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fix: re-add yeast #27

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Merged
tristan-f-r merged 3 commits into from
Jul 2, 2025
Merged

fix: re-add yeast #27

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0c4b2d0
fix: re-add yeast
tristan-f-r Jul 1, 2025
87b1775
docs: mention old configs
tristan-f-r Jul 1, 2025
c0a0caf
docs: remove inconsistent placeholder cmt
tristan-f-r Jul 1, 2025
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9 changes: 8 additions & 1 deletion configs/dmmm.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,14 +43,21 @@ algorithms:
g: [0]

datasets:
# TODO: use old paramaters for datasets
# HIV: https://github.com/Reed-CompBio/spras-benchmarking/blob/0293ae4dc0be59502fac06b42cfd9796a4b4413e/hiv-benchmarking/spras-config/config.yaml
- label: dmmmhiv060
node_files: ["processed_prize_060.txt"]
edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
# Placeholder
other_files: []
data_dir: "datasets/hiv/processed"
- label: dmmmhiv05
node_files: ["processed_prize_05.txt"]
edge_files: ["phosphosite-irefindex13.0-uniprot.txt"]
other_files: []
data_dir: "datasets/hiv/processed"
# Yeast: https://github.com/tristan-f-r/spras-benchmarking/blob/9477d85871024a5e3a4b0b8b9be7e78c0d0ee961/yeast-osmotic-stress/config.yaml
- label: dmmmyeast
node_files: ["prizes1_dummies.txt"]
edge_files: ["network1.txt"]
other_files: []
data_dir: "datasets/yeast-osmotic-stress/processed"
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