Background: Evidence synthesis facilitates evidence-based medicine. This task becomes increasingly difficult to accomplished with applying computational solutions, since the medical literature grows at astonishing rates. Objective: This study evaluates an information retrieval-driven workflow, CASMA, to enhance the efficiency, transparency, and reproducibility of systematic reviews. Endometriosis recurrence serves as the ideal case due to its complex and ambiguous literature. Methods: The hybrid approach integrates PRISMA guidelines with fuzzy matching and regular expression (regex) to facilitate semi-automated deduplication and filtered records before manual screening. The workflow synthesised evidence from randomised controlled trials on the efficacy of a subclass of gonadotropin-releasing hormone agonists (GnRH-a). A modified splitting method addressed unit-of-analysis errors in multi-arm trials. Results: The workflow sharply reduced the screening workload, taking only 11 days to fetch and filter 33,444 records. Seven eligible RCTs were synthesized (841 patients). The pooled random-effects model yielded a Risk Ratio (RR) of $0.64$ ($95\%$ CI $0.48$ to $0.86$), demonstrating a $36\%$ reduction in recurrence, with non-significant heterogeneity ($I^2=0.00\%$, $τ^2=0.00$). The findings were robust and stable, as they were backed by sensitivity analyses. Conclusion: This study demonstrates an application of an information-retrieval-driven workflow for medical evidence synthesis. The approach yields valuable clinical results and a generalisable framework to scale up the evidence synthesis, bridging the gap between clinical research and computer science.

Relation extraction between drugs plays a crucial role in identifying drug drug interactions and predicting side effects. The advancement of machine learning methods in relation extraction, along with the development of large medical text databases, has enabled the low cost extraction of such relations compared to other approaches that typically require expert knowledge. However, to the best of our knowledge, there are limited datasets specifically designed for drug drug relation extraction currently available. Therefore, employing transfer learning becomes necessary to apply machine learning methods in this domain. In this study, we propose DREAM, a method that first employs a trained relation extraction model to discover relations between entities and then applies this model to a corpus of medical texts to construct an ontology of drug relationships. The extracted relations are subsequently validated using a large language model. Quantitative results indicate that the LLM agreed with 71 of the relations extracted from a subset of PubMed abstracts. Furthermore, our qualitative analysis indicates that this approach can uncover ambiguities in the medical domain, highlighting the challenges inherent in relation extraction in this field.

Constructing comprehensive knowledge graphs requires the use of multiple ontologies in order to fully contextualize data into a domain. Ontology matching finds equivalences between concepts interconnecting ontologies and creating a cohesive semantic layer. While the simple pairwise state of the art is well established, simple equivalence mappings cannot provide full semantic integration of related but disjoint ontologies. Complex multi-ontology matching (CMOM) aligns one source entity to composite logical expressions of multiple target entities, establishing more nuanced equivalences and provenance along the ontological hierarchy. We present CMOMgen, the first end-to-end CMOM strategy that generates complete and semantically sound mappings, without establishing any restrictions on the number of target ontologies or entities. Retrieval-Augmented Generation selects relevant classes to compose the mapping and filters matching reference mappings to serve as examples, enhancing In-Context Learning. The strategy was evaluated in three biomedical tasks with partial reference alignments. CMOMgen outperforms baselines in class selection, demonstrating the impact of having a dedicated strategy. Our strategy also achieves a minimum of 63% in F1-score, outperforming all baselines and ablated versions in two out of three tasks and placing second in the third. Furthermore, a manual evaluation of non-reference mappings showed that 46% of the mappings achieve the maximum score, further substantiating its ability to construct semantically sound mappings.

Evaluating competing systems in a comparable way, i.e., benchmarking them, is an undeniable pillar of the scientific method. However, system performance is often summarized via a small number of metrics. The analysis of the evaluation details and the derivation of insights for further development or use remains a tedious manual task with often biased results. Thus, this paper argues for a new type of benchmarking, which is dubbed explainable benchmarking. The aim of explainable benchmarking approaches is to automatically generate explanations for the performance of systems in a benchmark. We provide a first instantiation of this paradigm for knowledge-graph-based question answering systems. We compute explanations by using a novel concept learning approach developed for large knowledge graphs called PruneCEL. Our evaluation shows that PruneCEL outperforms state-of-the-art concept learners on the task of explainable benchmarking by up to 0.55 points F1 measure. A task-driven user study with 41 participants shows that in 80\% of the cases, the majority of participants can accurately predict the behavior of a system based on our explanations. Our code and data are available at https://github.com/dice-group/PruneCEL/tree/K-cap2025

Timeseries foundation models (TSFMs) have multiplied, yet lightweight supervised baselines and even classical models often match them. We argue this gap stems from the naive importation of NLP or CV pipelines. In language and vision, large web-scale corpora densely capture human concepts i.e. there are countless images and text of apples. In contrast, timeseries data is built to complement the image and text modalities. There are no timeseries dataset that contains the concept apple. As a result, the scrape-everything-online paradigm fails for TS. We posit that progress demands a shift from opportunistic aggregation to principled design: constructing datasets that systematically span the space of invariance that preserve temporal semantics. To this end, we suggest that the ontology of timeseries invariances should be built based on first principles. Only by ensuring representational completeness through invariance coverage can TSFMs achieve the aligned structure necessary for generalisation, reasoning, and truly emergent behaviour.

A formalization of a subject-event ontology is proposed for modeling complex dynamic systems without reliance on global time. Key principles: (1) event as an act of fixation - a subject discerns and fixes changes according to models (conceptual templates) available to them; (2) causal order via happens-before - the order of events is defined by explicit dependencies, not timestamps; (3) making the ontology executable via a declarative dataflow mechanism, ensuring determinism; (4) models as epistemic filters - a subject can only fix what falls under its known concepts and properties; (5) presumption of truth - the declarative content of an event is available for computation from the moment of fixation, without external verification. The formalization includes nine axioms (A1-A9), ensuring the correctness of executable ontologies: monotonicity of history (I1), acyclicity of causality (I2), traceability (I3). Special attention is given to the model-based approach (A9): event validation via schemas, actor authorization, automatic construction of causal chains (W3) without global time. Practical applicability is demonstrated on the boldsea system - a workflow engine for executable ontologies, where the theoretical constructs are implemented in BSL (Boldsea Semantic Language). The formalization is applicable to distributed systems, microservice architectures, DLT platforms, and multiperspectivity scenarios (conflicting facts from different subjects).

Large Language Models (LLMs) have been extensively adopted in Knowledge Graph Completion (KGC), showcasing significant research advancements. However, as black-box models driven by deep neural architectures, current LLM-based KGC methods rely on implicit knowledge representation with parallel propagation of erroneous knowledge, thereby hindering their ability to produce conclusive and decisive reasoning outcomes. We aim to integrate neural-perceptual structural information with ontological knowledge, leveraging the powerful capabilities of LLMs to achieve a deeper understanding of the intrinsic logic of the knowledge. We propose an ontology enhanced KGC method using LLMs -- OL-KGC. It first leverages neural perceptual mechanisms to effectively embed structural information into the textual space, and then uses an automated extraction algorithm to retrieve ontological knowledge from the knowledge graphs (KGs) that needs to be completed, which is further transformed into a textual format comprehensible to LLMs for providing logic guidance. We conducted extensive experiments on three widely-used benchmarks -- FB15K-237, UMLS and WN18RR. The experimental results demonstrate that OL-KGC significantly outperforms existing mainstream KGC methods across multiple evaluation metrics, achieving state-of-the-art performance.

Traditional knowledge graphs are constrained by fixed ontologies that organize concepts within rigid hierarchical structures. The root cause lies in treating domains as implicit context rather than as explicit, reasoning-level components. To overcome these limitations, we propose the Domain-Contextualized Concept Graph (CDC), a novel knowledge modeling framework that elevates domains to first-class elements of conceptual representation. CDC adopts a C-D-C triple structure - - where domain specifications serve as dynamic classification dimensions defined on demand. Grounded in a cognitive-linguistic isomorphic mapping principle, CDC operationalizes how humans understand concepts through contextual frames. We formalize more than twenty standardized relation predicates (structural, logical, cross-domain, and temporal) and implement CDC in Prolog for full inference capability. Case studies in education, enterprise knowledge systems, and technical documentation demonstrate that CDC enables context-aware reasoning, cross-domain analogy, and personalized knowledge modeling - capabilities unattainable under traditional ontology-based frameworks.

An essential component for evaluating and comparing physical and cognitive capabilities between populations is the testing of various factors related to human performance. As a core part of sports science research, testing motor performance enables the analysis of the physical health of different demographic groups and makes them comparable. The Motor Research (MO|RE) data repository, developed at the Karlsruhe Institute of Technology, is an infrastructure for publishing and archiving research data in sports science, particularly in the field of motor performance research. In this paper, we present our vision for creating a knowledge graph from MO|RE data. With an ontology rooted in the Basic Formal Ontology, our approach centers on formally representing the interrelation of plan specifications, specific processes, and related measurements. Our goal is to transform how motor performance data are modeled and shared across studies, making it standardized and machine-understandable. The idea presented here is developed within the Leibniz Science Campus ``Digital Transformation of Research'' (DiTraRe).

Context: Modern Systems of Systems (SoSs) increasingly operate in dynamic environments (e.g., smart cities, autonomous vehicles) where runtime composition -- the on-the-fly discovery, integration, and coordination of constituent systems (CSs)--is crucial for adaptability. Despite growing interest, the literature lacks a cohesive synthesis of runtime composition in dynamic SoSs. Objective: This study synthesizes research on runtime composition in dynamic SoSs and identifies core challenges, solution strategies, supporting tools, and evaluation methods. Methods: We conducted a Systematic Literature Review (SLR), screening 1,774 studies published between 2019 and 2024 and selecting 80 primary studies for thematic analysis (TA). Results: Challenges fall into four categories: modeling and analysis, resilient operations, system orchestration, and heterogeneity of CSs. Solutions span seven areas: co-simulation and digital twins, semantic ontologies, integration frameworks, adaptive architectures, middleware, formal methods, and AI-driven resilience. Service-oriented frameworks for composition and integration dominate tooling, while simulation platforms support evaluation. Interoperability across tools, limited cross-toolchain workflows, and the absence of standardized benchmarks remain key gaps. Evaluation approaches include simulation-based, implementation-driven, and human-centered studies, which have been applied in domains such as smart cities, healthcare, defense, and industrial automation. Conclusions: The synthesis reveals tensions, including autonomy versus coordination, the modeling-reality gap, and socio-technical integration. It calls for standardized evaluation metrics, scalable decentralized architectures, and cross-domain frameworks. The analysis aims to guide researchers and practitioners in developing and implementing dynamically composable SoSs.