arXiv subjects

Heiko Paulheim

Publications and source records attributed to Heiko Paulheim.

At least 19 recordsLinked to original sources

arXiv2026

Aligning Biomedical Texts and Knowledge Graphs: A Systematic Comparison of Lightweight Alignment Strategies

Biomedical knowledge exists in two complementary but distinct forms: unstructured scientific literature and structured knowledge graphs (KGs). Aligning them is essential for knowledge grounding, evidence retrieval, and KG completion, yet existing methods do not explicitly align free-text evidence with KG triples. We present a unified framework for systematically studying design choices for aligning biomedical text and KGs. With a text encoder and a KG embedding model both frozen, we learn only a lightweight projection between their spaces via a contrastive objective. This enables a fair comparison across six design dimensions: text encoder, KG embedding model, projection head, triple composition, training direction, and hard-negatives sampling. We construct CTD-Align, a corpus of over 22K one-to-one tripledocument pairs linking chemical-gene interactions from the Comparative Toxicogenomics Database to supporting PubMed passages. We evaluate alignment on it in two retrieval settings: document-to-triple and triple-to-document. We find that the triple composition and the training direction (i.e., shared retrieval space) have the greatest impact, whereas the text encoder and hard-negatives sampling matter little. Overall, simple choices win: projecting text into the KG space with a linear head over concatenated subject, predicate, and object embeddings performs best. These findings establish lightweight contrastive alignment as an effective, practical foundation for bridging biomedical text and KGs.

cs.CL↗

arXiv2026

MultiGlobeQA: A Multilingual and Globally Diverse Benchmark for Geospatial Reasoning

Geospatial reasoning, i.e., computing distances, containment, and other spatial relations over real-world entities, is central to navigation and logistics, yet large language models (LLMs) struggle with the required geometric and topological computation despite storing considerable geographic knowledge. Existing benchmarks localize these failures only partially: they are synthetic or smallscale, largely monolingual, and offer limited control over geographic coverage. We introduce MultiGlobeQA, a multilingual benchmark of 46,060 question-answer pairs spanning 14 spatial-function families and 15 answer formats, with execution-based ground truth over three knowledge graphs. It covers 201 countries and territories via income- and density-stratified sampling, with parallel questions in English and 16 additional high- and low-resource languages. Across parametric, reasoning, and agentic settings, LLMs collapse on tasks requiring grid indexing and shape computation, while topological relations and directions fare best. Retrieval and tool use yield considerable gains, yet performance plateaus below two thirds even when gold facts are supplied, indicating that computation, not access to knowledge, is the bottleneck. Models also underperform on low-income regions, a gap that gold facts widen rather than close.

cs.CL↗

arXiv2026

Integrating Meta-Features with Knowledge Graph Embeddings for Meta-Learning

The vast collection of machine learning records available on the web presents a significant opportunity for meta-learning, where past experiments are leveraged to improve performance. Two crucial meta-learning tasks are pipeline performance estimation (PPE), which predicts pipeline performance on target datasets, and dataset performance-based similarity estimation (DPSE), which identifies datasets with similar performance patterns. Existing approaches primarily rely on dataset meta-features (e.g., number of instances, class entropy, etc.) to represent datasets numerically and approximate these meta-learning tasks. However, these approaches often overlook the wealth of past experimental results and pipeline metadata available. This limits their ability to capture dataset - pipeline interactions that reveal performance similarity patterns. In this work, we propose KGmetaSP, a knowledge-graph-embeddings approach that leverages existing experiment data to capture these interactions and improve both PPE and DPSE. We represent datasets and pipelines within a unified knowledge graph (KG) and derive embeddings that support pipeline-agnostic meta-models for PPE and distance-based retrieval for DPSE. To validate our approach, we construct a large-scale benchmark comprising 144,177 OpenML experiments, enabling a rich cross-dataset evaluation. KGmetaSP enables accurate PPE using a single pipeline-agnostic meta-model and improves DPSE over baselines. The proposed KGmetaSP, KG, and benchmark are released, establishing a new reference point for meta-learning and demonstrating how consolidating open experiment data into a unified KG advances the field.

cs.LG↗

arXiv2025

Improving Knowledge Graph Embeddings through Contrastive Learning with Negative Statements

Knowledge graphs represent information as structured triples and serve as the backbone for a wide range of applications, including question answering, link prediction, and recommendation systems. A prominent line of research for exploring knowledge graphs involves graph embedding methods, where entities and relations are represented in low-dimensional vector spaces that capture underlying semantics and structure. However, most existing methods rely on assumptions such as the Closed World Assumption or Local Closed World Assumption, treating missing triples as false. This contrasts with the Open World Assumption underlying many real-world knowledge graphs. Furthermore, while explicitly stated negative statements can help distinguish between false and unknown triples, they are rarely included in knowledge graphs and are often overlooked during embedding training. In this work, we introduce a novel approach that integrates explicitly declared negative statements into the knowledge embedding learning process. Our approach employs a dual-model architecture, where two embedding models are trained in parallel, one on positive statements and the other on negative statements. During training, each model generates negative samples by corrupting positive samples and selecting the most likely candidates as scored by the other model. The proposed approach is evaluated on both general-purpose and domain-specific knowledge graphs, with a focus on link prediction and triple classification tasks. The extensive experiments demonstrate that our approach improves predictive performance over state-of-the-art embedding models, demonstrating the value of integrating meaningful negative knowledge into embedding learning.

cs.LG↗

arXiv2025

Bio-KGvec2go: Serving up-to-date Dynamic Biomedical Knowledge Graph Embeddings

Knowledge graphs and ontologies represent entities and their relationships in a structured way, having gained significance in the development of modern AI applications. Integrating these semantic resources with machine learning models often relies on knowledge graph embedding models to transform graph data into numerical representations. Therefore, pre-trained models for popular knowledge graphs and ontologies are increasingly valuable, as they spare the need to retrain models for different tasks using the same data, thereby helping to democratize AI development and enabling sustainable computing. In this paper, we present Bio-KGvec2go, an extension of the KGvec2go Web API, designed to generate and serve knowledge graph embeddings for widely used biomedical ontologies. Given the dynamic nature of these ontologies, Bio-KGvec2go also supports regular updates aligned with ontology version releases. By offering up-to-date embeddings with minimal computational effort required from users, Bio-KGvec2go facilitates efficient and timely biomedical research.

cs.LG↗

arXiv2025

Knowledge Graph Completion for Action Prediction on Situational Graphs -- A Case Study on Household Tasks

Knowledge Graphs are used for various purposes, including business applications, biomedical analyses, or digital twins in industry 4.0. In this paper, we investigate knowledge graphs describing household actions, which are beneficial for controlling household robots and analyzing video footage. In the latter case, the information extracted from videos is notoriously incomplete, and completing the knowledge graph for enhancing the situational picture is essential. In this paper, we show that, while a standard link prediction problem, situational knowledge graphs have special characteristics that render many link prediction algorithms not fit for the job, and unable to outperform even simple baselines.

cs.AI↗

arXiv2025

ExeKGLib: A Platform for Machine Learning Analytics based on Knowledge Graphs

Nowadays machine learning (ML) practitioners have access to numerous ML libraries available online. Such libraries can be used to create ML pipelines that consist of a series of steps where each step may invoke up to several ML libraries that are used for various data-driven analytical tasks. Development of high-quality ML pipelines is non-trivial; it requires training, ML expertise, and careful development of each step. At the same time, domain experts in science and engineering may not possess such ML expertise and training while they are in pressing need of ML-based analytics. In this paper, we present our ExeKGLib, a Python library enhanced with a graphical interface layer that allows users with minimal ML knowledge to build ML pipelines. This is achieved by relying on knowledge graphs that encode ML knowledge in simple terms accessible to non-ML experts. ExeKGLib also allows improving the transparency and reusability of the built ML workflows and ensures that they are executable. We show the usability and usefulness of ExeKGLib by presenting real use cases.

cs.LG↗

arXiv2025

gpuRDF2vec -- Scalable GPU-based RDF2vec

Generating Knowledge Graph (KG) embeddings at web scale remains challenging. Among existing techniques, RDF2vec combines effectiveness with strong scalability. We present gpuRDF2vec, an open source library that harnesses modern GPUs and supports multi-node execution to accelerate every stage of the RDF2vec pipeline. Extensive experiments on both synthetically generated graphs and real-world benchmarks show that gpuRDF2vec achieves up to a substantial speedup over the currently fastest alternative, i.e., jRDF2vec. In a single-node setup, our walk-extraction phase alone outperforms pyRDF2vec, SparkKGML, and jRDF2vec by a substantial margin using random walks on large/ dense graphs, and scales very well to longer walks, which typically lead to better quality embeddings. Our implementation of gpuRDF2vec enables practitioners and researchers to train high-quality KG embeddings on large-scale graphs within practical time budgets and builds on top of Pytorch Lightning for the scalable word2vec implementation.

cs.AI↗

arXiv2025

Analysing semantic data storage in Distributed Ledger Technologies for Data Spaces

Data spaces are emerging as decentralised infrastructures that enable sovereign, secure, and trustworthy data exchange among multiple participants. To achieve semantic interoperability within these environments, the use of semantic web technologies and knowledge graphs has been proposed. Although distributed ledger technologies (DLT) fit as the underlying infrastructure for data spaces, there remains a significant gap in terms of the efficient storage of semantic data on these platforms. This paper presents a systematic evaluation of semantic data storage across different types of DLT (public, private, and hybrid), using a real-world knowledge graph as an experimental basis. The study compares performance, storage efficiency, resource consumption, and the capabilities to update and query semantic data. The results show that private DLTs are the most efficient for storing and managing semantic content, while hybrid DLTs offer a balanced trade-off between public auditability and operational efficiency. This research leads to a discussion on the selection of the most appropriate DLT infrastructure based on the data sovereignty requirements of decentralised data ecosystems.

cs.DC↗

arXiv2025

Walk&Retrieve: Simple Yet Effective Zero-shot Retrieval-Augmented Generation via Knowledge Graph Walks

Large Language Models (LLMs) have showcased impressive reasoning abilities, but often suffer from hallucinations or outdated knowledge. Knowledge Graph (KG)-based Retrieval-Augmented Generation (RAG) remedies these shortcomings by grounding LLM responses in structured external information from a knowledge base. However, many KG-based RAG approaches struggle with (i) aligning KG and textual representations, (ii) balancing retrieval accuracy and efficiency, and (iii) adapting to dynamically updated KGs. In this work, we introduce Walk&Retrieve, a simple yet effective KG-based framework that leverages walk-based graph traversal and knowledge verbalization for corpus generation for zero-shot RAG. Built around efficient KG walks, our method does not require fine-tuning on domain-specific data, enabling seamless adaptation to KG updates, reducing computational overhead, and allowing integration with any off-the-shelf backbone LLM. Despite its simplicity, Walk&Retrieve performs competitively, often outperforming existing RAG systems in response accuracy and hallucination reduction. Moreover, it demonstrates lower query latency and robust scalability to large KGs, highlighting the potential of lightweight retrieval strategies as strong baselines for future RAG research.

cs.IR↗

arXiv2025

GeoRDF2Vec Learning Location-Aware Entity Representations in Knowledge Graphs

Many knowledge graphs contain a substantial number of spatial entities, such as cities, buildings, and natural landmarks. For many of these entities, exact geometries are stored within the knowledge graphs. However, most existing approaches for learning entity representations do not take these geometries into account. In this paper, we introduce a variant of RDF2Vec that incorporates geometric information to learn location-aware embeddings of entities. Our approach expands different nodes by flooding the graph from geographic nodes, ensuring that each reachable node is considered. Based on the resulting flooded graph, we apply a modified version of RDF2Vec that biases graph walks using spatial weights. Through evaluations on multiple benchmark datasets, we demonstrate that our approach outperforms both non-location-aware RDF2Vec and GeoTransE.

cs.LG↗

arXiv2025

ReaLitE: Enrichment of Relation Embeddings in Knowledge Graphs using Numeric Literals

Most knowledge graph embedding (KGE) methods tailored for link prediction focus on the entities and relations in the graph, giving little attention to other literal values, which might encode important information. Therefore, some literal-aware KGE models attempt to either integrate numerical values into the embeddings of the entities or convert these numerics into entities during preprocessing, leading to information loss. Other methods concerned with creating relation-specific numerical features assume completeness of numerical data, which does not apply to real-world graphs. In this work, we propose ReaLitE, a novel relation-centric KGE model that dynamically aggregates and merges entities' numerical attributes with the embeddings of the connecting relations. ReaLitE is designed to complement existing conventional KGE methods while supporting multiple variations for numerical aggregations, including a learnable method. We comprehensively evaluated the proposed relation-centric embedding using several benchmarks for link prediction and node classification tasks. The results showed the superiority of ReaLitE over the state of the art in both tasks.

cs.LG↗

arXiv2025

Multi-dataset and Transfer Learning Using Gene Expression Knowledge Graphs

Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of disease pathology. Therefore, machine learning has been used to process gene expression data, with patient diagnosis emerging as one of the most popular applications. Although gene expression data can provide valuable insights, challenges arise because the number of patients in expression datasets is usually limited, and the data from different datasets with different gene expressions cannot be easily combined. This work proposes a novel methodology to address these challenges by integrating multiple gene expression datasets and domain-specific knowledge using knowledge graphs, a unique tool for biomedical data integration. Then, vector representations are produced using knowledge graph embedding techniques, which are used as inputs for a graph neural network and a multi-layer perceptron. We evaluate the efficacy of our methodology in three settings: single-dataset learning, multi-dataset learning, and transfer learning. The experimental results show that combining gene expression datasets and domain-specific knowledge improves patient diagnosis in all three settings.

cs.LG↗

arXiv2025

News Without Borders: Domain Adaptation of Multilingual Sentence Embeddings for Cross-lingual News Recommendation

Rapidly growing numbers of multilingual news consumers pose an increasing challenge to news recommender systems in terms of providing customized recommendations. First, existing neural news recommenders, even when powered by multilingual language models (LMs), suffer substantial performance losses in zero-shot cross-lingual transfer (ZS-XLT). Second, the current paradigm of fine-tuning the backbone LM of a neural recommender on task-specific data is computationally expensive and infeasible in few-shot recommendation and cold-start setups, where data is scarce or completely unavailable. In this work, we propose a news-adapted sentence encoder (NaSE), domain-specialized from a pretrained massively multilingual sentence encoder (SE). To this end, we construct and leverage PolyNews and PolyNewsParallel, two multilingual news-specific corpora. With the news-adapted multilingual SE in place, we test the effectiveness of (i.e., question the need for) supervised fine-tuning for news recommendation, and propose a simple and strong baseline based on (i) frozen NaSE embeddings and (ii) late click-behavior fusion. We show that NaSE achieves state-of-the-art performance in ZS-XLT in true cold-start and few-shot news recommendation.

cs.IR↗

arXiv2024

Peeling Back the Layers: An In-Depth Evaluation of Encoder Architectures in Neural News Recommenders

Encoder architectures play a pivotal role in neural news recommenders by embedding the semantic and contextual information of news and users. Thus, research has heavily focused on enhancing the representational capabilities of news and user encoders to improve recommender performance. Despite the significant impact of encoder architectures on the quality of news and user representations, existing analyses of encoder designs focus only on the overall downstream recommendation performance. This offers a one-sided assessment of the encoders' similarity, ignoring more nuanced differences in their behavior, and potentially resulting in sub-optimal model selection. In this work, we perform a comprehensive analysis of encoder architectures in neural news recommender systems. We systematically evaluate the most prominent news and user encoder architectures, focusing on their (i) representational similarity, measured with the Central Kernel Alignment, (ii) overlap of generated recommendation lists, quantified with the Jaccard similarity, and (iii) the overall recommendation performance. Our analysis reveals that the complexity of certain encoding techniques is often empirically unjustified, highlighting the potential for simpler, more efficient architectures. By isolating the effects of individual components, we provide valuable insights for researchers and practitioners to make better informed decisions about encoder selection and avoid unnecessary complexity in the design of news recommenders.

cs.IR↗

arXiv2024

Train Once, Use Flexibly: A Modular Framework for Multi-Aspect Neural News Recommendation

Recent neural news recommenders (NNRs) extend content-based recommendation (1) by aligning additional aspects (e.g., topic, sentiment) between candidate news and user history or (2) by diversifying recommendations w.r.t. these aspects. This customization is achieved by ``hardcoding`` additional constraints into the NNR's architecture and/or training objectives: any change in the desired recommendation behavior thus requires retraining the model with a modified objective. This impedes widespread adoption of multi-aspect news recommenders. In this work, we introduce MANNeR, a modular framework for multi-aspect neural news recommendation that supports on-the-fly customization over individual aspects at inference time. With metric-based learning as its backbone, MANNeR learns aspect-specialized news encoders and then flexibly and linearly combines the resulting aspect-specific similarity scores into different ranking functions, alleviating the need for ranking function-specific retraining of the model. Extensive experimental results show that MANNeR consistently outperforms state-of-the-art NNRs on both standard content-based recommendation and single- and multi-aspect customization. Lastly, we validate that MANNeR's aspect-customization module is robust to language and domain transfer.

cs.IR↗

arXiv2024

SnapE -- Training Snapshot Ensembles of Link Prediction Models

Snapshot ensembles have been widely used in various fields of prediction. They allow for training an ensemble of prediction models at the cost of training a single one. They are known to yield more robust predictions by creating a set of diverse base models. In this paper, we introduce an approach to transfer the idea of snapshot ensembles to link prediction models in knowledge graphs. Moreover, since link prediction in knowledge graphs is a setup without explicit negative examples, we propose a novel training loop that iteratively creates negative examples using previous snapshot models. An evaluation with four base models across four datasets shows that this approach constantly outperforms the single model approach, while keeping the training time constant.

cs.LG↗

arXiv2024

Do LLMs Really Adapt to Domains? An Ontology Learning Perspective

Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.

cs.CL↗