Unsupervised Representation Learning of DNA Sequences

Autor:	Agarwal, Vishal, Reddy, N Jayanth Kumar, Anand, Ashish
Rok vydání:	2019
Předmět:	Quantitative Biology - Genomics Computer Science - Machine Learning
Druh dokumentu:	Working Paper
Popis:	Recently several deep learning models have been used for DNA sequence based classification tasks. Often such tasks require long and variable length DNA sequences in the input. In this work, we use a sequence-to-sequence autoencoder model to learn a latent representation of a fixed dimension for long and variable length DNA sequences in an unsupervised manner. We evaluate both quantitatively and qualitatively the learned latent representation for a supervised task of splice site classification. The quantitative evaluation is done under two different settings. Our experiments show that these representations can be used as features or priors in closely related tasks such as splice site classification. Further, in our qualitative analysis, we use a model attribution technique Integrated Gradients to infer significant sequence signatures influencing the classification accuracy. We show the identified splice signatures resemble well with the existing knowledge. Comment: Accepted at 2019 ICML Workshop on Computational Biology
Databáze:	arXiv
Externí odkaz:	http://arxiv.org/abs/1906.03087 Zobrazit plný text záznamu View this record from Arxiv