loss func

tutorials/compute_contact_prob/README.md

@@ -1,6 +1,6 @@
 ## contact_prob computation code
 
-- compute_contact_prob.ipynb: call and computes the contact probabilities (DamID, TSASeq, and chr-chr)
+- compute_contact_prob.ipynb: this notebook includes the contact probablity calculation of chromosome-lamina (DamID) and chromosome-speckle (TSA-Seq), where the cluster analysis of speckles are also involved. The number of clusters with respect to the time are plotted. In addition, We show how to visualize the comparison between experimental contacts and simulated contacts, including DamID, TSA-Seq, ideal, compt-compt, and inter-chromosomal contact probs.
 
 - contact_calculation: execution file compiled from Fortran code "../../openNucleome/utility/chromosome_contact_calculation.f90"
 

tutorials/optimization/chr_NL_optimization/README.md

@@ -1,6 +1,6 @@
 ## chromosome-nuclear landmarks optimization code
 
-- chr_NL_optimization.ipynb: call and optimizes the chromosome-nuclear landmarks interactions (chr-spe, chr-lam)
+chr_NL_optimization.ipynb logs the process of optimizing the chromosome-nuclear landmarks interactions. The users can use the notebook OpenNucleome/tutorials/compute_contact_prob/compute_contact_prob.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 $$L = \sum_i (\left< f_i\right> - f_i^\text{exp})^2$$
 
 - DamID-OE.txt: experimental DamID sequencing data
 

tutorials/optimization/chr_chr_optimization/README.md

@@ -1,6 +1,6 @@
 ## chromosome-chromosome optimization code
 
-- chr_chr_optimization.ipynb: call and optimizes the chromosome-chromosome interactions (ideal, compt-compt, interchr)
+chr_chr_optimization.ipynb logs the process of optimizing the chromosome-chromosome interactions. The users can use the notebook OpenNucleome/tutorials/compute_contact_prob/compute_contact_prob.ipynb to get the ideal, compt-compt, and inter-chromosomal contact probablities, then, use this notebook to optimize the interactions with the Adam Optimizer. The loss function is $$L = \sum_i (\left< f_i\right> - f_i^\text{exp})^2$$
 
 - adam_chr_chr_param: save all the parameters used in the adam optimization for the chromosome-chromosome interactions