v0.3.7

gao-lab · May 11, 2020 · a16819a · a16819a
1 parent fa1f30d
commit a16819a
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diff --git a/BLAST2CO_dev/BLAST2CO.py b/BLAST2CO_dev/BLAST2CO.py
diff --git a/Cell_BLAST/__init__.py b/Cell_BLAST/__init__.py
@@ -30,4 +30,4 @@
     "config"
 ]
 
-__version__ = "0.3.6"
+__version__ = "0.3.7"
diff --git a/Cell_BLAST/blast.py b/Cell_BLAST/blast.py
@@ -1292,9 +1292,6 @@ def gene_gradient(
         if normalize_deviation:
             deviation /= np.linalg.norm(deviation, axis=2, keepdims=True)
 
-        # TODO: We can do some sort of interpolation here to further improve
-        # reliability of the results?
-
         if eval_point in ("ref", "both"):
             gene_dev_ref = joblib.Parallel(
                 n_jobs=n_jobs, backend="threading"

diff --git a/Cell_BLAST/message.py b/Cell_BLAST/message.py
diff --git a/Cell_BLAST/rmbatch.py b/Cell_BLAST/rmbatch.py
@@ -112,13 +112,13 @@ def _build_regularizer(
                 input_tensor, [self.h_dim] * self.depth,
                 dropout=dropout.tolist(), training_flag=training_flag
             ), self.batch_dim), "batch_logit")
-            self.batch_d_loss = tf.cast(
+            self.batch_d_loss = tf.multiply(tf.cast(
                 epoch >= self.delay, tf.float32
-            ) * tf.reduce_mean(
+            ), tf.reduce_mean(
                 tf.nn.softmax_cross_entropy_with_logits_v2(
                     labels=batch, logits=batch_pred
-                ), name="d_loss"
-            )
+                ), name="raw_d_loss"
+            ), name="d_loss")
             self.batch_g_loss = tf.negative(self.batch_d_loss, name="g_loss")
 
         self.vars_to_save += tf.get_collection(

diff --git a/Datasets/collect/collect_pbmc_68k.R b/Datasets/collect/collect_pbmc_68k.R
diff --git a/Evaluation/batch_removal_config.json b/Evaluation/batch_removal_config.json
@@ -2,7 +2,7 @@
     "gene_space_method": [],
     "latent_space_method": [
         "PCA", "ComBat+PCA", "MNN+PCA", "CCA_anchor+PCA",
-        "CCA", "scVI", "Cell_BLAST"
+        "CCA", "Harmony", "SAUCIE", "scPhere", "scVI", "Cell_BLAST"
     ],
     "Null": {
         "dimensionality": ["NA"],
@@ -49,6 +49,21 @@
         "lambda_rmbatch_reg": ["NA"],
         "seed": 16
     },
+    "Harmony": {
+        "dimensionality": [2, 5, 10, 20, 50],
+        "lambda_rmbatch_reg": ["NA"],
+        "seed": 16
+    },
+    "SAUCIE": {
+        "dimensionality": [2],
+        "lambda_rmbatch_reg": ["NA"],
+        "seed": 16
+    },
+    "scPhere": {
+        "dimensionality": [2, 5, 10, 20, 50],
+        "lambda_rmbatch_reg": ["NA"],
+        "seed": 16
+    },
     "scVI": {
         "dimensionality": [2, 5, 10, 20, 50],
         "lambda_rmbatch_reg": ["NA"],