Cited by 602Advanced Graph Neural NetworksTopic ModelingRecommender Systems and Techniques

The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index; 34 of the 76 sources its claims cite were checked for support.

Knowledge Graph Embedding for Link Prediction

Open access
Rossi, Andrea, Barbosa, Denilson, Firmani, Donatella, Matinata, Antonio, Merialdo, Paolo·2021·ACM Transactions on Knowledge Discovery from Data

Abstract

Knowledge Graphs (KGs) have found many applications in industrial and in academic settings, which in turn, have motivated considerable research efforts towards large-scale information extraction from a variety of sources. Despite such efforts, it is well known that even the largest KGs suffer from incompleteness; Link Prediction (LP) techniques address this issue by identifying missing facts among entities already in the KG. Among the recent LP techniques, those based on KG embeddings have achieved very promising performance in some benchmarks. Despite the fast-growing literature on the subject, insufficient attention has been paid to the effect of the design choices in those methods. Moreover, the standard practice in this area is to report accuracy by aggregating over a large number of test facts in which some entities are vastly more represented than others; this allows LP methods to exhibit good results by just attending to structural properties that include such entities, while ignoring the remaining majority of the KG. This analysis provides a comprehensive comparison of embedding-based LP methods, extending the dimensions of analysis beyond what is commonly available in the literature. We experimentally compare the effectiveness and efficiency of 18 state-of-the-art methods, consider a rule-based baseline, and report detailed analysis over the most popular benchmarks in the literature.

Overview

AI snapshot

Written from the paper’s full text.

TL;DR

This paper presents a comparative analysis of 16 KG embedding link-prediction models plus a rule-based baseline across 5 standard benchmarks, evaluating effectiveness, efficiency, and structural factors. It finds that graph structure, relation properties, and tie-handling policies strongly affect results, with ComplEx-N3 and AnyBURL among the most consistently strong performers.

Key findings

  • Across 16 embedding models and the AnyBURL baseline on FB15k, WN18, FB15k-237, WN18RR, and YAGO3-10, Tensor Decomposition models were generally solid; ComplEx with N3 regularization was the only embedding-based model consistently comparable to AnyBURL. RotatE was consistent and particularly strong on H@10, while ConvR and RSN were the best deep-learning models in the study.
  • Structural features matter: more source peers usually improved H@1, while more target peers often worsened it; higher Relational Path Support (RPS) generally improved performance. A standalone RPS-based observable-feature model achieved H@1 of 50.49 on FB15k, 93.55 on WN18, 10.45 on FB15k-237, and 36.33 on WN18RR, which the authors use as evidence of test leakage in FB15k/WN18.
  • Relation properties affect models differently: translational models such as TransE, CrossE, and STransE struggled with symmetric and transitive relations; in FB15k-237 most models performed poorly on symmetric relations, possibly because sampling removes training facts that would reveal symmetry. In WN18/WN18RR, symmetric relations were handled well by most models except TransE and ConvKB.
  • Tie policy can dramatically change reported results: CapsE obtained FB15k H@1 of 73.01 under min policy versus 1.93 under average, and YAGO3-10 H@1 of 100.0 under min versus 0.00 under average; ConvKB obtained FB15k H@1 of 52.86 under min versus 11.43 under average. Saturating activations such as ReLU were identified as a main cause; replacing CapsE’s ReLUs with Leaky ReLUs reduced discrepancies, and removing CrossE’s final sigmoid eliminated them.

Methods

  • Comparative experimental design: 16 state-of-the-art KG embedding models organized into Tensor Decomposition, Geometric, and Deep Learning families, plus AnyBURL as a rule-based baseline. Models were trained and evaluated from scratch on 5 datasets: FB15k, WN18, FB15k-237, WN18RR, and YAGO3-10.
  • Evaluation used the filtered scenario with H@1, H@10, MR, and MRR; efficiency was measured as training time and prediction time. Hyperparameters were taken from authors where available and otherwise hand-tuned.
  • Structural analyses defined and measured: number of source/target peers; Relational Path Support via a TF-IDF-style cosine similarity over relational paths up to length 3; relation properties (reflexivity, irreflexivity, symmetry, anti-symmetry, transitivity) with a 0.5 tolerance threshold; and degree of original reified relations for FreeBase-derived datasets.

Limitations

  • Stated: hyperparameter tuning was not exhaustive and often used hand tuning rather than full grid/random search; AnyBURL was trained for 1,000s instead of 10,000s on FB15k-237 and YAGO3-10 because full-ranking prediction became prohibitively slow; the standalone RPS model used only 512 test facts and paths up to length 2, and was not run on YAGO3-10; Entity-Pair Ranking evaluation was considered but deemed too time-consuming.
  • Stated: the Star-to-Clique conversion of FreeBase reified relations is irreversible and loses information through deduplication; for some S2C test facts no CVT was found and degree was set to 2; WN18RR’s test set includes 212 entities absent from training, making about 6.7% of test facts impossible to predict reasonably.
  • Evident from the provided text: several tables are garbled or partially unreadable, so some numeric results cannot be reliably extracted from this version.

Model-written summary. Check it against the paper before relying on it.

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Crossref · 10.1145/3424672

Cites

67 of 67 references verified0 citation errors · 0 not checkable

Statistics

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Figures

Fig. 1 Taxonomyfor the LP models included in our analysis. Dotted arrows indicate that the target method builds on the source method by either generalizing or specializing the definition of its scoring function. The included models are: DistMult [71]; ComplEx [61]; ANALOGY [35]; SimplE [27]; HolE [45]; TuckER [6]; TransE [8]; STransE [42]; CrossE [72]; TorusE [13]; RotatE [55]; ConvE [11]; ConvKB [41]; ConvR [25]; CapsE [43]; RSN [19].
Fig. 1 Taxonomyfor the LP models included in our analysis. Dotted arrows indicate that the target method builds on the source method by either generalizing or specializing the definition of its scoring function. The included models are: DistMult [71]; ComplEx [61]; ANALOGY [35]; SimplE [27]; HolE [45]; TuckER [6]; TransE [8]; STransE [42]; CrossE [72]; TorusE [13]; RotatE [55]; ConvE [11]; ConvKB [41]; ConvR [25]; CapsE [43]; RSN [19].From the PDF
Image 2
From the PDF
Image 3
From the PDF
Fig. 2 Example of head peers and tail peers in a small portion of a KG.
Fig. 2 Example of head peers and tail peers in a small portion of a KG.From the PDF
Fig. 3 Example for Relational Path Support
Fig. 3 Example for Relational Path SupportFrom the PDF
Fig. 4 Example of how the Star2Clique process operates on a small portion of a KG.
Fig. 4 Example of how the Star2Clique process operates on a small portion of a KG.From the PDF
Fig. 5 Training times in hours for each LP model on each dataset. Y axis is in logscale.
Fig. 5 Training times in hours for each LP model on each dataset. Y axis is in logscale.From the PDF
Fig. 6 Prediction times in milliseconds for each LP model on each dataset. Y axis is in logscale.
Fig. 6 Prediction times in milliseconds for each LP model on each dataset. Y axis is in logscale.From the PDF
Fig. 7 Cumulative H@1 results for each LP model on the Freebase datasets, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.
Fig. 7 Cumulative H@1 results for each LP model on the Freebase datasets, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.From the PDF
Fig. 8 Cumulative H@1 results for each LP model on the Wordnet datasets, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.
Fig. 8 Cumulative H@1 results for each LP model on the Wordnet datasets, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.From the PDF
Fig. 9 Cumulative H@1 results for each LP model on YAGO3-10, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.
Fig. 9 Cumulative H@1 results for each LP model on YAGO3-10, and corresponding cumulative distribution of test facts, varying the number of source peers (left) and target peers (right). X axis is in logscale.From the PDF
Fig. 10 H@1 results for each LP model on the Freebase datasets varying the RPS of the test facts, and corresponding cumulative distribution of test facts.
Fig. 10 H@1 results for each LP model on the Freebase datasets varying the RPS of the test facts, and corresponding cumulative distribution of test facts.From the PDF
Fig. 11 H@1 results for each LP model on the Wordnet datasets varying the RPS of the test facts, and corresponding cumulative distribution of test facts.
Fig. 11 H@1 results for each LP model on the Wordnet datasets varying the RPS of the test facts, and corresponding cumulative distribution of test facts.From the PDF
Fig. 12 H@1 results for each LP model on YAGO3-10 varying the RPS of the test facts, and corresponding cumulative distribution.
Fig. 12 H@1 results for each LP model on YAGO3-10 varying the RPS of the test facts, and corresponding cumulative distribution.From the PDF
Fig. 13 H@1 results for each LP model on FB15k varying the RPS of the test facts, computing RPS with paths up to length 1 and up to length 2.
Fig. 13 H@1 results for each LP model on FB15k varying the RPS of the test facts, computing RPS with paths up to length 1 and up to length 2.From the PDF
Fig. 14 H@1 results for each LP model on the Freebase datasets and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.
Fig. 14 H@1 results for each LP model on the Freebase datasets and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.From the PDF
Fig. 15 H@1 results for each LP model on the Wordnet datasets, and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.
Fig. 15 H@1 results for each LP model on the Wordnet datasets, and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.From the PDF
Fig. 16 H@1 results for each LP model on YAGO3-10, and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.
Fig. 16 H@1 results for each LP model on YAGO3-10, and corresponding percentages of test facts, for various relation properties. The best results for each column are in bold and underlined.From the PDF
Fig. 17 H@1 results for each LP model on the Freebase datasets, and corresponding distribution of test facts, varying the degree of the original reified relation in FreeBase. The best results for each column are marked in bold and underlined.
Fig. 17 H@1 results for each LP model on the Freebase datasets, and corresponding distribution of test facts, varying the degree of the original reified relation in FreeBase. The best results for each column are marked in bold and underlined.From the PDF
Image 20
From the PDF
Image 21
From the PDF
Fig. 20 H@1 results for each LP model on Yago datasets varying the RPS of the test facts, computing RPS with paths up to length 1 and up to length 2.
Fig. 20 H@1 results for each LP model on Yago datasets varying the RPS of the test facts, computing RPS with paths up to length 1 and up to length 2.From the PDF

Verification

Claims the paper makes

41 Own result · 40 No basis given · 38 Own interpretation · 20 Supported · 17 Sources not found · 9 Own method · 8 Partly supported · 3 Not checked yet · 2 No full text of the sources · 1 Couldn’t confirm · accuracy not yet measured

Verify all 3 references — free account
  • Probably not a substantial claim. 44
  • It may state two separate claims as one. 60
  • The quote only partly states this claim. 5
96 of 96
  • The paper relies on this without support.

    The standard practice of reporting accuracy aggregated over test facts with over-represented entities allows LP methods to exhibit good performance by attending only to structural properties involving those entities, while ignoring the remaining majority of the KG.

    “One aspect that is common to the vast majority of papers in this area, but nevertheless also problematic, is that they report results aggregated over a large number of test facts in which few entities are over-represented. As a result, LP methods can exhibit good performance on these benchmarks by attending only to such entities while ignoring the others.”
  • The paper relies on this without support.

    The strengths, weaknesses and limitations of current LP techniques are still unknown; the circumstances allowing models to perform better have been hardly investigated.

    “the strengths, weaknesses and limitations of the current techniques are still unknown, that is, the circumstances allowing models to perform better have been hardly investigated.”
  • The paper relies on this without support.

    It is still unknown what makes a fact easy or hard to learn and predict.

    “Roughly speaking, we still do not really know what makes a fact easy or hard to learn and predict.”
  • The paper relies on this without support.

    Insufficient attention has been paid to the effect of various design choices in embedding-based LP methods.

    “Despite the fast growing literature in the subject, insufficient attention has been paid to the effect of the various design choices in those methods.”
  • The paper relies on this without support.

    Embedding-based LP methods have achieved very promising performances in some benchmarks.

    “Among the recent LP techniques, those based on KG embeddings have achieved very promising performances in some benchmarks.”
  • The paper relies on this without support.

    The 5 datasets used in the analysis are the best-established datasets in the LP field.

    “We conduct our analysis using the 5 best-established datasets in the LP field; we report some of their most important properties in Table 2.”
  • The paper relies on this without support.

    MRR is a very stable metric, while simple MR tends to be highly sensitive to outliers.

    “Similarly, we choose MRR because is a very stable metric, while simple MR tends to be highly sensitive to outliers.”
  • The authors state this as an assumption.

    In the very unlikely event that the target entity is not included in the full ranking, all entities that have not been predicted have identical score 0, and the avg policy for ties is applied.

    “In this very unlikely event, we assume that all the entities that have not been predicted have identical score 0, and we apply the avg policy for ties.”
  • The paper relies on this without support.

    The authors of a model usually define the space of acceptable values of each hyperparameter, and then run grid or random search to find the best performing combination.

    “The authors of a model usually define the space of acceptable values of each hyperparameter, and then run grid or random search to find the best performing combination.”
  • The paper relies on this without support.

    TransE, STransE, and CrossE are naturally inclined to represent symmetric relations with very small vectors in the embedding space.

    “TransE, STransE and CrossE are naturally inclined to represent symmetric relations with very small vectors in the embedding space:”
  • The paper relies on this without support.

    In their original implementations, ConvKB and CapsE use min policy by default, whereas CrossE uses ordinal policy by default.

    “Note that in their original implementations ConvKB and CapsE use min policy by default, whereas CrossE uses ordinal policy by default.”
  • The paper relies on this without support.

    Tie policies are today treated as almost negligible implementation details, and they are hardly ever even reported when presenting novel LP models.

    “As a matter of fact, such policies are today treated as almost negligible implementation details, and they are hardly ever even reported when presenting novel LP models.”
  • The paper relies on this without support.

    Due to the S2C transformation, original reified relations tend to generate a high number of facts containing symmetric relations.

    “due to the very nature of the S2C transformation, original reified relations tend to generate a high number of facts containing symmetric relations.”
  • The paper relies on this without support.

    This work is the first extensive comparative analysis on LP models based on KG embedding.

    “we have presented the first extensive comparative analysis on LP models based on KG embedding.”
  • The paper relies on this without support.

    The five datasets used are the most popular in the literature.

    “the 5 most popular datasets in literature”
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Citations

Cites

Show all 46 references

Research works printed but not linked: 32

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Metadata

Authors
Rossi, A., Barbosa, D., Firmani, D., Matinata, A., & Merialdo, P.
Affiliations
  • Roma Tre University (IT)
  • University of Alberta (CA)
  • Roma Tre University, Rome, Italy
Venue
ACM Transactions on Knowledge Discovery from Data
Published
2021-01-04
Volume
15
Issue
2
Pages
1-49
ISSN
  • 1556-4681 (ISSN-L)
  • 1556-472X
OpenAlex
W3120491054
Cited by
601
References
46
Citations by year
2026: 48 · 2025: 107 · 2024: 122 · 2023: 139 · 2022: 117 · 2021: 55
FWCI
37.66
Type
journal article
Language
en
Open access
Locations
  • ACM Transactions on Knowledge Discovery from Data (publishedVersion)
  • arXiv (Cornell University) (submittedVersion)
  • IRIS Research product catalog (Sapienza University of Rome) (submittedVersion, other-oa)
  • Iris (Roma Tre University) (submittedVersion)
  • arXiv (Cornell University)
Topics
  • Physical Sciences › Computer Science › Artificial Intelligence › Advanced Graph Neural Networks
  • Physical Sciences › Computer Science › Artificial Intelligence › Topic Modeling
  • Physical Sciences › Computer Science › Information Systems › Recommender Systems and Techniques
Keywords
knowledge graph embedding, link prediction, knowledge graph incompleteness, method comparison, evaluation benchmark

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