A hierarchy of faithfulness criteria for knowledge base completion
Authors: Olga Mashkova, Robert Hoehndorf
Organizations: Computer Science Program, Computer, Electrical, and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
Knowledge graph completion is evaluated by ranking observed triples above randomly corrupted ones, which treats every unobserved fact as false. When the object being completed is a description logic knowledge base rather than a plain graph, the open world assumption and deductive closure make this inadequate: relative to the knowledge base, a candidate axiom is entailed, contradictory, or undetermined, and a model that cannot separate a logically impossible axiom from a plausible novel one is not merely less accurate but semantically incorrect. We ask what it means for a knowledge base completion model to be logically faithful, and whether current embedding models are. We define a hierarchy of four increasingly strict criteria, discrimination, logical admissibility, monotonic logical faithfulness, and probabilistic logical faithfulness, and prove that they form a strict chain of implications. We ground the strongest criterion in the relative model count P(α∣O)=#(O∪{α})/#(O), which recovers the trichotomy at its endpoints and ranks undetermined axioms in between. Evaluating knowledge graph and logic-geometric embedding models on EL ontologies, with entailed, contradictory, and undetermined test sets generated by a reasoner, we find that ranking accuracy does not imply logical faithfulness and that none of the evaluated models is faithful across the hierarchy. The code is available at https://github.com/bio-ontology-research-group/kbc.
Figures & tables
Model
AUC+/−↑
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
Logic-geometric (KBC)
ELEmbeddings
0.70 ± 0.01
0.48 ± 0.00
- 0.62 ± 0.02
0.14 ± 0.00
0.42 ± 0.01
EmEL++
0.73 ± 0.01
0.49 ± 0.00
- 0.63 ± 0.05
0.15 ± 0.01
0.41 ± 0.04
Box2EL
0.74 ± 0.01
0.60 ± 0.01
- 0.53 ± 0.00
0.17 ± 0.01
0.51 ± 0.01
Geometric (KGC)
BoxE
0.42 ± 0.06
0.73 ± 0.02
- 0.16 ± 0.04
0.10 ± 0.00
0.23 ± 0.04
Table 1: Faithfulness across models on atomic subsumption ( C⊑D , GCI0) over the Pizza ontology. Higher AUC+/− and ρP are better; Pair-FVR near 0.5 means S? is not separated from S⊥ . Ranking accuracy (MRR, Hits@10) does not predict faithfulness. Full metrics, the GO-plus slice, and all normal forms are in Appendix 0.G .
Appendix figures & tables25 assets
Supplementary material from the paper’s appendix.
Appendix
Pizza
GO-plus
Classes ∣NC∣
106
653
Roles ∣NR∣
4
6
Domain size ∣Δ∣
2
2
Training axioms by normal form (GCI0 split)
GCI0 C⊑D
62
546
GCI1 C⊓D⊑E
6
18
Appendix
Table 2: Ontology sizes and evaluation-split composition. Axiom counts exclude trivial axioms; “n/a” marks a quantity that is not applicable (the GO-plus GCI1, GCI2, and GCI3 splits have no contradictory set, whereas Pizza has one for every normal form).
Normal form
Axiom
AUC+/−↑
Pair-FVR ↓
ρP↑
GCI0
C⊑D
0.72
0.53
- 0.59
GCI1
C⊓D⊑E
0.15
0.80
-0.27
GCI2
C⊑∃r.D
0.50
0.57
- 0.43
GCI3
∃r.C⊑D
0.84
0.55
- 0.22
GCI1 ⊥
C⊓D⊑⊥
0.97
0.06
- 0.42
Appendix
Table 3: Faithfulness is construct-dependent: mean over the logic-geometric models (ELEmbeddings, EmEL++, Box2EL) by normal form, on the Pizza ontology. Disjointness ( C⊓D⊑⊥ ) is the one construct handled faithfully (high AUC, Pair-FVR near 0 ); conjunctive subsumption ( C⊓D⊑E ) inverts (AUC below 0.5 , negative ρP ), driven by the ball models’ loss (Section 6.2 ; Appendix 0.C ).
Figure 1: Full negative-sampling sweep (Section 6.3 ) on the Pizza ontology: FVR (left axis, lower is better) and MRR (right axis) as the fraction of random-corruption negatives varies; the remainder p⊥=1−x is drawn from S⊥ . In all 12 panels the all-contradiction endpoint ( x=0 ) has lower FVR than the all-random endpoint ( x=1 ); the response is not monotone in between, and on GCI0 the ball-based models’ effect is within single-seed noise.
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.70 ± 0.01
0.98 ± 0.00
0.74 ± 0.00
0.48 ± 0.00
0.62 ± 0.02
0.14 ± 0.00
0.42 ± 0.01
Box2EL
0.74 ± 0.01
0.99 ± 0.00
0.76 ± 0.01
0.60 ± 0.01
0.53 ± 0.00
0.17 ± 0.01
0.51 ± 0.01
EmEL++
0.73 ± 0.01
0.98 ± 0.01
0.73 ± 0.01
0.49 ± 0.00
0.63 ± 0.05
0.15 ± 0.01
0.41 ± 0.04
BoxE
0.42 ± 0.06
0.94 ± 0.01
0.90 ± 0.03
0.73 ± 0.02
0.16 ± 0.04
0.10 ± 0.00
0.23 ± 0.04
ComplEx
0.53 ± 0.03
0.94 ± 0.01
0.82 ± 0.01
0.45 ± 0.01
-0.13 ± 0.03
0.08 ± 0.01
0.11 ± 0.01
DistMult
0.52 ± 0.09
0.94 ± 0.01
0.82 ± 0.05
0.47 ± 0.08
-0.03 ± 0.08
0.05 ± 0.02
0.08 ± 0.06
Appendix
Table 4: GCI0, Pizza
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.84 ± 0.01
1.00 ± 0.00
0.60 ± 0.01
0.47 ± 0.01
0.53 ± 0.01
0.16 ± 0.01
0.46 ± 0.01
Box2EL
0.82 ± 0.01
1.00 ± 0.00
0.50 ± 0.01
0.25 ± 0.02
0.63 ± 0.01
0.09 ± 0.00
0.26 ± 0.01
EmEL++
0.83 ± 0.01
1.00 ± 0.00
0.62 ± 0.02
0.49 ± 0.02
0.57 ± 0.01
0.15 ± 0.01
0.45 ± 0.02
BoxE
0.61 ± 0.01
1.00 ± 0.00
0.74 ± 0.01
0.33 ± 0.02
0.24 ± 0.02
0.16 ± 0.00
0.20 ± 0.00
ComplEx
0.55 ± 0.05
1.00 ± 0.00
0.78 ± 0.04
0.49 ± 0.08
0.01 ± 0.05
0.16 ± 0.00
0.19 ± 0.00
DistMult
0.27 ± 0.07
1.00 ± 0.00
0.95 ± 0.03
0.76 ± 0.13
0.01 ± 0.01
0.04 ± 0.02
0.09 ± 0.02
Appendix
Table 5: GCI0, GO-plus slice
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.57 ± 0.01
1.00 ± 0.00
0.78 ± 0.00
0.52 ± 0.01
0.51 ± 0.01
0.10 ± 0.00
0.29 ± 0.01
Box2EL
0.35 ± 0.02
1.00 ± 0.00
0.90 ± 0.01
0.73 ± 0.02
0.22 ± 0.01
0.09 ± 0.00
0.18 ± 0.01
EmEL++
0.59 ± 0.01
1.00 ± 0.00
0.76 ± 0.00
0.48 ± 0.01
0.55 ± 0.01
0.10 ± 0.00
0.29 ± 0.01
BoxE
0.34 ± 0.01
1.00 ± 0.00
0.91 ± 0.00
0.75 ± 0.01
0.22 ± 0.03
0.14 ± 0.01
0.20 ± 0.01
ComplEx
0.51 ± 0.03
1.00 ± 0.00
0.83 ± 0.01
0.51 ± 0.03
-0.05 ± 0.01
0.11 ± 0.01
0.19 ± 0.02
DistMult
0.47 ± 0.02
1.00 ± 0.00
0.86 ± 0.01
0.48 ± 0.06
-0.04 ± 0.03
0.09 ± 0.01
0.18 ± 0.02
Appendix
Table 6: GCI2, Pizza
Model name
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.43 ± 0.02
0.06 ± 0.00
0.22 ± 0.00
Box2EL
0.30 ± 0.00
0.01 ± 0.00
0.01 ± 0.01
EmEL++
0.49 ± 0.02
0.06 ± 0.00
0.22 ± 0.02
BoxE
0.15 ± 0.04
0.06 ± 0.00
0.07 ± 0.00
ComplEx
-0.15 ± 0.05
0.06 ± 0.00
0.07 ± 0.00
DistMult
-0.22 ± 0.14
0.01 ± 0.00
0.01 ± 0.01
Appendix
Table 7: GCI2, GO-plus slice
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.02 ± 0.00
1.00 ± 0.00
1.00 ± 0.00
0.94 ± 0.01
-0.34 ± 0.01
0.06 ± 0.00
0.11 ± 0.01
Box2EL
0.39 ± 0.01
1.00 ± 0.00
0.91 ± 0.00
0.55 ± 0.01
-0.09 ± 0.02
0.05 ± 0.00
0.13 ± 0.01
EmEL++
0.05 ± 0.01
1.00 ± 0.00
1.00 ± 0.00
0.91 ± 0.02
-0.31 ± 0.03
0.06 ± 0.00
0.11 ± 0.00
Appendix
Table 8: GCI1, Pizza
Model name
ρP↑
MRR ↑
Hits@10 ↑
ELEm
-0.39 ± 0.02
0.08 ± 0.00
0.20 ± 0.01
Box2EL
0.12 ± 0.01
0.04 ± 0.00
0.06 ± 0.01
EmEL++
-0.40 ± 0.01
0.09 ± 0.00
0.20 ± 0.01
Appendix
Table 9: GCI1, GO-plus slice
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.96 ± 0.00
1.00 ± 0.00
0.47 ± 0.01
0.08 ± 0.01
0.43 ± 0.00
0.03 ± 0.00
0.02 ± 0.00
Box2EL
1.00 ± 0.00
1.00 ± 0.00
0.17 ± 0.01
0.01 ± 0.00
0.41 ± 0.00
0.05 ± 0.00
0.01 ± 0.00
EmEL++
0.96 ± 0.00
1.00 ± 0.00
0.47 ± 0.01
0.07 ± 0.01
0.43 ± 0.00
0.03 ± 0.00
0.02 ± 0.00
Appendix
Table 10: GCI1 ⊥ , Pizza
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.95 ± 0.01
1.00 ± 0.00
0.65 ± 0.01
0.06 ± 0.00
0.61 ± 0.01
0.01 ± 0.00
0.03 ± 0.01
Box2EL
0.99 ± 0.00
1.00 ± 0.00
0.50 ± 0.01
0.03 ± 0.00
0.73 ± 0.00
0.01 ± 0.00
0.04 ± 0.00
EmEL++
0.95 ± 0.01
1.00 ± 0.00
0.65 ± 0.01
0.06 ± 0.00
0.61 ± 0.01
0.01 ± 0.00
0.03 ± 0.01
Appendix
Table 11: GCI1 ⊥ , GO-plus slice
Model name
AUC+/−↑
Adm@10 ↑
FVR ↓
Pair-FVR ↓
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.75 ± 0.01
1.00 ± 0.00
0.71 ± 0.02
0.56 ± 0.03
0.26 ± 0.01
0.23 ± 0.03
0.65 ± 0.01
Box2EL
0.97 ± 0.00
1.00 ± 0.00
0.62 ± 0.01
0.55 ± 0.01
0.09 ± 0.01
0.39 ± 0.02
0.77 ± 0.02
EmEL++
0.79 ± 0.02
1.00 ± 0.00
0.68 ± 0.01
0.54 ± 0.01
0.31 ± 0.01
0.22 ± 0.02
0.60 ± 0.03
Appendix
Table 12: GCI3, Pizza
Model name
ρP↑
MRR ↑
Hits@10 ↑
ELEm
0.55 ± 0.01
0.01 ± 0.00
0.01 ± 0.00
Box2EL
0.42 ± 0.01
0.01 ± 0.00
0.01 ± 0.00
EmEL++
0.53 ± 0.00
0.01 ± 0.00
0.01 ± 0.00
Appendix
Table 13: GCI3, GO-plus slice
x
FVR ↓
MRR ↑
0.0
0.7303±0.0087
0.1710±0.0076
0.2
0.7328±0.0122
0.1701±0.0093
0.4
0.7444±0.0054
0.1721±0.0067
0.6
0.7516±0.0050
0.1743±0.0066
0.8
0.7524±0.0082
0.1728±0.0048
1.0
0.7493±0.0114
0.1748±0.0057
Appendix
Table 14: Multi-seed (5 seeds) sweep for Box2EL, Pizza ontology, GCI0. x is the fraction of random-corruption negatives, with the remaining 1−x drawn from S⊥ (matching Figure 1 ). Values are mean ± standard deviation.
x
FVR ↓
MRR ↑
0.0
0.7335±0.0035
0.1401±0.0024
0.2
0.7377±0.0063
0.1426±0.0030
0.4
0.7344±0.0051
0.1439±0.0057
0.6
0.7383±0.0078
0.1431±0.0049
0.8
0.7395±0.0069
0.1470±0.0083
1.0
0.7431±0.0052
0.1452±0.0041
Appendix
Table 15: Multi-seed (5 seeds) sweep for ELEmbeddings, Pizza ontology, GCI0; conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.7304±0.0038
0.1409±0.0062
0.2
0.7357±0.0068
0.1402±0.0025
0.4
0.7340±0.0023
0.1461±0.0069
0.6
0.7354±0.0074
0.1444±0.0049
0.8
0.7357±0.0077
0.1485±0.0082
1.0
0.7398±0.0032
0.1458±0.0038
Appendix
Table 16: Multi-seed (5 seeds) sweep for EmEL++, Pizza ontology, GCI0; conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.1695±0.0042
0.0537±0.0013
0.2
0.1707±0.0051
0.0517±0.0003
0.4
0.1725±0.0087
0.0515±0.0013
0.6
0.1694±0.0070
0.0526±0.0012
0.8
0.1746±0.0075
0.0517±0.0020
1.0
0.1789±0.0066
0.0516±0.0020
Appendix
Table 17: Multi-seed (5 seeds) sweep for Box2EL, Pizza ontology, GCI1 ⊥ (disjointness); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.4323±0.0102
0.0351±0.0008
0.2
0.4452±0.0053
0.0341±0.0020
0.4
0.4484±0.0204
0.0343±0.0022
0.6
0.4452±0.0251
0.0340±0.0024
0.8
0.4563±0.0178
0.0335±0.0035
1.0
0.4580±0.0106
0.0325±0.0009
Appendix
Table 18: Multi-seed (5 seeds) sweep for ELEmbeddings, Pizza ontology, GCI1 ⊥ (disjointness); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.4330±0.0079
0.0351±0.0014
0.2
0.4475±0.0070
0.0339±0.0019
0.4
0.4516±0.0184
0.0339±0.0012
0.6
0.4436±0.0266
0.0346±0.0028
0.8
0.4574±0.0168
0.0331±0.0034
1.0
0.4581±0.0102
0.0333±0.0018
Appendix
Table 19: Multi-seed (5 seeds) sweep for EmEL++, Pizza ontology, GCI1 ⊥ (disjointness); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.8723±0.0119
0.0921±0.0074
0.2
0.8866±0.0128
0.0945±0.0060
0.4
0.8916±0.0094
0.0953±0.0063
0.6
0.8865±0.0089
0.0941±0.0085
0.8
0.8891±0.0030
0.0910±0.0034
1.0
0.9023±0.0026
0.0965±0.0096
Appendix
Table 20: Multi-seed (5 seeds) sweep for Box2EL, Pizza ontology, GCI2 ( C⊑∃r.D ); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.7406±0.0038
0.0937±0.0021
0.2
0.7552±0.0128
0.0955±0.0040
0.4
0.7636±0.0101
0.0974±0.0028
0.6
0.7732±0.0105
0.1015±0.0040
0.8
0.7739±0.0086
0.1008±0.0070
1.0
0.7832±0.0065
0.1022±0.0053
Appendix
Table 21: Multi-seed (5 seeds) sweep for ELEmbeddings, Pizza ontology, GCI2 ( C⊑∃r.D ); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.7269±0.0041
0.0853±0.0029
0.2
0.7312±0.0114
0.0875±0.0032
0.4
0.7402±0.0172
0.0911±0.0019
0.6
0.7526±0.0088
0.0938±0.0017
0.8
0.7528±0.0101
0.0948±0.0023
1.0
0.7607±0.0061
0.0976±0.0022
Appendix
Table 22: Multi-seed (5 seeds) sweep for EmEL++, Pizza ontology, GCI2 ( C⊑∃r.D ); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.4795±0.0152
0.3941±0.0327
0.2
0.5259±0.0326
0.3742±0.0425
0.4
0.5496±0.0217
0.3849±0.0347
0.6
0.5751±0.0082
0.3772±0.0402
0.8
0.5815±0.0257
0.3941±0.0250
1.0
0.6107±0.0055
0.3867±0.0149
Appendix
Table 23: Multi-seed (5 seeds) sweep for Box2EL, Pizza ontology, GCI3 ( ∃r.C⊑D ); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.6566±0.0077
0.2835±0.0148
0.2
0.6731±0.0103
0.2515±0.0214
0.4
0.6875±0.0205
0.2410±0.0203
0.6
0.7211±0.0350
0.2554±0.0241
0.8
0.6862±0.0091
0.2994±0.0135
1.0
0.7066±0.0297
0.2263±0.0400
Appendix
Table 24: Multi-seed (5 seeds) sweep for ELEmbeddings, Pizza ontology, GCI3 ( ∃r.C⊑D ); conventions as in Table 14 .
x
FVR ↓
MRR ↑
0.0
0.6340±0.0050
0.2507±0.0073
0.2
0.6459±0.0086
0.2315±0.0068
0.4
0.6666±0.0171
0.2144±0.0203
0.6
0.6897±0.0138
0.2198±0.0144
0.8
0.6603±0.0101
0.2599±0.0275
1.0
0.6834±0.0147
0.2128±0.0101
Appendix
Table 25: Multi-seed (5 seeds) sweep for EmEL++, Pizza ontology, GCI3 ( ∃r.C⊑D ); conventions as in Table 14 .
Knowledge graph completion models optimize ranking, although many downstream applications require calibrated probabilities. We present BLADE, a variational model that separates latent truth from graph recording and distills offline language-model judgments into a frozen teacher regularizer. The LLM is absent during inference. Posterior samples provide predictive probabilities and epistemic uncertainty, while the compact teacher remains available only as an optional triage factor. Across five benchmarks, BLADE remains competitive under a common ranking protocol and reduces adaptive ECE by a macro-average of 60.1% relative to deep ensembles and 78.1% relative to temperature-scaled RotatE. On identical FB15k-237 candidate sets, BLADE also improves ECE, Brier score, and NLL over validation-selected histogram binning and a matched generative ComplEx2 model, with these improvements persisting on a prespecified near-miss pool. Under controlled injected missingness, the full triage score achieves a mean AUC-PR of 0.863, compared with 0.805 for its strongest non-teacher variant. Leakage stress tests show that aligned semantics matter, but they cannot exclude knowledge acquired during LLM pretraining. We therefore claim calibration only for the declared candidate distributions, not for all unobserved triples.
Ibne Farabi Shihab, Rabeya Bosri Tamanna, Abdo El Karaky +2
Department of Computer Science, Iowa State University · Brac University · Department of Civil, Construction & Environmental Engineering, Iowa State University
Knowledge graph completion (KGC) aims to predict missing facts from an observed knowledge graph (KG), playing a crucial role in a wide range of real-world applications such as drug discovery, recommender systems, and retrieval-augmented generation (RAG). Although numerous KGC models have been proposed, the evaluation of KGC remains underexplored, despite its critical role in reliably assessing model performance and selecting appropriate models for real-world applications. In this paper, we introduce two important perspectives for KGC evaluation that are overlooked by existing evaluation metrics, (P1) predictive sharpness and (P2) popularity-bias robustness. To address both perspectives, we propose a generalized evaluation framework, PROBE, which consists of a rank transformer (RT) that estimates the score of each prediction based on a desired level of predictive sharpness and a rank aggregator (RA) that determines the final evaluation score by aggregating all prediction scores according to a desired level of popularity-bias robustness. We theoretically analyze PROBE by defining six key properties for reliable KGC evaluation and prove that PROBE satisfies all the properties, while existing metrics fail to satisfy some. In particular, due to the open-world nature of KGs, an evaluation metric should preserve the relative performance of KGC models even when only incomplete facts are observed. We show that PROBE better maintains such consistency, providing a more reliable estimate of intrinsic model performance than existing metrics. Extensive experiments with six KGC models on six real-world KGs reveal that existing metrics may over- or under-estimate model performance depending on different evaluation perspectives, whereas PROBE enables a more comprehensive, flexible, and consistent evaluation of KGC models.
Sooho Moon, Jian Kang, Yunyong Ko
Chung-Ang University, South Korea · Mohamed bin Zayed University of Artificial Intelligence, UAE
Incomplete Knowledge Graph Question Answering (IKGQA) requires completing missing edges to continue reasoning. A growing line of work verifies completed edges against retrieved text, treating textual support as a proxy for edge quality. We ask a question that, to our knowledge, has not been systematically tested: does textual verifiability actually track correctness? Exploiting the gold deleted triples provided by the standard random-deletion protocol, we measure both. The finding is counterintuitive: among gold-correct completed edges, 76-96% have no supporting passage even under exhaustive retrieval, robustly across deletion rates (20%/40%), datasets (CWQ/WebQSP), and relation types (structural, commonsense, long-tail). Most Freebase-style facts simply do not occur as head-tail co-mentions in text. Textual faithfulness therefore measures provenance, not correctness -- separated by a paradigm-level gap no in-corpus retrieval closes. This reframes edge completion. Since most completed edges -- correct or not -- are causally redundant for the answer (95-97% of correct answers do not depend on any unsupported edge), the central question shifts from "is the edge correct?" to "admit or abstain under provenance uncertainty?" Within this framing we present TGComplete, a provenance-favoring admission policy that retrieves evidence at a reasoning breakpoint, verifies a candidate through a lightweight loop, and abstains when support is absent. Against the generate-to-complete baseline GoG, it attains higher edge precision against gold (15-21% vs 3-14%), with no statistically detectable EM loss and 3.1-7.4 times higher strict faithfulness of admitted edges -- at the cost of lower recall. We position TGComplete not as uniformly better, but as a principled point on a precision/provenance-recall trade-off, appropriate when auditability matters.