scholarly journals Genomic pan-cancer classification using image-based deep learning

2021 ◽  
Vol 19 ◽  
pp. 835-846
Author(s):  
Taoyu Ye ◽  
Sen Li ◽  
Yang Zhang
Author(s):  
Moloud Abdar ◽  
Maryam Samami ◽  
Sajjad Dehghani Mahmoodabad ◽  
Thang Doan ◽  
Bogdan Mazoure ◽  
...  

2018 ◽  
Author(s):  
Yeping Lina Qiu ◽  
Hong Zheng ◽  
Olivier Gevaert

AbstractMotivationThe presence of missing values is a frequent problem encountered in genomic data analysis. Lost data can be an obstacle to downstream analyses that require complete data matrices. State-of-the-art imputation techniques including Singular Value Decomposition (SVD) and K-Nearest Neighbors (KNN) based methods usually achieve good performances, but are computationally expensive especially for large datasets such as those involved in pan-cancer analysis.ResultsThis study describes a new method: a denoising autoencoder with partial loss (DAPL) as a deep learning based alternative for data imputation. Results on pan-cancer gene expression data and DNA methylation data from over 11,000 samples demonstrate significant improvement over standard denoising autoencoder for both data missing-at-random cases with a range of missing percentages, and missing-not-at-random cases based on expression level and GC-content. We discuss the advantages of DAPL over traditional imputation methods and show that it achieves comparable or better performance with less computational burden.Availabilityhttps://github.com/gevaertlab/[email protected]


Electronics ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 445 ◽  
Author(s):  
Laith Alzubaidi ◽  
Omran Al-Shamma ◽  
Mohammed A. Fadhel ◽  
Laith Farhan ◽  
Jinglan Zhang ◽  
...  

Breast cancer is a significant factor in female mortality. An early cancer diagnosis leads to a reduction in the breast cancer death rate. With the help of a computer-aided diagnosis system, the efficiency increased, and the cost was reduced for the cancer diagnosis. Traditional breast cancer classification techniques are based on handcrafted features techniques, and their performance relies upon the chosen features. They also are very sensitive to different sizes and complex shapes. However, histopathological breast cancer images are very complex in shape. Currently, deep learning models have become an alternative solution for diagnosis, and have overcome the drawbacks of classical classification techniques. Although deep learning has performed well in various tasks of computer vision and pattern recognition, it still has some challenges. One of the main challenges is the lack of training data. To address this challenge and optimize the performance, we have utilized a transfer learning technique which is where the deep learning models train on a task, and then fine-tune the models for another task. We have employed transfer learning in two ways: Training our proposed model first on the same domain dataset, then on the target dataset, and training our model on a different domain dataset, then on the target dataset. We have empirically proven that the same domain transfer learning optimized the performance. Our hybrid model of parallel convolutional layers and residual links is utilized to classify hematoxylin–eosin-stained breast biopsy images into four classes: invasive carcinoma, in-situ carcinoma, benign tumor and normal tissue. To reduce the effect of overfitting, we have augmented the images with different image processing techniques. The proposed model achieved state-of-the-art performance, and it outperformed the latest methods by achieving a patch-wise classification accuracy of 90.5%, and an image-wise classification accuracy of 97.4% on the validation set. Moreover, we have achieved an image-wise classification accuracy of 96.1% on the test set of the microscopy ICIAR-2018 dataset.


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