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Describe the bug
After training a model on fb15k237 dataset, I tried running a test with predict_tails.

When using this function, I had a KeyError resulting from calling predict_tails, this is because the predict function calls this line head_id = self.triples_factory.entity_to_id[head_label] which is fetching the dictionary entry for the entity, id pair.

This happened for /m/05hyfin the test set of fb15k237 dataset after training and just calling the predict function. Should a keyerror happen if the key is not found?

To Reproduce
Steps to reproduce the behavior:

1. Run this code to train the model

from pykeen.triples.triples_factory import TriplesFactory
import pandas as pd
import torch
from pykeen.pipeline import pipeline
from numpy import asarray
from numpy import savetxt
import numpy as np

def main():
    result = pipeline(
        dataset= "fb15k237",
        model="DistMult",
        model_kwargs=dict(embedding_dim= 100),
        regularizer= "no",
        optimizer= "Adam",
        optimizer_kwargs=dict(lr=0.001),
        negative_sampler= "basic",
        negative_sampler_kwargs=dict(
            num_negs_per_pos= 500
        ),
        training_kwargs=dict(
            num_epochs=1,  # just to be fast
            batch_size=256,
        ),
    )
    model = result.model

    tf= TriplesFactory(path='test.txt') #this is the file from https://github.com/ZhenfengLei/KGDatasets/tree/master/FB15k-237
    triples = tf.triples
    results = []	
    model.predict_tails("/m/05hyf", "/film/film_subject/films") #KeyError here

3. KeyError: '/m/05hyf'

Expected behavior
Runs and results in a dataframe of predictions.

Environment (please complete the following information):

• OS: Linux
• Python version: 3.6.5
• Version of this software: 1.0.4
• Versions of required Python packages: # run pip list | grep -Eiw 'torch|numpy|Click|click-default-group|tqdm'
  • Torch: 1.6.0
  • Numpy: 1.19.2
  • Click: 7.1.2
  • Click_default_group: 1.2.2
  • Tqdm: 4.49.0

Describe the bug
I am trying to use pykeen on my own data and following the BYOD section of the docs I am doing the following:

from pykeen.triples import TriplesFactory
from pykeen.pipeline import pipeline

tf = TriplesFactory(path="/tmp/exampledata.txt")
training, testing = tf.split()

pipeline_result = pipeline(
    training_triples_factory=training, testing_triples_factory=testing, model="TransH"
)

Unfortunately I get the following:

Using random_state=1333753659 to split TriplesFactory(path="/tmp/out")
No random seed is specified. Setting to 2098687070.
No cuda devices were available. The model runs on CPU
Training epochs on cpu:   0%|                                                           | 0/5 [00:00<?, ?epoch/s]INFO:pykeen.training.training_loop:using stopper: <pykeen.stoppers.stopper.NopStopper object at 0x7f42e4842cc0>
Training epochs on cpu:   0%|                                                           | 0/5 [00:00<?, ?epoch/s]
Traceback (most recent call last):                                                                               
  File "test.py", line 8, in <module>
    training_triples_factory=training, testing_triples_factory=testing, model="TransH"
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/pipeline.py", line 815, in pipeline
    **training_kwargs,
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/training/training_loop.py", line 190, in train
    num_workers=num_workers,
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/training/training_loop.py", line 376, in _train
    slice_size,
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/training/training_loop.py", line 438, in _forward_pass
    slice_size=slice_size,
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/training/slcwa.py", line 101, in _process_batch
    positive_scores = self.model.score_hrt(positive_batch)
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/pykeen/models/unimodal/trans_h.py", line 134, in score_hrt
    d_r = self.relation_embeddings(hrt_batch[:, 1])
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/torch/nn/modules/module.py", line 550, in __call__
    result = self.forward(*input, **kwargs)
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/torch/nn/modules/sparse.py", line 114, in forward
    self.norm_type, self.scale_grad_by_freq, self.sparse)
  File "/home/dobraczka/.local/share/virtualenvs/embedding-transformers-I3i1Obsv/lib/python3.7/site-packages/torch/nn/functional.py", line 1724, in embedding
    return torch.embedding(weight, input, padding_idx, scale_grad_by_freq, sparse)
IndexError: index out of range in self

Loading e.g. the kinships dataset this way (i.e. concatenating train.txt, test.txt, valid.txt into a single file to have the same setting) I do not get this error. I have attached the data, which is a simple three-column tsv file.
exampledata.txt

To Reproduce
Steps to reproduce the behavior:

1. Execute the above script
2. See error

Expected behavior
Pipeline runs without errors and returns result.

Environment (please complete the following information):

• OS: Debian Buster
• Python version: 3.7
• Version of this software: 1.0.2
• Versions of required Python packages:
  click 7.1.2
  click-default-group 1.2.2
  numpy 1.19.0
  torch 1.5.1
  tqdm 4.48.0

As of the PyTorch 1.6 release on July 28th, 2020, there is a native type for tensors of complex numbers (see: https://pytorch.org/docs/stable/complex_numbers.html)

From @mberr: Referencing the 1.7.1 release tracker here, in case they mention something about it: pytorch/pytorch#47622

It would be interesting to test updated implementations of models using complex tensors such as RotatE and ComplEx to see if we can make them more elegant using this new trick. #292 is a good solution, but still not native. #134 presents a solution where the tensors themselves inside the Embedding are assigned the complex dtype like in:

...
# initialize weight outside of torch.nn.Embedding to sneak in the dtype definitiion
_weight = torch.empty((num_embeddings, embedding_dim), dtype=dtype)

self._embeddings = torch.nn.Embedding(
    num_embeddings=num_embeddings,
    embedding_dim=embedding_dim,
    _weight=_weight,
)
...

Then, the math in ComplEx can be updated like in:

# old
(h_re, h_im), (r_re, r_im), (t_re, t_im) = [split_complex(x=x) for x in (h, r, t)]

# new
h_re, h_im = h.real, h.imag
r_re, r_im = r.real, r.imag
t_re, t_im = t.real, t.imag

However, this update is blocked by a major issue - the torch.nn.functional.embedding function does not currently support automatic differentiation on complex tensors.

Traceback (most recent call last):
  File "/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.8/lib/python3.8/unittest/case.py", line 60, in testPartExecutor
    yield
  File "/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.8/lib/python3.8/unittest/case.py", line 676, in run
    self._callTestMethod(testMethod)
  File "/usr/local/opt/[email protected]/Frameworks/Python.framework/Versions/3.8/lib/python3.8/unittest/case.py", line 633, in _callTestMethod
    method()
  File "/Users/cthoyt/dev/pykeen/tests/test_models.py", line 439, in test_score_r_with_score_hrt_equality
    raise e
  File "/Users/cthoyt/dev/pykeen/tests/test_models.py", line 431, in test_score_r_with_score_hrt_equality
    scores_r = self.model.score_r(batch)
  File "/Users/cthoyt/dev/pykeen/src/pykeen/models/base.py", line 993, in score_r
    expanded_scores = self.score_hrt(hrt_batch=hrt_batch)
  File "/Users/cthoyt/dev/pykeen/src/pykeen/models/unimodal/complex.py", line 151, in score_hrt
    h = self.entity_embeddings(indices=hrt_batch[:, 0])
  File "/Users/cthoyt/.virtualenvs/pykeen/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/Users/cthoyt/dev/pykeen/src/pykeen/nn/emb.py", line 177, in forward
    x = self._embeddings(indices)
  File "/Users/cthoyt/.virtualenvs/pykeen/lib/python3.8/site-packages/torch/nn/modules/module.py", line 727, in _call_impl
    result = self.forward(*input, **kwargs)
  File "/Users/cthoyt/.virtualenvs/pykeen/lib/python3.8/site-packages/torch/nn/modules/sparse.py", line 124, in forward
    return F.embedding(
  File "/Users/cthoyt/.virtualenvs/pykeen/lib/python3.8/site-packages/torch/nn/functional.py", line 1852, in embedding
    return torch.embedding(weight, input, padding_idx, scale_grad_by_freq, sparse)
RuntimeError: embedding does not support automatic differentiation for outputs with complex dtype.

Mock mock mock mock

RotatE throws a cpu/gpu tensor mismatch error on the optimizer step when running on gpu

  File "/home/wwymak/code_experiments/pykeen_expts/hello_world_transe.py", line 19, in <module>
    training_kwargs=dict(num_epochs=100)
  File "/home/wwymak/libraries/pykeen/src/pykeen/pipeline.py", line 722, in pipeline
    **training_kwargs,
  File "/home/wwymak/libraries/pykeen/src/pykeen/training/training_loop.py", line 190, in train
    num_workers=num_workers,
  File "/home/wwymak/libraries/pykeen/src/pykeen/training/training_loop.py", line 370, in _train
    self.optimizer.step()
  File "/home/wwymak/anaconda3/envs/deep_graph/lib/python3.7/site-packages/torch/optim/adagrad.py", line 96, in step
    state['sum'].addcmul_(1, grad, grad)
RuntimeError: expected device cpu but got device cuda:0

To Reproduce
running this simple code snippet on a gpu machine

results = pipeline(
        dataset=Kinships,
        model='RotatE',
        random_seed=1235,
        training_kwargs=dict(num_epochs=100)
    )
print(results)

Environment (please complete the following information):

• OS: ubuntu 18.04
• Python version: 3.7
• Version of this software: 1.0.2dev
• Versions of required Python packages: # run pip list | grep -Eiw 'torch|numpy|Click|click-default-group|tqdm'
  • Torch: 1.4.0
  • Numpy: 1.18.1
  • Click: 7.1.2
  • Click_default_group:1.2.2
  • Tqdm: 4.46.1

(this error also happens on colab)

matplotlib, seaborn and word_cloud are needed for some of the plotting functionality and it would be useful to list them as optional installs in the documentation.

If I select the RGCN model, the trials return None:
Optuna init() got an unexpected keyword argument 'base_model_cls' ...
Choices for a categorical distribution should be a tuple of None, bool, int, float and str for persistent storage but contains <function symmetric_edge_weights at 0x2aac1328bb90> which is of type function.
Is there something I didn't realize? With other models it works fine.

I got the result of TransE on WN18RR dataset as follows, with 100 epoch and default parameter settings.

mean_rank={'best': 7396.350889192887, 'worst': 7396.3558481532145, 'avg': 7396.353368673051}, mean_reciprocal_rank={'best': 0.11426725607718224, 'worst': 0.11426725590337292, 'avg': 0.1142672559902559}, hits_at_k={'best': {1: 0.0032489740082079343, 3: 0.19493844049247605, 5: 0.24811901504787962, 10: 0.2973666210670315}, 'worst': {1: 0.0032489740082079343, 3: 0.19493844049247605, 5: 0.24811901504787962, 10: 0.2973666210670315}, 'avg': {1: 0.0032489740082079343, 3: 0.19493844049247605, 5: 0.24811901504787962, 10: 0.2973666210670315}}, adjusted_mean_rank=0.36492311337297334.

it seems a bit lower than the result reported in the paper

What about adding a mode that moves all entities that won't get used in evaluation over to training?

I suppose you mean the triples containing entities which are not in evaluation_entity_whitelist? We could think about this, but it would change the split ratio of the subsets' number of triples.

Maybe we add this functionality in our splitting functionalities (and emit appropriate warnings)? Or we look at it from a different perspective: we first split all triples of interest by split_ratio. Then we extend the training set by additional triples. Practically we need to make sure that the ID-mapping stays consistent.

Originally posted by @mberr in #62 (comment)

On which paper(s) is your requested model based.

Low-Dimensional Hyperbolic Knowledge Graph Embeddings
Chami et al. (2021)
https://arxiv.org/abs/2005.00545

List the original and other existing implementations of this model
Official pytorch implementation: https://github.com/HazyResearch/KGEmb
Tensorflow implementation: https://github.com/tensorflow/neural-structured-learning/tree/master/research/kg_hyp_emb

Relevance of this model

1. Hyperbolic thing blow my mind
2. More variety
3. Performing pretty well

Ability to help and additional context
Your background and ability to help with the implementation of the model.

On which paper(s) is your requested model based.

https://arxiv.org/abs/2006.04986

List the original and other existing implementations of this model

No link provided in the paper

Relevance of this model

This model is a logical successor of RotatE, ComplEx, etc. @mali-git can also probably the authors to help implement it in PyKEEN since they're in his group

Ability to help and additional context
Your background and ability to help with the implementation of the model.

Make Block and Bases Decomposition are individual modules so the R-GCN class is agnostic to the chosen relation matrix decomposition.

Move the PR from https://github.com/mali-git/POEM_develop/pull/529

I am having difficulty which format my KG data should be in to be used with pykeen. What is the structure that it should have ?

Describe the bug
for a model trained on gpu, when I do `model.predict_tails(...) it gives an error of

....
/usr/local/lib/python3.6/dist-packages/pykeen/models/base.py in _novel(self, h, r, t)
    399         """Return if the triple is novel with respect to the training triples."""
    400         triple = torch.tensor(data=[h, r, t], dtype=torch.long, device=self.device).view(1, 3)
--> 401         return (triple == self.triples_factory.mapped_triples).all(dim=1).any().item()
    402 
    403     def predict_scores_all_relations(

/usr/local/lib/python3.6/dist-packages/torch/tensor.py in wrapped(*args, **kwargs)
     26     def wrapped(*args, **kwargs):
     27         try:
---> 28             return f(*args, **kwargs)
     29         except TypeError:
     30             return NotImplemented

RuntimeError: expected device cuda:0 but got device cpu

(not sure if the model should always be on the cpu? but if so would be nice to update the docs to point this out, since if I trained the model on gpu I should expect to be able to do inference on the gpu as well?)

To Reproduce
Steps to reproduce the behavior:

1. train a model on gpu
2. do model.predict_tail('entity', 'relation')
3. device mismatch error

Expected behavior
there shouldn't be a device mismatch

Environment (please complete the following information):

• OS: ubuntu 18.04
• Python version: 3.7
• Version of this software: 1.0.2dev
  Versions of required Python packages: # run pip list | grep -Eiw 'torch|numpy|Click|click-default-group|tqdm'
• Torch: 1.4.0
• Numpy: 1.18.1
• Click: 7.1.2
• Click_default_group:1.2.2
• Tqdm: 4.46.1

Additional information
an example on colab here

I have created a toy example as follows:

Brussels	locatedIn	Belgium
Belgium	partOf	EU
EU	hasCapital	Brussels

As far as I understand, there should be a trivial embedding solution in two dimensions (the three entities form a triangle, with the three relations being their connecting vectors). The code I use for this is as follows:

results = pipeline(
    training_triples_factory=tf,
    testing_triples_factory=tf,
    model = 'TransE',
    model_kwargs=dict(embedding_dim=2),
    random_seed=1,
    device='cpu',
)

However, the result looks kind of unexpected:

I also played with different random seeds and training parameters, but I never came to a sensible solution. DistMult and HolE, among others, come up with a similar solution.

Am I doing something wrong? Or is my conceptual understanding of the expected outcome incorrect?

As suggested, we're adding a list of projects that include Optuna to our docs. Can you confirm you're ok with this reference and the URL here? optuna/optuna#1605

Thanks!

You thought the 1.5 upgrade was confusing? Get ready for 2.0.0!

The release of v2.0 is approaching and we are going through the final details 🎯 Let us know if you need any last minute fixes or changes through this release candidate.

pip install optuna==2.0.0rc0https://t.co/4K8Oyc5a2K pic.twitter.com/CeL5JQ9jbv

— OptunaAutoML (@OptunaAutoML) July 6, 2020

Since #17 was merged before I got a chance to make a fuss about there not being documentation, it needs to be revisited.

1. Since you touched it last, you're responsible for writing the documentation for the RankBasedEvaluator.__init__() which should include explanations of what all parameters do (ks and filtered) as well as an explanation of integer hits@k versus fractional hits@k. References required.
2. What happens when somebody uses a fractional hits@k downstream? right now all code interprets whatever happens after the @ as an integer. This will break all usages of pipeline() and hpo_pipeline. Please provide unittests showing fractional hits@k in use

Blocked by #18

Cross entropy loss and NSSA loss are the only two setwise loss formulations described in our paper. Its also a bit confusing becuase technically in the implementation, NSSA loss is inheriting from PairwiseLoss. Are there other setwise loss functions we could add, so there's more than 1?

Can you perhaps help me realize how I can use your framework properly? I tried following the documentation on how to train and evaluate embedding models in pykeen but after the OpenBioLink Dataset caused CUDA oom issues (partly because for most models slicing is not implemented or can I adapt any parameters to fit it?) (sidenote: how are the OBLF1 and F2 supposed to me used?) and I did not get the Neural Network implementations I was particularly interested in using to run I now tested some data set model combination that was actually used in your experiments and still the results seem far off anything you report (I am aware I did not run the same hyper parameter search -because different to your way where 24 hours get you through a good of parameters, for a training time of 107170 sec that was not feasible for a simple try out for me) the results are around hits@3 : 0.0005 and hits@10: 0.0007 for the attatched configuration. I have the 1.0.1-dev version installed and use Geforce GTX1080 2560 Cude-Kerne 11GB GDDR5 AERO GPUs.

from pykeen.pipeline import pipeline

pipeline_result = pipeline(
    dataset='WN18RR',
    model='RotatE',
    model_kwargs=dict(
        embedding_dim=500,
        #automatic_memory_optimization=True,
        ),
    training_kwargs=dict(num_epochs=1000),
    optimizer='Adam',
    optimizer_kwargs=dict(
        lr=0.00008,
        weight_decay=0.91,
    ),
    training_loop='sLCWA',
    loss='MarginRankingLoss',
    evaluator='RankBasedEvaluator',
    evaluator_kwargs=dict(filtered=True,),
    negative_sampler="basic",
    negative_sampler_kwargs=dict(num_negs_per_pos=1024)
)
print(pipeline_result)

In #51 the novelty computation is introduced.
To enhance the computational efficiency and usability, automatic memory optimization as well as filtering has to be implemented.

Blocked by #18

The pointwise hinge loss sets the score of positive examples larger than a margin parameterλwhile reducing the scores of negative examples to values below−λ:

L(t_i,l_i) = max(0,λ−ˆl_i * f(ti))

where ˆl_i ∈ {−1,1}. The loss penalizes scores of positive examples which are smaller than λ, but does not impose any restriction on value s> λ. Similarly, negative scores larger than−λcontribute to the loss, whereas all values smaller than−λ do not have any loss contribution. Thereby, the model is not encouraged to further optimize triples which are already predicted well enough (according to the margin parameter λ).

Since each interaction model has a different range (e.g., the values of some interaction functions could be between [-inf,inf], some could be [0, inf], some could be [0, 1]), it makes the interpretation difficult. Even worse, this also has to do with interaction models' constrains on embeddings, etc.

It would be good for all interaction functions to define an "interpretation function" that remaps the results onto the range of [0,1]

From @mberr:

Obtaining such is an active research area and neither straight-forward, nor exists a "unique" solution. In case you are interested, you may want to look for keywords "model calibration" (e.g. Platt scaling), and for KG "triple classification".

needs step-by-step tutorial with screenshots

Give a directory and periodicity, save the model at the given state every x epochs into a new folder in the directory

Enable saving of models to AWS S3 using boto3. Will look very similar to the results from #28.

Add FTP saving to pipeline results and HPO results classes

Move from https://github.com/mali-git/POEM_develop/pull/478/files

Is your feature request related to a problem? Please describe.
I am trying to run experiments from a landmark. When the experiment runs, the results are config files and pkl file. There are files that contain MRR and Hits@1,3,10.

Describe the solution you'd like
I would like to see the predictions, not just the aggregate numerical results (like predictions for all triples). It is not clear how to do that from this point (especially after spending a lot of time training the model, then not being able to access the predictions).

Describe alternatives you've considered
Would it be possible to load from the pkl file and make predictions? I tried this but it did not work out. Please provide an example so this becomes more clear.

Additional context
Add any other context or screenshots about the feature request here.

Given an entity, its position (either head or tail), and a relation, return a ranked list of all entities and their scores. It should be clear if higher score or lower score means more likely to be a real edge. We might want to have it automatically filter out entities corresponding to edges already in the original knowledge graph.

This should be implemented in the top-level Model class, as all models should have this functionality.

Question: do models trained under LCWA or sLCWA have to behave differently here? Does this functionality have to behave differently based on the loss function?

Is your feature request related to a problem? Please describe.
I have trained some of the models so far by using the parameters in the experiments config files and some of them have taken an hour or less while others timed out after running on our university's supercomputer for over 23 hours. It's a little frustrating because I can't tell if something is wrong and I lose all the progress after training for a whole day.

Describe the solution you'd like
It would be great if we can have some estimates of how long the models would take so we know if something is wrong? Or maybe some hardware requirements to run them for that given time? I am running on one GPU and I can't tell if this timing is normal.

Describe alternatives you've considered

• I have made changes in the parameters, I have tried running pykeen experiments command and also just taking the config file and using the parameters in the code by creating a pipeline and the experiments continue to take a long time.
• Other than taking a long time, when I run experiments on another server with 10 GE Force RTX GPUs with 11019MiB memory each, the code only runs on 1 GPU (changing CUDA_VISIBLE_DEVICES does not change this). Even when I try to load the pickle file and use it to make predictions, I get an out of memory error. Are there instructions on running this on multiple GPUs so that I don't get this error?

Additional context
Out of memory error screenshot here, triggered by running this code:
import torch map_location=torch.device('cpu') model = torch.load('trained_model.pkl') #distmult wn18 predictions_df = model.score_all_triples()

And also by running any predict all_triples experiment on the server I mentioned.

Blocked by #18

The pairwise logistic loss is defined as:

L(∆) = log(1 + exp(∆))

Thus, it can be seen as a soft-margin formulation of the pairwise hinge loss (MRL) with a margin of zero.

Currently, we support BCE and BCEAfterSigmoidLoss. However, training will fail when training a model with BCE because we do not provide the option predict_with_sigmoid in the scort_hrt/h/r/t() functions (we only support it in the predict_scores_all_heads/tails/relations() functions) .

We could remove the support for blank BCE, or we need to add the option predict_with_sigmoid in the scoring functions.

Enable the use of the HPO helper-functions for customized datasets.

Since all classes are now implemented directly in PyKEEN, we can move the default HPO ranges into the classes themselves rather than in the external dictionary

Thank you for the library. My usecase is to embed relations/entities in ConceptNet. The Conceptnet is not in RDF form, instead it is a csv file. So I need to convert a format compatible with PyKEEN.
I checked your source code and found this example Is this the data format for reading custom KGs?
Thanks in advance.

I'm interested in getting the resulting embeddings of entities and relations.
How to get this, please?
I couldn't find a method which could gives this.
It seems to me that the PipelineResult may have a method for this purpose?

Describe the bug

In the Bring Your Own Data section of the documentation, the results of a pipeline run are saved to the variable pipeline_result. Directly after result.save_to_directory('test_pre_stratified_transe') is called, triggering an error: NameError: name 'result' is not defined.

To Reproduce
Steps to reproduce the behavior:

1. Copy pasting the examples from Bring Your Own Data trigger a NameError.

Expected behavior

Rename result to pipeline_result (or vice versa) to prevent the NameError when copy pasting the example.

Environment (please complete the following information):

N/A. The issue is with the documentation.

Additional information

I looked for open or closed issues mentioning this typo and did not find them. Apologies if this typo is already known.

In the opposite scenario to #62/#83, we want to report several different sets of metrics based on each relation type. For example, for hetionet, you might want to specify edges or groups of edges to evaluate together:

from pykeen.pipeline import pipeline

pipeline_results = pipeline(
    dataset='Hetionet',
    model='RotatE',
    evaluation_relation_whitelist=[
         {'CtD', 'CpD'},  # evaluate the compund treats disease and compounds palliates disease relations together
        'CcSE',  # evaluate the compound causes side effect alone
        {'CdG', 'CuG', 'CbG'},  # compound/gene regulations/bindings
        {'GiG', 'GcG',  'Gr>G'},  # gene/gene relations,
        None,  # special entry None should group all remaining that haven't appeared in the rest
    ],
)

• It should theoretically possible to have duplicates appearing throughout the subsets.
• None should be a special entry that groups everything you haven't considered. Maybe raise error if all have been covered and None is also added?
• all (or something else that can be written in a JSON configuration) should be a special entry that will do everything. Alternatively, "all" could always be reported

Alternate idea, using a dict for named subsets

from pykeen.pipeline import pipeline

pipeline_results = pipeline(
    dataset='Hetionet',
    model='RotatE',
    evaluation_relation_whitelist={
        'Compound-Disease': {'CtD', 'CpD'},
        'Compound-SideEffect': 'CcSE',
        'Compound-Gene': {'CdG', 'CuG', 'CbG'},
        'Gene-Gene': {'GiG', 'GcG',  'Gr>G'},
        'Remainder': None,
    },
)

It might be better overall to force usage of dictionaries so we can switch on the type (mapping vs. collection)

I just read through the pipeline and it seems like this is going to be quite a pain in the butt to do this...

When trying to use my own data I get the following error. I am not very experienced and don't know how to solve this or why this is happening.

ValueError                                Traceback (most recent call last)
<ipython-input-13-ef15ccdc9011> in <module>
      3 
      4 tf = TriplesFactory(path=work_path + '/eucalyptus_triplets.txt')
----> 5 training, testing = tf.split()
      6 
      7 pipeline_result = pipeline(

~\anaconda3\envs\pykeen\lib\site-packages\pykeen\triples\triples_factory.py in split(self, ratios, random_state, randomize_cleanup)
    419         idx = np.arange(n_triples)
    420         if random_state is None:
--> 421             random_state = np.random.randint(0, 2 ** 32 - 1)
    422             logger.warning(f'Using random_state={random_state} to split {self}')
    423         if isinstance(random_state, int):

mtrand.pyx in numpy.random.mtrand.RandomState.randint()

_bounded_integers.pyx in numpy.random._bounded_integers._rand_int32()

ValueError: high is out of bounds for int32

Is your feature request related to a problem? Please describe.
The usage of Tensor.nonzero() (without arguments) has been deprecated, cf. pytorch/pytorch#40187

At least in

we use the now deprecated version.

Describe the solution you'd like
Change all usages of nonzero to use to future-proof variant, i.e. in the above mentioned case

filter_batch = (entity_filter_test & relation_filter).nonzero(as_tuple=False) 

Describe alternatives you've considered
Keep it as it is. This might lead to problems once PyTorch removes the deprecated behaviour.

Additional context
Warning found in this notebook: https://gist.github.com/cthoyt/190233fd98a11306ceb13f2ee0e95a9e (scroll all the way to the bottom)

Right now, the margin and adversarial_temperature parameters do not have a default for NSSA loss. We need to pick reasonable ones and set it.

Issue #2 brought attention to the ConceptNet as a possible dataset to include with PyKEEN. They provide a tab-separated dump of the database here. It is not pre-stratified into training/testing/evaluation sets.

Because this file has additional columns besides head, relation, and tail, its inclusion will also require an updated to the SingleTabbedDataset such that the usecols keyword argument can be specified in the dataset's __init__()

Blocked by #196 because splitting algorithm is currently too slow for big datasets (with more than ~5 million triples)

We need to merge from the private development repository. It will take an awful lot dark magic to get to there:

1. Make a new branch on pykeen/pykeen (optional - delete everything, and commit?)
2. Add the following to the .git/config file

[remote "poem"]
    url = [email protected]:mali-git/POEM_develop.git
    fetch = +refs/heads/*:refs/remotes/origin/*

3. git pull poem master --allow-unrelated-histories --no-commit -S and pray to rebased god. Figured this out with lots of googling and eventually the perfect article, so thanks a bunch to the author @fdv
4. Commit
5. Profit

Blocked by #18

The square error loss function computes the squared difference between the predicted scores and the labels l_i ∈ {0,1}:

L(t_i,l_i) = (1/2)(f(t_i)−l_i)^2

The squared error loss strongly penalizes predictions that deviate considerably from the labels, and is usually used for regression problems. For simple models it often permits more efficient optimization algorithms involving analytical solutions of sub-problems, e.g. the Alternating Least Squares algorithm

After I train the model on my own dataset, I got a file named trained_model.pkl ,how to load the saved model and use it to predict?

Currently, it is difficult to understand the data structure (i.e. what I am passing to the model).
It may be useful to add a description page to help in developing custom models and datasets and therefore, extend the framework.

Furthermore, I think that an example based on Graph Neural Networks (maybe with PyTorch Geometric) will be very appreciated.

I am trying to use the RGCN algorithm and run into the following error.

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-6-231451742934> in <module>
      5 training, testing = tf.split()
      6 
----> 7 pipeline_result = pipeline(
      8     training_triples_factory=training,
      9     testing_triples_factory=testing,

~\anaconda3\envs\pykeen\lib\site-packages\pykeen\pipeline.py in pipeline(dataset, dataset_kwargs, training_triples_factory, testing_triples_factory, validation_triples_factory, evaluation_entity_whitelist, evaluation_relation_whitelist, model, model_kwargs, loss, loss_kwargs, regularizer, regularizer_kwargs, optimizer, optimizer_kwargs, clear_optimizer, training_loop, negative_sampler, negative_sampler_kwargs, training_kwargs, stopper, stopper_kwargs, evaluator, evaluator_kwargs, evaluation_kwargs, result_tracker, result_tracker_kwargs, metadata, device, random_seed, use_testing_data)
    711 
    712     model = get_model_cls(model)
--> 713     model_instance: Model = model(
    714         triples_factory=training_triples_factory,
    715         **model_kwargs,

~\anaconda3\envs\pykeen\lib\site-packages\pykeen\models\unimodal\rgcn.py in __init__(self, triples_factory, embedding_dim, automatic_memory_optimization, loss, predict_with_sigmoid, preferred_device, random_seed, num_bases_or_blocks, num_layers, use_bias, use_batch_norm, activation_cls, activation_kwargs, base_model, sparse_messages_slcwa, edge_dropout, self_loop_dropout, edge_weighting, decomposition, buffer_messages)
    231                 num_bases_or_blocks = triples_factory.num_relations // 2 + 1
    232             if num_bases_or_blocks > triples_factory.num_relations:
--> 233                 raise ValueError('The number of bases should not exceed the number of relations.')
    234         elif self.decomposition == 'block':
    235             if num_bases_or_blocks is None:

ValueError: The number of bases should not exceed the number of relations.

I assumed that bases are the same as nodes. When changing the number of relation types to be more than the different number of nodes It seemed to work.

However I want to apply the RGCN approach to a graph with 30 000 different nodes and only 6 different relation types between the nodes. From what I understand about the mathematics behind the RGCN model this should be possible, why is it recommended then in the error to have so many different relation types?

I am also sorry if this is not the platform to ask questions like this, but it seems to be the only platform where I consistently get answers about this package, presumably due to how new it still is.

Can we generalize this part?
We should consider that we could also pass experiment_id, and experiment_name to the MLFlow tracker.

Originally posted by @mali-git in #69