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[WIP] feat: create and train GNN for gene expression prediction using gene regulatory network #1

Merged
merged 49 commits into from
Feb 3, 2025
Merged

[WIP] feat: create and train GNN for gene expression prediction using gene regulatory network #1

merged 49 commits into from
Feb 3, 2025

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@macwiatrak macwiatrak changed the title feat: create and train GNN for gene expression prediction using gene regulatory network [WIP] feat: create and train GNN for gene expression prediction using gene regulatory network Jan 31, 2025
@macwiatrak
feat: add support for training the model including the data reader an…
fc74910 
…d trainer
@macwiatrak
feat: add support for training the model including the data reader an…
ecd388f 
…d trainer
@macwiatrak
debug: debug data processing
1348c13
@macwiatrak
fix: add output_dim as an argument
c3d3b2e
@macwiatrak
fix: n_unique genes
b75af59
@macwiatrak
fix: fix passing args to trainer
55a5903
@macwiatrak
fix: fix fetching protein embeddings in the dataset.py
306e38e
@macwiatrak
fix: fix fetching protein embeddings in the dataset.py
e20ea14
@macwiatrak
fix: convert edge indices to long tensors
1af18b6
@macwiatrak
fix: fix adding bias to the output
0e5357e
@macwiatrak
fix: fix adding bias to the output
89982db
@macwiatrak
fix: fix adding bias to the output
53695c1
@macwiatrak
debug: debug nan in loss
e40d0a9
@macwiatrak
debug: debug nan in loss
0e99651
@macwiatrak
debug: remove debugging print
90ee5bc
@macwiatrak
feat: experience with removing bias
f832fd4
@macwiatrak
feat: group embeddings by label
4eb351a
@macwiatrak
feat: add gene matrix parameter
f296ab8
@macwiatrak
feat: add gene matrix parameter
cf6a6ed
@macwiatrak
feat: add gene matrix parameter
520f1c7
@macwiatrak
feat: add gene matrix parameter
840824e
@macwiatrak
feat: add gene matrix parameter
75c699c
@macwiatrak
feat: add gene matrix parameter
d0961a8
@macwiatrak
debug: randomize the network
45aca53
@macwiatrak
debug: revert randomize the network
472cb4b
@macwiatrak
feat: add cosine annealing LR
ed06cc3
@macwiatrak
feat: add t_max for cosine annealing LR
3cbc1bf
@macwiatrak
exp: remove cosine annealing LR
ece65d5
@macwiatrak
exp: don't use softplus
5fc2447
@macwiatrak
feat: add gene_layers instead of gene_matrix
7d33bd0
@macwiatrak
feat: only add biad, no gene layers
0183303
@macwiatrak
feat: only add bias, no gene layers
18c7300
@macwiatrak
feat: only add bias, no gene layers
f33bd93
@macwiatrak
feat: try to revert back to previous version with gene matrix
f07330b
@macwiatrak
feat: experiment with a single non-gene specific layer
fb07df1
@macwiatrak
feat: experiment with no gene specific layer
bee8c49
@macwiatrak
feat: do testing on val and test after training
9a68d94
@macwiatrak
feat: change the train_size
fb87742
@macwiatrak
feat: randomize the network experiment
1c224e2
@macwiatrak
feat: fully connected network experiment
3702143
@macwiatrak
exp: subset to half of genes
954a359
@macwiatrak
exp: subset to quarter of genes
b12e6a6
@macwiatrak
exp: run expn with gene matrix and randomizing the network
a5665d4
@macwiatrak
exp: revert randomizing the network
fc084bc
@macwiatrak
exp: flip network direction
014a040
@macwiatrak
refactor: revert to previous version
3f6df87
@macwiatrak macwiatrak merged commit 4bac5ad into main Feb 3, 2025
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@macwiatrak