updates to sir, group figures, couple other things

.gitignore

@@ -8,4 +8,5 @@ __pycache__/
 docs/examples
 docs/*.pt
 docs/*.csv
-docs/_build/
+docs/_build/
+manuscript/experiments/

manuscript/Snakefile

@@ -86,6 +86,11 @@ rule train_torch:
             "experiments/{dataset}/lantern/full/model.pt",
             dataset=["gfp-brightness", "laci-joint", "covid-joint"],
         ),
+        expand(
+            "experiments/{dataset}/lantern/full-r{r}/model.pt",
+            dataset=["gfp-brightness", "laci-joint", "covid-joint"],
+            r = range(2)
+        ),
         expand(
             "experiments/{dataset}/{model}/cv{cv}-n{n}000/model.pt",
             dataset=["laci-joint", "gfp-brightness"],
@@ -169,7 +174,17 @@ rule exp_figures:
                 "covid-joint/bind",
                 "gfp-brightness/brightness",
             ],
-            fig=["surface", "gradient", "robustness", "laplacian", "additivity", "sir-effects", "sir-dims"],
+            fig=[
+                "surface",
+                "gradient",
+                "robustness",
+                "laplacian",
+                "additivity",
+                # "sir-effects",
+                # "sir-effects-corr",
+                # "sir-dims",
+                # "sir-variance",
+            ],
         ),
         expand(
             "figures/{dataset}/anglehist.png",
@@ -195,10 +210,10 @@ rule pred_figures:
     input:
         "figures/cvr2.png",
         "figures/laci-joint/sample-size-ec50-norm.png",
-        "figures/laci-joint/sample-size-ginf-norm.png",
+        #"figures/laci-joint/sample-size-ginf-norm.png",
         "figures/gfp-brightness/sample-size-phenotype.png",
-        "figures/covid-joint/sample-size-func_score_norm_exp.png",
-        "figures/covid-joint/sample-size-func_score_norm_bind.png",
+        #"figures/covid-joint/sample-size-func_score_norm_exp.png",
+        #"figures/covid-joint/sample-size-func_score_norm_bind.png",
     shell:
         "tar -czf figures.tar.gz figures/*"
 
@@ -224,10 +239,3 @@ rule help:
 rule environment:
     shell:
         """conda env export -n lantern > environment.yml"""
-
-# rule a:
-#     input: expand("tmp/in/{a}.txt", a=range(10))
-#     output: "tmp/out/a.txt"
-# 
-# rule b:
-#     input: "tmp/{a}/out.txt"

manuscript/config.yaml

@@ -7,11 +7,11 @@ gfp:
 
   lantern:
     prediction:
-      cuda: True
+      cuda: False
 
   feedforward:
     prediction:
-      cuda: True
+      cuda: False
 
   alphabet: ["A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y","*"]
 
@@ -30,11 +30,11 @@ laci:
 
   lantern:
     prediction:
-      cuda: True
+      cuda: False
 
   feedforward:
     prediction:
-      cuda: True
+      cuda: False
 
 covid:
   N: 125000
@@ -54,11 +54,11 @@ covid:
 
   lantern:
     prediction:
-      cuda: True
+      cuda: False
 
   feedforward:
     prediction:
-      cuda: True
+      cuda: False
 
 figures:
   surface:

manuscript/environment.yml

@@ -1,4 +1,4 @@
-name: lantern
+name: lantern-response
 channels:
   - defaults
   - conda-forge

manuscript/smk/figures/calibration.smk

@@ -7,7 +7,7 @@ rule calibration:
         expand("experiments/{dataset}-{phenotype}/{model}/cv{cv}/pred-val.csv", cv=range(10), allow_missing=True)
     output:
         "figures/{dataset}-{phenotype}/{model}/cv-calibration.png"
-
+    group: "figure"
     run:
         scores = pd.concat([pd.read_csv(pth) for pth in input])
         D = len(get(config, f"{wildcards.dataset}/phenotypes/{wildcards.phenotype}"))

manuscript/smk/figures/diffops.smk

@@ -4,6 +4,7 @@ rule diffops:
     output:
         "figures/diffops-curvature.png",
         "figures/diffops-slope.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("laci", "joint", "lantern", "full", 8)
 

manuscript/smk/figures/dimensions.smk

@@ -7,6 +7,7 @@ rule dimensions:
         )
     output:
         "figures/dimensions.png"
+    group: "figure"
     run:
         mn = 1e-4
         mx = 1

manuscript/smk/figures/highlight.smk

@@ -9,6 +9,7 @@ rule gfp_surface_focus:
         "experiments/gfp-brightness/lantern/full/model.pt"
     output:
         "figures/gfp-brightness/brightness/surface-focus.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("gfp", "brightness", "lantern", "full", 8)
         model.eval()
@@ -52,6 +53,7 @@ rule gfp_surface_bfp1:
         "experiments/gfp-brightness/lantern/full/model.pt"
     output:
         "figures/gfp-brightness/brightness/surface-bfp1.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("gfp", "brightness", "lantern", "full", 8)
         model.eval()
@@ -124,6 +126,7 @@ rule gfp_surface_bfp2:
         "experiments/gfp-brightness/lantern/full/model.pt"
     output:
         "figures/gfp-brightness/brightness/surface-bfp2.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("gfp", "brightness", "lantern", "full", 8)
         model.eval()
@@ -196,6 +199,7 @@ rule gfp_surface_bfp_all:
         "experiments/gfp-brightness/lantern/full/model.pt"
     output:
         "figures/gfp-brightness/brightness/surface-bfp-all.png"
+    group: "figure"
     run:
         import matplotlib.patches as mpatches
 
@@ -343,6 +347,7 @@ rule laci_parametric:
         "experiments/laci-joint/lantern/full/model.pt"
     output:
         "figures/laci-joint/parametric.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("laci", "joint", "lantern", "full", 8)
         model.eval()
@@ -521,6 +526,7 @@ rule covid_anglehist:
         "experiments/covid-joint/lantern/full/model.pt"
     output:
         "figures/covid-joint/anglehist-highlight.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("covid", "joint", "lantern", "full", 8)
         model.eval()
@@ -633,6 +639,7 @@ rule covid_axes_parametric:
         "experiments/covid-joint/lantern/full/model.pt"
     output:
         "figures/covid-joint/axes-surface.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("covid", "joint", "lantern", "full", 8)
         model.eval()
@@ -741,6 +748,7 @@ rule covid_parametric:
         "experiments/covid-joint/lantern/full/model.pt"
     output:
         "figures/covid-joint/parametric.png"
+    group: "figure"
     run:
         df, ds, model = util.load_run("covid", "joint", "lantern", "full", 8)
         model.eval()
@@ -852,6 +860,7 @@ rule covid_variants:
     output:
         "figures/covid-joint/variants.png",
         "figures/covid-joint/variants_project.png"
+    group: "figure"
     run:
         from cycler import cycler
 
@@ -1085,6 +1094,7 @@ rule covid_axes_surface:
         "figures/covid-joint/axes-binding.png",
         "figures/covid-joint/axes-expression.png",
         # "figures/covid-joint/axes-expression-with-hist.png"
+    group: "figure"
     run:
 
         df, ds, model = util.load_run("covid", "joint", "lantern", "full", 8)