Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psychological CIH approaches in standard terminologies. We also intended to apply advanced Natural Language Processing (NLP) models such as Bidirectional Encoder Representations from Transformers (BERT) and GPT-3.5 Turbo for CIH named entity recognition, evaluating their performance against established models like MetaMap and CLAMP. Materials and Methods: We constructed the CIHLex by integrating various resources, compiling and integrating data from biomedical literature and relevant knowledge bases. The Lexicon encompasses 198 unique concepts with 1090 corresponding unique terms. We matched these concepts to the Unified Medical Language System (UMLS). Additionally, we developed and utilized BERT models and compared their efficiency in CIH named entity recognition to that of other models such as MetaMap, CLAMP, and GPT3.5-turbo. Results: From the 198 unique concepts in CIHLex, 62.1% could be matched to at least one term in the UMLS. Moreover, 75.7% of the mapped UMLS Concept Unique Identifiers (CUIs) were categorized as "Therapeutic or Preventive Procedure." Among the models applied to CIH named entity recognition, BLUEBERT delivered the highest macro average F1-score of 0.90, surpassing other models. Conclusion: Our CIHLex significantly augments representation of CIH approaches in biomedical literature. Demonstrating the utility of advanced NLP models, BERT notably excelled in CIH entity recognition. These results highlight promising strategies for enhancing standardization and recognition of CIH terminology in biomedical contexts.

Objective: To create a commons for infectious disease (ID) epidemiology in which epidemiologists, public health officers, data producers, and software developers can not only share data and software, but receive assistance in improving their interoperability. Materials and Methods: We represented 586 datasets, 54 software, and 24 data formats in OWL 2 and then used logical queries to infer potentially interoperable combinations of software and datasets, as well as statistics about the FAIRness of the collection. We represented the objects in DATS 2.2 and a software metadata schema of our own design. We used these representations as the basis for the Content, Search, FAIR-o-meter, and Workflow pages that constitute the MIDAS Digital Commons. Results: Interoperability was limited by lack of standardization of input and output formats of software. When formats existed, they were human-readable specifications (22/24; 92%); only 3 formats (13%) had machine-readable specifications. Nevertheless, logical search of a triple store based on named data formats was able to identify scores of potentially interoperable combinations of software and datasets. Discussion: We improved the findability and availability of a sample of software and datasets and developed metrics for assessing interoperability. The barriers to interoperability included poor documentation of software input/output formats and little attention to standardization of most types of data in this field. Conclusion: Centralizing and formalizing the representation of digital objects within a commons promotes FAIRness, enables its measurement over time and the identification of potentially interoperable combinations of data and software.

Ontologies play a crucial role in organizing and representing knowledge. However, even current ontologies do not encompass all relevant concepts and relationships. Here, we explore the potential of large language models (LLM) to expand an existing ontology in a semi-automated fashion. We demonstrate our approach on the biomedical ontology SNOMED-CT utilizing semantic relation types from the widely used UMLS semantic network. We propose a method that uses conversational interactions with an LLM to analyze clinical practice guidelines (CPGs) and detect the relationships among the new medical concepts that are not present in SNOMED-CT. Our initial experimentation with the conversational prompts yielded promising preliminary results given a manually generated gold standard, directing our future potential improvements.

It is commonly known that the conjunctive query entailment problem for certain extensions of (the well-known ontology language) ALC is computationally harder than their knowledge base satisfiability problem while for others the complexities coincide, both under the standard and the finite-model semantics. We expose a uniform principle behind this divide by identifying a wide class of (finitely) locally-forward description logics, for which we prove that (finite) query entailment problem can be solved by a reduction to exponentially many calls of the (finite) knowledge base satisfiability problem. Consequently, our algorithm yields tight ExpTime upper bounds for locally-forward logics with ExpTime-complete knowledge base satisfiability problem, including logics between ALC and µALCHbregQ (and more), as well as ALCSCC with global cardinality constraints, for which the complexity of querying remained open. Moreover, to make our technique applicable in future research, we provide easy-to-check sufficient conditions for a logic to be locally-forward based several versions of the on model-theoretic notion of unravellings. Together with existing results, this provides a nearly complete classification of the “benign” vs. “malign” primitive modelling features extending ALC, missing out only the Self operator. We then show a rather counter-intuitive result, namely that the conjunctive entailment problem for ALCSelf is exponentially harder than for ALC. This places the seemingly innocuous Self operator among the “malign” modelling features, like inverses, transitivity or nominals.

This study aims to comprehend linguistic and socio-demographic features, encompassing English language styles, conveyed sentiments, and lexical diversity within spatial online social media review data. To this end, we undertake a case study that scrutinizes reviews composed by two distinct and demographically diverse groups. Our analysis entails the extraction and examination of various statistical, grammatical, and sentimental features from these two groups. Subsequently, we leverage these features with machine learning (ML) classifiers to discern their potential in effectively differentiating between the groups. Our investigation unveils substantial disparities in certain linguistic attributes between the two groups. When integrated into ML classifiers, these attributes exhibit a marked efficacy in distinguishing the groups, yielding a macro F1 score of approximately 0.85. Furthermore, we conduct a comparative evaluation of these linguistic features with word n-gram-based lexical features in discerning demographically diverse review data. As expected, the n-gram lexical features, coupled with fine-tuned transformer-based models, show superior performance, attaining accuracies surpassing 95\% and macro F1 scores exceeding 0.96. Our meticulous analysis and comprehensive evaluations substantiate the efficacy of linguistic and sentimental features in effectively discerning demographically diverse review data. The findings of this study provide valuable guidelines for future research endeavors concerning the analysis of demographic patterns in textual content across various social media platforms.

Manual ontology construction takes time, resources, and domain specialists. Supporting a component of this process for automation or semi-automation would be good. This project and dissertation provide a Formal Concept Analysis and WordNet framework for learning concept hierarchies from free texts. The process has steps. First, the document is Part-Of-Speech labeled, then parsed to produce sentence parse trees. Verb/noun dependencies are derived from parse trees next. After lemmatizing, pruning, and filtering the word pairings, the formal context is created. The formal context may contain some erroneous and uninteresting pairs because the parser output may be erroneous, not all derived pairs are interesting, and it may be large due to constructing it from a large free text corpus. Deriving lattice from the formal context may take longer, depending on the size and complexity of the data. Thus, decreasing formal context may eliminate erroneous and uninteresting pairs and speed up idea lattice derivation. WordNet-based and Frequency-based approaches are tested. Finally, we compute formal idea lattice and create a classical concept hierarchy. The reduced concept lattice is compared to the original to evaluate the outcomes. Despite several system constraints and component discrepancies that may prevent logical conclusion, the following data imply idea hierarchies in this project and dissertation are promising. First, the reduced idea lattice and original concept have commonalities. Second, alternative language or statistical methods can reduce formal context size. Finally, WordNet-based and Frequency-based approaches reduce formal context differently, and the order of applying them is examined to reduce context efficiently.

Clinicians are increasingly looking towards machine learning to gain insights about patient evolutions. We propose a novel approach named Multi-Modal UMLS Graph Learning (MMUGL) for learning meaningful representations of medical concepts using graph neural networks over knowledge graphs based on the unified medical language system. These representations are aggregated to represent entire patient visits and then fed into a sequence model to perform predictions at the granularity of multiple hospital visits of a patient. We improve performance by incorporating prior medical knowledge and considering multiple modalities. We compare our method to existing architectures proposed to learn representations at different granularities on the MIMIC-III dataset and show that our approach outperforms these methods. The results demonstrate the significance of multi-modal medical concept representations based on prior medical knowledge.

Competency Questions (CQs) are a form of ontology functional requirements expressed as natural language questions. Inspecting CQs together with the axioms in an ontology provides critical insights into the intended scope and applicability of the ontology. CQs also underpin a number of tasks in the development of ontologies e.g. ontology reuse, ontology testing, requirement specification, and the definition of patterns that implement such requirements. Although CQs are integral to the majority of ontology engineering methodologies, the practice of publishing CQs alongside the ontological artefacts is not widely observed by the community. In this context, we present an experiment in retrofitting CQs from existing ontologies. We propose RETROFIT-CQs, a method to extract candidate CQs directly from ontologies using Generative AI. In the paper we present the pipeline that facilitates the extraction of CQs by leveraging Large Language Models (LLMs) and we discuss its application to a number of existing ontologies.

This paper discusses the different roles that explicit knowledge, in particular ontologies, can play in Explainable AI and in the development of human-centric explainable systems and intelligible explanations. We consider three main perspectives in which ontologies can contribute significantly, namely reference modelling, common-sense reasoning, and knowledge refinement and complexity management. We overview some of the existing approaches in the literature, and we position them according to these three proposed perspectives. The paper concludes by discussing what challenges still need to be addressed to enable ontology-based approaches to explanation and to evaluate their human-understandability and effectiveness.

Multi-modal Large Language Models (MLLMs) have demonstrated impressive instruction abilities across various open-ended tasks. However, previous methods primarily focus on enhancing multi-modal capabilities. In this work, we introduce a versatile multi-modal large language model, mPLUG-Owl2, which effectively leverages modality collaboration to improve performance in both text and multi-modal tasks. mPLUG-Owl2 utilizes a modularized network design, with the language decoder acting as a universal interface for managing different modalities. Specifically, mPLUG-Owl2 incorporates shared functional modules to facilitate modality collaboration and introduces a modality-adaptive module that preserves modality-specific features. Extensive experiments reveal that mPLUG-Owl2 is capable of generalizing both text tasks and multi-modal tasks and achieving state-of-the-art performances with a single generic model. Notably, mPLUG-Owl2 is the first MLLM model that demonstrates the modality collaboration phenomenon in both pure-text and multi-modal scenarios, setting a pioneering path in the development of future multi-modal foundation models.