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Aggregated Weight Matrices Used in Transformers Enhance the Predictive Power of Network Medicine
Jonah Spector, Andrés Aldana Gonzalez, Michael Sebek, Joseph Ehlert, Christian DeFrondeville, Susan Dina Ghiassian, and 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.
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