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ReadoutFunction.py
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ReadoutFunction.py
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#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
MessageFunction.py: Propagates a message depending on two nodes and their common edge.
Usage:
"""
from __future__ import print_function
# Own modules
import datasets
from MessageFunction import MessageFunction
from UpdateFunction import UpdateFunction
from models.nnet import NNet
import time
import torch
import torch.nn as nn
import os
import argparse
import numpy as np
from torch.autograd.variable import Variable
#dtype = torch.cuda.FloatTensor
dtype = torch.FloatTensor
__author__ = "Pau Riba, Anjan Dutta"
__email__ = "priba@cvc.uab.cat, adutta@cvc.uab.cat"
class ReadoutFunction(nn.Module):
# Constructor
def __init__(self, readout_def='nn', args={}):
super(ReadoutFunction, self).__init__()
self.r_definition = ''
self.r_function = None
self.args = {}
self.__set_readout(readout_def, args)
# Readout graph given node values at las layer
def forward(self, h_v):
return self.r_function(h_v)
# Set a readout function
def __set_readout(self, readout_def, args):
self.r_definition = readout_def.lower()
self.r_function = {
'duvenaud': self.r_duvenaud,
'ggnn': self.r_ggnn,
'intnet': self.r_intnet,
'mpnn': self.r_mpnn
}.get(self.r_definition, None)
if self.r_function is None:
print('WARNING!: Readout Function has not been set correctly\n\tIncorrect definition ' + readout_def)
quit()
init_parameters = {
'duvenaud': self.init_duvenaud,
'ggnn': self.init_ggnn,
'intnet': self.init_intnet,
'mpnn': self.init_mpnn
}.get(self.r_definition, lambda x: (nn.ParameterList([]), nn.ModuleList([]), {}))
self.learn_args, self.learn_modules, self.args = init_parameters(args)
# Get the name of the used readout function
def get_definition(self):
return self.r_definition
## Definition of various state of the art update functions
# Duvenaud
def r_duvenaud(self, h):
# layers
aux = []
for l in range(len(h)):
param_sz = self.learn_args[l].size()
parameter_mat = torch.t(self.learn_args[l])[None, ...].expand(h[l].size(0), param_sz[1],
param_sz[0])
aux.append(torch.transpose(torch.bmm(parameter_mat, torch.transpose(h[l], 1, 2)), 1, 2))
for j in range(0, aux[l].size(1)):
# Mask whole 0 vectors
aux[l][:, j, :] = nn.Softmax()(aux[l][:, j, :].clone())*(torch.sum(aux[l][:, j, :] != 0, 1) > 0).expand_as(aux[l][:, j, :]).type_as(aux[l])
aux = torch.sum(torch.sum(torch.stack(aux, 3), 3), 1)
return self.learn_modules[0](torch.squeeze(aux))
def init_duvenaud(self, params):
learn_args = []
learn_modules = []
args = {}
args['out'] = params['out']
# Define a parameter matrix W for each layer.
for l in range(params['layers']):
learn_args.append(nn.Parameter(torch.randn(params['in'][l], params['out'])))
# learn_modules.append(nn.Linear(params['out'], params['target']))
learn_modules.append(NNet(n_in=params['out'], n_out=params['target']))
return nn.ParameterList(learn_args), nn.ModuleList(learn_modules), args
# GG-NN, Li et al.
def r_ggnn(self, h):
aux = Variable( torch.Tensor(h[0].size(0), self.args['out']).type_as(h[0].data).zero_() )
# For each graph
for i in range(h[0].size(0)):
nn_res = nn.Sigmoid()(self.learn_modules[0](torch.cat([h[0][i,:,:], h[-1][i,:,:]], 1)))*self.learn_modules[1](h[-1][i,:,:])
# Delete virtual nodes
nn_res = (torch.sum(h[0][i,:,:],1).expand_as(nn_res)>0).type_as(nn_res)* nn_res
aux[i,:] = torch.sum(nn_res,0)
return aux
def init_ggnn(self, params):
learn_args = []
learn_modules = []
args = {}
# i
learn_modules.append(NNet(n_in=2*params['in'], n_out=params['target']))
# j
learn_modules.append(NNet(n_in=params['in'], n_out=params['target']))
args['out'] = params['target']
return nn.ParameterList(learn_args), nn.ModuleList(learn_modules), args
# Battaglia et al. (2016), Interaction Networks
def r_intnet(self, h):
aux = torch.sum(h[-1],1)
return self.learn_modules[0](aux)
def init_intnet(self, params):
learn_args = []
learn_modules = []
args = {}
learn_modules.append(NNet(n_in=params['in'], n_out=params['target']))
return nn.ParameterList(learn_args), nn.ModuleList(learn_modules), args
def r_mpnn(self, h):
aux = Variable( torch.Tensor(h[0].size(0), self.args['out']).type_as(h[0].data).zero_() )
# For each graph
for i in range(h[0].size(0)):
nn_res = nn.Sigmoid()(self.learn_modules[0](torch.cat([h[0][i,:,:], h[-1][i,:,:]], 1)))*self.learn_modules[1](h[-1][i,:,:])
# Delete virtual nodes
nn_res = (torch.sum(h[0][i,:,:],1).expand_as(nn_res)>0).type_as(nn_res)* nn_res
aux[i,:] = torch.sum(nn_res,0)
return aux
def init_mpnn(self, params):
learn_args = []
learn_modules = []
args = {}
# i
learn_modules.append(NNet(n_in=2*params['in'], n_out=params['target']))
# j
learn_modules.append(NNet(n_in=params['in'], n_out=params['target']))
args['out'] = params['target']
return nn.ParameterList(learn_args), nn.ModuleList(learn_modules), args
if __name__ == '__main__':
# Parse optios for downloading
parser = argparse.ArgumentParser(description='QM9 Object.')
# Optional argument
parser.add_argument('--root', nargs=1, help='Specify the data directory.', default=['./data/qm9/dsgdb9nsd/'])
args = parser.parse_args()
root = args.root[0]
files = [f for f in os.listdir(root) if os.path.isfile(os.path.join(root, f))]
idx = np.random.permutation(len(files))
idx = idx.tolist()
valid_ids = [files[i] for i in idx[0:10000]]
test_ids = [files[i] for i in idx[10000:20000]]
train_ids = [files[i] for i in idx[20000:]]
data_train = datasets.Qm9(root, train_ids)
data_valid = datasets.Qm9(root, valid_ids)
data_test = datasets.Qm9(root, test_ids)
# d = datasets.utils.get_graph_stats(data_train, 'degrees')
d = [1, 2, 3, 4]
## Define message
m = MessageFunction('duvenaud')
## Parameters for the update function
# Select one graph
g_tuple, l = data_train[0]
g, h_t, e = g_tuple
m_v = m.forward(h_t[0], h_t[1], e[list(e.keys())[0]])
in_n = len(m_v)
out_n = 30
## Define Update
u = UpdateFunction('duvenaud', args={'deg': d, 'in': in_n, 'out': out_n})
in_n = len(h_t[0])
## Define Readout
r = ReadoutFunction('duvenaud', args={'layers': 2, 'in': [in_n, out_n], 'out': 50, 'target': len(l)})
print(m.get_definition())
print(u.get_definition())
print(r.get_definition())
start = time.time()
# Layers
h = []
# Select one graph
g_tuple, l = data_train[0]
g, h_in, e = g_tuple
h.append(h_in)
# Layer
t = 1
h.append({})
for v in g.nodes_iter():
neigh = g.neighbors(v)
m_neigh = dtype()
for w in neigh:
if (v, w) in e:
e_vw = e[(v, w)]
else:
e_vw = e[(w, v)]
m_v = m.forward(h[t-1][v], h[t-1][w], e_vw)
if len(m_neigh):
m_neigh += m_v
else:
m_neigh = m_v
# Duvenaud
opt = {'deg': len(neigh)}
h[t][v] = u.forward(h[t-1][v], m_neigh, opt)
# Readout
res = r.forward(h)
end = time.time()
print(res)
print('Time')
print(end - start)