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TuftsBCB · Mar 26, 2024 · 199e187 · 199e187
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Showing 1 changed file with 20 additions and 3 deletions.
diff --git a/docs/index.rst b/docs/index.rst
@@ -48,11 +48,14 @@ Understanding the Inferred Networks
 After the ``RegDiffusion`` model converges, what you get is simply an 
 `adjacency` matrix. When you have thousands or tens of thousands of genes, 
 it's getting difficult to analyze matrix at that scale. In our paper, we 
-propose to analyze the local network by focusing on the local networks around 
-genes you care the most. 
+propose a way to analyze the local network by focusing on the genes you care 
+the most. With this package, you could visualize the network directly. 
+Alternatively, we can also extract the network first, identify some node 
+clusters, and then perform a gene set enrichment analysis to find out the 
+corresponding pathways. 
 
 .. image:: https://github.com/TuftsBCB/RegDiffusion/blob/master/resources/apoe_reg.png?raw=true
-    :width: 400
+    :width: 500
     :alt: Inferred network around ApoE
 
 Inference Speed
@@ -63,6 +66,20 @@ device. Even if you don't have access to those fancy GPU cards, RegDiffusion
 still works. Inference on the same large network takes roughly 3 hours on a 
 mid-range 12-core CPU. 
 
++--------------+-----------+-----------+-----------+-----------+
+|              | hESC      | hHep      | Hammond   | Atlas     |
++==============+===========+===========+===========+===========+
+| # of Genes   | 1,410     | 1,448     | 14,065    | 15,547    |
+| # of Cells   | 758       | 425       | 8,258     | 1,296     |
++--------------------------------------------------------------+
+| GENIE3       | 1hr 58min | 48min 51s | -         | -         |
+| GRNBoost2    | 34min 12s | 16min 32s | -         | -         |
+| DeepSEM      | 29s       | 15s       | 4hr 21min | 59min     |
+| DAZZLE       | 31s       | 16s       | 4hr 47min | 1hr 10min |
++--------------------------------------------------------------|
+| RegDiffusion | 7s        | 8s        | 3min 28s  | 4min 10s  |
++--------------+-----------+-----------+-----------+-----------+
+
 Citation
 --------
 Please consider cite our work if you found it useful for your work: