Add experimental implementation for sparse datasets

Author: DesmondYuan

configs/debugger.compile.json

@@ -2,18 +2,16 @@
   "experiment_id": "Debugging",
   "experiment_type": "random partition",
   "model": "CellBox",
-  "sparse_data": false,
-  "pert_file": "data/pert.csv",
-  "expr_file": "data/expr.csv",
-  "node_index_file": "data/node_Index.csv",
-  "pert_v_file": "data/prediction_in.csv",
+  "sparse_data": true,
+  "pert_file": "data/pert_subset.npz",
+  "expr_file": "data/expr_subset.npz",
   "prediction_output_file": "data/Predicted_Valid.csv",
   "n_protein_nodes": 82,
   "n_activity_nodes": 87,
-  "n_x" : 99,
+  "n_x" : 105,
   "trainset_ratio": 0.7,
   "validset_ratio": 0.8,
-  "batchsize": 4,
+  "batchsize": 8,
 
   "envelop_form": "hill",
   "dT": 0.1,
@@ -31,11 +29,12 @@
   "stages":[{
     "nT": 10,
     "sub_stages":[
-        {"lr_val": 0.1,"l1lamda": 0.01}
+        {"lr_val": 0.1,"l1lamda": 0.01},
+        {"lr_val": 0.01,"l1lamda": 0.01}
     ]}, {
     "nT": 20,
     "sub_stages":[
-        {"lr_val": 0.1,"l1lamda": 0.01}
+        {"lr_val": 0.01,"l1lamda": 0.01}
     ]}],
 
     "export_verbose": 3,

configs/debugger.sparse_matrix.json

@@ -0,0 +1,46 @@
+{
+  "experiment_id": "Weissman",
+  "experiment_type": "random partition",
+  "model": "CellBox",
+  "sparse_data": true,
+  "pert_file": "data/pert_subset.npz",
+  "expr_file": "data/expr_subset.npz",
+  "prediction_output_file": "data/Predicted_Valid.csv",
+  "n_protein_nodes": 105,
+  "n_activity_nodes": 105,
+  "n_x" : 105,
+  "trainset_ratio": 0.7,
+  "validset_ratio": 0.8,
+  "batchsize": 32,
+
+  "envelop_form": "hill",
+  "dT": 0.1,
+  "polynomial_k": 3,
+  "envelop":2,
+  "ode_degree": 1,
+  "ode_solver": "heun",
+  "ode_last_steps": 20,
+
+  "n_epoch": 10,
+  "n_iter": 1000,
+  "n_iter_buffer":5,
+  "n_iter_patience":50,
+
+  "stages":[{
+    "nT": 20,
+    "sub_stages":[
+        {"lr_val": 0.1,"l1lamda": 0.01, "n_iter_patience":100},
+        {"lr_val": 0.01,"l1lamda": 0.01},
+        {"lr_val": 0.01,"l1lamda": 0.0001},
+        {"lr_val": 0.001,"l1lamda": 0.00001}
+    ]},{
+    "nT": 100,
+    "sub_stages":[
+        {"lr_val": 0.001,"l1lamda": 0.0001}
+    ]}
+  ],
+
+    "export_verbose": 3,
+    "model_prefix": "b11",
+    "ckpt_name": "model11.ckpt"
+}

pertbio/pertbio/version.py

@@ -66,6 +66,9 @@ def get_msg():
         version 0.2.2
         -- Apr23, 2020 --
         * Add support to tf.Datasets
+        * Add support to tf.sparse
+        * Prepare for sparse single-cell data
+
         """
 
     print(changelog)