README.md

Treat Different Negatives Differently: Enriching Loss Functions with Domain and Range Constraints for Link Prediction

Datasets

The datasets/ folder contains the following datasets: FB15k187, DBpedia77k, and YAGO14k. These are the filtered versions of FB15k-237, DBpedia93k, and YAGO19k, respectively [1].

The code for generating semantically valid and semantically invalid negative triples is provided for each dataset: neg_freebase.py, neg_dbpedia.py, and neg_yago.py. These .py files only need to be run once. The generated files are: sem_hr.pkl and sem_tr.pkl for the semantically valid negative triples; dumb_hr.pkl and dumb_tr.pkl for the semantically invalid negative triples.

Running a model in the command-line

To run a model with vanilla loss functions (the full list of parameters is available in the Usage Section):

Template: python main_vanilla.py -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

Example: python main_vanilla.py -dataset FB15k187 -model TransE -batch_size 2048 -lr 0.001 -reg 0.001 -dim 200 -lossfunc pairwise

To run a model with vanilla loss functions (the full list of parameters is available in the Usage Section):

Template: python main_sem.py -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

Example: python main_sem.py -dataset FB15k187 -model TransE -batch_size 2048 -lr 0.001 -reg 0.001 -dim 200 -lossfunc pairwise

Alternatively, one can choose run either the training or testing procedure with the pipeline argument:

Template (training): python main_vanilla.py -pipeline train -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

Template (testing): python main_vanilla.py -pipeline test -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

It is also possible to run the ablation study with main_vanilla_bucket.py and main_sem_bucket.py:

python main_vanilla_bucket.py -epoch epoch -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

python main_sem_bucket.py -epoch epoch -dataset dataset -model model -batch_size batchsize -lr lr -reg reg -dim dim -lossfunc lossfunc

where the epoch parameter specifies at which epoch to test your model. In our experiments, the epoch parameter is set at the best epoch (w.r.t. MRR) found on the validation set.

Details about all the user-defined parameters are available in the Usage Section below.

Usage

To run your model on a given dataset, the following parameters are to be defined:

ne: number of epochs

lr: learning rate

reg: regularization weight

dataset: the dataset to be used

model: the knowledge graph embedding model to be used

dim: embedding dimension

batch_size: batch size

save_each: validate every k epochs

pipeline: whether training or testing your model from a pre-trained model (or both)

lossfunc: the loss function to be used

monitor_metrics: whether to keep track of MRR/Hits@/Sem@K during training

gamma1: value for gamma1 (pairwise hinge loss)

gamma2: value for gamma2 (pairwise hinge loss). This equals $\gamma \cdot \epsilon$ with $\epsilon$ being the semantic factor

labelsem: semantic factor (binary cross-entropy loss)

alpha: semantic factor (pointwise logistic loss)

ConvE

ConvE has additional parameters:

input_drop: input dropout

hidden_drop: hidden dropout

feat_drop: feature dropout

hidden_size: hidden size

embedding_shape1: first dimension of embeddings

TuckER

ConvE has additional parameters:

dim_e: embedding dimension for entities

dim_r: embedding dimension for relations

input_dropout: input dropout

hidden_dropout1: hidden dropout (first layer)

hidden_dropout2: hidden dropout (second layer)

label_smoothing: label smoothing

Full hyperparameter space

All models were tested with the following combinations of hyperparameters:

Hyperparameters	Range
Batch Size	{128, 256, 512, 1024, 2048}
Embedding Dimension	{50, 100, 150, 200}
Regularizer Type	{None, L1, L2}
Regularizer Weight ($\lambda$)	{1e-2, 1e-3, 1e-4, 1e-5}
Learning Rate ($lr$)	{1e-2, 5e-3, 1e-3, 5e-4, 1e-4}
Margin $\gamma~(\mathcal{L}_{PHL})$	{1, 2, 3, 5, 10, 20}
Semantic Factor $\epsilon~(\mathcal{L}^{S}_{PHL})$	{0.01, 0.1, 0.25, 0.5, 0.75}
Semantic Factor $\epsilon~(\mathcal{L}^{S}_{PLL})$	{0.05, 0.10, 0.15, 0.25}
Semantic Factor $\epsilon~(\mathcal{L}^{S}_{BCEL})$	{1e-1, 1e-2, 1e-3, 1e-4, 1e-5}

Chosen hyperparamters (main experiment)

Model	Hyperparameters	DBpedia77k	FB15k187	Yago14k
TransE	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	0.001	0.001	0.001
	Regularization Weight	0.001	0.001	0.001
	Semantic Factor	0.5	0.25	0.25
TransH	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	0.001	0.001	0.001
	Regularization Weight	0.00001	0.00001	0.00001
	Semantic Factor	0.5	0.25	0.25
DistMult	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	0.1	10.0	0.0001
	Regularization Weight	0.00001	0.00001	0.00001
	Semantic Factor	0.5	0.25	0.25
ComplEx	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	0.001	0.001	0.01
	Regularization Weight	0.1	0.1	0.1
	Semantic Factor	0.15	0.15	0.015
SimplE	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	0.1	0.1	0.1
	Regularization Weight	0.01	0.1	0.00001
	Semantic Factor	0.15	0.15	0.15
ConvE	Batch Size	512	128	512
	Embedding Dimension	200	200	200
	Learning Rate	0.001	0.001	0.001
	Regularization Weight	0.0	0.0	0.0
	Semantic Factor	0.0001	0.001	0.001
TuckER	Batch Size	128	128	128
	Embedding Dimension	200	200	100
	Learning Rate	0.001	0.0005	0.001
	Regularization Weight	0.0	0.0	0.0
	Semantic Factor	0.00001	0.0001	0.0001
RGCN	Embedding Dimension	500	500	500
	Learning Rate	0.01	0.01	0.01
	Regularization Weight	0.01	0.01	0.01
	Semantic Factor	0.1	0.1	0.1

Appendices

This section aims at providing implementation details that could not be discussed in the paper's content due to page limitations.

Chosen hyperparameters for the KGEMs trained with the alternative semantic-driven loss function

Model	Hyperparameters	DBpedia77k	FB15k187	Yago14k
ComplEx	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	1e-4	1e-4	1e-3
	Regularization Weight	1e-1	1e-1	1e-1
	Semantic Factor	-1e-1	-1e-1	1e-2
SimplE	Batch Size	2048	2048	1024
	Embedding Dimension	200	200	100
	Learning Rate	1e-3	1e-4	1e-3
	Regularization Weight	1e-1	1e-1	1e-1
	Semantic Factor	-1e-1	1e-2	1e-2
ConvE	Batch Size	512	128	512
	Embedding Dimension	200	200	200
	Learning Rate	1e-3	1e-3	1e-3
	Regularization Weight	0	0	0
	Semantic Factor	1e-6	1e-5	1e-4
TuckER	Batch Size	128	128	128
	Embedding Dimension	200	200	100
	Learning Rate	1e-3	5e-4	1e-3
	Regularization Weight	0	0	0
	Semantic Factor	1e-6	1e-5	1e-5
RGCN	Embedding Dimension	500	500	500
	Learning Rate	1e-2	1e-2	1e-2
	Regularization Weight	1e-2	1e-2	1e-2
	Semantic Factor	1e-4	1e-5	1e-4

Cut-offs for FB15k187, DBpedia77k, and Yago14k

Cut-offs for FB15k187, DBpedia77k, and Yago14k. B1, B2, and B3 denote the buckets of relations with narrow, intermediate, and large sets of semantically valid heads or tails, respectively. $|\mathcal{R}|$ denotes the number of unique relations in a given bucket and $|\text{Sem. Val}|$ indicates the interval of the number of semantically valid entities for the bucket relations. To illustrate, $|\text{Sem. Val}|$ = [11, 216] for the head side means that relations in the bucket have at least $11$ and at most $216$ semantically valid heads.

Bucket	Side	Sem. Val Range	Unique Relations	Sem. Val Range	Unique Relations	Sem. Val Range	Unique Relations
		FB15k187		DBpedia77k		Yago14k
		Sem. Val Range	Unique Relations	Sem. Val Range	Unique Relations	Sem. Val Range	Unique Relations
--------	------	----------------	------------------	----------------	------------------	----------------	------------------
B1	Head	[11, 216]	69	[12, 930]	62	[93, 811]	10
	Tail	[12, 244]	80	[19, 801]	44	[35, 678]	13
B2	Head	[278, 1391]	55	[1295, 11586]	58	[2102, 3624]	15
	Tail	[278, 1391]	49	[1419, 11586]	55	[2102, 3624]	16
B3	Head	[1473, 4500]	63	[22252, 57242]	25	{5730}	12
	Tail	[1473, 4500]	58	{57242}	50	{5730}	8

Rank-based and Semantic-based Results on DBpedia77k (Intermediate and Large Sets)

Rank-based and semantic-based results on DBpedia77k for buckets of relations that feature an intermediate (B2) and large (B3) set of semantically valid heads or tails.

Model	MRR	H@10	S@10	MRR	H@10	S@10
	B2	B2	B2	B3	B3	B3
	MRR	H@10	S@10	MRR	H@10	S@10
--------------	-------	-------	-------	-------	-------	-------
TransE-V	.450	.607	.838	.317	.429	.995
TransE-S	.404	.556	.987	.300	.407	1
--------------	-------	-------	-------	-------	-------	-------
TransH-V	.449	.610	.729	.311	.425	.971
TransH-S	.423	.592	.981	.296	.413	1
--------------	-------	-------	-------	-------	-------	-------
DistMult-V	.446	.553	.669	.505	.413	.742
DistMult-S	.450	.566	.790	.506	.422	.920
--------------	-------	-------	-------	-------	-------	-------
ComplEx-V	.442	.538	.551	.582	.453	.787
ComplEx-S	.448	.545	.707	.505	.426	.975
--------------	-------	-------	-------	-------	-------	-------
SimplE-V	.381	.461	.716	.485	.357	.954
SimplE-S	.350	.404	.649	.386	.276	.960
--------------	-------	-------	-------	-------	-------	-------
ConvE-V	.388	.535	.890	.489	.371	.960
ConvE-S	.429	.559	.977	.450	.399	.999
--------------	-------	-------	-------	-------	-------	-------
TuckER-V	.438	.547	.874	.591	.436	.898
TuckER-S	.444	.568	.923	.564	.444	.983
--------------	-------	-------	-------	-------	-------	-------
RGCN-V	.282	.413	.670	.367	.322	.971
RGCN-S	.275	.423	.861	.362	.357	.999

Rank-based and Semantic-based Results on FB15k-187 (Intermediate and Large Sets)

Rank-based and semantic-based results on FB15k187 for the buckets of relations that feature an intermediate (B2) and large (B3) set of semantically valid heads or tails.

Model	MRR	H@10	S@10	MRR	H@10	S@10
	B2	B2	B2	B3	B3	B3
	MRR	H@10	S@10	MRR	H@10	S@10
--------------	-------	-------	-------	-------	-------	-------
TransE-V	.330	.526	.934	.141	.255	.953
TransE-S	.385	.588	.972	.169	.290	.993
--------------	-------	-------	-------	-------	-------	-------
TransH-V	.330	.517	.846	.161	.262	.963
TransH-S	.380	.590	.967	.171	.291	.993
--------------	-------	-------	-------	-------	-------	-------
DistMult-V	.336	.527	.780	.177	.274	.946
DistMult-S	.388	.579	.962	.187	.309	.995
--------------	-------	-------	-------	-------	-------	-------
ComplEx-V	.327	.476	.318	.197	.306	.717
ComplEx-S	.351	.537	.769	.191	.310	.942
--------------	-------	-------	-------	-------	-------	-------
SimplE-V	.283	.432	.331	.179	.274	.694
SimplE-S	.283	.448	.671	.159	.243	.923
--------------	-------	-------	-------	-------	-------	-------
ConvE-V	.347	.529	.974	.172	.277	.977
ConvE-S	.354	.543	.998	.188	.283	.999
--------------	-------	-------	-------	-------	-------	-------
TuckER-V	.387	.574	.987	.215	.330	.994
TuckER-S	.396	.585	.991	.222	.337	.997

Rank-based and Semantic-based Results on Yago14k (Intermediate and Large Sets)

Rank-based and semantic-based results on Yago14k for the buckets of relations that feature an intermediate (B2) and large (B3) set of semantically valid heads or tails.

Model	MRR	H@10	S@10	MRR	H@10	S@10
	B2	B2	B2	B3	B3	B3
	MRR	H@10	S@10	MRR	H@10	S@10
--------------	-------	-------	-------	-------	-------	-------
TransE-V	.879	.928	.892	.841	.923	.974
TransE-S	.861	.922	.997	.854	.917	1
--------------	-------	-------	-------	-------	-------	-------
TransH-V	.854	.922	.567	.788	.92	.803
TransH-S	.865	.921	.876	.778	.926	.996
--------------	-------	-------	-------	-------	-------	-------
DistMult-V	.852	.915	.443	.941	.911	.536
DistMult-S	.862	.911	.441	.941	.911	.584
--------------	-------	-------	-------	-------	-------	-------
ComplEx-V	.883	.921	.352	.932	.914	.619
ComplEx-S	.881	.918	.738	.922	.914	.964
--------------	-------	-------	-------	-------	-------	-------
SimplE-V	.882	.915	.378	.932	.914	.656
SimplE-S	.883	.918	.841	.930	.905	.991
--------------	-------	-------	-------	-------	-------	-------
ConvE-V	.893	.928	.858	.941	.917	.904
ConvE-S	.892	.925	.931	.939	.923	.956
--------------	-------	-------	-------	-------	-------	-------
TuckER-V	.884	.928	.791	.941	.917	.915
TuckER-S	.894	.935	.930	.942	.917	.983

References

[1] Hubert, N., Monnin, P., Brun, A., & Monticolo, D. (2023). Sem@K: Is my knowledge graph embedding model semantic-aware?