy. The calculated AUC values were 1.0 in all models. Pericystic fibrosis and necrotic areas, as well as germinative and laminated layers of the metacestodes played an important role in decision tasks according to the superimposed GradCAM heatmaps. CONCLUSION: Deep learning models achieved a high predictive performance in classifying E. multilocularis liver lesions. A possible next step could be to validate the model using other datasets and test it against other pathologic entities as well, such as, for example, Echinococcus granulosus infection.


Asunto(s)
Aprendizaje Profundo , Equinococosis , Echinococcus granulosus , Echinococcus multilocularis , Neoplasias Hepáticas , Animales , Humanos , Equinococosis/parasitología
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