Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data.

Publication date: Nov 29, 2019

Precision medicine in oncology aims at obtaining data from heterogeneous sources to have a precise estimation of a given patient’s state and prognosis. With the purpose of advancing to personalized medicine framework, accurate diagnoses allow prescription of more effective treatments adapted to the specificities of each individual case. In the last years, next-generation sequencing has impelled cancer research by providing physicians with an overwhelming amount of gene-expression data from RNA-seq high-throughput platforms. In this scenario, data mining and machine learning techniques have widely contribute to gene-expression data analysis by supplying computational models to supporting decision-making on real-world data. Nevertheless, existing public gene-expression databases are characterized by the unfavorable imbalance between the huge number of genes (in the order of tenths of thousands) and the small number of samples (in the order of a few hundreds) available. Despite diverse feature selection and extraction strategies have been traditionally applied to surpass derived over-fitting issues, the efficacy of standard machine learning pipelines is far from being satisfactory for the prediction of relevant clinical outcomes like follow-up end-points or patient’s survival. Using the public Pan-Cancer dataset, in this study we pre-train convolutional neural network architectures for survival prediction on a subset composed of thousands of gene-expression samples from thirty-one tumor types. The resulting architectures are subsequently fine-tuned to predict lung cancer progression-free interval. The application of convolutional networks to gene-expression data has many limitations, derived from the unstructured nature of these data. In this work we propose a methodology to rearrange RNA-seq data by transforming RNA-seq samples into gene-expression images, from which convolutional networks can extract high-level features. As an additional objective, we investigate whether leveraging the information extracted from other tumor-type samples contributes to the extraction of high-level features that improve lung cancer progression prediction, compared to other machine learning approaches.

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L’opez-Garc’ia, G., Jerez, J.M., Franco, L., and Veredas, F.J. Transfer learning with convolutional neural networks for cancer survival prediction using gene-expression data. 06568. 2019 PLoS One (15):3.

Concepts Keywords
Convolutional Neural Network Artificial neural networks
Convolutional Neural Networks Machine learning
Gene Molecular biology
Lung RNA
Prognosis Gene expression
RNA Seq Biochemistry
Sequencing Branches of biology
Throughput Tumor
Tumor RNA-Seq
Convolutional neural network
Neural network
Gene expression

Semantics

Type Source Name
disease MESH cancer
disease MESH diagnoses
disease MESH lung cancer

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