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Update README.md
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binzhangMIT authored Feb 29, 2024
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## chromosome-nuclear landmarks optimization code

ChrNLOptimization.ipynb logs the process of optimizing the chromosome-nuclear landmarks interactions. The users can use the notebook OpenNucleome/tutorials/compute_contact_prob/ComputeContactProb.ipynb to get the DamID and TSA-Seq, then, use this notebook to optimize the interactions with the Adam Optimizer. The loss function is similar to the chr-chr optimization $$L = \sum_i (\left< f_i\right> - f_i^\text{exp})^2$$
ChrNLOptimization.ipynb logs the process of optimizing interaction parameters between chromosome and nuclear landmarks.

The pipline is the same as that in the folder "../chr_chr_optimization"

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