Create README.md
Browse files# Aggregated Weight Matrices Used in *Transformers Enhance the Predictive Power of Network Medicine*
*Jonah Spector, Andrés Aldana Gonzalez, Michael Sebek, Joseph Ehlert, Christian DeFrondeville, Albert-László Barabási*
## Data Structure
This directory contains all aggregated weight matrices used to make figures in the manuscript. The data structure is as follows
```
aggregated_matrices
aggregated_attentions
dcm_samples
fine_tuned
max
layer_0
layer_1
layer_2
layer_3
layer_4
layer_5
pretrained
max
genecorpus
fine_tuned
max
pretrained
max
aggregated_embeddings
dcm_samples
fine_tuned
max
layer_input
layer_0
layer_1
layer_2
layer_3
layer_4
layer_5
pretrained
max
genecorpus
fine_tuned
max
pretrained
max
```
In the folder at the end of each branch there are 3 files, called ```counts.pkl```, ```vals.pkl```, ```gene_dict.pkl```. The counts matrix is a square matrix of size NxN, where N is the number of unique genes in the sample set. It counts how many times each pair of genes co-occurs in a sample. The vals matrix is the same shape, and contains the aggregated weight between each pair of genes. ```gene_dict.pkl``` is a dictionary that specifies the index of each gene in the matrix.