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Running
Eachan Johnson
commited on
Commit
·
6cf1162
1
Parent(s):
fd0246d
Update examples
Browse files- app.py +4 -4
- example-data/examples.json +83 -33
- example-data/liu23-abau-1000.csv +0 -0
- example-data/liu23-abau.csv +0 -0
- example-data/stokes20-eco-1000.csv +0 -0
- example-data/stokes2020-eco.csv +0 -0
- example-data/wong24-sau-tox-1000.csv +0 -0
- example-data/wong24-sau-tox-5000.csv +0 -0
app.py
CHANGED
@@ -32,8 +32,8 @@ THEME = gr.themes.Default()
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DEVICE = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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CACHE = "./cache"
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-
MAX_ROWS =
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-
BATCH_SIZE =
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HEADER_FILE = os.path.join("sources", "header.md")
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with open("repos.json", "r") as f:
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MODEL_REPOS = json.load(f)
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@@ -676,7 +676,7 @@ if __name__ == "__main__":
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"\n".join(eg["strings"]),
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"smiles",
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eg["species"],
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-
list(EXTRA_METRICS)[:
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]
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for eg in EXAMPLES["line input examples"]
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],
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@@ -732,7 +732,7 @@ if __name__ == "__main__":
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"smiles",
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eg["species"],
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"",
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-
list(EXTRA_METRICS)[:
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] for eg in EXAMPLES["file examples"]
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],
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example_labels=[
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DEVICE = torch.device("cuda" if torch.cuda.is_available() else "cpu")
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CACHE = "./cache"
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+
MAX_ROWS = 1000
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+
BATCH_SIZE = 16
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HEADER_FILE = os.path.join("sources", "header.md")
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with open("repos.json", "r") as f:
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MODEL_REPOS = json.load(f)
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"\n".join(eg["strings"]),
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"smiles",
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eg["species"],
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+
list(EXTRA_METRICS)[:3],
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]
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for eg in EXAMPLES["line input examples"]
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],
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"smiles",
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eg["species"],
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"",
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+
list(EXTRA_METRICS)[:3],
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] for eg in EXAMPLES["file examples"]
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],
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example_labels=[
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example-data/examples.json
CHANGED
@@ -1,25 +1,47 @@
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{
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"line input examples": [
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{
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-
"label": "Y. pestis (plague) vs Ciprofloxacin, Ceftriaxone, Cefiderocol
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"strings": [
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"Ciprofloxacin: C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O",
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"Ceftriaxone: CN1C(=NC(=O)C(=O)N1)SCC2=C(N3[C@@H]([C@@H](C3=O)NC(=O)/C(=N\\OC)/C4=CSC(=N4)N)SC2)C(=O)O",
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"Cefiderocol: CC(C)(C(=O)O)O/N=C(/C1=CSC(=N1)N)\\C(=O)N[C@H]2[C@@H]3N(C2=O)C(=C(CS3)C[N+]4(CCCC4)CCNC(=O)C5=C(C(=C(C=C5)O)O)Cl)C(=O)[O-]",
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-
"Linezolid: CC(=O)NC[C@H]1CN(C(=O)O1)C2=CC(=C(C=C2)N3CCOCC3)F",
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-
"Gepotidacin: C1CC2=CC(=NC=C2OC1)CNC3CCN(CC3)C[C@@H]4CN5C(=O)C=CC6=C5N4C(=O)C=N6"
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],
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"species": [
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"Yersinia pestis"
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]
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},
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{
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"label": "S. aureus vs
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"strings": [
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"Doxorubicin: C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](CC3=C2C(=C4C(=C3O)C(=O)C5=C(C4=O)C(=CC=C5)OC)O)(C(=O)CO)O)N)O",
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"Ampicillin: CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=CC=C3)N)C(=O)O)C",
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"Amoxicillin: CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=C(C=C3)O)N)C(=O)O)C",
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-
"Meropenem: C[C@@H]1[C@@H]2[C@H](C(=O)N2C(=C1S[C@H]3C[C@H](NC3)C(=O)N(C)C)C(=O)O)[C@@H](C)O"
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"Tetracycline: C[C@@]1([C@H]2C[C@H]3[C@@H](C(=O)C(=C([C@]3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O",
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"Anhydrotetracycline: CC1=C2C=CC=C(C2=C(C3=C1C[C@H]4[C@@H](C(=O)C(=C([C@]4(C3=O)O)O)C(=O)N)N(C)C)O)O"
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],
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@@ -28,43 +50,70 @@
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]
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},
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{
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-
"label": "E. coli
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"strings": [
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-
"Halicin: C1=C(SC(=N1)SC2=NN=C(S2)N)[N+](=O)[O-]",
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-
"Abaucin: C1CN(CCC12C3=CC=CC=C3NC(=O)O2)CCC4=CC=C(C=C4)C(F)(F)F",
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"Trimethoprim: COC1=CC(=CC(=C1OC)OC)CC2=CN=C(N=C2N)N",
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-
"Amikacin: CC1=CC(=NO1)NS(=O)(=O)C2=CC=C(C=C2)N",
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"Sulfamethoxazole: C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)O)N",
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-
"Isoniazid: C1=CN=CC=C1C(=O)NN"
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],
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"species": [
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"Escherichia coli"
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"Acinetobacter baumannii"
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]
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},
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{
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"label": "A. baumannii vs
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"strings": [
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"
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"
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"
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-
"Plazomicin: C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC=C(O3)CNCCO)N)N)NC(=O)[C@H](CCN)O)O",
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"Gentamicin: CC(C1CCC(C(O1)OC2C(CC(C(C2O)OC3C(C(C(CO3)(C)O)NC)O)N)N)N)NC",
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-
"Rifampicin: C[C@H]1/C=C/C=C(\\C(=O)NC2=C(C(=C3C(=C2O)C(=C(C4=C3C(=O)[C@](O4)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]1O)C)O)C)OC(=O)C)C)OC)C)C)O)O)/C=N/N5CCN(CC5)C)/CC"
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],
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"species": [
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"
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]
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},
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{
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"label": "E. coli vs Debio-1452, Debio-1452-NH3, Fabimycin
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"strings": [
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"Debio-1452: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)CC4)N=C3",
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"Debio-1452-NH3: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)[C@@H](C4)N)N=C3",
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-
"Fabimycin: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)[C@H](CC4)[NH3+])N=C3.[Cl-]"
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"5-FU: C1=C(C(=O)NC(=O)N1)F",
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"Carmofur: CCCCCCNC(=O)N1C=C(C(=O)NC1=O)F",
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-
"Etoposide: C[C@@H]1OC[C@@H]2[C@@H](O1)[C@@H]([C@H]([C@@H](O2)O[C@H]3[C@H]4COC(=O)[C@@H]4[C@@H](C5=CC6=C(C=C35)OCO6)C7=CC(=C(C(=C7)OC)O)OC)O)O"
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],
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"species": [
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"Escherichia coli"
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]
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},
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{
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"label": "K. pneumoniae vs CHIR-090, SCH79797, DBeQ, Tenovin-6, Pyrimethamine, Aminopterin",
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"strings": [
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"CHIR-090: C[C@H]([C@@H](C(=O)NO)NC(=O)C1=CC=C(C=C1)C#CC2=CC=C(C=C2)CN3CCOCC3)O",
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"SCH79797: CC(C)C1=CC=C(C=C1)CN2C=CC3=C2C=CC4=C3C(=NC(=N4)NC5CC5)N",
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"Aminopterin: C1=CC(=CC=C1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCC2=CN=C3C(=N2)C(=NC(=N3)N)N"
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],
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"species": [
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"Klebsiella pneumoniae"
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]
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}
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@@ -102,20 +152,20 @@
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"file examples": [
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{
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"label": "E. coli training data from Stokes J. et al., Cell (2020)",
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"file": "example-data/stokes2020-eco.csv",
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"column": "
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"species": "Escherichia coli"
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},
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{
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"label": "A. baumannii training data from Liu (2023)",
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"file": "example-data/liu23-abau.csv",
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"column": "
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"species": "Acinetobacter baumannii"
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},
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{
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"label": "S. aureus training data from Wong (2024)",
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"file": "example-data/wong24-sau-tox-
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"column": "
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"species": "Staphylococcus aureus"
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}
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]
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{
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"line input examples": [
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{
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"label": "Y. pestis (plague) vs Ciprofloxacin, Ceftriaxone, Cefiderocol",
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"strings": [
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"Ciprofloxacin: C1CC1N2C=C(C(=O)C3=CC(=C(C=C32)N4CCNCC4)F)C(=O)O",
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"Ceftriaxone: CN1C(=NC(=O)C(=O)N1)SCC2=C(N3[C@@H]([C@@H](C3=O)NC(=O)/C(=N\\OC)/C4=CSC(=N4)N)SC2)C(=O)O",
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"Cefiderocol: CC(C)(C(=O)O)O/N=C(/C1=CSC(=N1)N)\\C(=O)N[C@H]2[C@@H]3N(C2=O)C(=C(CS3)C[N+]4(CCCC4)CCNC(=O)C5=C(C(=C(C=C5)O)O)Cl)C(=O)[O-]",
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],
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"species": [
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"Yersinia pestis"
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]
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},
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{
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"label": "E. coli, K. pneumoniae, & S. aureus vs Ampicillin, Linezolid, Amoxicillin, Meropenem",
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"strings": [
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"Ampicillin: CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=CC=C3)N)C(=O)O)C",
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"Linezolid: CC(=O)NC[C@H]1CN(C(=O)O1)C2=CC(=C(C=C2)N3CCOCC3)F",
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"Amoxicillin: CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](C3=CC=C(C=C3)O)N)C(=O)O)C",
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"Meropenem: C[C@@H]1[C@@H]2[C@H](C(=O)N2C(=C1S[C@H]3C[C@H](NC3)C(=O)N(C)C)C(=O)O)[C@@H](C)O"
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],
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"species": [
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"Escherichia coli",
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"Klebsiella pneumoniae",
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"Staphylococcus aureus"
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]
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},
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{
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"label": "E. coli, P. aeruginosa, & S. aureus vs Gepotidacin, Murepavadin, Zosurabalpin, Plazomicin",
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"strings": [
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"Murepavadin: CC[C@H](C)[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N2CCC[C@@H]2C(=O)N3CCC[C@H]3C(=O)N[C@H](C(=O)N[C@H](C(=O)N1)CC4=CNC5=CC=CC=C54)[C@@H](C)O)CO)C)CCN)CCN)CC6=CNC7=CC=CC=C76)CCN)CCN)CCCN)CCN",
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+
"Gepotidacin: C1CC2=CC(=NC=C2OC1)CNC3CCN(CC3)C[C@@H]4CN5C(=O)C=CC6=C5N4C(=O)C=N6",
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"Zosurabalpin: CN1[C@H](C(=O)NCC2=C(C=CC=C2SC3=C(CN[C@H](C(=O)N[C@H](C1=O)CCCCN)CCCN)C=CC=N3)C4=CC=C(C=C4)C(=O)O)CC5=CNC6=CC=CC=C65",
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"Plazomicin: C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H](CC=C(O3)CNCCO)N)N)NC(=O)[C@H](CCN)O)O"
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],
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"species": [
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"Escherichia coli",
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"Pseudomonas aeruginosa",
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"Staphylococcus aureus"
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]
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},
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{
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"label": "S. aureus vs Tetracycline, Anhydrotetracycline",
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"strings": [
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"Tetracycline: C[C@@]1([C@H]2C[C@H]3[C@@H](C(=O)C(=C([C@]3(C(=O)C2=C(C4=C1C=CC=C4O)O)O)O)C(=O)N)N(C)C)O",
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"Anhydrotetracycline: CC1=C2C=CC=C(C2=C(C3=C1C[C@H]4[C@@H](C(=O)C(=C([C@]4(C3=O)O)O)C(=O)N)N(C)C)O)O"
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],
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]
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},
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{
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"label": "E. coli & A. baumannii vs Trimethoprim, Sulfamethoxazole",
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"strings": [
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"Trimethoprim: COC1=CC(=CC(=C1OC)OC)CC2=CN=C(N=C2N)N",
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"Sulfamethoxazole: C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CN)O)O)O)N",
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],
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"species": [
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"Escherichia coli"
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]
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},
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{
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"label": "E. coli, A. baumannii, & S. aureus vs Halicin, Abaucin, Compound 1 (from Wong, 2024)",
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"strings": [
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"Halicin: C1=C(SC(=N1)SC2=NN=C(S2)N)[N+](=O)[O-]",
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"Abaucin: C1CN(CCC12C3=CC=CC=C3NC(=O)O2)CCC4=CC=C(C=C4)C(F)(F)F",
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"Compound 1: ClC1=CC(Cl)=CC=C1OCC(NC2=C(C(O)=O)C=CC(Cl)=C2)=O"
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],
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"species": [
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"Escherichia coli",
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"Acinetobacter baumannii",
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"Staphylococcus aureus"
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]
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},
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{
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"label": "E. coli, P. aeruginosa & S. aureus vs Debio-1452, Debio-1452-NH3, Fabimycin",
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"strings": [
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"Debio-1452: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)CC4)N=C3",
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"Debio-1452-NH3: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)[C@@H](C4)N)N=C3",
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"Fabimycin: CC1=C(OC2=CC=CC=C12)CN(C)C(=O)/C=C/C3=CC4=C(NC(=O)[C@H](CC4)[NH3+])N=C3.[Cl-]"
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],
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"species": [
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"Escherichia coli",
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"Pseudomonas aeruginosa",
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"Staphylococcus aureus"
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]
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},
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{
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"label": "E. coli, A. baumannii, K. pneumoniae, P. aeruginosa & S. aureus vs 6NDM, 6NDM-NH3",
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"strings": [
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"6NDM: CN1C(C=C(C)C2=CC3=C(N4C(C=C3C)=O)C(OCC4)=C12)=O",
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"6NDM-NH3: CN1C(C=C(C)C2=CC3=C(N4C(C=C3C)=O)C(OCC4C[NH3+])=C12)=O",
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],
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"species": [
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96 |
+
"Escherichia coli",
|
97 |
+
"Acinetobacter baumannii",
|
98 |
+
"Klebsiella pneumoniae",
|
99 |
+
"Pseudomonas aeruginosa",
|
100 |
+
"Staphylococcus aureus"
|
101 |
+
]
|
102 |
+
},
|
103 |
+
{
|
104 |
+
"label": "E. coli vs Doxorubicin, 5-FU, Carmofur, Etoposide, Bleomycin, Cyclophosphamide, Vincristine, Procarbazine, Oxaliplatin, Docetaxel, Gemcitabine",
|
105 |
+
"strings": [
|
106 |
+
"Doxorubicin: C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](CC3=C2C(=C4C(=C3O)C(=O)C5=C(C4=O)C(=CC=C5)OC)O)(C(=O)CO)O)N)O",
|
107 |
"5-FU: C1=C(C(=O)NC(=O)N1)F",
|
108 |
"Carmofur: CCCCCCNC(=O)N1C=C(C(=O)NC1=O)F",
|
109 |
+
"Etoposide: C[C@@H]1OC[C@@H]2[C@@H](O1)[C@@H]([C@H]([C@@H](O2)O[C@H]3[C@H]4COC(=O)[C@@H]4[C@@H](C5=CC6=C(C=C35)OCO6)C7=CC(=C(C(=C7)OC)O)OC)O)O",
|
110 |
+
"Bleomycin: CC1=C(N=C(N=C1N)[C@H](CC(=O)N)NC[C@@H](C(=O)N)N)C(=O)N[C@@H]([C@H](C2=CN=CN2)OC3C(C(C(C(O3)CO)O)O)OC4C(C(C(C(O4)CO)O)OC(=O)N)O)C(=O)N[C@H](C)[C@H]([C@H](C)C(=O)N[C@@H]([C@@H](C)O)C(=O)NCCC5=NC(=CS5)C6=NC(=CS6)C(=O)NCCC[S+](C)C)O",
|
111 |
+
"Cyclophosphamide: C1CNP(=O)(OC1)N(CCCl)CCCl ",
|
112 |
+
"Vincristine: CC[C@@]1(C[C@@H]2C[C@@](C3=C(CCN(C2)C1)C4=CC=CC=C4N3)(C5=C(C=C6C(=C5)[C@]78CCN9[C@H]7[C@@](C=CC9)([C@H]([C@@]([C@@H]8N6C=O)(C(=O)OC)O)OC(=O)C)CC)OC)C(=O)OC)O ",
|
113 |
+
"Procarbazine: CC(C)NC(=O)C1=CC=C(C=C1)CNNC",
|
114 |
+
"Oxaliplatin: C1CC[C@H]([C@@H](C1)[NH-])[NH-].C(=O)(C(=O)O)O.[Pt+2]",
|
115 |
+
"Docetaxel: CC1=C2[C@H](C(=O)[C@@]3([C@H](C[C@@H]4[C@]([C@H]3[C@@H]([C@@](C2(C)C)(C[C@@H]1OC(=O)[C@@H]([C@H](C5=CC=CC=C5)NC(=O)OC(C)(C)C)O)O)OC(=O)C6=CC=CC=C6)(CO4)OC(=O)C)O)C)O",
|
116 |
+
"Gemcitabine: C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO)O)(F)F"
|
117 |
],
|
118 |
"species": [
|
119 |
"Escherichia coli"
|
|
|
134 |
]
|
135 |
},
|
136 |
{
|
137 |
+
"label": "E. coli & K. pneumoniae vs CHIR-090, SCH79797, DBeQ, Tenovin-6, Pyrimethamine, Aminopterin",
|
138 |
"strings": [
|
139 |
"CHIR-090: C[C@H]([C@@H](C(=O)NO)NC(=O)C1=CC=C(C=C1)C#CC2=CC=C(C=C2)CN3CCOCC3)O",
|
140 |
"SCH79797: CC(C)C1=CC=C(C=C1)CN2C=CC3=C2C=CC4=C3C(=NC(=N4)NC5CC5)N",
|
|
|
144 |
"Aminopterin: C1=CC(=CC=C1C(=O)N[C@@H](CCC(=O)O)C(=O)O)NCC2=CN=C3C(=N2)C(=NC(=N3)N)N"
|
145 |
],
|
146 |
"species": [
|
147 |
+
"Escherichia coli",
|
148 |
"Klebsiella pneumoniae"
|
149 |
]
|
150 |
}
|
|
|
152 |
"file examples": [
|
153 |
{
|
154 |
"label": "E. coli training data from Stokes J. et al., Cell (2020)",
|
155 |
+
"file": "example-data/stokes2020-eco-1000.csv",
|
156 |
+
"column": "smiles",
|
157 |
"species": "Escherichia coli"
|
158 |
},
|
159 |
{
|
160 |
+
"label": "A. baumannii training data from Liu G., Nature Chemical Biology (2023)",
|
161 |
+
"file": "example-data/liu23-abau-1000.csv",
|
162 |
+
"column": "smiles",
|
163 |
"species": "Acinetobacter baumannii"
|
164 |
},
|
165 |
{
|
166 |
+
"label": "S. aureus training data from Wong F., Nature (2024)",
|
167 |
+
"file": "example-data/wong24-sau-tox-1000.csv",
|
168 |
+
"column": "smiles",
|
169 |
"species": "Staphylococcus aureus"
|
170 |
}
|
171 |
]
|
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