3. [Tsubaki, Tomii, and Sese, 2018 in Bioinformatics]
[Tsubaki and Mizoguchi, 2018 in Journal of physical chemistry letters]
AIST AIRC machine learning team
Masashi Tsubaki
7. AIST AIRC machine learning team
SMILES
Masashi Tsubaki
(SMILES 0 or 1)
(SMILES )
(※GitHub )
8. AIST AIRC machine learning team
GitHub ( )
Masashi Tsubaki
Atom x y z
O 0.03 0.98 0.008
H 0.06 0.02 0.002
H 0.87 1.30 0.0007
Water molecule
GNN
(e.g., )
https://github.com/masashitsubaki/molecularGNN_3Dstructure
9. AIST AIRC machine learning team
Masashi Tsubaki
Molecular property types
Data index
Each atom and its 3D coordinate
in the molecule CH4
Properties in order of the above types
In the following, each data is
described with the same format
( README)
18. [Tsubaki, Tomii, and Sese, 2018 in Bioinformatics]
[Tsubaki and Mizoguchi, 2018 in Journal of physical chemistry letters]
AIST AIRC machine learning team
Masashi Tsubaki
21. (1)
( )
(2) (or )
( )
(3)
( )
O C
H
H
AIST AIRC machine learning team
Masashi Tsubaki
: GNN
22. NN ( )
( transition propagation( ) message passing )
O C
H
H
AIST AIRC machine learning team
Masashi Tsubaki
: GNN
x
(`+1)
i = x
(`)
i +
X
j
f(x
(`)
j )
e.g, ReLu(Wx+b)
NN
(4)
(5)
26. [Tsubaki, Tomii, and Sese, 2018 in Bioinformatics]
[Tsubaki and Mizoguchi, 2018 in Journal of physical chemistry letters]
AIST AIRC machine learning team
Masashi Tsubaki
35. [Tsubaki, Tomii, and Sese, 2018 in Bioinformatics]
[Tsubaki and Mizoguchi, 2018 in Journal of physical chemistry letters]
AIST AIRC machine learning team
Masashi Tsubaki
36. AIST AIRC machine learning team
Masashi Tsubaki
Atom x y z
O 0.03 0.98 0.008
H 0.06 0.02 0.002
H 0.87 1.30 0.0007
3
( )
-9.24 eV
Water molecule ( …)
( …)
( …)
37. AIST AIRC machine learning team
Nature comm PRL ( …)
Masashi Tsubaki
( )
46. AIST AIRC machine learning team
Masashi Tsubaki
Atom x y z
O 0.03 0.98 0.008
H 0.06 0.02 0.002
H 0.87 1.30 0.0007
( )
=
1
-9.24 eV
Water molecule
=
etc…
…
( )
🤭
47. AIST AIRC machine learning team
Masashi Tsubaki
SchNOrb extends the deep tensor neural network SchNet to represent electronic
wavefunctions, ...model uses about 93 million parameters to predict a large Hamiltonian…
48. AIST AIRC machine learning team
Masashi Tsubaki
https://github.com/masashitsubaki
tsubaki.masashi@aist.go.jp