This study aimed to develop a deep learning (DL) model for predicting the recurrence risk of lung adenocarcinoma (LUAD) based on its histopathological features. Clinicopathological data and whole slide images from 164 LUAD cases were collected and used to train DL models with an ImageNet pre-trained efficientnet-b2 architecture, densenet201, and resnet152. The models were trained to classify each image patch into high-risk or low-risk groups, and the case-level result was determined by multiple instance learning with final FC layer's features from a model from all patches. Analysis of the clinicopathological and genetic characteristics of the model-based risk group was performed. For predicting recurrence, the model had an area under the curve score of 0.763 with 0.750, 0.633 and 0.680 of sensitivity, specificity, and accuracy in the test set, respectively. High-risk cases for recurrence predicted by the model (HR group) were significantly associated with shorter recurrence-free survival and a higher stage (both, p < 0.001). The HR group was associated with specific histopathological features such as poorly differentiated components, complex glandular pattern components, tumor spread through air spaces, and a higher grade. In the HR group, pleural invasion, necrosis, and lymphatic invasion were more frequent, and the size of the invasion was larger (all, p < 0.001). Several genetic mutations, including TP53 (p = 0.007) mutations, were more frequently found in the HR group. The results of stages I-II were similar to those of the general cohort. DL-based model can predict the recurrence risk of LUAD and identify the presence of the TP53 gene mutation by analyzing histopathologic features.
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http://dx.doi.org/10.1038/s41598-024-56867-9 | DOI Listing |
Brief Bioinform
November 2024
School of Engineering, Westlake University, No. 600 Dunyu Road, 310030 Zhejiang, P.R. China.
Single-cell RNA sequencing (scRNA-seq) offers remarkable insights into cellular development and differentiation by capturing the gene expression profiles of individual cells. The role of dimensionality reduction and visualization in the interpretation of scRNA-seq data has gained widely acceptance. However, current methods face several challenges, including incomplete structure-preserving strategies and high distortion in embeddings, which fail to effectively model complex cell trajectories with multiple branches.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Biotherapeutics Molecule Discovery, Boehringer Ingelheim Pharmaceutical Inc., 900 Ridgebury Road, Ridgefield, CT 06877, United States.
Antibody generation requires the use of one or more time-consuming methods, namely animal immunization, and in vitro display technologies. However, the recent availability of large amounts of antibody sequence and structural data in the public domain along with the advent of generative deep learning algorithms raises the possibility of computationally generating novel antibody sequences with desirable developability attributes. Here, we describe a deep learning model for computationally generating libraries of highly human antibody variable regions whose intrinsic physicochemical properties resemble those of the variable regions of the marketed antibody-based biotherapeutics (medicine-likeness).
View Article and Find Full Text PDFFood Chem X
December 2024
School of Pharmacy, Naval Medical University, Shanghai 200433, China.
With the rising demand of saffron, it is essential to standardize the confirmation of its origin and identify any adulteration to maintain a good quality led market product. However, a rapid and reliable strategy for identifying the adulteration saffron is still lacks. Herein, a combination of headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS) and convolutional neural network (CNN) was developed.
View Article and Find Full Text PDFFront Public Health
January 2025
Department of Computer Science, College of Engineering and Computer Science, Jazan University, Jazan, Saudi Arabia.
Introduction: The growing demand for real-time, affordable, and accessible healthcare has underscored the need for advanced technologies that can provide timely health monitoring. One such area is predicting arterial blood pressure (BP) using non-invasive methods, which is crucial for managing cardiovascular diseases. This research aims to address the limitations of current healthcare systems, particularly in remote areas, by leveraging deep learning techniques in Smart Health Monitoring (SHM).
View Article and Find Full Text PDFFront Artif Intell
January 2025
Department of Computer Science, University of Saskatchewan, Saskatoon, SK, Canada.
Introduction: Active learning can significantly decrease the labeling cost of deep learning workflows by prioritizing the limited labeling budget to high-impact data points that have the highest positive impact on model accuracy. Active learning is especially useful for semantic segmentation tasks where we can selectively label only a few high-impact regions within these high-impact images. Most established regional active learning algorithms deploy a static-budget querying strategy where a fixed percentage of regions are queried in each image.
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