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refactor general readout: move to links. #305

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Jan 23, 2019
Merged

refactor general readout: move to links. #305

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7a49af0
refactor general readout: move to links.
Jan 21, 2019
01a6464
update
Jan 21, 2019
27dbbcc
update docstring
Jan 23, 2019
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2 changes: 0 additions & 2 deletions chainer_chemistry/functions/__init__.py
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Expand Up @@ -7,5 +7,3 @@
from chainer_chemistry.functions.loss.mean_squared_error import MeanSquaredError # NOQA

from chainer_chemistry.functions.math.matmul import matmul # NOQA

from chainer_chemistry.functions.readout.general_readout import GeneralReadout # NOQA
Empty file removed chainer_chemistry/functions/readout/__init__.py
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1 change: 1 addition & 0 deletions chainer_chemistry/links/__init__.py
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Expand Up @@ -3,6 +3,7 @@

from chainer_chemistry.links.normalization.graph_batch_normalization import GraphBatchNormalization # NOQA

from chainer_chemistry.links.readout.general_readout import GeneralReadout # NOQA
from chainer_chemistry.links.readout.ggnn_readout import GGNNReadout # NOQA
from chainer_chemistry.links.readout.nfp_readout import NFPReadout # NOQA
from chainer_chemistry.links.readout.schnet_readout import SchNetReadout # NOQA
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9 changes: 7 additions & 2 deletions ...stry/functions/readout/general_readout.py → ...hemistry/links/readout/general_readout.py
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Expand Up @@ -2,13 +2,18 @@
from chainer import functions


class GeneralReadout(chainer.Chain):
class GeneralReadout(chainer.Link):
"""General submodule for readout part.

This class can be used for rsgcn and weavenet.
This class can be used for `rsgcn` and `weavenet`.
Note that this class has no learnable parameter,
even though this is subclass of `chainer.Link`.
This class is under `links` module for consistency
with other readout module.

Args:
mode (str):
activation (callable): activation function
"""

def __init__(self, mode='sum', activation=None):
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6 changes: 4 additions & 2 deletions chainer_chemistry/models/rsgcn.py
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Expand Up @@ -12,7 +12,7 @@

import chainer_chemistry
from chainer_chemistry.config import MAX_ATOMIC_NUM
from chainer_chemistry.functions.readout.general_readout import GeneralReadout
from chainer_chemistry.links.readout.general_readout import GeneralReadout
from chainer_chemistry.links.update.rsgcn_update import RSGCNUpdate


Expand Down Expand Up @@ -55,6 +55,8 @@ def __init__(self, out_dim, hidden_dim=32, n_layers=4,
in_dims = [hidden_dim for _ in range(n_layers)]
out_dims = [hidden_dim for _ in range(n_layers)]
out_dims[n_layers - 1] = out_dim
if readout is None:
readout = GeneralReadout()
with self.init_scope():
self.embed = chainer_chemistry.links.EmbedAtomID(
in_size=n_atom_types, out_size=hidden_dim)
Expand All @@ -70,7 +72,7 @@ def __init__(self, out_dim, hidden_dim=32, n_layers=4,
if isinstance(readout, chainer.Link):
self.readout = readout
if not isinstance(readout, chainer.Link):
self.readout = readout or GeneralReadout()
self.readout = readout
self.out_dim = out_dim
self.hidden_dim = hidden_dim
self.n_layers = n_layers
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2 changes: 1 addition & 1 deletion chainer_chemistry/models/weavenet.py
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Expand Up @@ -4,7 +4,7 @@

from chainer_chemistry.config import MAX_ATOMIC_NUM
from chainer_chemistry.config import WEAVE_DEFAULT_NUM_MAX_ATOMS
from chainer_chemistry.functions.readout.general_readout import GeneralReadout
from chainer_chemistry.links.readout.general_readout import GeneralReadout
from chainer_chemistry.links.connection.embed_atom_id import EmbedAtomID


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5 changes: 3 additions & 2 deletions ...ons_tests/readout/test_general_readout.py → ...sts/readout_tests/test_general_readout.py
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Expand Up @@ -5,7 +5,7 @@
import pytest

from chainer_chemistry.config import MAX_ATOMIC_NUM
from chainer_chemistry.functions.readout.general_readout import GeneralReadout
from chainer_chemistry.links.readout.general_readout import GeneralReadout
from chainer_chemistry.utils.permutation import permute_node

atom_size = 5
Expand Down Expand Up @@ -74,8 +74,9 @@ def test_backward_gpu(readouts, data):
readout.to_gpu()
if readout.mode == 'summax':
y_grad = functions.concat((y_grad, y_grad), axis=1).data
# TODO (nakago): check why tolerance is so high.
gradient_check.check_backward(
readout, atom_data, y_grad, atol=1e-2, rtol=1e-2)
readout, atom_data, y_grad, atol=1e-1, rtol=1e-1)


def test_forward_cpu_graph_invariant(readouts, data):
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