Update docs and rerun training, fix small bugs in save model.

aimat-lab · Dec 12, 2023 · 9246d83 · 9246d83
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diff --git a/README.md b/README.md
@@ -114,7 +114,7 @@ e_idx = ks.layers.Input(shape=(None, 2), dtype="int64", name="edge_indices")
 total_n = ks.layers.Input(shape=(), dtype="int64", name="total_nodes")  # Or mask
 total_e = ks.layers.Input(shape=(), dtype="int64", name="total_edges")  # Or mask
 
-n, idx, batch_id, _, _, _, _, _ = CastBatchedIndicesToDisjoint()([ns, e_idx, total_n, total_e])
+n, idx, batch_id, _, _, _, _, _ = CastBatchedIndicesToDisjoint(uses_mask=False)([ns, e_idx, total_n, total_e])
 n_in_out = GatherNodes()([n, idx])
 node_messages = ks.layers.Dense(64, activation='relu')(n_in_out)
 node_updates = AggregateLocalEdges()([n, node_messages, idx])
@@ -177,6 +177,7 @@ original implementations (with proper licencing).
 * **[MAT](kgcnn/literature/MAT)**: [Molecule Attention Transformer](https://arxiv.org/abs/2002.08264) by Maziarka et al. (2020)
 * **[MEGAN](kgcnn/literature/MEGAN)**: [MEGAN: Multi-explanation Graph Attention Network](https://link.springer.com/chapter/10.1007/978-3-031-44067-0_18) by Teufel et al. (2023)
 * **[Megnet](kgcnn/literature/Megnet)**: [Graph Networks as a Universal Machine Learning Framework for Molecules and Crystals](https://doi.org/10.1021/acs.chemmater.9b01294) by Chen et al. (2019)
+* **[MoGAT](kgcnn/literature/MoGAT)**: [Multi-order graph attention network for water solubility prediction and interpretation](https://www.nature.com/articles/s41598-022-25701-5) by Lee et al. (2023)
 * **[MXMNet](kgcnn/literature/MXMNet)**: [Molecular Mechanics-Driven Graph Neural Network with Multiplex Graph for Molecular Structures](https://arxiv.org/abs/2011.07457) by Zhang et al. (2020)
 * **[NMPN](kgcnn/literature/NMPN)**: [Neural Message Passing for Quantum Chemistry](http://arxiv.org/abs/1704.01212) by Gilmer et al. (2017)
 * **[Unet](kgcnn/literature/Unet)**: [Graph U-Nets](http://proceedings.mlr.press/v97/gao19a/gao19a.pdf) by H. Gao and S. Ji (2019)

diff --git a/docs/source/kgcnn.backend.rst b/docs/source/kgcnn.backend.rst
@@ -0,0 +1,10 @@
+kgcnn.backend package
+=====================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.backend
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.layers.rst b/docs/source/kgcnn.layers.rst
@@ -60,6 +60,14 @@ kgcnn.layers.geom module
    :undoc-members:
    :show-inheritance:
 
+kgcnn.layers.message module
+---------------------------
+
+.. automodule:: kgcnn.layers.message
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 kgcnn.layers.mlp module
 -----------------------
 
@@ -84,6 +92,14 @@ kgcnn.layers.norm module
    :undoc-members:
    :show-inheritance:
 
+kgcnn.layers.polynom module
+---------------------------
+
+.. automodule:: kgcnn.layers.polynom
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 kgcnn.layers.pooling module
 ---------------------------
 
@@ -92,6 +108,14 @@ kgcnn.layers.pooling module
    :undoc-members:
    :show-inheritance:
 
+kgcnn.layers.relational module
+------------------------------
+
+.. automodule:: kgcnn.layers.relational
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 kgcnn.layers.scale module
 -------------------------
 
@@ -100,6 +124,22 @@ kgcnn.layers.scale module
    :undoc-members:
    :show-inheritance:
 
+kgcnn.layers.set2set module
+---------------------------
+
+.. automodule:: kgcnn.layers.set2set
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+kgcnn.layers.update module
+--------------------------
+
+.. automodule:: kgcnn.layers.update
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 Module contents
 ---------------
 

diff --git a/docs/source/kgcnn.literature.AttentiveFP.rst b/docs/source/kgcnn.literature.AttentiveFP.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.AttentiveFP package
+====================================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.AttentiveFP
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.CGCNN.rst b/docs/source/kgcnn.literature.CGCNN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.CGCNN package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.CGCNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.CMPNN.rst b/docs/source/kgcnn.literature.CMPNN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.CMPNN package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.CMPNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.DGIN.rst b/docs/source/kgcnn.literature.DGIN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.DGIN package
+=============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.DGIN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.DMPNN.rst b/docs/source/kgcnn.literature.DMPNN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.DMPNN package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.DMPNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.DimeNetPP.rst b/docs/source/kgcnn.literature.DimeNetPP.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.DimeNetPP package
+==================================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.DimeNetPP
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.EGNN.rst b/docs/source/kgcnn.literature.EGNN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.EGNN package
+=============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.EGNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.GNNExplain.rst b/docs/source/kgcnn.literature.GNNExplain.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.GNNExplain package
+===================================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.GNNExplain
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.GNNFilm.rst b/docs/source/kgcnn.literature.GNNFilm.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.GNNFilm package
+================================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.GNNFilm
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.HDNNP2nd.rst b/docs/source/kgcnn.literature.HDNNP2nd.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.HDNNP2nd package
+=================================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.HDNNP2nd
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.HamNet.rst b/docs/source/kgcnn.literature.HamNet.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.HamNet package
+===============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.HamNet
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.INorp.rst b/docs/source/kgcnn.literature.INorp.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.INorp package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.INorp
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.MAT.rst b/docs/source/kgcnn.literature.MAT.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.MAT package
+============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.MAT
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.MEGAN.rst b/docs/source/kgcnn.literature.MEGAN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.MEGAN package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.MEGAN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.MXMNet.rst b/docs/source/kgcnn.literature.MXMNet.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.MXMNet package
+===============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.MXMNet
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.Megnet.rst b/docs/source/kgcnn.literature.Megnet.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.Megnet package
+===============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.Megnet
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.MoGAT.rst b/docs/source/kgcnn.literature.MoGAT.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.MoGAT package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.MoGAT
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.NMPN.rst b/docs/source/kgcnn.literature.NMPN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.NMPN package
+=============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.NMPN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.PAiNN.rst b/docs/source/kgcnn.literature.PAiNN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.PAiNN package
+==============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.PAiNN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.RGCN.rst b/docs/source/kgcnn.literature.RGCN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.RGCN package
+=============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.RGCN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.rGIN.rst b/docs/source/kgcnn.literature.rGIN.rst
@@ -0,0 +1,10 @@
+kgcnn.literature.rGIN package
+=============================
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.literature.rGIN
+   :members:
+   :undoc-members:
+   :show-inheritance:
diff --git a/docs/source/kgcnn.literature.rst b/docs/source/kgcnn.literature.rst
@@ -7,12 +7,33 @@ Subpackages
 .. toctree::
    :maxdepth: 4
 
+   kgcnn.literature.AttentiveFP
+   kgcnn.literature.CGCNN
+   kgcnn.literature.CMPNN
+   kgcnn.literature.DGIN
+   kgcnn.literature.DMPNN
+   kgcnn.literature.DimeNetPP
+   kgcnn.literature.EGNN
    kgcnn.literature.GAT
    kgcnn.literature.GATv2
    kgcnn.literature.GCN
    kgcnn.literature.GIN
+   kgcnn.literature.GNNExplain
+   kgcnn.literature.GNNFilm
    kgcnn.literature.GraphSAGE
+   kgcnn.literature.HDNNP2nd
+   kgcnn.literature.HamNet
+   kgcnn.literature.INorp
+   kgcnn.literature.MAT
+   kgcnn.literature.MEGAN
+   kgcnn.literature.MXMNet
+   kgcnn.literature.Megnet
+   kgcnn.literature.MoGAT
+   kgcnn.literature.NMPN
+   kgcnn.literature.PAiNN
+   kgcnn.literature.RGCN
    kgcnn.literature.Schnet
+   kgcnn.literature.rGIN
 
 Module contents
 ---------------

diff --git a/docs/source/kgcnn.models.rst b/docs/source/kgcnn.models.rst
@@ -4,6 +4,14 @@ kgcnn.models package
 Submodules
 ----------
 
+kgcnn.models.casting module
+---------------------------
+
+.. automodule:: kgcnn.models.casting
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 kgcnn.models.force module
 -------------------------
 

diff --git a/docs/source/kgcnn.optimizers.rst b/docs/source/kgcnn.optimizers.rst
@@ -0,0 +1,21 @@
+kgcnn.optimizers package
+========================
+
+Submodules
+----------
+
+kgcnn.optimizers.optimizers module
+----------------------------------
+
+.. automodule:: kgcnn.optimizers.optimizers
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: kgcnn.optimizers
+   :members:
+   :undoc-members:
+   :show-inheritance: