Link Prediction

Structural reasoning, the ability to recognize and make inferences over the relational structure between objects and concepts, is a hallmark of human cognition, yet prevailing methods often collapse relational topology into flat embeddings, cannot discover hidden structure and lack interpretability. We introduce Neural Structural Reasoner (NSR), a brain-inspired network that preserves relational structure directly in the connectivity and dynamics of coupled neuronal populations. NSR draws inspiration from three biological mechanisms: multi-layered architecture for encoding hierarchical knowledge, stable representations of entity and concepts, and path integration for input-driven state inference. At query time, NSR parallelizes computation over candidate relational structures and leverages confidence-weighted scores to perform link prediction. Across standard knowledge-graph benchmarks, NSR achieves competitive accuracy without leading on every dataset, and has lower reported training times than several neural baselines. Because reasoning is implemented through sequences of human-readable neuron activations, NSR affords native interpretability by tracking intermediate inference steps. The model further extracts latent relational hierarchies and compositional rules, demonstrating the brain-inspired architecture as an effective, efficient, and highly interpretable substrate for structural reasoning.

Many temporal link predictors summarize past interactions through learned node representations. We examine whether simple counts of recurring interaction patterns can provide competitive predictions without learning these representations. We propose a temporal link predictor based on statistical language modelling. It pools transition and co-occurrence counts across sources to predict links that a source has never formed. We smooth sparse estimates using destination frequencies or Kneser-Ney continuation counts. A shared log-linear rule combines these estimates with popularity, source history, and recency, without node embeddings. In our main evaluation, the model achieves the highest MRR among the compared methods on 7 out of 16 datasets from TGB and TGB-Seq. It also outperforms EdgeBank and Base3 on all 16 datasets and the heuristic family on 14. These gains extend to datasets designed to limit repeated edges. With only 9--13 learned parameters, our model provides a simple and competitive baseline for evaluating future neural temporal link predictors.

Graph Neural Networks (GNNs) are effective for learning node and link embeddings through permutation-equivariant aggregation. However, standard GNNs collapse automorphic nodes, i.e., those with identical structural roles (or orbits) into indistinguishable representations, leading to the node automorphism problem. This collapse limits their expressive power and degrades link prediction performance. Existing approaches to characterize GNN expressiveness rely primarily on Weisfeiler-Lehman (WL) analyses, but these methods are typically qualitative and often misaligned with empirical results. To address this gap, we begin by introducing a novel quantitative framework to assess GNN expressiveness for link prediction. We first formalize edge-level automorphism through edge orbits, which capture the set of structural role pairs for nodes that share a link. Then, we introduce the edge automorphism ratio (EAR), a scalar metric that quantifies a GNN's ability to distinguish links in a given graph. We empirically demonstrate that EAR correlates strongly with performance, validating its practical benefit. Building on this insight, we design EDGE-ORBIT EQUIVARIANT GRAPH NEURAL NETWORK (EO-GNN), a GNN architecture that addresses automorphism collapse while preserving equivariance and incurring minimal computational overhead. EO-GNN accomplishes this through two core designs combined with WL-based node hashes: (i) automorphism-aware dropouts and (ii) subgraph orbit-biased aggregation. Empirical evaluations on synthetic and real graphs show improvements of up to 42.36% and 28.44%, respectively, in predicting links in scenarios with high automorphism.

Temporal link prediction on the Temporal Graph Benchmark 2.0 (TGB 2.0) faces a scalability ceiling: on the benchmark's three largest datasets, every existing embedding method runs out of memory or exceeds the time budget. These large-scale graphs are the ones nearest real deployment scale, so failing on them is a real production limitation. EdgeReMIND sets the highest reported test mean reciprocal rank (MRR) on six of eight TGB 2.0 datasets and is the only relation-aware method that runs on all of them. This linear memorization model, with learned per-relation weights over data-calibrated features, is therefore not merely a fallback where embeddings fail but a practical state-of-the-art baseline across the benchmark.

Knowledge graph foundation models such as ULTRA achieve zero-shot link prediction on unseen graphs through dedicated architectures that hard-code a transfer mechanism. In this work we move that mechanism out of the architecture and into the representation, by \emph{reifying} the input graph: every fact becomes a node, connected to its subject, object, and relation type through a fixed vocabulary of six meta-relations, with relation types as anonymous shared nodes rather than model parameters. On this representation, five textbook GNNs (GAT, GINE with sum and with mean+max aggregation, GraphSAGE, R-GCN), each trained on a single knowledge graph of 4,245 triples for 30 minutes on one NVIDIA A100, transfer zero-shot to 40 inductive link-prediction benchmarks. The best of them, an off-the-shelf GAT, matches ULTRA, a dedicated foundation model pretrained on three graphs, across ULTRA's own evaluation suite. The same fixed vocabulary extends to relational databases, a row becoming an entity and a foreign-key column a relation type; a preliminary probe on two unseen databases, with no cell values, schema text or in-context labels, shows a model of this family pretrained on three knowledge graphs ranking foreign-key targets far above random-initialization and degree controls. We release the code, the checkpoints, and the evaluation pipeline for all 40 benchmarks.

Knowledge graph embedding (KGE) demonstrates its effectiveness for predicting missing links in knowledge graphs (KGs) by projecting entities and relations into a low-dimensional vector space. It is crucial for KGE models to effectively capture inference patterns (patterns) inherent in KGs, such as symmetry/antisymmetry, inversion and composition. Although recent KGE models exhibit strong capabilities in modeling such diverse patterns, they suffer from inherent limitations stemming from pattern over-generalization, where embeddings learned from only a single pattern instance inevitably generalize that pattern to all related instances, i.e., generalize the pattern universally. To address this issue, we propose PogRE (Pattern Over-Generalization Robust Embedding), a simple but effective method that utilizes dense linear transformations and compound operations for relation representation. Our theoretical analysis demonstrates that a dense linear transformation allows a pattern to become progressively universal as more triples are observed in the pattern. Furthermore, after observing d+1 linearly independent entities (d+1 denotes the dimension of entity), the linear transformation guarantees universal generalization of the pattern across all related instances. Experimental results on three standard benchmark datasets show that PogRE outperforms existing state-of-the-art KGE models in link prediction. Moreover, our empirical results indicate that PogRE effectively addresses the negative impact of over-generalization.

Uncertain knowledge graphs (UKGs) extend knowledge graphs by assigning each triple a continuous confidence score. Since most possible triples lack observed confidences, recent methods rely on semi-supervised learning to generate pseudo-labels. These methods initialize entity embeddings without using the confidence-weighted graph, discarding its global community and hub structure. We introduce QUEST, which adds no trainable parameters to the standard confidence-distribution learning pipeline. First, QUEST initializes entity embeddings using the smallest non-trivial eigenvectors of the confidence-weighted graph Laplacian, incorporating community and hub structure before training. Second, QUEST applies an unbiased mini-batch Dirichlet energy regularizer to enforce early-stage structural consistency. On two UKG datasets, QUEST improves confidence prediction and link prediction on six of eight metric-dataset pairs over prior methods and matches the previous best on the remaining two, while removing the instability spike observed on dense graphs. These results indicate that spectral structural priors combined with a graph Dirichlet energy regularizer improve accuracy, training stability, and checkpoint reliability in UKG completion.

Music recommendation relies primarily on two signals: user-item interactions, which fail in the cold-start regime, and intrinsic musical content, available for any recording. We argue that a third, largely untapped signal is both richer and more principled: critical adjacency, the pairwise relation established when an expert critic explicitly links two artists in long-form prose. It encodes deliberate judgments about which artists belong together. Prior work established its internal validity, showing it recovers coherent, interpretable communities and can match collaborative filtering in user-satisfaction simulations, with no user data. What has been missing is external validation: whether this critic-sourced relation is grounded in the music itself versus sociological context. We test it against acoustic content, reframing the question as one of construct validity. Representing artists as empirical distributions over 80 low-level Essentia acoustic descriptors and modeling pairwise proximity via marginal optimal-transport (Wasserstein) distances, we evaluate how far critical adjacency is sonically recoverable under a cold-start, artist-disjoint split. Our ensemble recovers these edges at out-of-sample AUC of 0.767 (95% CI 0.761-0.775). Recoverability rises monotonically with critical consensus, reaching 0.865 on multi-source attested edges. Stratified evaluations align with sociological models of genre: tightly bounded, scene-based genres show higher recoverability than broad industry umbrella terms. Critical discourse is thus a rich source of information for recommendation, decomposing into a reproducible "sonic core" and a "sociological remainder" driven by narrative positioning, subcultural context, and canonical placement. The work offers both a scalable cold-start discovery mechanism and a sociologically grounded approach to MIR and MRS research.

In fair ranked link prediction, demographic parity ($Δ_\mathrm{DP}$) is a common fairness metric. Yet, Mattos et al. (2025) argue that it fails to detect exposure bias because it ignores where links appear in the ranking. In this study, we reproduce this claim by showing that $Δ_\mathrm{DP}$ can indicate aggregate parity even when some subgroup-pair links are systematically ranked lower than others. The proposed rank-aware Normalized Discounted KL-divergence (NDKL), however, does detect such disparities. We also reproduce the effectiveness of MORAL, a post-processing method that improves exposure-based fairness while maintaining competitive utility. Beyond reproduction, we assess robustness using synthetic homophily settings, categorical sensitive attributes, and additional fairness and utility metrics, including subgroup-pair-adapted Attention-Weighted Rank Fairness (AWRF). Overall, our results show that exposure-based metrics uncover biases hidden by $Δ_\mathrm{DP}$ and that MORAL reduces these biases with minimal utility loss across diverse settings and datasets. We release a corrected, reproducible implementation at https://github.com/Floris93100/reproducing-MORAL.

Hyperbolic embeddings provide compact geometric representations of complex networks in hyperbolic spaces, but systematic comparisons of methods developed in machine learning, network science, and algorithmics remain rare. We benchmark 13 unsupervised hyperbolic graph embedders under a unified protocol for link prediction and topology reconstruction on synthetic and empirical networks. The protocol captures both missing-link recovery and the preservation of local and global network structure. Maximum-likelihood and representation-learning-based approaches, including hybrid variants, achieve the strongest overall performance, although no method dominates across all tasks and structural regimes. Performance is more strongly associated with embedding paradigm than with disciplinary origin. We identify the network regimes in which different paradigms succeed or fail and provide practical guidance for method selection in downstream applications.

Dynamic graph prompting freezes a pre-trained temporal backbone and adapts it to label-scarce downstream tasks using lightweight prompts. However, existing methods operate within a single, fixed embedding space. In this work, we reveal that temporal shifts in local clustering and degree heterogeneity actively reorganize the edge curvature spectrum---indicating that the optimal representation geometry dynamically evolves with local topology over time. We formalize this unaddressed mismatch as geometry under-adaptation. To overcome this limitation, we propose CurvPrompt, a topology-routed geometry prompting framework for dynamic graphs. Instead of relying on a single space, CurvPrompt maintains a bank of curvature-diverse Riemannian experts, each paired with a learnable prompt. A topology-aware gate dynamically routes each node--time instance to a sparse subset of experts, constructing a personalized mixed-curvature representation. To ensure parameter efficiency and training stability under extreme label scarcity, CurvPrompt employs soft routing during pre-training to build a continuous topology--geometry mapping, and transitions to hard Top-K routing with uniform weights during downstream adaptation. Extensive experiments across four benchmark datasets show that CurvPrompt significantly advances few-shot link prediction while delivering strong, consistent performance on node classification tasks, validating the necessity of geometry-adaptive prompting.

Predicting the existence and type of links (edges) between nodes in a multi-relational graph is key for applications from social interaction prediction to knowledge relationship identification. Enhancing local features with relevant global information is crucial for accurate link prediction, yet it remains challenging. We address this by modeling the relationship between node pairs as node influence. That is, whether the node influence can be propagated and what type of influence is propagated indicates where and what type the edge is, which will be the most relevant local and global information to predict the edges. To this end, we extend the Susceptible-Infectious-Recovered (SIR) epidemic model to capture the influence propagation of nodes on a large scale through sub-graph structures. Subsequently, these sub-graphs are compressed using virtual edges, thereby substantially reducing the computation associated with utilizing the global graph structure. Finally, we propose the Influential Graph Neural Predictor, referred to as IGNP, a link prediction framework guided by influence propagation. Extensive experiments demonstrate the superiority of the proposed method, which outperforms strong baselines by a large margin on the widely used and real-world datasets.

Prerequisite relation learning is central to adaptive instruction, yet existing methods often formulate it as conventional link prediction, limiting their ability to adaptively integrate complementary educational evidence for individual candidate pairs and to discourage contradictory reverse predictions. We propose ProPRL, a Property-aware Prerequisite Relation Learning framework. ProPRL first learns complementary concept representations from a concept-resource hypergraph and a directed learning-behavior graph, where direction-preserving personalized propagation aggregates multi-hop behavioral evidence. It then employs a Pair-conditioned Gate to adaptively weight and fuse the two views for each candidate ordered concept pair. Finally, an \textit{Irreversibility Constraint} introduces an anti-symmetry regularizer that penalizes simultaneously high confidence in both directions of the same concept pair. Experiments on multiple real-world educational datasets show that ProPRL achieves state-of-the-art performance on prerequisite relation learning.

Link prediction aims to identify potential or future connections within a given graph structure. Position information is essential for link prediction, as it distinguishes homogeneous nodes through their relative relationships, facilitating the accurate capture of structural patterns and implicit connections. Previous studies derive node positional information as distances to single-granularity landmarks, defined as the centers of homophilic regions, while neglecting the multi-granularity nature of homophilic structures and their hierarchical interrelations. We propose the Multi-Granularity Position Embedding of Graphs via Granular-Ball for Link Prediction (MGLP) method to obtain multi-granularity position embedding of graphs. Specifically, MGLP introduces an Adaptive Granular-Ball Graph Refinement mechanism to adaptively refine the graph into homophilic subdomains with optimal levels of granularity. The central nodes within subdomains are treated as landmarks, which form a Hierarchical Central Graph. Moreover, a novel Multi-granularity Hierarchical Distance encoding mechanism is proposed to capture both the homophilic structures within a graph and their hierarchical correlations, improving the discriminative power of nodes. Experimental results demonstrate that the multi-granularity position embedding generated by our method exhibits excellent performance and strong competitiveness compared to baseline algorithms for link prediction. Our codes are available in https://anonymous.4open.science/r/MGLP-D3C5/.

Many real-world graphs support multiple predictive tasks over the same underlying structure, creating an opportunity to reuse supervision across node classification (NC) and link prediction (LP). However, existing evaluations often rely on incompatible splits, observed-graph assumptions, and negative sampling rules, making conclusions about same-graph cross-task transfer unreliable. We formalize same-graph NC-LP transfer and propose a leakage-free protocol that fixes node and edge splits, uses a shared message-passing graph that excludes evaluated edges, and employs fixed negatives for LP. Across three backbones (GCN, GraphSAGE, GPS), we find that transfer is strongly directional and predictable: NC $\to$ LP is consistently beneficial on homophilic graphs, while LP $\to$ NC is fragile and can even degrade accuracy under naive representation reuse. LP $\to$ NC becomes reliably positive mainly in a structure-dominant regime where LP is easy but NC is unsaturated, suggesting that LP acts as structural pretraining. Finally, we introduce the CoTask Score (CTS) to summarize joint NC+LP utility when a shared encoder must serve both tasks, and show that simple dataset statistics, especially homophily, can guide mechanism choice and help avoid negative transfer.

In production processes for consumer products, assembly instructions are essential not only for planning but also for executing the production process. Likewise in robotics, it is crucial for an assembly robot to understand how components fit together and can be assembled. To facilitate these tasks, we contribute a method for constructing scene graphs to represent and characterize assembly relationships between components. Our approach does not rely on semantic data and is capable of handling a very small dataset. To realize this, the output of a Faster R-CNN model is used to create geometric representations, which are then processed by a transformer architecture to generate an adjacency matrix. This matrix serves as input to a Siamese network that uses message passing based on an attentional graph convolutional network (aGCN) architecture to characterize the connections between the components. We validate our method on a study dataset of toy model components which can be assembled into transportation vehicles.

Inferring gene regulatory networks (GRNs) from single-cell transcriptomic data is crucial for biological discovery, yet existing approaches suffer from a fundamental misalignment with real-world needs. Researchers typically seek a small set of high-confidence regulatory interactions for experimental validation, often involving previously unseen genes. However, current benchmarks rely on transductive splits with global classification metrics, while prevailing models struggle to generalize under inductive settings. To bridge this gap, we reformulate GRN inference as an inductive, ranking-centric graph completion problem and introduce \textbf{\benchmark}, a new benchmark that incorporates an inductive gene-holdout split together with knowledge graph completion metrics to better evaluate top-ranked predictions. Building on this, we propose \textbf{\method}, the first co-evolutionary discrete diffusion framework that jointly models biologically coherent discretized gene expression states and regulatory interactions for robust inductive generalization and improved top-ranked regulatory discovery. We further introduce TF-ALL Subgraph Sampling (TASS) for scalable training. Extensive experiments on {\benchmark} show that {\method} establishes new state-of-the-art performance, significantly outperforming existing methods in novel regulatory discovery, and ablation studies further verify the effectiveness of our design.

Institutional equity holdings disclosed in SEC Form 13F filings provide a rich temporal record of portfolio decisions by large investment managers. However, forecasting future allocations and modeling future demand remains challenging due to disclosure lags, reporting noise, and strong persistence in institutional behavior. We introduce the first benchmark for these tasks using temporal graph machine learning, framing holdings prediction as node affinity prediction -- i.e., forecasting portfolio weights -- on a discrete-time temporal bipartite graph of managers and securities extracted from preprocessed filings. On a sampled dataset comprising 99 managers and the S&P 500 index (503 securities, 209,351 temporal edges across 48 quarters from 2013--2025), Node Affinity prediction model using Virtual State (NAVIS) achieves a state-of-the-art test Normalized Discounted Cumulative Gain (NDCG) of 0.9127 with features (0.9121 without), outperforming all dynamic graph representation learning competitors by a substantial margin, and outperforming all heuristic methods. Remarkably, a simple Exponential Moving Average baseline achieves 0.8882, surpassing all dynamic graph models except NAVIS and all heuristics except Persistent Forecast (0.8891), highlighting the strong smoothness and persistence of institutional portfolios. Domain-specific node features provide only marginal gains (<1.2%), indicating that temporal and structural signals in the 13F ownership graph already capture most of the predictable information. By benchmarking a suite of Temporal Graph Benchmark (TGB) models under the node affinity prediction setting, both with and without features, on real-world 13F data, this work provides a reproducible foundation for temporal graph machine learning in holdings prediction and portfolio allocation.

Text-attributed graphs (TAGs), where each node carries a natural language description, require models to jointly reason over text and graph topology. Existing approaches often handle the two modalities separately: graph neural networks operate on shallow text features, while hybrids of LLMs and graphs use the language model mainly as a text encoder and delegate structure learning to a separate graph module. We propose method that unifies textual reasoning and graph message passing within a masked diffusion language model, a language model with bidirectional attention and generative decoding. For each graph instance, method linearises a sampled local neighbourhood into a token sequence and injects graph structure through a topology attention mask, which realises message passing over the graph. Because the diffusion language model can both interpret and generate text, the method adapts to different tasks simply by changing the prompt, supporting node classification, link prediction, and cross-dataset transfer with no target-specific fine-tuning. Experiments show that method outperforms graph neural networks, graph transformers, and LLM-based baselines on all three TAG benchmarks across two tasks, improving over the strongest baseline by up to 3.9 points.

Graph Neural Networks are great for link prediction in various network-like structures; however, the question of their speed/quality tradeoff has been barely studied. While in practice the time it takes to do inference matters little for small benchmarks, the latency does limit applicability in large-scale domains. In this work, we explore early-exiting strategies that can be applied to Graph Neural Networks to solve the problem of link-prediction faster. We use no auxiliary losses to enforce early exiting, allowing it to emerge as an implicit property of the architecture. We show that our method enables early exiting in several setups, moving the Pareto frontier on the HeaRT benchmark for GCN and SAS-GNN backbones. Our findings show that inference speed of GNNs on many link-prediction problems can be improved, while losing little, or even winning in terms of prediction quality. The code is available in our repository: https://github.com/knyazer/link_prediction.

Map generalization remains one of the fundamental tasks in cartography, especially for the simplification and aggregation of complex building footprints. This study presents the first exploratory application of graph-based deep learning to both tasks, reformulating simplification as node movement prediction and aggregation as link prediction within a unified graph learning framework. We evaluate representative graph neural network architectures (GCN, GAT, and GraphSAGE) on multi-scale building datasets, showing that GraphSAGE demonstrates relative strengths in link prediction accuracy, while also revealing persistent challenges in precise node movement prediction. Beyond quantitative performance, the results highlight that aggregation poses greater complexity and challenges than simplification, underscoring the difficulty of capturing higher-level spatial relationships in map generalization with current deep learning approaches. Although limitations such as data imbalance and the need for post-processing remain, the study provides valuable insights and methodological directions for advancing automated map generalization with deep learning approaches.

The problem of predicting links in complex networks appears in different disciplines and has led to a variety of ingenious human-designed methods. We use this rich program space to explore the performance and behavior of automated code-evolution systems tasked to obtain machine-designed methods for link prediction. Despite being trained on limited data, algorithms evolved through code evolution outperform human-designed methods (with an average AUC score of 0.915 vs. 0.783, computed over 580 networks) and show improved computational efficiency, allowing them to be applied to networks with millions of links. The discovered methods follow approaches that have been employed in human-designed methods, but contain key innovations in the selection and combination of node- and link-features. This illustrates the role modern large language models and genetic algorithms can play in algorithmic innovation and scientific discovery more generally.

Multi-agent AI systems are increasingly used to automate software engineering tasks including requirements analysis, architecture design, test generation, and traceability linking. When these agents operate as a sequential pipeline over shared software artifacts, errors and low-confidence decisions made by upstream agents propagate to downstream stages, producing orphaned requirements, contradictory links, and compliance gaps that pose significant risks in safety-critical domains. We propose a trust-aware coordination framework where a shared knowledge graph serves as both centralized semantic memory and a coordination surface through which agents assess and build upon each other's contributions using calibrated confidence scores. Our approach introduces a two-stage traceability link prediction pipeline combining embedding-based retrieval with LLM-based multi-criteria analysis, a traceability seeding mechanism that enables comparison between derivation-time and validation-time confidence, and a consistency protocol governing pipeline interactions through confidence threshold gating, confidence divergence detection, and conflict resolution. We evaluate on an automotive software engineering case study measuring link prediction calibration, protocol effectiveness, threshold sensitivity, and the impact of traceability seeding. Ablation studies confirm that confidence calibration is essential for effective pipeline coordination.

Link prediction in knowledge graphs fundamentally depends on the quality of learned embeddings for entities and relations. However, most existing methods derive these embeddings by aggregating only the local neighborhood of each entity, neglecting the global structure of the knowledge graph. This limited view prevents models from capturing higher-level structural patterns that are essential for accurate and generalizable link prediction. To address these limitations, we introduce Model Graph Inductive Learning (\textbf{MGIL}), a framework that constructs a model graph by clustering entities based on the similarity of their incoming and outgoing relational structures or their entity types. A GNN is then applied to this model graph to produce embeddings that capture the global view of the knowledge graph. These embeddings subsequently serve as high-quality initial features %embeddings for the original knowledge graph, replacing random initialization and leading to more stable and expressive representations. Extensive experiments on standard and recently proposed inductive benchmarks demonstrate that MGIL achieves state-of-the-art or highly competitive performance in inductive link prediction, highlighting its effectiveness across diverse graph settings.

Embedding models (KGEMs) constitute the main link prediction approach to complete knowledge graphs. Standard evaluation protocols emphasize rank-based metrics such as MRR or Hits@$K$, but usually overlook the influence of random seeds on result stability. Moreover, these metrics conceal potential instabilities in individual predictions and in the organization of embedding spaces. In this work, we conduct a systematic stability analysis of multiple KGEMs across several datasets. We find that high-performance models actually produce divergent predictions at the triple level and highly variable embedding spaces. By isolating stochastic factors (i.e., initialization, triple ordering, negative sampling, dropout, hardware), we show that each independently induces instability of comparable magnitude. Furthermore, for a given model, hyperparameter configurations with better MRR are not guaranteed to be more stable. Moreover, voting, albeit a known remediation mechanism, only provides a limited enhancement of stability. These findings highlight critical limitations of current benchmarking protocols, and raise concerns about the reliability of KGEMs for knowledge graph completion.

Recently, instance discrimination models have emerged as a major solution for self-supervised learning. Having already demonstrated its effectiveness in the image domain, instance discrimination learning is now proving equally convincing in the graph domain, in particular for node classification. However, fewer contributions have tackled the link prediction task. In this contribution, we propose to adapt existing methods to this context. We first provide a rigorous evaluation of existing self-supervised models in the field of link prediction, showing that the main performance depends on the augmentation process (like in computer vision). We then propose a new structural augmentation based on the community structure that is relevant for link prediction. Our main contribution introduces two new models, L-GRACE and L-BGRL, based on link representations instead of node representations, which improve the performance of the existing methods, especially on unattributed graphs, and we show that they perform on par with the state of the art, both in supervised and self-supervised contexts.

Scientific artifacts such as models and datasets are foundations for research. With the rapid growth of platforms like HuggingFace, researchers now have access to a large number of artifacts. Yet, a key challenge remains: how can we automatically discover the state-of-the-art (SOTA) model for a given dataset by fully leveraging existing artifacts? We formalize this task as automatic SOTA discovery by modeling HuggingFace as an artifact graph, where nodes are models/datasets and edges represent evaluations. We propose ArtifactLinker, a two-stage framework: (1) ranking promising unobserved model--dataset links using Graph Neural Networks (GNNs) or graph-augmented Large Language Models (LLMs), and (2) verifying top-ranked links via coding experiments with LLM-based agents. We further introduce a benchmark named ArtifactBench with 14,053 artifacts and 51,337 relations to evaluate the performance of both stages. Results show that (1) graph structures between existing artifacts are effective for missing link prediction; (2) end-to-end ranking and verification with ArtifactLinker help discover potential SOTA results and research insights.

Link prediction (inferring missing or future connections between nodes in a graph) is a fundamental problem in network science with widespread applications in, e.g., biological systems, recommender systems, finance and cybersecurity. The ability to accurately predict links has significant real-world applications, such as detecting fraudulent financial transactions or identifying drug-target interactions in biomedicine. Despite a rich literature, link prediction is still challenging, especially for graphs enriched with information on edges (direction) and nodes (attributes). In fact, research on link prediction, especially the one based on Graph Deep Learning (GDL), has mostly focused on undirected graphs, without fully leveraging node attributes. Here, we fill this gap by proposing Gravity-GraphSAGE (GG-SAGE), a modified version of GraphSAGE, a GDL model for node embeddings, composed of a gravity-inspired decoder. This implementation is the first example in the literature of a GraphSAGE backbone adopted for directed link prediction. Using the benchmark datasets Cora, Citeseer, PubMed and 16 real-world graphs from the online Netzschleuder repository, we show that our proposed model outperforms state-of-the-art GDL link prediction techniques. Using further experimental evidence, we relate the quality of the output of our model with various characteristics of the graph, suggesting that our framework scales well when applied to data of increasing complexity.

Accurate prediction of physician referral links is essential for optimizing care coordination and reducing fragmentation in healthcare delivery. However, existing computational methods, ranging from triadic closure heuristics to graph neural networks, fail to capture the intrinsic properties of physician referral networks, including sparsity, disassortative degree mixing, and hub-dominated topology. Here, we propose H3, a healthcare three-hop index that addresses these limitations by modeling indirect referral pathways through intermediate physicians, with degree-based normalization and a redundancy penalty to mitigate hub-mediated noise. Using Medicare Physician Shared Patient Patterns data, we evaluate H3 under two complementary prediction regimes: within-period prediction, which assesses recovery of contemporaneous referral links under sparse conditions, and cross-period prediction, which tests robustness to temporal shift as referral windows expand. Across both regimes, H3 consistently outperforms classical heuristics and deep learning-based baselines. Unlike black-box neural network approaches, H3 produces fully decomposable predictions traceable to specific intermediary physicians, offering a transparent and deployable solution for referral network completion.

Prior work on node classification has shown that Graph Neural Networks (GNNs) can learn representations that transfer across graphs, when underlying graph properties are shared. For a fixed graph, one would then expect GNNs trained for link prediction to learn a representation consistent with that learnt for node classification. We show this intuition does not hold in the general case. Instead, we find popular link prediction models can learn a trivial mini-batch dependent heuristic, enabled by batch-normalisation layers, to solve the edge classification task. When correcting for this, we observe increased alignment of the network representation with node-class relevant features, suggesting the network has learnt a graph representation that better aligns with the underlying graph's properties. Our findings suggest that standard link prediction training may be leading us to overestimate link predictors' ability to learn a generalised representation of a graph that is consistent across tasks.