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[WIP] Super nodes #17

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Merged
vict0rsch merged 56 commits into from
Sep 16, 2022
Merged

[WIP] Super nodes #17

vict0rsch merged 56 commits into from
Sep 16, 2022

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@vict0rsch
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@vict0rsch vict0rsch commented Jun 15, 2022 •
edited by AlexDuvalinho
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  • verify importance of tag 0 nodes in prediction
  • remove all tag 0 nodes
  • one super node per graph
  • one supernode per atom type
  • one supernode per atom type with min distance
  • positional embeddings

AlexDuvalinho
AlexDuvalinho reviewed Jun 21, 2022
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get_data_sample.py
sn_pos = [b.pos[sub_nodes[i]].mean(0) for i in range(batch_size)]
# target relaxed position is the mean of the super node's aggregates
# (per batch)
sn_pos_relaxed = [
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@AlexDuvalinho AlexDuvalinho Jun 21, 2022

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Same as sn_pos since tag-0 nodes are fixed. No need to compute it.

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@vict0rsch vict0rsch Jun 21, 2022

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indeed ; very small overhead though

@RolnickLab RolnickLab deleted a comment from vict0rsch Jun 22, 2022
@AlexDuvalinho
first draft one supernode per node type
c10d62f
@AlexDuvalinho
In process creation of supernode per atom type --Co-authored-by: Vict…
2197d1c 
…or Schmidt
@AlexDuvalinho
second draft supernode extensions
ca01b36
@AlexDuvalinho
refine phys_embeddings: remove col + add ionization energy
1a69889
@AlexDuvalinho
proper implem of one-supernode-per-graph graph rewiring
4ba7c77
@AlexDuvalinho
working supernodes implem
a34036b
@AlexDuvalinho
refactor one-supernode-per-atom-type inside dist fct, not finished
e58ff99
@AlexDuvalinho
continue refactor one-supernode-per-atom-type inside dist fct
f600539
@AlexDuvalinho
good version of one-supernode-per-graph
d6e683e
@AlexDuvalinho
correct typo in names
a3824cc
@AlexDuvalinho
supernode with min. subnode distance to other atoms
9df1170
@AlexDuvalinho
one tensor not on correct device
5825615
@AlexDuvalinho
clean graph rewiring
b7bdf8e
@AlexDuvalinho
relaxed_pos correction
73dc673
@AlexDuvalinho
add positional encoding for schnet, supernode extensions only
5f5dc1e
@AlexDuvalinho
positional encoding for all methods
8071768
@AlexDuvalinho
fix one-supernode-per-graph issue (part 1)
91ffd9d
@AlexDuvalinho
fix pe + one-supernode-per-graph issue
629ee8f
@AlexDuvalinho AlexDuvalinho marked this pull request as ready for review July 13, 2022 15:13
@vict0rsch vict0rsch merged commit 4ca9b47 into main Sep 16, 2022
@vict0rsch vict0rsch deleted the supernode branch September 16, 2022 17:10
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@vict0rsch @AlexDuvalinho