scholarly journals Deep learning of pharmacogenomics resources: moving towards precision oncology

2019 ◽  
Vol 21 (6) ◽  
pp. 2066-2083 ◽  
Author(s):  
Yu-Chiao Chiu ◽  
Hung-I Harry Chen ◽  
Aparna Gorthi ◽  
Milad Mostavi ◽  
Siyuan Zheng ◽  
...  
Keyword(s):  
Deep Learning ◽  
Drug Response ◽  
Cancer Genomics ◽  
Drug Repositioning ◽  
Precision Oncology ◽  
Response Patterns ◽  
Cancer Subtypes ◽  
Drug Synergy ◽  
Typical Model

Abstract The recent accumulation of cancer genomic data provides an opportunity to understand how a tumor’s genomic characteristics can affect its responses to drugs. This field, called pharmacogenomics, is a key area in the development of precision oncology. Deep learning (DL) methodology has emerged as a powerful technique to characterize and learn from rapidly accumulating pharmacogenomics data. We introduce the fundamentals and typical model architectures of DL. We review the use of DL in classification of cancers and cancer subtypes (diagnosis and treatment stratification of patients), prediction of drug response and drug synergy for individual tumors (treatment prioritization for a patient), drug repositioning and discovery and the study of mechanism/mode of action of treatments. For each topic, we summarize current genomics and pharmacogenomics data resources such as pan-cancer genomics data for cancer cell lines (CCLs) and tumors, and systematic pharmacologic screens of CCLs. By revisiting the published literature, including our in-house analyses, we demonstrate the unprecedented capability of DL enabled by rapid accumulation of data resources to decipher complex drug response patterns, thus potentially improving cancer medicine. Overall, this review provides an in-depth summary of state-of-the-art DL methods and up-to-date pharmacogenomics resources and future opportunities and challenges to realize the goal of precision oncology.

scholarly journals Artificial Intelligence in Bulk and Single-Cell RNA-Sequencing Data to Foster Precision Oncology

2021 ◽  
Vol 22 (9) ◽  
pp. 4563
Author(s):  
Marco Del Giudice ◽  
Serena Peirone ◽  
Sarah Perrone ◽  
Francesca Priante ◽  
Fabiola Varese ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Rna Sequencing ◽  
Large Scale ◽  
Cancer Genomics ◽  
Computational Algorithms ◽  
Precision Oncology ◽  
Rare Cancer ◽  
Sequencing Data ◽  
Cancer Subtypes ◽  
Single Cell Rna Sequencing

Artificial intelligence, or the discipline of developing computational algorithms able to perform tasks that requires human intelligence, offers the opportunity to improve our idea and delivery of precision medicine. Here, we provide an overview of artificial intelligence approaches for the analysis of large-scale RNA-sequencing datasets in cancer. We present the major solutions to disentangle inter- and intra-tumor heterogeneity of transcriptome profiles for an effective improvement of patient management. We outline the contributions of learning algorithms to the needs of cancer genomics, from identifying rare cancer subtypes to personalizing therapeutic treatments.

A Study on the Auxiliary Diagnosis of Thyroid Disease Images Based on Multiple Dimensional Deep Learning Algorithms

2020 ◽  
Vol 16 (3) ◽  
pp. 199-205
Author(s):  
Yuejun Liu ◽  
Yifei Xu ◽  
Xiangzheng Meng ◽  
Xuguang Wang ◽  
Tianxu Bai
Keyword(s):  
Deep Learning ◽  
Learning Algorithms ◽  
Region Of Interest ◽  
Classification Performance ◽  
Thyroid Diseases ◽  
Great Success ◽  
Learning Models ◽  
Good Classification Performance ◽  
Spect Images

Background: Medical imaging plays an important role in the diagnosis of thyroid diseases. In the field of machine learning, multiple dimensional deep learning algorithms are widely used in image classification and recognition, and have achieved great success. Objective: The method based on multiple dimensional deep learning is employed for the auxiliary diagnosis of thyroid diseases based on SPECT images. The performances of different deep learning models are evaluated and compared. Methods: Thyroid SPECT images are collected with three types, they are hyperthyroidism, normal and hypothyroidism. In the pre-processing, the region of interest of thyroid is segmented and the amount of data sample is expanded. Four CNN models, including CNN, Inception, VGG16 and RNN, are used to evaluate deep learning methods. Results: Deep learning based methods have good classification performance, the accuracy is 92.9%-96.2%, AUC is 97.8%-99.6%. VGG16 model has the best performance, the accuracy is 96.2% and AUC is 99.6%. Especially, the VGG16 model with a changing learning rate works best. Conclusion: The standard CNN, Inception, VGG16, and RNN four deep learning models are efficient for the classification of thyroid diseases with SPECT images. The accuracy of the assisted diagnostic method based on deep learning is higher than that of other methods reported in the literature.

scholarly journals Deep Learning Model Comparison for Vision-Based Classification of Full/Empty-Load Trucks in Earthmoving Operations

2019 ◽  
Vol 9 (22) ◽  
pp. 4871 ◽  
Author(s):  
Quan Liu ◽  
Chen Feng ◽  
Zida Song ◽  
Joseph Louis ◽  
Jian Zhou
Keyword(s):  
Deep Learning ◽  
Model Comparison ◽  
Surveillance Systems ◽  
Comparison Study ◽  
Learning Models ◽  
The Core ◽  
Dump Trucks ◽  
Deep Learning Model ◽  
Contact Field

Earthmoving is an integral civil engineering operation of significance, and tracking its productivity requires the statistics of loads moved by dump trucks. Since current truck loads’ statistics methods are laborious, costly, and limited in application, this paper presents the framework of a novel, automated, non-contact field earthmoving quantity statistics (FEQS) for projects with large earthmoving demands that use uniform and uncovered trucks. The proposed FEQS framework utilizes field surveillance systems and adopts vision-based deep learning for full/empty-load truck classification as the core work. Since convolutional neural network (CNN) and its transfer learning (TL) forms are popular vision-based deep learning models and numerous in type, a comparison study is conducted to test the framework’s core work feasibility and evaluate the performance of different deep learning models in implementation. The comparison study involved 12 CNN or CNN-TL models in full/empty-load truck classification, and the results revealed that while several provided satisfactory performance, the VGG16-FineTune provided the optimal performance. This proved the core work feasibility of the proposed FEQS framework. Further discussion provides model choice suggestions that CNN-TL models are more feasible than CNN prototypes, and models that adopt different TL methods have advantages in either working accuracy or speed for different tasks.

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