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chainer / chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
MIT License
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[WIP] Inputsize invariant dev #308

Open corochann opened 5 years ago

corochann commented 5 years ago

fixing relgcn, relgat calculation as well, due to ggnnpreprocessor change.

corochann commented 5 years ago

performance comparison with tox21

PR #241 : v0.4.0 eval_results_tox21

PR #302 : after module refactoring, before input size invariant.

eval_results_tox21

This PR #308 : input size invariant eval_results_tox21

corochann commented 5 years ago

performance comparison with qm9

It is difficult to see the difference after scaling...

In [1]: scaler.mean_
Out[1]:
array([ 9.81423703e+00,  1.40609910e+00,  1.12491609e+00,  2.70606047e+00,
        7.51916720e+01, -2.39976429e-01,  1.11237232e-02,  2.51099679e-01,
        1.18952558e+03,  1.48523891e-01, -4.11610053e+02, -4.11594996e+02,
       -4.11593263e+02, -4.11665414e+02,  3.16009336e+01])

In [2]: scaler.var_
Out[2]:
array([3.27409900e+06, 2.50771379e+00, 1.20007181e+00, 2.34202719e+00,
       6.70371780e+01, 4.89749655e-04, 2.20295275e-03, 2.25798483e-03,
       7.82604766e+04, 1.10710843e-03, 1.60476355e+03, 1.60471277e+03,
       1.60470911e+03, 1.60495593e+03, 1.65031147e+01])

In [3]: scaler.scale_
Out[3]:
array([1.80944715e+03, 1.58357627e+00, 1.09547789e+00, 1.53036832e+00,
       8.18762347e+00, 2.21302882e-02, 4.69356234e-02, 4.75182579e-02,
       2.79750740e+02, 3.32732389e-02, 4.00595001e+01, 4.00588663e+01,
       4.00588206e+01, 4.00619013e+01, 4.06240258e+00])

PR #241 : v0.4.0 eval_mean_abs_error_qm9

PR #302 : after module refactoring, before input size invariant. eval_mean_abs_error_qm9

This PR #308 : input size invariant eval_mean_abs_error_qm9

It seems metric for how to scale mean_abs_error has changed... I need to investigate.

codecov-io commented 5 years ago

Codecov Report

Merging #308 into master will increase coverage by 0.29%. The diff coverage is 97.95%.

@@            Coverage Diff             @@
##           master     #308      +/-   ##
==========================================
+ Coverage   83.66%   83.95%   +0.29%     
==========================================
  Files         179      179              
  Lines        8098     8171      +73     
==========================================
+ Hits         6775     6860      +85     
+ Misses       1323     1311      -12