Source code for experiments in the papers "Complex Embeddings for Simple Link Prediction" (ICML 2016) and "Knowledge Graph Completion via Complex Tensor Factorization" (JMLR 2017).
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README.md

Complex Embeddings for Simple Link Prediction

This repository contains the code of the main experiments presented in the papers:

Complex Embeddings for Simple Link Prediction, Théo Trouillon, Johannes Welbl, Sebastian Riedel, Éric Gaussier and Guillaume Bouchard, ICML 2016.

Knowledge Graph Completion via Complex Tensor Factorization, Théo Trouillon, Christopher R. Dance, Éric Gaussier, Johannes Welbl, Sebastian Riedel and Guillaume Bouchard, JMLR 2017.

Install

First clone the repository:

git clone https://github.com/ttrouill/complex.git

The code depends on downhill, a theano-based Stochastic Gradient Descent implementation.

Install it, along with other dependencies with:

pip install -r requirements.txt

The code is compatible with Python 2 and 3.

Run the experiments

To run the experiments, unpack the datasets first:

unzip datasets/fb15k.zip -d datasets/
unzip datasets/wn18.zip -d datasets/

And run the corresponding python scripts, for Freebase (FB15K):

python fb15k_run.py

And for Wordnet (WN18):

python wn18_run.py

By default, it runs the ComplEx (Complex Embeddings) model, edit the files and uncomment the corresponding lines to run DistMult, TransE, RESCAL or CP models. The given hyper-parameters for each model are the best validated ones by the grid-search described in the paper.

To run on GPU (approx 5x faster), simply add the following theano flag before the python call:

THEANO_FLAGS='device=gpu' python fb15k_run.py

Export the produced embeddings

Simply uncomment the last lines in fb15k_run.py and wn18_run.py (and the import scipy.io line (requires scipy module)), this will save the embeddings of the ComplEx model in the common matlab .mat format. If you want to save the embeddings of other models, just edit the embedding variable names corresponding to the desired model (see models.py).

Run on your own data

Create a subfolder in the datasets folder, and put your data in three files train.txt, valid.txt and test.txt. Each line is a triple, in the format: 

subject_entity_id	relation_id	object_entity_id

separated with tabs. Then modify fb15k_run.py for example, by changing the name argument in the build_data function call to your data set folder name:

fb15kexp = build_data(name = 'your_dataset_folder_name',path = tools.cur_path + '/datasets/')

Implement your own model

Models are defined as classes in models.py, that all inherit the class Abstract_Model defined in the same file. The Abstract_Model class handles all the common stuff (training functions, ...), and child classes (the actual models) just need to define their embeddings shape and initialization, and their scoring and loss function.

To properly understand the following, one must be comfortable with Theano basics.

The Abstract_Model class contains the symbolic 1D tensor variables self.rows, self.cols, self.tubes and self.ys that will instantiate at runtime the corresponding: subject entity indexes, relation indexes, object entity indexes and truth values (1 or -1) respectively, of the triples of the current batch. It also contains the number of subject entities, relations and object entities of the dataset in self.n, self.m, self.l respectively, as well as the current embedding size in self.k.

Two functions must be overridden in the child classes to define a proper model: get_init_params(self) and define_loss(self).

Let's have a look at the DistMult_Model class and its get_init_params(self) function:

def get_init_params(self):
	params = { 'e' : randn(max(self.n,self.l),self.k),
			   'r' : randn(self.m,self.k)}
	return params

This function both defines the embedding-matrix shapes (number of entities * rank for e, number of relations * rank for r), and their initial value (randn is numpy.random.randn), by returning a dictionnary where the key names correspond to the class attribute names. From this dict the mother class will create shared tensor variables initialized with the given values, and assigned to the corresponding attribute names (self.e and self.r).

Now the define_loss(self) function must define three Theano expressions: the scoring function, the loss, and the regularization. Here is the DistMult_Model one:

def define_loss(self):
	self.pred_func = TT.sum(self.e[self.rows,:] * self.r[self.cols,:] * self.e[self.tubes,:], 1)

	self.loss = TT.sqr(self.ys - self.pred_func).mean()

	self.regul_func = TT.sqr(self.e[self.rows,:]).mean() \
					+ TT.sqr(self.r[self.cols,:]).mean() \
					+ TT.sqr(self.e[self.tubes,:]).mean()

The corresponding expressions must be written in their batched form, i.e. to compute the scores of multiple triples at once. For a given batch, the corresponding embeddings are retrieved with self.e[self.rows,:], self.r[self.cols,:] and self.e[self.tubes,:].

In the case of the DistMult model, the trilinear product between these embeddings is computed, here by doing first two element-wise multiplications and then a sum over the columns in the self.pred_func expression. The self.pred_func expression must yield a vector of the size of the batch (the size of self.rows, self.cols, ...). The loss defined in self.loss is the squared-loss here (see the DistMult_Logistic_Model class for the logistic loss), and is averaged over the batch, as the self.loss expression must yield a scalar value. The regularization defined here is the L2 regularization over the corresponding embeddings of the batch, and must also yield a scalar value.

That's all you need to implement your own tensor factorization model! All gradient computation is handled by Theano auto-differentiation, and all the training functions by the downhill module and the Abstract_Model class.

Cite ComplEx

If you use this package for published work, please cite either or both papers, here is the BibTeX:

@inproceedings{trouillon2016complex,
	title = {{Complex embeddings for simple link prediction}},
	author = {Trouillon, Th\'eo and Welbl, Johannes and Riedel, Sebastian and Gaussier, \'Eric and Bouchard, Guillaume},
	booktitle = {International Conference on Machine Learning (ICML)},
	volume={48},
	pages={2071--2080},
	year = {2016}
}
@article{trouillon2017knowledge,
	title={Knowledge graph completion via complex tensor factorization},
	author={Trouillon, Th{\'e}o and Dance, Christopher R and Gaussier, {\'E}ric and Welbl, Johannes and Riedel, Sebastian and Bouchard, Guillaume},
	journal={Journal of Machine Learning Research (JMLR)},
	volume={18},
	number={130},
	pages={1--38},
	year={2017}
}

License

This software comes under a non-commercial use license, please see the LICENSE file.