search

Knowledge-Graph-Hub / neat-ml

Network Embedding All the Things
BSD 3-Clause "New" or "Revised" License
18 stars 1 forks source link

error when not specifying validation sets? #13

Open realmarcin opened 3 years ago

realmarcin commented 3 years ago

When these two keys are missing in the yaml:

pos_validation neg_validation

Then get the following error:

can't find key in YAML: 'pos_validation' can't find key in YAML: 'neg_validation' Traceback (most recent call last): File "/global/scratch/marcin/N2V/NEAT/venv/bin/neat", line 10, in sys.exit(cli()) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/cli.py", line 61, in run yhelp.edge_embedding_method()) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data these_params.update(graph_args) TypeError: 'NoneType' object is not iterable

justaddcoffee commented 3 years ago

It'd be helpful to have the YAML you are using

justaddcoffee commented 3 years ago

Also it'd be helpful to have the graphs if possible.

These are likely just harmless warnings:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'

The error is here:

File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data
these_params.update(graph_args)
TypeError: 'NoneType' object is not iterable
realmarcin commented 3 years ago

Here is another potentially related error:

can't find key in YAML: 'pos_validation' can't find key in YAML: 'neg_validation' Traceback (most recent call last): File "/global/scratch/marcin/N2V/NEAT/venv/bin/neat", line 10, in sys.exit(cli()) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/cli.py", line 61, in run yhelp.edge_embedding_method()) File "/global/scratch/marcin/N2V/NEAT/venv/lib/python3.7/site-packages/neat/link_prediction/model.py", line 71, in make_link_prediction_data these_params.update(graph_args) TypeError: 'NoneType' object is not iterable

justaddcoffee commented 3 years ago

I think I'd need the graph files (nodes and edges tsv) to figure out what the problem is here. Seems to be an issue parsing the callbacks for MLP here.

It's nothing to do with these warning messages:

can't find key in YAML: 'pos_validation'
can't find key in YAML: 'neg_validation'