LEC-KG: An LLM-Embedding Collaborative Framework for Domain-Specific Knowledge Graph Construction -- A Case Study on SDGs

Constructing domain-specific knowledge graphs from unstructured text remains challenging due to heterogeneous entity mentions, long-tail relation distributions, and the absence of standardized schemas. We present LEC-KG, a bidirectional collaborative framework that integrates the semantic understanding of Large Language Models (LLMs) with the structural reasoning of Knowledge Graph Embeddings (KGE). Our approach features three key components: (1) hierarchical coarse-to-fine relation extraction that mitigates long-tail bias, (2) evidence-guided Chain-of-Thought feedback that grounds structural suggestions in source text, and (3) semantic initialization that enables structural validation for unseen entities. The two modules enhance each other iteratively-KGE provides structure-aware feedback to refine LLM extractions, while validated triples progressively improve KGE representations. We evaluate LEC-KG on Chinese Sustainable Development Goal (SDG) reports, demonstrating substantial improvements over LLM baselines, particularly on low-frequency relations. Through iterative refinement, our framework reliably transforms unstructured policy text into validated knowledge graph triples.

Ontology-to-tools compilation for executable semantic constraint enforcement in LLM agents

We introduce ontology-to-tools compilation as a proof-of-principle mechanism for coupling large language models (LLMs) with formal domain knowledge. Within The World Avatar (TWA), ontological specifications are compiled into executable tool interfaces that LLM-based agents must use to create and modify knowledge graph instances, enforcing semantic constraints during generation rather than through post-hoc validation. Extending TWA's semantic agent composition framework, the Model Context Protocol (MCP) and associated agents are integral components of the knowledge graph ecosystem, enabling structured interaction between generative models, symbolic constraints, and external resources. An agent-based workflow translates ontologies into ontology-aware tools and iteratively applies them to extract, validate, and repair structured knowledge from unstructured scientific text. Using metal-organic polyhedra synthesis literature as an illustrative case, we show how executable ontological semantics can guide LLM behaviour and reduce manual schema and prompt engineering, establishing a general paradigm for embedding formal knowledge into generative systems.

Embedding Learning on Multiplex Networks for Link Prediction

Over the past years, embedding learning on networks has shown tremendous results in link prediction tasks for complex systems, with a wide range of real-life applications. Learning a representation for each node in a knowledge graph allows us to capture topological and semantic information, which can be processed in downstream analyses later. In the link prediction task, high-dimensional network information is encoded into low-dimensional vectors, which are then fed to a predictor to infer new connections between nodes in the network. As the network complexity (that is, the numbers of connections and types of interactions) grows, embedding learning turns out increasingly challenging. This review covers published models on embedding learning on multiplex networks for link prediction. First, we propose refined taxonomies to classify and compare models, depending on the type of embeddings and embedding techniques. Second, we review and address the problem of reproducible and fair evaluation of embedding learning on multiplex networks for the link prediction task. Finally, we tackle evaluation on directed multiplex networks by proposing a novel and fair testing procedure. This review constitutes a crucial step towards the development of more performant and tractable embedding learning approaches for multiplex networks and their fair evaluation for the link prediction task. We also suggest guidelines on the evaluation of models, and provide an informed perspective on the challenges and tools currently available to address downstream analyses applied to multiplex networks.

LIEREx: Language-Image Embeddings for Robotic Exploration

Semantic maps allow a robot to reason about its surroundings to fulfill tasks such as navigating known environments, finding specific objects, and exploring unmapped areas. Traditional mapping approaches provide accurate geometric representations but are often constrained by pre-designed symbolic vocabularies. The reliance on fixed object classes makes it impractical to handle out-of-distribution knowledge not defined at design time. Recent advances in Vision-Language Foundation Models, such as CLIP, enable open-set mapping, where objects are encoded as high-dimensional embeddings rather than fixed labels. In LIEREx, we integrate these VLFMs with established 3D Semantic Scene Graphs to enable target-directed exploration by an autonomous agent in partially unknown environments.

ROG: Retrieval-Augmented LLM Reasoning for Complex First-Order Queries over Knowledge Graphs

Answering first-order logic (FOL) queries over incomplete knowledge graphs (KGs) is difficult, especially for complex query structures that compose projection, intersection, union, and negation. We propose ROG, a retrieval-augmented framework that combines query-aware neighborhood retrieval with large language model (LLM) chain-of-thought reasoning. ROG decomposes a multi-operator query into a sequence of single-operator sub-queries and grounds each step in compact, query-relevant neighborhood evidence. Intermediate answer sets are cached and reused across steps, improving consistency on deep reasoning chains. This design reduces compounding errors and yields more robust inference on complex and negation-heavy queries. Overall, ROG provides a practical alternative to embedding-based logical reasoning by replacing learned operators with retrieval-grounded, step-wise inference. Experiments on standard KG reasoning benchmarks show consistent gains over strong embedding-based baselines, with the largest improvements on high-complexity and negation-heavy query types.

RAG-GNN: Integrating Retrieved Knowledge with Graph Neural Networks for Precision Medicine

Network topology excels at structural predictions but fails to capture functional semantics encoded in biomedical literature. We present a retrieval-augmented generation (RAG) embedding framework that integrates graph neural network representations with dynamically retrieved literature-derived knowledge through contrastive learning. Benchmarking against ten embedding methods reveals task-specific complementarity: topology-focused methods achieve near-perfect link prediction (GCN: 0.983 AUROC), while RAG-GNN is the only method achieving positive silhouette scores for functional clustering (0.001 vs. negative scores for all baselines). Information-theoretic decomposition shows network topology contributes 77.3% of predictive information, while retrieved documents provide 8.6% unique information. Applied to cancer signaling networks (379 proteins, 3,498 interactions), the framework identifies DDR1 as a therapeutic target based on retrieved evidence of synthetic lethality with KRAS mutations. These results establish that topology-only and retrieval-augmented approaches serve complementary purposes: structural prediction tasks are solved by network topology alone, while functional interpretation uniquely benefits from retrieved knowledge.

EGAM: Extended Graph Attention Model for Solving Routing Problems

Neural combinatorial optimization (NCO) solvers, implemented with graph neural networks (GNNs), have introduced new approaches for solving routing problems. Trained with reinforcement learning (RL), the state-of-the-art graph attention model (GAM) achieves near-optimal solutions without requiring expert knowledge or labeled data. In this work, we generalize the existing graph attention mechanism and propose the extended graph attention model (EGAM). Our model utilizes multi-head dot-product attention to update both node and edge embeddings, addressing the limitations of the conventional GAM, which considers only node features. We employ an autoregressive encoder-decoder architecture and train it with policy gradient algorithms that incorporate a specially designed baseline. Experiments show that EGAM matches or outperforms existing methods across various routing problems. Notably, the proposed model demonstrates exceptional performance on highly constrained problems, highlighting its efficiency in handling complex graph structures.

Rethinking Federated Graph Foundation Models: A Graph-Language Alignment-based Approach

Recent studies of federated graph foundational models (FedGFMs) break the idealized and untenable assumption of having centralized data storage to train graph foundation models, and accommodate the reality of distributed, privacy-restricted data silos. Despite their simplicity and intuition, existing studies that project aligned generalizable knowledge onto a discrete token space via vector-quantized backbones suffer from irreversible knowledge loss during the quantization process. In this context, we argue that reconciling the semantic-structural orthogonality and integrity between pre-trained language models (PLMs) and graph neural networks (GNNs) is paramount for developing effective FedGFMs while simultaneously mitigating the severe data heterogeneity and communication constraints inherent in distributed, resource-limited environments. To address these issues, we propose FedGALA (Federated Graph And Language Alignment), a framework that resolves graph-based semantic-structural orthogonality and integrity in federated settings by employing unsupervised contrastive learning to align GNNs and frozen PLMs within a continuous embedding space, thereby capturing robust, transferable general knowledge. Subsequently, FedGALA leverages a communication-efficient prompt tuning mechanism to steer these pre-aligned encoders and frozen PLMs, facilitating effective adaptation to diverse downstream tasks while circumventing the prohibitive overhead of full-parameter fine-tuning. The comprehensive experiments validate that FedGALA outperforms all competitive baselines across multi-domain datasets on multiple tasks with up to 14.37% performance improvement.

Structurally Human, Semantically Biased: Detecting LLM-Generated References with Embeddings and GNNs

Large language models are increasingly used to curate bibliographies, raising the question: are their reference lists distinguishable from human ones? We build paired citation graphs, ground truth and GPT-4o-generated (from parametric knowledge), for 10,000 focal papers ($\approx$ 275k references) from SciSciNet, and added a field-matched random baseline that preserves out-degree and field distributions while breaking latent structure. We compare (i) structure-only node features (degree/closeness/eigenvector centrality, clustering, edge count) with (ii) 3072-D title/abstract embeddings, using an RF on graph-level aggregates and Graph Neural Networks with node features. Structure alone barely separates GPT from ground truth (RF accuracy $\approx$ 0.60) despite cleanly rejecting the random baseline ($\approx$ 0.89--0.92). By contrast, embeddings sharply increase separability: RF on aggregated embeddings reaches $\approx$ 0.83, and GNNs with embedding node features achieve 93\% test accuracy on GPT vs.\ ground truth. We show the robustness of our findings by replicating the pipeline with Claude Sonnet 4.5 and with multiple embedding models (OpenAI and SPECTER), with RF separability for ground truth vs.\ Claude $\approx 0.77$ and clean rejection of the random baseline. Thus, LLM bibliographies, generated purely from parametric knowledge, closely mimic human citation topology, but leave detectable semantic fingerprints; detection and debiasing should target content signals rather than global graph structure.

JAF: Judge Agent Forest

Judge agents are fundamental to agentic AI frameworks: they provide automated evaluation, and enable iterative self-refinement of reasoning processes. We introduce JAF: Judge Agent Forest, a framework in which the judge agent conducts joint inference across a cohort of query--response pairs generated by a primary agent, rather than evaluating each in isolation. This paradigm elevates the judge from a local evaluator to a holistic learner: by simultaneously assessing related responses, the judge discerns cross-instance patterns and inconsistencies, whose aggregate feedback enables the primary agent to improve by viewing its own outputs through the judge's collective perspective. Conceptually, JAF bridges belief propagation and ensemble-learning principles: overlapping in-context neighborhoods induce a knowledge-graph structure that facilitates propagation of critique, and repeated, randomized evaluations yield a robust ensemble of context-sensitive judgments. JAF can be instantiated entirely via ICL, with the judge prompted for each query using its associated primary-agent response plus a small, possibly noisy set of peer exemplars. While kNN in embedding space is a natural starting point for exemplars, this approach overlooks categorical structure, domain metadata, or nuanced distinctions accessible to modern LLMs. To overcome these limitations, we develop a flexible locality-sensitive hashing (LSH) algorithm that learns informative binary codes by integrating semantic embeddings, LLM-driven hash predicates, supervision from categorical labels, and relevant side information. These hash codes support efficient, interpretable, and relation-aware selection of diverse exemplars, and further optimize exploration of CoT reasoning paths. We validate JAF with an empirical study on the demanding task of cloud misconfigs triage in large-scale cloud environments.