Robust Deep Multi-task Learning Framework for Cancer Survival Analysis

Author(s):  
Shuang Yun ◽  
Bo Du ◽  
Yuren Mao
2020 ◽  
Author(s):  
Yeping Lina Qiu ◽  
Hong Zheng ◽  
Arnout Devos ◽  
Olivier Gevaert

AbstractRNA sequencing has emerged as a promising approach in cancer prognosis as sequencing data becomes more easily and affordably accessible. However, it remains challenging to build good predictive models especially when the sample size is limited and the number of features is high, which is a common situation in biomedical settings. To address these limitations, we propose a meta-learning framework based on neural networks for survival analysis and evaluate it in a genomic cancer research setting. We demonstrate that, compared to regular transfer-learning, meta-learning is a significantly more effective paradigm to leverage high-dimensional data that is relevant but not directly related to the problem of interest. Specifically, meta-learning explicitly constructs a model, from abundant data of relevant tasks, to learn a new task with few samples effectively. For the application of predicting cancer survival outcome, we also show that the meta-learning framework with a few samples is able to achieve competitive performance with learning from scratch with a significantly larger number of samples. Finally, we demonstrate that the meta-learning model implicitly prioritizes genes based on their contribution to survival prediction and allows us to identify important pathways in cancer.


2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yeping Lina Qiu ◽  
Hong Zheng ◽  
Arnout Devos ◽  
Heather Selby ◽  
Olivier Gevaert

AbstractRNA sequencing has emerged as a promising approach in cancer prognosis as sequencing data becomes more easily and affordably accessible. However, it remains challenging to build good predictive models especially when the sample size is limited and the number of features is high, which is a common situation in biomedical settings. To address these limitations, we propose a meta-learning framework based on neural networks for survival analysis and evaluate it in a genomic cancer research setting. We demonstrate that, compared to regular transfer-learning, meta-learning is a significantly more effective paradigm to leverage high-dimensional data that is relevant but not directly related to the problem of interest. Specifically, meta-learning explicitly constructs a model, from abundant data of relevant tasks, to learn a new task with few samples effectively. For the application of predicting cancer survival outcome, we also show that the meta-learning framework with a few samples is able to achieve competitive performance with learning from scratch with a significantly larger number of samples. Finally, we demonstrate that the meta-learning model implicitly prioritizes genes based on their contribution to survival prediction and allows us to identify important pathways in cancer.


2021 ◽  
Vol 13 (5) ◽  
pp. 168781402110131
Author(s):  
Junfeng Wu ◽  
Li Yao ◽  
Bin Liu ◽  
Zheyuan Ding ◽  
Lei Zhang

As more and more sensor data have been collected, automated detection, and diagnosis systems are urgently needed to lessen the increasing monitoring burden and reduce the risk of system faults. A plethora of researches have been done on anomaly detection, event detection, anomaly diagnosis respectively. However, none of current approaches can explore all these respects in one unified framework. In this work, a Multi-Task Learning based Encoder-Decoder (MTLED) which can simultaneously detect anomalies, diagnose anomalies, and detect events is proposed. In MTLED, feature matrix is introduced so that features are extracted for each time point and point-wise anomaly detection can be realized in an end-to-end way. Anomaly diagnosis and event detection share the same feature matrix with anomaly detection in the multi-task learning framework and also provide important information for system monitoring. To train such a comprehensive detection and diagnosis system, a large-scale multivariate time series dataset which contains anomalies of multiple types is generated with simulation tools. Extensive experiments on the synthetic dataset verify the effectiveness of MTLED and its multi-task learning framework, and the evaluation on a real-world dataset demonstrates that MTLED can be used in other application scenarios through transfer learning.


2021 ◽  
Author(s):  
Zhilong Lv ◽  
Yuexiao Lin ◽  
Rui Yan ◽  
Zhenghe Yang ◽  
Ying Wang ◽  
...  

Author(s):  
David Korfkamp ◽  
Stefan Gudenkauf ◽  
Martin Rohde ◽  
Eunice Sirri ◽  
Joachim Kieschke ◽  
...  

Author(s):  
Jie Yang ◽  
Zhiquan Qi ◽  
Yong Shi

This paper develops a multi-task learning framework that attempts to incorporate the image structure knowledge to assist image inpainting, which is not well explored in previous works. The primary idea is to train a shared generator to simultaneously complete the corrupted image and corresponding structures --- edge and gradient, thus implicitly encouraging the generator to exploit relevant structure knowledge while inpainting. In the meantime, we also introduce a structure embedding scheme to explicitly embed the learned structure features into the inpainting process, thus to provide possible preconditions for image completion. Specifically, a novel pyramid structure loss is proposed to supervise structure learning and embedding. Moreover, an attention mechanism is developed to further exploit the recurrent structures and patterns in the image to refine the generated structures and contents. Through multi-task learning, structure embedding besides with attention, our framework takes advantage of the structure knowledge and outperforms several state-of-the-art methods on benchmark datasets quantitatively and qualitatively.


F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 919 ◽  
Author(s):  
Manali Rupji ◽  
Xinyan Zhang ◽  
Jeanne Kowalski

We present CASAS, a shiny R based tool for interactive survival analysis and visualization of results. The tool provides a web-based one stop shop to perform the following types of survival analysis:  quantile, landmark and competing risks, in addition to standard survival analysis.  The interface makes it easy to perform such survival analyses and obtain results using the interactive Kaplan-Meier and cumulative incidence plots.  Univariate analysis can be performed on one or several user specified variable(s) simultaneously, the results of which are displayed in a single table that includes log rank p-values and hazard ratios along with their significance. For several quantile survival analyses from multiple cancer types, a single summary grid is constructed. The CASAS package has been implemented in R and is available via http://shinygispa.winship.emory.edu/CASAS/. The developmental repository is available at https://github.com/manalirupji/CASAS/.


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