Link Prediction

We present a semantic-structural atlas of transportation research built from 120{,}323 papers across 34 peer-reviewed journals published between 1967 and 2025, roughly an order of magnitude larger than and a decade beyond Sun and Rahwan's~(2017) coauthorship study. We use OpenAlex and Crossref as open, CC0-licensed data sources, resolve author identity through OpenAlex author IDs, ORCID records, and manual alias resolution, and embed every paper with SPECTER2 with Arora-style whitening concatenated with concept TF--IDF and venue linear-discriminant projections. On this substrate we report three findings. First, Leiden on the author-level semantic k-nearest-neighbor graph yields 23 topic communities that agree only weakly with the 172 coauthor communities (normalized mutual information $0.23$), opening room for a predictive layer that neither source encodes alone. Second, a multiplex Leiden partition combining both edge types recovers 181 communities and localizes where collaboration and topic structure decouple. Third -- the paper's core methodological contribution -- we define \emph{phantom collaborators}, pairs of authors who are top-$K$ semantic neighbors yet $\geq 3$ hops apart in the coauthor graph, and show via a temporal hold-out (training cutoff 2019) that phantom pairs become real coauthors in 2020--2025 at a rate $16$ to $33$ times above random, popularity-weighted, and same-venue baselines, with a $68$-fold monotone gradient between the highest- and lowest-similarity buckets. All artifacts are released as a live, reproducible web atlas at https://choi-seongjin.github.io/transport-atlas/.

Knowledge Graphs (KGs) are composed of triples, and the goal of Knowledge Graph Completion (KGC) is to infer the missing factual triples. Traditional KGC tasks predict missing elements in a triple given one or two of its elements. As a more realistic task, the Triple Set Prediction (TSP) task aims to infer the set of missing triples conditioned only on the observed knowledge graph, without assuming any partial information about the missing triples. Existing TSP methods predict the set of missing triples in a triple-by-triple manner, falling short in capturing the dependencies among the predicted triples to ensure consistency. To address this issue, we propose a novel discrete diffusion model termed DiffTSP that treats TSP as a generative task. DiffTSP progressively adds noise to the KG through a discrete diffusion process, achieved by masking relational edges. The reverse process then gradually recovers the complete KG conditioned on the incomplete graph. To this end, we design a structure-aware denoising network that integrates a relational context encoder with a relational graph diffusion transformer for knowledge graph generation. DiffTSP can generate the complete set of triples in a one-pass manner while ensuring the dependencies among the predicted triples. Our approach achieves state-of-the-art performance on three public datasets. Code: https://github.com/ADMIS-TONGJI/DiffTSP.

Predicting links in sparse, continuously evolving networks is a central challenge in network science. Conventional heuristic methods and deep learning models, including Graph Neural Networks (GNNs), are typically designed for static graphs and thus struggle to capture temporal dependencies. Snapshot-based techniques partially address this issue but often encounter data sparsity and class imbalance, particularly in networks with transient interactions such as telecommunication call detail records (CDRs). Temporal Graph Networks (TGNs) model dynamic graphs by updating node embeddings over time; however, their predictive accuracy under sparse conditions remains limited. In this study, we improve the TGN framework by extracting enclosing subgraphs around candidate links, enabling the model to jointly learn structural and temporal information. Experiments on a sparse CDR, email, message dataset show that our approach increases average precision by at least 2% over standard TGNs, demonstrating the advantages of integrating local topology for robust link prediction in dynamic networks.

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities. Our code is publicly available at https://github.com/quang-truong/pencil.