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[WIP] Inputsize invariant dev #308

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[WIP] Inputsize invariant dev #308

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

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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

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corochann commented Jan 23, 2019 •
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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.

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codecov-io commented Jan 23, 2019 •
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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

@corochann corochann mentioned this pull request Jan 23, 2019
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corochann added 2 commits January 23, 2019 14:08
Merge branch 'master' into inputsize_invariant_ggnn2
cb577d2 
# Conflicts:
#	chainer_chemistry/links/readout/ggnn_readout.py
Merge branch 'inputsize_invariant_ggnn2' into inputsize_invariant_dev
e5fffb5 
# Conflicts:
#	chainer_chemistry/links/readout/ggnn_readout.py
@mottodora mottodora added this to the 0.6.0 milestone Feb 7, 2019
@mottodora mottodora modified the milestones: 0.6.0, 0.7.0 Sep 11, 2019
@corochann corochann removed this from the 0.7.0 milestone Dec 9, 2019
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@corochann @codecov-io @mottodora