Integrating Meta-Features with Knowledge Graph Embeddings for Meta-Learning
Authors: Antonis Klironomos, Ioannis Dasoulas, Francesco Periti, Mohamed Gad-Elrab, Heiko Paulheim, Anastasia Dimou, Evgeny Kharlamov
Organizations: Bosch Center for Artificial Intelligence, Germany · University of Mannheim, Germany · KU Leuven, Belgium · Leuven.AI - KU Leuven Institute for AI, Belgium · Flanders Make, Belgium · Univesity of Oslo, Norway
The vast collection of machine learning records available on the web presents a significant opportunity for meta-learning, where past experiments are leveraged to improve performance. Two crucial meta-learning tasks are pipeline performance estimation (PPE), which predicts pipeline performance on target datasets, and dataset performance-based similarity estimation (DPSE), which identifies datasets with similar performance patterns. Existing approaches primarily rely on dataset meta-features (e.g., number of instances, class entropy, etc.) to represent datasets numerically and approximate these meta-learning tasks. However, these approaches often overlook the wealth of past experimental results and pipeline metadata available. This limits their ability to capture dataset - pipeline interactions that reveal performance similarity patterns. In this work, we propose KGmetaSP, a knowledge-graph-embeddings approach that leverages existing experiment data to capture these interactions and improve both PPE and DPSE. We represent datasets and pipelines within a unified knowledge graph (KG) and derive embeddings that support pipeline-agnostic meta-models for PPE and distance-based retrieval for DPSE. To validate our approach, we construct a large-scale benchmark comprising 144,177 OpenML experiments, enabling a rich cross-dataset evaluation. KGmetaSP enables accurate PPE using a single pipeline-agnostic meta-model and improves DPSE over baselines. The proposed KGmetaSP, KG, and benchmark are released, establishing a new reference point for meta-learning and demonstrating how consolidating open experiment data into a unified KG advances the field.
Figures & tables
Figure 1: Comparison of the information leveraged by our proposed approach (green) versus existing approaches (orange) for representing datasets in meta-learning. For a pair of datasets, A and B, existing approaches represent datasets using only intrinsic meta-feature vectors (top-right). Our proposed approach also includes past pipeline configurations metadata (top left) as additional context into a KG, to represent datasets.
Figure 2: KGmetaSP overview.
Figure 3: ML pipeline configuration example represented as an ExeKG .
Figure 4
Entities
Properties
Triples
Attributes
Literals
ExeKGs
1,502,140
293
4,492,036
149
371,534
ExeKGs + MLSea
1,514,836
317
4,522,216
155
385,246
Table 1: MetaExe-KG statistics.
Figure 6: Overview of MetaExe-Bench constructed by sparsely training and evaluating MetaExe-KG datasets with MetaExe-KG pipeline configurations. Resulting performance values are used to assess the ground truth performance-based similarity between datasets and train PPE meta-models.
Figure 7: High-level depiction of PPE meta-models. a) Common approach: Pipeline configuration-specific meta-models predict the performance of a pipeline-configuration for a dataset given a dataset’s representation. b) Our approach: A single common pipeline configuration-agnostic meta-model predicts the performance of a pipeline configuration for a dataset given the dataset’s and pipeline configuration’s representations.
Dataset
Pipeline
Meta-
Meta-Regr.
Meta-Classif.
Embedding
Strategy
Models
MSE
R2
Accuracy
F1
Target: Accuracy
MF All
Conf.-specific
1,028
0.0081
0.6748
0.7363
0.7358
KGmetaSP PE
1
0.0101
0.6181
0.7413
0.7427
MF Info. Theory [ 26 ]
Conf.-specific
1,028
0.0249
-0.0737
0.4428
0.4423
KGmetaSP PE
1
0.0401
-0.5135
0.4773
0.4789
Table 2: PPE meta-regression and meta-classification for unseen datasets. We compare a single, configuration-agnostic model trained on meta-features and KGmetaSP embeddings against an average evaluation of 1,028 configuration-specific specialized models trained on meta-features. Meta-regression targets are raw performance values. Meta-classification targets are binned into 3 classes (low, medium, high). The highest score per metric is underlined; the best score per dataset embedding group is bold.
Method
Meta-Regression
Meta-Classification
MSE
R2
Accuracy
F1
Target: Accuracy
Average performance
0.0267
-0.0005
0.3303
0.1640
Closest embedding
0.0127
0.5241
0.7748
0.7747
MF All + KGmetaSP PE
0.0070
0.7361
0.8250
0.8244
Target: Precision
Table 3: PPE meta-regression and meta-classification for unseen pipeline configurations. Meta-Regression targets are the raw performance values. Meta-classification targets are binned into 3 classes (low, medium, high). The best scores are in bold.
Hit@k ( ST =0.8)
Hit@k ( ST =0.9)
Method
k=1
k=2
k=5
Avg.
k=1
k=2
k=5
Avg.
GED [ 36 ]
0.5743
0.8243
0.9054
0.7680
0.4527
0.7432
0.8514
0.6824
MF [ 13 ]
0.6892
0.8243
0.8851
0.7996
0.6622
0.8041
0.8716
0.7793
MF Norm. [ 13 ]
0.6892
0.8851
0.9324
0.8356
0.7905
0.8446
0.9122
0.8491
SiFi-Dat. [ 6 , 44 ]
0.8514
0.8851
0.9054
0.8806
0.7973
0.8649
0.8919
0.8514
SiFi-Pip. [ 6 , 44 ]
0.6351
0.8176
0.9527
0.8018
0.6216
0.7568
0.9324
0.7703
Table 4: Hit@k of similarity measures according to performance-based ground truth. A hit is recorded when a dataset retrieved within the top-k has a ground-truth similarity with the query dataset greater than a similarity threshold ( ST ). Results are reported for ST=0.8 and ST=0.9 . The highest score per metric is in bold and the second highest is underlined.
NDCG@k
Method
k=1
k=2
k=5
Avg.
GED [ 36 ]
0.5684
0.6308
0.6847
0.6280
MF [ 13 ]
0.6939
0.6874
0.7016
0.6943
MF Norm. [ 13 ]
0.8561
0.8418
0.8358
0.8446
SiFi-Dat. [ 6 , 44 ]
0.8753
0.8768
0.8693
0.8738
SiFi-Pip. [ 6 , 44 ]
0.8255
0.8073
0.8248
0.8192
Table 5: NDCG@k of similarity measures according to performance-based ground truth. The highest score per metric is in bold and the second highest is underlined.
Method
MLSea-KG
Meta-Regression
Meta-Classification
MSE
R2
Accuracy
F1
Target: Accuracy
MF All + KGmetaSP PE
With
0.0101
0.6181
0.7413
0.7427
MF All + KGmetaSP PE
Without
0.0103
0.6114
0.7302
0.7320
Target: Precision
MF All + KGmetaSP PE
With
0.0164
0.5449
0.7492
0.7516
Table 6: Ablation of MLSea-KG integration for PPE for the unseen datasets. Experimental setup follows Table 2 . The best score per column is in bold.
Method
MLSea-KG
Meta-Regression
Meta-Classification
MSE
R2
Accuracy
F1
Target: Accuracy
MF All + KGmetaSP PE
With
0.0070
0.7361
0.8250
0.8244
MF All + KGmetaSP PE
Without
0.0074
0.7246
0.8225
0.8220
Target: Precision
MF All + KGmetaSP PE
With
0.0131
0.6264
0.8251
0.8247
Table 7: Ablation of MLSea-KG integration for PPE for the unseen pipeline configurations. Experimental setup follows Table 3 . The best score per column is in bold.
Hit@k
NDCG@k
Method
MLSea-KG
k=1
k=2
k=5
k=1
k=2
k=5
KGmetaSP DEpip
With
0.7905
0.8649
0.9257
0.8811
0.8642
0.8541
KGmetaSP DEpip
Without
0.7432
0.8649
0.9527
0.8551
0.8606
0.8560
Table 8: Ablation of MLSea-KG integration on DPSE . For Hit@k, datasets with similarity > 0.9 are considered hits.
Appendix figures & tables2 assets
Supplementary material from the paper’s appendix.
Appendix
Dataset
Pipeline
Meta-
Meta-Regr.
Meta-Classif.
Emb.
Strategy
Models
MSE
R2
Accuracy
F1
Target: Accuracy
MF All
Conf.-specific
1028
0.0081
0.6748
0.7363
0.7358
KGmetaSP PE (ComplEx)
1
0.0106
0.6006
0.7343
0.7361
KGmetaSP PE (TransE)
1
0.0105
0.6032
0.7351
0.7368
KGmetaSP PE (DistMult)
1
0.0103
0.6104
0.7380
0.7393
Appendix
Table 9: PPE results for unseen datasets. Setup follows Table 2 .
Method
Meta-Regr.
Meta-Classif.
MSE
R2
Accuracy
F1
Target: Accuracy
Average performance
0.0267
-0.0005
0.3303
0.1640
Closest embedding
0.0127
0.5241
0.7748
0.7747
MF All + KGmetaSP PE (ComplEx)
0.0083
0.6911
0.8072
0.8062
MF All + KGmetaSP PE (TransE)
0.0081
0.6976
0.8092
0.8083
Appendix
Table 10: PPE results for unseen pipeline configurations. Setup follows Table 3 .