remove redundant tutorials; simplify

BIMSBbioinfo · Jul 18, 2024 · 2ce3fbc · 2ce3fbc
1 parent 21303c9
commit 2ce3fbc
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Showing 8 changed files with 881 additions and 3,197 deletions.
diff --git a/.github/workflows/tutorials.yml b/.github/workflows/tutorials.yml
@@ -58,12 +58,6 @@ jobs:
         notebook='examples/tutorials/brca_subtypes'
         papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel 
         
-    - name: Compile modeling_drug_response
-      shell: bash -l {0}
-      run: |
-        conda activate my_env
-        notebook='examples/tutorials/modeling_drug_response'
-        papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel
         
     - name: Compile survival_subtypes_LGG_GBM
       shell: bash -l {0}
@@ -72,21 +66,7 @@ jobs:
         notebook='examples/tutorials/survival_subtypes_LGG_GBM'
         papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel
 
-    - name: Compile scrnaseq_bonemarrow
-      shell: bash -l {0}
-      run: |
-        conda activate my_env
-        notebook='examples/tutorials/scrnaseq_bonemarrow'
-        papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel
-        
-    - name: Compile neuroblastoma_data_integration
-      shell: bash -l {0}
-      run: |
-        conda activate my_env
-        notebook='examples/tutorials/neuroblastoma_data_integration' 
-        papermill "${notebook}.ipynb" "${notebook}_out.ipynb" -p HPO_ITER 1 -k my_env_kernel
-
-    - name: Compile unsupervised_analysis_single_cell
+    - name: Compile unsupervised-analysis
       shell: bash -l {0}
       run: |
         conda activate my_env

diff --git a/examples/tutorials/brca_subtypes.ipynb b/examples/tutorials/brca_subtypes.ipynb
diff --git a/examples/tutorials/conf.yaml b/examples/tutorials/conf.yaml
@@ -2,68 +2,74 @@ DirectPred:
   - type: Integer
     name: latent_dim
     low: 16
-    high: 64
+    high: 128
+  - type: Real
+    name: hidden_dim_factor
+    low: 0.5
+    high: 2
   - type: Integer
-    name: hidden_dim
-    low: 64
-    high: 512
+    name: supervisor_hidden_dim
+    low: 16
+    high: 128
   - type: Real
     name: lr
     low: 0.0001
     high: 0.01
     prior: log-uniform
-  - type: Integer
+  - type: Categorical
     name: batch_size
-    low: 32
-    high: 128
+    categories: [32, 64, 128]
   - type: Categorical
     name: epochs
     categories: [200]
 
-DirectPredCNN:
+CrossModalPred:
   - type: Integer
     name: latent_dim
     low: 16
-    high: 64
+    high: 128
+  - type: Real
+    name: hidden_dim_factor
+    low: 0.5
+    high: 2
   - type: Integer
-    name: hidden_dim
-    low: 64
-    high: 512
+    name: supervisor_hidden_dim
+    low: 16
+    high: 128
   - type: Real
     name: lr
     low: 0.0001
     high: 0.01
     prior: log-uniform
-  - type: Integer
+  - type: Categorical
     name: batch_size
-    low: 32
-    high: 128
+    categories: [32, 64, 128]
   - type: Categorical
     name: epochs
     categories: [200]
 
+
 supervised_vae:
   - type: Integer
     name: latent_dim
     low: 16
     high: 128
-  - type: Integer
-    name: hidden_dim
-    low: 64
-    high: 512
+  - type: Real
+    name: hidden_dim_factor
+    low: 0.5
+    high: 2
   - type: Integer
     name: supervisor_hidden_dim
-    low: 8
-    high: 32
+    low: 16
+    high: 128
   - type: Real
     name: lr
     low: 0.0001
     high: 0.01
     prior: log-uniform
-  - type: Integer
+  - type: Categorical
     name: batch_size
-    low: 32
-    high: 128
+    categories: [32, 64, 128]
   - type: Categorical
     name: epochs
     categories: [200]
@@ -73,23 +79,22 @@ MultiTripletNetwork:
     name: latent_dim
     low: 16
     high: 128
-  - type: Integer
-    name: hidden_dim
-    low: 64
-    high: 512
+  - type: Real
+    name: hidden_dim_factor
+    low: 0.5
+    high: 2
   - type: Integer
     name: supervisor_hidden_dim
-    low: 8
-    high: 32
+    low: 16
+    high: 128
   - type: Real
     name: lr
     low: 0.0001
     high: 0.01
     prior: log-uniform
-  - type: Integer
+  - type: Categorical
     name: batch_size
-    low: 32
-    high: 128
+    categories: [32, 64, 128]
   - type: Categorical
     name: epochs
     categories: [200]

diff --git a/examples/tutorials/modeling_drug_response.ipynb b/examples/tutorials/modeling_drug_response.ipynb
diff --git a/examples/tutorials/neuroblastoma_data_integration.ipynb b/examples/tutorials/neuroblastoma_data_integration.ipynb