Recent advances in natural language processing (NLP) owe their success to pre-training language models on large amounts of unstructured data. Still, there is an increasing effort to combine the unstructured nature of LMs with structured knowledge and reasoning. Particularly in the rapidly evolving field of biomedical NLP, knowledge-enhanced language models (KELMs) have emerged as promising tools to bridge the gap between large language models and domain-specific knowledge, considering the available biomedical knowledge graphs (KGs) curated by experts over the decades. In this paper, we develop an approach that uses lightweight adapter modules to inject structured biomedical knowledge into pre-trained language models (PLMs). We use two large KGs, the biomedical knowledge system UMLS and the novel biochemical ontology OntoChem, with two prominent biomedical PLMs, PubMedBERT and BioLinkBERT. The approach includes partitioning knowledge graphs into smaller subgraphs, fine-tuning adapter modules for each subgraph, and combining the knowledge in a fusion layer. We test the performance on three downstream tasks: document classification,question answering, and natural language inference. We show that our methodology leads to performance improvements in several instances while keeping requirements in computing power low. Finally, we provide a detailed interpretation of the results and report valuable insights for future work.

The escalating complexity of modern computing frameworks has resulted in a surge in the cybersecurity vulnerabilities reported to the National Vulnerability Database (NVD) by practitioners. Despite the fact that the stature of NVD is one of the most significant databases for the latest insights into vulnerabilities, extracting meaningful trends from such a large amount of unstructured data is still challenging without the application of suitable technological methodologies. Previous efforts have mostly concentrated on software vulnerabilities; however, a holistic strategy incorporates approaches for mitigating vulnerabilities, score prediction, and a knowledge-generating system that may extract relevant insights from the Common Weakness Enumeration (CWE) and Common Vulnerability Exchange (CVE) databases is notably absent. As the number of hardware attacks on Internet of Things (IoT) devices continues to rapidly increase, we present the Hardware Vulnerability to Weakness Mapping (HW-V2W-Map) Framework, which is a Machine Learning (ML) framework focusing on hardware vulnerabilities and IoT security. The architecture that we have proposed incorporates an Ontology-driven Storytelling framework, which automates the process of updating the ontology in order to recognize patterns and evolution of vulnerabilities over time and provides approaches for mitigating the vulnerabilities. The repercussions of vulnerabilities can be mitigated as a result of this, and conversely, future exposures can be predicted and prevented. Furthermore, our proposed framework utilized Generative Pre-trained Transformer (GPT) Large Language Models (LLMs) to provide mitigation suggestions.

The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.

Materialisation facilitates Datalog reasoning by precomputing all consequences of the facts and the rules so that queries can be directly answered over the materialised facts. However, storing all materialised facts may be infeasible in practice, especially when the rules are complex and the given set of facts is large. We observe that for certain combinations of rules, there exist data structures that compactly represent the reasoning result and can be efficiently queried when necessary. In this paper, we present a general framework that allows for the integration of such optimised storage schemes with standard materialisation algorithms. Moreover, we devise optimised storage schemes targeting at transitive rules and union rules, two types of (combination of) rules that commonly occur in practice. Our experimental evaluation shows that our approach significantly improves memory consumption, sometimes by orders of magnitude, while remaining competitive in terms of query answering time.

This paper proposes an approach to build 3D scene graphs in arbitrary (indoor and outdoor) environments. Such extension is challenging; the hierarchy of concepts that describe an outdoor environment is more complex than for indoors, and manually defining such hierarchy is time-consuming and does not scale. Furthermore, the lack of training data prevents the straightforward application of learning-based tools used in indoor settings. To address these challenges, we propose two novel extensions. First, we develop methods to build a spatial ontology defining concepts and relations relevant for indoor and outdoor robot operation. In particular, we use a Large Language Model (LLM) to build such an ontology, thus largely reducing the amount of manual effort required. Second, we leverage the spatial ontology for 3D scene graph construction using Logic Tensor Networks (LTN) to add logical rules, or axioms (e.g., "a beach contains sand"), which provide additional supervisory signals at training time thus reducing the need for labelled data, providing better predictions, and even allowing predicting concepts unseen at training time. We test our approach in a variety of datasets, including indoor, rural, and coastal environments, and show that it leads to a significant increase in the quality of the 3D scene graph generation with sparsely annotated data.

Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources, necessitating substantial collaborative efforts of domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). This method can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies, as well as unstructured textual sources. We assessed DRAGON-AI across ten diverse ontologies, making use of extensive manual evaluation of results. We demonstrate high precision for relationship generation, close to but lower than precision from logic-based reasoning. We also demonstrate definition generation comparable with but lower than human-generated definitions. Notably, expert evaluators were better able to discern subtle flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues. These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.

In this paper, we introduce the problem of rewriting finite formal languages using syntactic macros such that the rewriting is minimal in size. We present polynomial-time algorithms to solve variants of this problem and show their correctness. To demonstrate the practical relevance of the proposed problems and the feasibility and effectiveness of our algorithms in practice, we apply these to biomedical ontologies authored in OWL. We find that such rewritings can significantly reduce the size of ontologies by capturing repeated expressions with macros. In addition to offering valuable assistance in enhancing ontology quality and comprehension, the presented approach introduces a systematic way of analysing and evaluating features of rewriting systems (including syntactic macros, templates, or other forms of rewriting rules) in terms of their influence on computational problems.

Knowledge graph embedding models (KGEMs) developed for link prediction learn vector representations for graph entities, known as embeddings. A common tacit assumption is the KGE entity similarity assumption, which states that these KGEMs retain the graph's structure within their embedding space, i.e., position similar entities close to one another. This desirable property make KGEMs widely used in downstream tasks such as recommender systems or drug repurposing. Yet, the alignment of graph similarity with embedding space similarity has rarely been formally evaluated. Typically, KGEMs are assessed based on their sole link prediction capabilities, using ranked-based metrics such as Hits@K or Mean Rank. This paper challenges the prevailing assumption that entity similarity in the graph is inherently mirrored in the embedding space. Therefore, we conduct extensive experiments to measure the capability of KGEMs to cluster similar entities together, and investigate the nature of the underlying factors. Moreover, we study if different KGEMs expose a different notion of similarity. Datasets, pre-trained embeddings and code are available at: https://github.com/nicolas-hbt/similar-embeddings.

Trajectory prediction in traffic scenes involves accurately forecasting the behaviour of surrounding vehicles. To achieve this objective it is crucial to consider contextual information, including the driving path of vehicles, road topology, lane dividers, and traffic rules. Although studies demonstrated the potential of leveraging heterogeneous context for improving trajectory prediction, state-of-the-art deep learning approaches still rely on a limited subset of this information. This is mainly due to the limited availability of comprehensive representations. This paper presents an approach that utilizes knowledge graphs to model the diverse entities and their semantic connections within traffic scenes. Further, we present nuScenes Knowledge Graph (nSKG), a knowledge graph for the nuScenes dataset, that models explicitly all scene participants and road elements, as well as their semantic and spatial relationships. To facilitate the usage of the nSKG via graph neural networks for trajectory prediction, we provide the data in a format, ready-to-use by the PyG library. All artefacts can be found here: https://github.com/boschresearch/nuScenes_Knowledge_Graph

In research of manufacturing systems and autonomous robots, the term capability is used for a machine-interpretable specification of a system function. Approaches in this research area develop information models that capture all information relevant to interpret the requirements, effects and behavior of functions. These approaches are intended to overcome the heterogeneity resulting from the various types of processes and from the large number of different vendors. However, these models and associated methods do not offer solutions for automated process planning, i.e. finding a sequence of individual capabilities required to manufacture a certain product or to accomplish a mission using autonomous robots. Instead, this is a typical task for AI planning approaches, which unfortunately require a high effort to create the respective planning problem descriptions. In this paper, we present an approach that combines these two topics: Starting from a semantic capability model, an AI planning problem is automatically generated. The planning problem is encoded using Satisfiability Modulo Theories and uses an existing solver to find valid capability sequences including required parameter values. The approach also offers possibilities to integrate existing human expertise and to provide explanations for human operators in order to help understand planning decisions.