A curated list of awesome deep learning applications on gene expression data

Ahmed Elmahy
Jul 11 · 2 min read

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A curated list of awesome deep learning applications on gene expression data (RNASeq and microarray data). The list is on github, Feel free to send a pull request.

https://github.com/ahmedelmahy/awesome-deep-gene-expression

Convolutional neural networks on gene expression data

  • 2017–10 | Convolutional neural networks for structured omics: OmicsCNN and the OmicsConv layer | Giuseppe Jurman, Valerio Maggio, et al | Arxiv
  • 2017–11 | Tumor gene expression data classification via sample expansion-based deep learning | Jian Liu, Xuesong Wang | Oncotarget
  • 2018–4 | OmicsMapNet: Transforming omics data to take advantage of Deep Convolutional Neural Network for discovery | Shiyong Ma, Zhen Zhang | Arxiv | Github
  • 2018–7 | Deep Learning Based Tumor Type Classification Using Gene Expression Data | Boyu Lyu, Anamul Haque | Arxiv | Github
  • 2019–6 | Convolutional neural network models for cancer type prediction based on gene expression | Milad Mostavi, Yu-Chiao Chiu, Yufei Huang, Yidong Chen | Arxiv | Github

Autoencoders on gene expression data

  • 2016–12 | A DEEP LEARNING APPROACH FOR CANCER DETECTION AND RELEVANT GENE IDENTIFICATION | PADIDEH DANAEE, REZA GHAEINI and DAVID A. HENDRIX | Biocomputing 2018
  • 2018–1 | Extracting a biologically relevant latent space from cancer transcriptomes with variational autoencoders | Gregory P. Way and Casey S. Greene | Biocomputing 2018
  • 2018–12 | GSAE: an autoencoder with embedded gene-set nodes for genomics functional characterization | Hung-I Harry Chen, Yu-Chiao Chiu, et al | BMC Systems Biology
  • 2018–12 | OUTRIDER: A Statistical Method for Detecting Aberrantly Expressed Genes in RNA Sequencing Data | Felix Brechtmann, Christian Mertes, et al | American Journal of Human Genetics
  • 2018–5 | DeepProfile: Deep learning of cancer molecular profiles for precision medicine | Ayse Berceste Dincer, Safiye Celik, Naozumi Hiranuma, Su-In Lee | biorxiv | Github

Transfer learning on gene expression data

Ensemble learning integrated with deep learning on gene expression data

Generative adversarial networks on gene expression data

  • 2016–12 | DeepCancer: Detecting Cancer through Gene Expressions via Deep Generative Learning | * Rajendra Rana Bhat, Vivek Viswanath, Xiaolin Li* | arxiv

Densely connected neural nets (DNN) on gene expression data

Deep clustering

  • 2014–8 | Molecular subtyping of bladder cancer using Kohonen self‐organizing maps | * Edyta M. Borkowska, Andrzej Kruk, et al* | Cancer Medicine
  • 2017–2 | Clustering cancer gene expression data by projective clustering ensemble | * Xianxue Yu, Guoxian Yu, Jun Wang* | plos one