As the immense opportunities enabled by large language models become more apparent, NLP systems will be increasingly expected to excel in real-world settings. However, in many instances, powerful models alone will not yield translational NLP solutions, especially if the formulated problem is not well aligned with the real-world task. In this work, we study the case of UMLS vocabulary insertion, an important real-world task in which hundreds of thousands of new terms, referred to as atoms, are added to the UMLS, one of the most comprehensive open-source biomedical knowledge bases. Previous work aimed to develop an automated NLP system to make this time-consuming, costly, and error-prone task more efficient. Nevertheless, practical progress in this direction has been difficult to achieve due to a problem formulation and evaluation gap between research output and the real-world task. In order to address this gap, we introduce a new formulation for UMLS vocabulary insertion which mirrors the real-world task, datasets which faithfully represent it and several strong baselines we developed through re-purposing existing solutions. Additionally, we propose an effective rule-enhanced biomedical language model which enables important new model behavior, outperforms all strong baselines and provides measurable qualitative improvements to editors who carry out the UVI task. We hope this case study provides insight into the considerable importance of problem formulation for the success of translational NLP solutions.

Individuals and organizations cope with an always-growing amount of data, which is heterogeneous in its contents and formats. An adequate data management process yielding data quality and control over its lifecycle is a prerequisite to getting value out of this data and minimizing inherent risks related to multiple usages. Common data governance frameworks rely on people, policies, and processes that fall short of the overwhelming complexity of data. Yet, harnessing this complexity is necessary to achieve high-quality standards. The latter will condition any downstream data usage outcome, including generative artificial intelligence trained on this data. In this paper, we report our concrete experience establishing a simple, cost-efficient framework that enables metadata-driven, agile and (semi-)automated data governance (i.e. Data Governance 4.0). We explain how we implement and use this framework to integrate 25 years of clinical study data at an enterprise scale in a fully productive environment. The framework encompasses both methodologies and technologies leveraging semantic web principles. We built a knowledge graph describing avatars of data assets in their business context, including governance principles. Multiple ontologies articulated by an enterprise upper ontology enable key governance actions such as FAIRification, lifecycle management, definition of roles and responsibilities, lineage across transformations and provenance from source systems. This metadata model is the keystone to data governance 4.0: a semi-automatised data management process that considers the business context in an agile manner to adapt governance constraints to each use case and dynamically tune it based on business changes.

One of the significant barriers to the training of statistical models on knowledge graphs is the difficulty that scientists have in finding the best input data to address their prediction goal. In addition to this, a key challenge is to determine how to manipulate these relational data, which are often in the form of particular triples (i.e., subject, predicate, object), to enable the learning process. Currently, many high-quality catalogs of knowledge graphs, are available. However, their primary goal is the re-usability of these resources, and their interconnection, in the context of the Semantic Web. This paper describes the LiveSchema initiative, namely, a first version of a gateway that has the main scope of leveraging the gold mine of data collected by many existing catalogs collecting relational data like ontologies and knowledge graphs. At the current state, LiveSchema contains - 1000 datasets from 4 main sources and offers some key facilities, which allow to: i) evolving LiveSchema, by aggregating other source catalogs and repositories as input sources; ii) querying all the collected resources; iii) transforming each given dataset into formal concept analysis matrices that enable analysis and visualization services; iv) generating models and tensors from each given dataset.

The availability of representative datasets is an essential prerequisite for many successful artificial intelligence and machine learning models. However, in real life applications these models often encounter scenarios that are inadequately represented in the data used for training. There are various reasons for the absence of sufficient data, ranging from time and cost constraints to ethical considerations. As a consequence, the reliable usage of these models, especially in safety-critical applications, is still a tremendous challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches. Knowledge augmented machine learning approaches offer the possibility of compensating for deficiencies, errors, or ambiguities in the data, thus increasing the generalization capability of the applied models. Even more, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-driven models with existing knowledge. The identified approaches are structured according to the categories knowledge integration, extraction and conformity. In particular, we address the application of the presented methods in the field of autonomous driving.

Recent years witnessed a rising interest towards Datalog-based ontological reasoning systems, both in academia and industry. These systems adopt languages, often shared under the collective name of Datalog$+/-$, that extend Datalog with the essential feature of existential quantification, while introducing syntactic limitations to sustain reasoning decidability and achieve a good trade-off between expressive power and computational complexity. From an implementation perspective, modern reasoners borrow the vast experience of the database community in developing streaming-based data processing systems, such as volcano-iterator architectures, that sustain a limited memory footprint and good scalability. In this paper, we focus on two extremely promising, expressive, and tractable languages, namely, Shy and Warded Datalog$+/-$. We leverage their theoretical underpinnings to introduce novel reasoning techniques, technically, "chase variants", that are particularly fit for efficient reasoning in streaming-based architectures. We then implement them in Vadalog, our reference streaming-based engine, to efficiently solve ontological reasoning tasks over real-world settings.

We explore developing rich semantic models of systems. Specifically, we consider structured causal explanations about state changes in those systems. Essentially, we are developing process-based dynamic knowledge graphs. As an example, we construct a model of the causal threads for geological changes proposed by the Snowball Earth theory. Further, we describe an early prototype of a graphical interface to present the explanations. Unlike statistical approaches to summarization and explanation such as Large Language Models (LLMs), our approach of direct representation can be inspected and verified directly.

Domain experts often rely on most recent knowledge for apprehending and disseminating specific biological processes that help them design strategies for developing prevention and therapeutic decision-making in various disease scenarios. A challenging scenarios for artificial intelligence (AI) is using biomedical data (e.g., texts, imaging, omics, and clinical) to provide diagnosis and treatment recommendations for cancerous conditions.~Data and knowledge about biomedical entities like cancer, drugs, genes, proteins, and their mechanism is spread across structured (knowledge bases (KBs)) and unstructured (e.g., scientific articles) sources. A large-scale knowledge graph (KG) can be constructed by integrating and extracting facts about semantically interrelated entities and relations. Such a KG not only allows exploration and question answering (QA) but also enables domain experts to deduce new knowledge. However, exploring and querying large-scale KGs is tedious for non-domain users due to their lack of understanding of the data assets and semantic technologies. In this paper, we develop a domain KG to leverage cancer-specific biomarker discovery and interactive QA. For this, we constructed a domain ontology called OncoNet Ontology (ONO), which enables semantic reasoning for validating gene-disease (different types of cancer) relations. The KG is further enriched by harmonizing the ONO, metadata, controlled vocabularies, and biomedical concepts from scientific articles by employing BioBERT- and SciBERT-based information extractors. Further, since the biomedical domain is evolving, where new findings often replace old ones, without having access to up-to-date scientific findings, there is a high chance an AI system exhibits concept drift while providing diagnosis and treatment. Therefore, we fine-tune the KG using large language models (LLMs) based on more recent articles and KBs.

Automated driving vehicles~(ADV) promise to enhance driving efficiency and safety, yet they face intricate challenges in safety-critical scenarios. As a result, validating ADV within generated safety-critical scenarios is essential for both development and performance evaluations. This paper investigates the complexities of employing two major scenario-generation solutions: data-driven and knowledge-driven methods. Data-driven methods derive scenarios from recorded datasets, efficiently generating scenarios by altering the existing behavior or trajectories of traffic participants but often falling short in considering ADV perception; knowledge-driven methods provide effective coverage through expert-designed rules, but they may lead to inefficiency in generating safety-critical scenarios within that coverage. To overcome these challenges, we introduce BridgeGen, a safety-critical scenario generation framework, designed to bridge the benefits of both methodologies. Specifically, by utilizing ontology-based techniques, BridgeGen models the five scenario layers in the operational design domain (ODD) from knowledge-driven methods, ensuring broad coverage, and incorporating data-driven strategies to efficiently generate safety-critical scenarios. An optimized scenario generation toolkit is developed within BridgeGen. This expedites the crafting of safety-critical scenarios through a combination of traditional optimization and reinforcement learning schemes. Extensive experiments conducted using Carla simulator demonstrate the effectiveness of BridgeGen in generating diverse safety-critical scenarios.

Coding of unstructured clinical free-text to produce interoperable structured data is essential to improve direct care, support clinical communication and to enable clinical research.However, manual clinical coding is difficult and time consuming, which motivates the development and use of natural language processing for automated coding. This work evaluates the quality and consistency of both manual and automated clinical coding of diagnoses from hospital outpatient letters. Using 100 randomly selected letters, two human clinicians performed coding of diagnosis lists to SNOMED CT. Automated coding was also performed using IMO's Concept Tagger. A gold standard was constructed by a panel of clinicians from a subset of the annotated diagnoses. This was used to evaluate the quality and consistency of both manual and automated coding via (1) a distance-based metric, treating SNOMED CT as a graph, and (2) a qualitative metric agreed upon by the panel of clinicians. Correlation between the two metrics was also evaluated. Comparing human and computer-generated codes to the gold standard, the results indicate that humans slightly out-performed automated coding, while both performed notably better when there was only a single diagnosis contained in the free-text description. Automated coding was considered acceptable by the panel of clinicians in approximately 90% of cases.

Since ChatGPT offers detailed responses without justifications, and erroneous facts even for popular persons, events and places, in this paper we present a novel pipeline that retrieves the response of ChatGPT in RDF and tries to validate the ChatGPT facts using one or more RDF Knowledge Graphs (KGs). To this end we leverage DBpedia and LODsyndesis (an aggregated Knowledge Graph that contains 2 billion triples from 400 RDF KGs of many domains) and short sentence embeddings, and introduce an algorithm that returns the more relevant triple(s) accompanied by their provenance and a confidence score. This enables the validation of ChatGPT responses and their enrichment with justifications and provenance. To evaluate this service (such services in general), we create an evaluation benchmark that includes 2,000 ChatGPT facts; specifically 1,000 facts for famous Greek Persons, 500 facts for popular Greek Places, and 500 facts for Events related to Greece. The facts were manually labelled (approximately 73% of ChatGPT facts were correct and 27% of facts were erroneous). The results are promising; indicatively for the whole benchmark, we managed to verify the 85.3% of the correct facts of ChatGPT and to find the correct answer for the 58% of the erroneous ChatGPT facts.