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Atlas of Computational Cell Reprogramming

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L3 · Explicit model-based inverse intervention I D

DeepNEU

Danter WR

2019 · Orphanet journal of rare diseases

BACKGROUND: Conversion of human somatic cells into induced pluripotent stem cells (iPSCs) is often an inefficient, time consuming and expensive process.

Abstract

From the original paper, Orphanet journal of rare diseases · PubMed

BACKGROUND: Conversion of human somatic cells into induced pluripotent stem cells (iPSCs) is often an inefficient, time consuming and expensive process. Also, the tendency of iPSCs to revert to their original somatic cell type over time continues to be problematic. A computational model of iPSCs identifying genes/molecules necessary for iPSC generation and maintenance could represent a crucial step forward for improved stem cell research. The combination of substantial genetic relationship data, advanced computing hardware and powerful nonlinear modeling software could make the possibility of artificially-induced pluripotent stem cells (aiPSC) a reality. We have developed an unsupervised deep machine learning technology, called DeepNEU that is based on a fully-connected recurrent neural network architecture with one network processing layer for each input. DeepNEU was used to simulate aiPSC systems using a defined set of reprogramming transcription factors. Genes/proteins that were reported to be essential in human pluripotent stem cells (hPSC) were used for system modelling. RESULTS: The Mean Squared Error (MSE) function was used to assess system learning. System convergence was defined at MSE < 0.001. The markers of human iPSC pluripotency (N = 15) were all upregulated in the aiPSC final model. These upregulated/expressed genes in the aiPSC system were entirely consistent with results obtained for iPSCs. CONCLUSION: This research introduces and validates the potential use of aiPSCs as computer models of human pluripotent stem cell systems. Disease-specific aiPSCs have the potential to improve disease modeling, prototyping of wet lab experiments, and prediction of genes relevant and necessary for aiPSC production and maintenance for both common and rare diseases in a cost-effective manner.

Summary

Editorial summary pending review by the maintainer. The paper's own abstract appears above; the Atlas summary in the maintainer's voice will explain how DeepNEU relates to the cross-modality inverse-design framework of the review.

Why this level

Level 3 because candidate interventions enter an explicit forward operator FθuF_{\theta_u} and the predicted post-intervention outcome is what scores each candidate. Representation family is executable intervention model. Cited in §3.4 of the review. Editorial rationale pending review by the maintainer.

Classification

Level
L3
Representation
Executable intervention model
Modalities
D, I
Intervention
Transcription factors
Framework
Boolean network

Software

Code
Not available
Reproducibility
0 of 4
FAIR4RS
0 of 5

Last audited 2026-05-24

Citation

Danter WR (2019). DeepNEU: cellular reprogramming comes of age - a machine learning platform with application to rare diseases research., Orphanet journal of rare diseases.

DOI: 10.1186/s13023-018-0983-3

PMID: 30630505

BibTeX 
@article{deepneu2019,
  title  = {DeepNEU: cellular reprogramming comes of age - a machine learning platform with application to rare diseases research.},
  author = {Danter WR},
  year   = {2019},
  journal = {Orphanet journal of rare diseases},
  pmid = {30630505},
  doi  = {10.1186/s13023-018-0983-3}
}