THOR: Inductive Link Prediction over Hyper-Relational Knowledge Graphs

Knowledge graphs (KGs) have become a key ingredient supporting a variety of applications. Beyond the traditional triplet representation of facts where a relation connects two entities, modern KGs observe an increasing number of hyper-relational facts, where an arbitrary number of qualifiers associated with a triplet provide auxiliary information to further describe the rich semantics of the triplet, which can effectively boost the reasoning performance in link prediction tasks. However, existing link prediction techniques over such hyper-relational KGs (HKGs) mostly focus on a transductive setting, where KG embedding models are learned from the specific vocabulary of a given KG and subsequently can only make predictions within the same vocabulary, limiting their generalizability to previously unseen vocabularies. Against this background, we propose THOR, an inducTive link prediction technique for Hyper-relational knOwledge gRaphs. Specifically, we first introduce both relation and entity foundation graphs, modeling their fundamental inter- and intra-fact interactions in HKGs, which are agnostic to any specific relations and entities. Afterward, THOR is designed to learn from the two foundation graphs with two parallel graph encoders followed by a transformer decoder, which supports efficient masked training and fully-inductive inference. We conduct a thorough evaluation of THOR in hyper-relational link prediction tasks on 12 datasets with different settings. Results show that THOR outperforms a sizable collection of baselines, yielding 66.1%, 55.9%, and 20.4% improvement over the best-performing rule-based, semi-inductive, and fully-inductive techniques, respectively. A series of ablation studies also reveals our key design factors capturing the structural invariance transferable across HKGs for inductive tasks.

A Domain-Specific Curated Benchmark for Entity and Document-Level Relation Extraction

Information Extraction (IE), encompassing Named Entity Recognition (NER), Named Entity Linking (NEL), and Relation Extraction (RE), is critical for transforming the rapidly growing volume of scientific publications into structured, actionable knowledge. This need is especially evident in fast-evolving biomedical fields such as the gut-brain axis, where research investigates complex interactions between the gut microbiota and brain-related disorders. Existing biomedical IE benchmarks, however, are often narrow in scope and rely heavily on distantly supervised or automatically generated annotations, limiting their utility for advancing robust IE methods. We introduce GutBrainIE, a benchmark based on more than 1,600 PubMed abstracts, manually annotated by biomedical and terminological experts with fine-grained entities, concept-level links, and relations. While grounded in the gut-brain axis, the benchmark's rich schema, multiple tasks, and combination of highly curated and weakly supervised data make it broadly applicable to the development and evaluation of biomedical IE systems across domains.

Graph-Augmented Reasoning with Large Language Models for Tobacco Pest and Disease Management

This paper proposes a graph-augmented reasoning framework for tobacco pest and disease management that integrates structured domain knowledge into large language models. Building on GraphRAG, we construct a domain-specific knowledge graph and retrieve query-relevant subgraphs to provide relational evidence during answer generation. The framework adopts ChatGLM as the Transformer backbone with LoRA-based parameter-efficient fine-tuning, and employs a graph neural network to learn node representations that capture symptom-disease-treatment dependencies. By explicitly modeling diseases, symptoms, pesticides, and control measures as linked entities, the system supports evidence-aware retrieval beyond surface-level text similarity. Retrieved graph evidence is incorporated into the LLM input to guide generation toward domain-consistent recommendations and to mitigate hallucinated or inappropriate treatments. Experimental results show consistent improvements over text-only baselines, with the largest gains observed on multi-hop and comparative reasoning questions that require chaining multiple relations.

SynCABEL: Synthetic Contextualized Augmentation for Biomedical Entity Linking

We present SynCABEL (Synthetic Contextualized Augmentation for Biomedical Entity Linking), a framework that addresses a central bottleneck in supervised biomedical entity linking (BEL): the scarcity of expert-annotated training data. SynCABEL leverages large language models to generate context-rich synthetic training examples for all candidate concepts in a target knowledge base, providing broad supervision without manual annotation. We demonstrate that SynCABEL, when combined with decoder-only models and guided inference establish new state-of-the-art results across three widely used multilingual benchmarks: MedMentions for English, QUAERO for French, and SPACCC for Spanish. Evaluating data efficiency, we show that SynCABEL reaches the performance of full human supervision using up to 60% less annotated data, substantially reducing reliance on labor-intensive and costly expert labeling. Finally, acknowledging that standard evaluation based on exact code matching often underestimates clinically valid predictions due to ontology redundancy, we introduce an LLM-as-a-judge protocol. This analysis reveals that SynCABEL significantly improves the rate of clinically valid predictions. Our synthetic datasets, models, and code are released to support reproducibility and future research.

Breaking the Reasoning Horizon in Entity Alignment Foundation Models

Entity alignment (EA) is critical for knowledge graph (KG) fusion. Existing EA models lack transferability and are incapable of aligning unseen KGs without retraining. While using graph foundation models (GFMs) offer a solution, we find that directly adapting GFMs to EA remains largely ineffective. This stems from a critical "reasoning horizon gap": unlike link prediction in GFMs, EA necessitates capturing long-range dependencies across sparse and heterogeneous KG structuresTo address this challenge, we propose a EA foundation model driven by a parallel encoding strategy. We utilize seed EA pairs as local anchors to guide the information flow, initializing and encoding two parallel streams simultaneously. This facilitates anchor-conditioned message passing and significantly shortens the inference trajectory by leveraging local structural proximity instead of global search. Additionally, we incorporate a merged relation graph to model global dependencies and a learnable interaction module for precise matching. Extensive experiments verify the effectiveness of our framework, highlighting its strong generalizability to unseen KGs.

PathReasoner-R1: Instilling Structured Reasoning into Pathology Vision-Language Model via Knowledge-Guided Policy Optimization

Vision-Language Models (VLMs) are advancing computational pathology with superior visual understanding capabilities. However, current systems often reduce diagnosis to directly output conclusions without verifiable evidence-linked reasoning, which severely limits clinical trust and hinders expert error rectification. To address these barriers, we construct PathReasoner, the first large-scale dataset of whole-slide image (WSI) reasoning. Unlike previous work reliant on unverified distillation, we develop a rigorous knowledge-guided generation pipeline. By leveraging medical knowledge graphs, we explicitly align structured pathological findings and clinical reasoning with diagnoses, generating over 20K high-quality instructional samples. Based on the database, we propose PathReasoner-R1, which synergizes trajectory-masked supervised fine-tuning with reasoning-oriented reinforcement learning to instill structured chain-of-thought capabilities. To ensure medical rigor, we engineer a knowledge-aware multi-granular reward function incorporating an Entity Reward mechanism strictly aligned with knowledge graphs. This effectively guides the model to optimize for logical consistency rather than mere outcome matching, thereby enhancing robustness. Extensive experiments demonstrate that PathReasoner-R1 achieves state-of-the-art performance on both PathReasoner and public benchmarks across various image scales, equipping pathology models with transparent, clinically grounded reasoning capabilities. Dataset and code are available at https://github.com/cyclexfy/PathReasoner-R1.

FinMetaMind: A Tech Blueprint on NLQ Systems for Financial Knowledge Search

Natural Language Query (NLQ) allows users to search and interact with information systems using plain, human language instead of structured query syntax. This paper presents a technical blueprint on the design of a modern NLQ system tailored to financial knowledge search. The introduction of NLQ not only enhances the precision and recall of the knowledge search compared to traditional methods, but also facilitates deeper insights by efficiently linking disparate financial objects, events, and relationships. Using core constructs from natural language processing, search engineering, and vector data models, the proposed system aims to address key challenges in discovering, relevance ranking, data freshness, and entity recognition intrinsic to financial data retrieval. In this work, we detail the unique requirements of NLQ for financial datasets and documents, outline the architectural components for offline indexing and online retrieval, and discuss the real-world use cases of enhanced knowledge search in financial services. We delve into the theoretical underpinnings and experimental evidence supporting our proposed architecture, ultimately providing a comprehensive analysis on the subject matter. We also provide a detailed elaboration of our experimental methodology, the data used, the results and future optimizations in this study.

Implementing Tensor Logic: Unifying Datalog and Neural Reasoning via Tensor Contraction

The unification of symbolic reasoning and neural networks remains a central challenge in artificial intelligence. Symbolic systems offer reliability and interpretability but lack scalability, while neural networks provide learning capabilities but sacrifice transparency. Tensor Logic, proposed by Domingos, suggests that logical rules and Einstein summation are mathematically equivalent, offering a principled path toward unification. This paper provides empirical validation of this framework through three experiments. First, we demonstrate the equivalence between recursive Datalog rules and iterative tensor contractions by computing the transitive closure of a biblical genealogy graph containing 1,972 individuals and 1,727 parent-child relationships, converging in 74 iterations to discover 33,945 ancestor relationships. Second, we implement reasoning in embedding space by training a neural network with learnable transformation matrices, demonstrating successful zero-shot compositional inference on held-out queries. Third, we validate the Tensor Logic superposition construction on FB15k-237, a large-scale knowledge graph with 14,541 entities and 237 relations. Using Domingos's relation matrix formulation $R_r = E^\top A_r E$, we achieve MRR of 0.3068 on standard link prediction and MRR of 0.3346 on a compositional reasoning benchmark where direct edges are removed during training, demonstrating that matrix composition enables multi-hop inference without direct training examples.

It's All About the Confidence: An Unsupervised Approach for Multilingual Historical Entity Linking using Large Language Models

Despite the recent advancements in NLP with the advent of Large Language Models (LLMs), Entity Linking (EL) for historical texts remains challenging due to linguistic variation, noisy inputs, and evolving semantic conventions. Existing solutions either require substantial training data or rely on domain-specific rules that limit scalability. In this paper, we present MHEL-LLaMo (Multilingual Historical Entity Linking with Large Language MOdels), an unsupervised ensemble approach combining a Small Language Model (SLM) and an LLM. MHEL-LLaMo leverages a multilingual bi-encoder (BELA) for candidate retrieval and an instruction-tuned LLM for NIL prediction and candidate selection via prompt chaining. Our system uses SLM's confidence scores to discriminate between easy and hard samples, applying an LLM only for hard cases. This strategy reduces computational costs while preventing hallucinations on straightforward cases. We evaluate MHEL-LLaMo on four established benchmarks in six European languages (English, Finnish, French, German, Italian and Swedish) from the 19th and 20th centuries. Results demonstrate that MHEL-LLaMo outperforms state-of-the-art models without requiring fine-tuning, offering a scalable solution for low-resource historical EL. The implementation of MHEL-LLaMo is available on Github.

Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval

Retrieving evidence for language model queries from knowledge graphs requires balancing broad search across the graph with multi-hop traversal to follow relational links. Similarity-based retrievers provide coverage but remain shallow, whereas traversal-based methods rely on selecting seed nodes to start exploration, which can fail when queries span multiple entities and relations. We introduce ARK: Adaptive Retriever of Knowledge, an agentic KG retriever that gives a language model control over this breadth-depth tradeoff using a two-operation toolset: global lexical search over node descriptors and one-hop neighborhood exploration that composes into multi-hop traversal. ARK alternates between breadth-oriented discovery and depth-oriented expansion without depending on a fragile seed selection, a pre-set hop depth, or requiring retrieval training. ARK adapts tool use to queries, using global search for language-heavy queries and neighborhood exploration for relation-heavy queries. On STaRK, ARK reaches 59.1% average Hit@1 and 67.4 average MRR, improving average Hit@1 by up to 31.4% and average MRR by up to 28.0% over retrieval-based and agentic training-free methods. Finally, we distill ARK's tool-use trajectories from a large teacher into an 8B model via label-free imitation, improving Hit@1 by +7.0, +26.6, and +13.5 absolute points over the base 8B model on AMAZON, MAG, and PRIME datasets, respectively, while retaining up to 98.5% of the teacher's Hit@1 rate.