gHAWK: Local and Global Structure Encoding for Scalable Training of Graph Neural Networks on Knowledge Graphs

Knowledge Graphs (KGs) are a rich source of structured, heterogeneous data, powering a wide range of applications. A common approach to leverage this data is to train a graph neural network (GNN) on the KG. However, existing message-passing GNNs struggle to scale to large KGs because they rely on the iterative message passing process to learn the graph structure, which is inefficient, especially under mini-batch training, where a node sees only a partial view of its neighborhood. In this paper, we address this problem and present gHAWK, a novel and scalable GNN training framework for large KGs. The key idea is to precompute structural features for each node that capture its local and global structure before GNN training even begins. Specifically, gHAWK introduces a preprocessing step that computes: (a)~Bloom filters to compactly encode local neighborhood structure, and (b)~TransE embeddings to represent each node's global position in the graph. These features are then fused with any domain-specific features (e.g., text embeddings), producing a node feature vector that can be incorporated into any GNN technique. By augmenting message-passing training with structural priors, gHAWK significantly reduces memory usage, accelerates convergence, and improves model accuracy. Extensive experiments on large datasets from the Open Graph Benchmark (OGB) demonstrate that gHAWK achieves state-of-the-art accuracy and lower training time on both node property prediction and link prediction tasks, topping the OGB leaderboard for three graphs.

HyperComplEx: Adaptive Multi-Space Knowledge Graph Embeddings

Knowledge graphs have emerged as fundamental structures for representing complex relational data across scientific and enterprise domains. However, existing embedding methods face critical limitations when modeling diverse relationship types at scale: Euclidean models struggle with hierarchies, vector space models cannot capture asymmetry, and hyperbolic models fail on symmetric relations. We propose HyperComplEx, a hybrid embedding framework that adaptively combines hyperbolic, complex, and Euclidean spaces via learned attention mechanisms. A relation-specific space weighting strategy dynamically selects optimal geometries for each relation type, while a multi-space consistency loss ensures coherent predictions across spaces. We evaluate HyperComplEx on computer science research knowledge graphs ranging from 1K papers (~25K triples) to 10M papers (~45M triples), demonstrating consistent improvements over state-of-the-art baselines including TransE, RotatE, DistMult, ComplEx, SEPA, and UltraE. Additional tests on standard benchmarks confirm significantly higher results than all baselines. On the 10M-paper dataset, HyperComplEx achieves 0.612 MRR, a 4.8% relative gain over the best baseline, while maintaining efficient training, achieving 85 ms inference per triple. The model scales near-linearly with graph size through adaptive dimension allocation. We release our implementation and dataset family to facilitate reproducible research in scalable knowledge graph embeddings.

Is Architectural Complexity Overrated? Competitive and Interpretable Knowledge Graph Completion with RelatE

We revisit the efficacy of simple, real-valued embedding models for knowledge graph completion and introduce RelatE, an interpretable and modular method that efficiently integrates dual representations for entities and relations. RelatE employs a real-valued phase-modulus decomposition, leveraging sinusoidal phase alignments to encode relational patterns such as symmetry, inversion, and composition. In contrast to recent approaches based on complex-valued embeddings or deep neural architectures, RelatE preserves architectural simplicity while achieving competitive or superior performance on standard benchmarks. Empirically, RelatE outperforms prior methods across several datasets: on YAGO3-10, it achieves an MRR of 0.521 and Hit@10 of 0.680, surpassing all baselines. Additionally, RelatE offers significant efficiency gains, reducing training time by 24%, inference latency by 31%, and peak GPU memory usage by 22% compared to RotatE. Perturbation studies demonstrate improved robustness, with MRR degradation reduced by up to 61% relative to TransE and by up to 19% compared to RotatE under structural edits such as edge removals and relation swaps. Formal analysis further establishes the model's full expressiveness and its capacity to represent essential first-order logical inference patterns. These results position RelatE as a scalable and interpretable alternative to more complex architectures for knowledge graph completion.

MuCoS: Efficient Drug Target Discovery via Multi Context Aware Sampling in Knowledge Graphs

Accurate prediction of drug target interactions is critical for accelerating drug discovery and elucidating complex biological mechanisms. In this work, we frame drug target prediction as a link prediction task on heterogeneous biomedical knowledge graphs (KG) that integrate drugs, proteins, diseases, pathways, and other relevant entities. Conventional KG embedding methods such as TransE and ComplEx SE are hindered by their reliance on computationally intensive negative sampling and their limited generalization to unseen drug target pairs. To address these challenges, we propose Multi Context Aware Sampling (MuCoS), a novel framework that prioritizes high-density neighbours to capture salient structural patterns and integrates these with contextual embeddings derived from BERT. By unifying structural and textual modalities and selectively sampling highly informative patterns, MuCoS circumvents the need for negative sampling, significantly reducing computational overhead while enhancing predictive accuracy for novel drug target associations and drug targets. Extensive experiments on the KEGG50k dataset demonstrate that MuCoS outperforms state-of-the-art baselines, achieving up to a 13\% improvement in mean reciprocal rank (MRR) in predicting any relation in the dataset and a 6\% improvement in dedicated drug target relation prediction.

MuCo-KGC: Multi-Context-Aware Knowledge Graph Completion

Knowledge graph completion (KGC) seeks to predict missing entities (e.g., heads or tails) or relationships in knowledge graphs (KGs), which often contain incomplete data. Traditional embedding-based methods, such as TransE and ComplEx, have improved tail entity prediction but struggle to generalize to unseen entities during testing. Textual-based models mitigate this issue by leveraging additional semantic context; however, their reliance on negative triplet sampling introduces high computational overhead, semantic inconsistencies, and data imbalance. Recent approaches, like KG-BERT, show promise but depend heavily on entity descriptions, which are often unavailable in KGs. Critically, existing methods overlook valuable structural information in the KG related to the entities and relationships. To address these challenges, we propose Multi-Context-Aware Knowledge Graph Completion (MuCo-KGC), a novel model that utilizes contextual information from linked entities and relations within the graph to predict tail entities. MuCo-KGC eliminates the need for entity descriptions and negative triplet sampling, significantly reducing computational complexity while enhancing performance. Our experiments on standard datasets, including FB15k-237, WN18RR, CoDEx-S, and CoDEx-M, demonstrate that MuCo-KGC outperforms state-of-the-art methods on three datasets. Notably, MuCo-KGC improves MRR on WN18RR, and CoDEx-S and CoDEx-M datasets by $1.63\%$, and $3.77\%$ and $20.15\%$ respectively, demonstrating its effectiveness for KGC tasks.

SparseTransX: Efficient Training of Translation-Based Knowledge Graph Embeddings Using Sparse Matrix Operations

Knowledge graph (KG) learning offers a powerful framework for generating new knowledge and making inferences. Training KG embedding can take a significantly long time, especially for larger datasets. Our analysis shows that the gradient computation of embedding is one of the dominant functions in the translation-based KG embedding training loop. We address this issue by replacing the core embedding computation with SpMM (Sparse-Dense Matrix Multiplication) kernels. This allows us to unify multiple scatter (and gather) operations as a single operation, reducing training time and memory usage. We create a general framework for training KG models using sparse kernels and implement four models, namely TransE, TransR, TransH, and TorusE. Our sparse implementations exhibit up to 5.3x speedup on the CPU and up to 4.2x speedup on the GPU with a significantly low GPU memory footprint. The speedups are consistent across large and small datasets for a given model. Our proposed sparse approach can be extended to accelerate other translation-based (such as TransC, TransM, etc.) and non-translational (such as DistMult, ComplEx, RotatE, etc.) models as well.

MuCoS: Efficient Drug-Target Prediction through Multi-Context-Aware Sampling

Drug-target interactions are critical for understanding biological processes and advancing drug discovery. However, traditional methods such as ComplEx-SE, TransE, and DistMult struggle with unseen relationships and negative triplets, which limits their effectiveness in drug-target prediction. To address these challenges, we propose Multi-Context-Aware Sampling (MuCoS), an efficient and positively accurate method for drug-target prediction. MuCoS reduces computational complexity by prioritizing neighbors of higher density to capture informative structural patterns. These optimized neighborhood representations are integrated with BERT, enabling contextualized embeddings for accurate prediction of missing relationships or tail entities. MuCoS avoids the need for negative triplet sampling, reducing computation while improving performance over unseen entities and relations. Experiments on the KEGG50k biomedical dataset show that MuCoS improved over existing models by 13\% on MRR, 7\% on Hits@1, 4\% on Hits@3, and 18\% on Hits@10 for the general relationship, and by 6\% on MRR, 1\% on Hits@1, 3\% on Hits@3, and 12\% on Hits@10 for prediction of drug-target relationship.

A Contextualized BERT model for Knowledge Graph Completion

Knowledge graphs (KGs) are valuable for representing structured, interconnected information across domains, enabling tasks like semantic search, recommendation systems and inference. A pertinent challenge with KGs, however, is that many entities (i.e., heads, tails) or relationships are unknown. Knowledge Graph Completion (KGC) addresses this by predicting these missing nodes or links, enhancing the graph's informational depth and utility. Traditional methods like TransE and ComplEx predict tail entities but struggle with unseen entities. Textual-based models leverage additional semantics but come with high computational costs, semantic inconsistencies, and data imbalance issues. Recent LLM-based models show improvement but overlook contextual information and rely heavily on entity descriptions. In this study, we introduce a contextualized BERT model for KGC that overcomes these limitations by utilizing the contextual information from neighbouring entities and relationships to predict tail entities. Our model eliminates the need for entity descriptions and negative triplet sampling, reducing computational demands while improving performance. Our model outperforms state-of-the-art methods on standard datasets, improving Hit@1 by 5.3% and 4.88% on FB15k-237 and WN18RR respectively, setting a new benchmark in KGC.

Unified Interpretation of Smoothing Methods for Negative Sampling Loss Functions in Knowledge Graph Embedding

Knowledge Graphs (KGs) are fundamental resources in knowledge-intensive tasks in NLP. Due to the limitation of manually creating KGs, KG Completion (KGC) has an important role in automatically completing KGs by scoring their links with KG Embedding (KGE). To handle many entities in training, KGE relies on Negative Sampling (NS) loss that can reduce the computational cost by sampling. Since the appearance frequencies for each link are at most one in KGs, sparsity is an essential and inevitable problem. The NS loss is no exception. As a solution, the NS loss in KGE relies on smoothing methods like Self-Adversarial Negative Sampling (SANS) and subsampling. However, it is uncertain what kind of smoothing method is suitable for this purpose due to the lack of theoretical understanding. This paper provides theoretical interpretations of the smoothing methods for the NS loss in KGE and induces a new NS loss, Triplet Adaptive Negative Sampling (TANS), that can cover the characteristics of the conventional smoothing methods. Experimental results of TransE, DistMult, ComplEx, RotatE, HAKE, and HousE on FB15k-237, WN18RR, and YAGO3-10 datasets and their sparser subsets show the soundness of our interpretation and performance improvement by our TANS.

Vehicle Lane Change Prediction based on Knowledge Graph Embeddings and Bayesian Inference

Prediction of vehicle lane change maneuvers has gained a lot of momentum in the last few years. Some recent works focus on predicting a vehicle's intention by predicting its trajectory first. This is not enough, as it ignores the context of the scene and the state of the surrounding vehicles (as they might be risky to the target vehicle). Other works assessed the risk made by the surrounding vehicles only by considering their existence around the target vehicle, or by considering the distance and relative velocities between them and the target vehicle as two separate numerical features. In this work, we propose a solution that leverages Knowledge Graphs (KGs) to anticipate lane changes based on linguistic contextual information in a way that goes well beyond the capabilities of current perception systems. Our solution takes the Time To Collision (TTC) with surrounding vehicles as input to assess the risk on the target vehicle. Moreover, our KG is trained on the HighD dataset using the TransE model to obtain the Knowledge Graph Embeddings (KGE). Then, we apply Bayesian inference on top of the KG using the embeddings learned during training. Finally, the model can predict lane changes two seconds ahead with 97.95% f1-score, which surpassed the state of the art, and three seconds before changing lanes with 93.60% f1-score.