Added ISOMAP embedding.

Lanny · Dec 11, 2019 · e5df789 · e5df789
1 parent 0781fd2
commit e5df789
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Showing 3 changed files with 9 additions and 2 deletions.
diff --git a/cspace/jobs/compute_facet.py b/cspace/jobs/compute_facet.py
@@ -69,12 +69,18 @@ def embedf(dist_mat):
                 return embedding
 
             return embedf
-        if job.embedding == '3/TSNE':
+        elif job.embedding == '3/TSNE':
             TSNE = manifold.TSNE(
                 n_components=3,
                 metric='precomputed'
             )
             return lambda d: TSNE.fit(np.array(d)).embedding_
+        elif job.embedding == '3/ISOMAP':
+            Isomap = manifold.Isomap(
+                n_components=3,
+                metric='precomputed'
+            )
+            return lambda d: Isomap.fit(np.array(d)).embedding_
         else:
             raise Exception('Unknown embedding: %s' % job.embedding)
 

diff --git a/cspace/models.py b/cspace/models.py
@@ -17,6 +17,7 @@
     ('3/RDK/SMACOF', '3/RDKit/SMACOF Multidimensional Scaling'),
     ('3/RDK/NM-SMACOF', '3/RDKit/Non-Metric SMACOF Multidimensional Scaling'),
     ('3/TSNE', '3/TSNE'),
+    ('3/ISOMAP', '3/ISOMAP'),
 )
 
 class ChemicalTag(models.Model):

diff --git a/requirements.txt b/requirements.txt
@@ -2,4 +2,4 @@ Django==2.2.6
 numpy==1.17.3
 pytz==2019.3
 sqlparse==0.3.0
-sklearn==0.0
+scikit-learn==0.22