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README.md
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- biology
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size_categories:
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- 100B<n<1T
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- biology
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size_categories:
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- 100B<n<1T
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---
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# Aggregated Weight Matrices Used in *Transformers Enhance the Predictive Power of Network Medicine*
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*Jonah Spector, Andrés Aldana Gonzalez, Michael Sebek, Joseph Ehlert, Christian DeFrondeville, Albert-László Barabási*
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## Data Structure
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This directory contains all aggregated weight matrices used to make figures in the manuscript. The data structure is as follows
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```
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aggregated_matrices
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aggregated_attentions
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dcm_samples
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fine_tuned
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max
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layer_0
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layer_1
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layer_2
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layer_3
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layer_4
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layer_5
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pretrained
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max
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genecorpus
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fine_tuned
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max
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pretrained
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max
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aggregated_embeddings
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dcm_samples
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fine_tuned
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max
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layer_input
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layer_0
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layer_1
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layer_2
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layer_3
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layer_4
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layer_5
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pretrained
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max
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genecorpus
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fine_tuned
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max
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pretrained
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max
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```
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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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