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GraphConvModel compute_saliency #1706

abanerjee10 opened this issue Nov 4, 2019 · 1 comment


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@abanerjee10 abanerjee10 commented Nov 4, 2019

Platform: Linux64
Installed with conda

Hello, I followed the tutorial at to construct a graphconv model as shown below.

import deepchem as dc
from deepchem.models.graph_models import GraphConvModel
# Load Tox21 dataset
tox21_tasks, tox21_datasets, transformers = dc.molnet.load_tox21(featurizer='GraphConv')
train_dataset, valid_dataset, test_dataset = tox21_datasets
n_tasks = len(tox21_tasks)
model = GraphConvModel(n_tasks, batch_size=50, mode='classification')
num_epochs = 10
losses = []
for i in range(num_epochs):
 loss =, nb_epoch=1)
 print("Epoch %d loss: %f" % (i, loss))

The Issue
After doing this, I would like to find the gradients of the model with respect to its inputs. I thought this would be supported by the compute_saliency method. I cannot find any documentation or examples indicating how to do this.

Minimum Failing Examples
I have tried


with AttributeError: 'DiskDataset' object has no attribute 'shape'.
I have also tried


with TypeError: float() argument must be a string or a number, not 'ConvMol'.
Based on the source code I found for the model as well the TensorGraphTutorial, I also tried

from deepchem.feat.mol_graphs import ConvMol
import numpy as np
for ind, (X_b, y_b, w_b, ids_b) in enumerate(
            batch_size=1, pad_batches=True, deterministic=True)):
    multiConvMol = ConvMol.agglomerate_mols(X_b)
    inputs = [multiConvMol.get_atom_features(), multiConvMol.deg_slice, np.array(multiConvMol.membership)]
    for i in range(1, len(multiConvMol.get_deg_adjacency_lists())):

with TypeError: Failed to convert object of type <class 'list'> to Tensor. Contents: [<tensorflow.python.framework.ops.IndexedSlices object at 0x7fbe46f66f28>]. Consider casting elements to a supported type.

I am out of ideas. I have the same problems when trying to make predictions with the model. What should the model's input look like?

Thank you!


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@peastman peastman commented Nov 5, 2019

compute_saliency() doesn't work with GraphConvModel. It's designed for models that take a simple numpy array as input and produce one or more arrays as output. It computes the gradient of each output element with respect to each input element. But GraphConvModel takes a ConvMol object as input, then implements default_generator() to construct a bunch of arrays describing the molecule in a somewhat complicated way. To make compute_saliency() work with that, we would somehow have to reverse that process and compute gradients with respect to... I'm not really sure what.

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