LLMs4Life: Large Language Models for Ontology Learning in Life Sciences

Ontology learning in complex domains, such as life sciences, poses significant challenges for current Large Language Models (LLMs). Existing LLMs struggle to generate ontologies with multiple hierarchical levels, rich interconnections, and comprehensive class coverage due to constraints on the number of tokens they can generate and inadequate domain adaptation. To address these issues, we extend the NeOn-GPT pipeline for ontology learning using LLMs with advanced prompt engineering techniques and ontology reuse to enhance the generated ontologies' domain-specific reasoning and structural depth. Our work evaluates the capabilities of LLMs in ontology learning in the context of highly specialized and complex domains such as life science domains. To assess the logical consistency, completeness, and scalability of the generated ontologies, we use the AquaDiva ontology developed and used in the collaborative research center AquaDiva as a case study. Our evaluation shows the viability of LLMs for ontology learning in specialized domains, providing solutions to longstanding limitations in model performance and scalability.

Empowering the Deaf and Hard of Hearing Community: Enhancing Video Captions Using Large Language Models

In today's digital age, video content is prevalent, serving as a primary source of information, education, and entertainment. However, the Deaf and Hard of Hearing (DHH) community often faces significant challenges in accessing video content due to the inadequacy of automatic speech recognition (ASR) systems in providing accurate and reliable captions. This paper addresses the urgent need to improve video caption quality by leveraging Large Language Models (LLMs). We present a comprehensive study that explores the integration of LLMs to enhance the accuracy and context-awareness of captions generated by ASR systems. Our methodology involves a novel pipeline that corrects ASR-generated captions using advanced LLMs. It explicitly focuses on models like GPT-3.5 and Llama2-13B due to their robust performance in language comprehension and generation tasks. We introduce a dataset representative of real-world challenges the DHH community faces to evaluate our proposed pipeline. Our results indicate that LLM-enhanced captions significantly improve accuracy, as evidenced by a notably lower Word Error Rate (WER) achieved by ChatGPT-3.5 (WER: 9.75%) compared to the original ASR captions (WER: 23.07%), ChatGPT-3.5 shows an approximate 57.72% improvement in WER compared to the original ASR captions.

F -- A Model of Events based on the Foundational Ontology DOLCE+DnS Ultralite

The lack of a formal model of events hinders interoperability in distributed event-based systems. In this paper, we present a formal model of events, called Event-Model-F. The model is based on the foundational ontology DOLCE+DnS Ultralite (DUL) and provides comprehensive support to represent time and space, objects and persons, as well as mereological, causal, and correlative relationships between events. In addition, the Event-Model-F provides a flexible means for event composition, modeling event causality and event correlation, and representing different interpretations of the same event. The Event-Model-F is developed following the pattern-oriented approach of DUL, is modularized in different ontologies, and can be easily extended by domain specific ontologies.

DAGE: DAG Query Answering via Relational Combinator with Logical Constraints

Predicting answers to queries over knowledge graphs is called a complex reasoning task because answering a query requires subdividing it into subqueries. Existing query embedding methods use this decomposition to compute the embedding of a query as the combination of the embedding of the subqueries. This requirement limits the answerable queries to queries having a single free variable and being decomposable, which are called tree-form queries and correspond to the $\mathcal{SROI}^-$ description logic. In this paper, we define a more general set of queries, called DAG queries and formulated in the $\mathcal{ALCOIR}$ description logic, propose a query embedding method for them, called DAGE, and a new benchmark to evaluate query embeddings on them. Given the computational graph of a DAG query, DAGE combines the possibly multiple paths between two nodes into a single path with a trainable operator that represents the intersection of relations and learns DAG-DL from tautologies. We show that it is possible to implement DAGE on top of existing query embedding methods, and we empirically measure the improvement of our method over the results of vanilla methods evaluated in tree-form queries that approximate the DAG queries of our proposed benchmark.

Visual Representation Learning Guided By Multi-modal Prior Knowledge

Despite the remarkable success of deep neural networks (DNNs) in computer vision, they fail to remain high-performing when facing distribution shifts between training and testing data. In this paper, we propose Knowledge-Guided Visual representation learning (KGV), a distribution-based learning approach leveraging multi-modal prior knowledge, to improve generalization under distribution shift. We use prior knowledge from two distinct modalities: 1) a knowledge graph (KG) with hierarchical and association relationships; and 2) generated synthetic images of visual elements semantically represented in the KG. The respective embeddings are generated from the given modalities in a common latent space, i.e., visual embeddings from original and synthetic images as well as knowledge graph embeddings (KGEs). These embeddings are aligned via a novel variant of translation-based KGE methods, where the node and relation embeddings of the KG are modeled as Gaussian distributions and translations respectively. We claim that incorporating multi-model prior knowledge enables more regularized learning of image representations. Thus, the models are able to better generalize across different data distributions. We evaluate KGV on different image classification tasks with major or minor distribution shifts, namely road sign classification across datasets from Germany, China, and Russia, image classification with the mini-ImageNet dataset and its variants, as well as the DVM-CAR dataset. The results demonstrate that KGV consistently exhibits higher accuracy and data efficiency than the baselines across all experiments.

Is Complex Query Answering Really Complex?

Complex query answering (CQA) on knowledge graphs (KGs) is gaining momentum as a challenging reasoning task. In this paper, we show that the current benchmarks for CQA are not really complex, and the way they are built distorts our perception of progress in this field. For example, we find that in these benchmarks, most queries (up to 98% for some query types) can be reduced to simpler problems, e.g., link prediction, where only one link needs to be predicted. The performance of state-of-the-art CQA models drops significantly when such models are evaluated on queries that cannot be reduced to easier types. Thus, we propose a set of more challenging benchmarks, composed of queries that require models to reason over multiple hops and better reflect the construction of real-world KGs. In a systematic empirical investigation, the new benchmarks show that current methods leave much to be desired from current CQA methods.

Predictive Multiplicity of Knowledge Graph Embeddings in Link Prediction

Knowledge graph embedding (KGE) models are often used to predict missing links for knowledge graphs (KGs). However, multiple KG embeddings can perform almost equally well for link prediction yet suggest conflicting predictions for certain queries, termed \textit{predictive multiplicity} in literature. This behavior poses substantial risks for KGE-based applications in high-stake domains but has been overlooked in KGE research. In this paper, we define predictive multiplicity in link prediction. We introduce evaluation metrics and measure predictive multiplicity for representative KGE methods on commonly used benchmark datasets. Our empirical study reveals significant predictive multiplicity in link prediction, with $8\%$ to $39\%$ testing queries exhibiting conflicting predictions. To address this issue, we propose leveraging voting methods from social choice theory, significantly mitigating conflicts by $66\%$ to $78\%$ according to our experiments.

Conformalized Answer Set Prediction for Knowledge Graph Embedding

Knowledge graph embeddings (KGE) apply machine learning methods on knowledge graphs (KGs) to provide non-classical reasoning capabilities based on similarities and analogies. The learned KG embeddings are typically used to answer queries by ranking all potential answers, but rankings often lack a meaningful probabilistic interpretation - lower-ranked answers do not necessarily have a lower probability of being true. This limitation makes it difficult to distinguish plausible from implausible answers, posing challenges for the application of KGE methods in high-stakes domains like medicine. We address this issue by applying the theory of conformal prediction that allows generating answer sets, which contain the correct answer with probabilistic guarantees. We explain how conformal prediction can be used to generate such answer sets for link prediction tasks. Our empirical evaluation on four benchmark datasets using six representative KGE methods validates that the generated answer sets satisfy the probabilistic guarantees given by the theory of conformal prediction. We also demonstrate that the generated answer sets often have a sensible size and that the size adapts well with respect to the difficulty of the query.

eSPARQL: Representing and Reconciling Agnostic and Atheistic Beliefs in RDF-star Knowledge Graphs

Over the past few years, we have seen the emergence of large knowledge graphs combining information from multiple sources. Sometimes, this information is provided in the form of assertions about other assertions, defining contexts where assertions are valid. A recent extension to RDF which admits statements over statements, called RDF-star, is in revision to become a W3C standard. However, there is no proposal for a semantics of these RDF-star statements nor a built-in facility to operate over them. In this paper, we propose a query language for epistemic RDF-star metadata based on a four-valued logic, called eSPARQL. Our proposed query language extends SPARQL-star, the query language for RDF-star, with a new type of FROM clause to facilitate operating with multiple and sometimes conflicting beliefs. We show that the proposed query language can express four use case queries, including the following features: (i) querying the belief of an individual, (ii) the aggregating of beliefs, (iii) querying who is conflicting with somebody, and (iv) beliefs about beliefs (i.e., nesting of beliefs).

Approximating Probabilistic Inference in Statistical EL with Knowledge Graph Embeddings

Statistical information is ubiquitous but drawing valid conclusions from it is prohibitively hard. We explain how knowledge graph embeddings can be used to approximate probabilistic inference efficiently using the example of Statistical EL (SEL), a statistical extension of the lightweight Description Logic EL. We provide proofs for runtime and soundness guarantees, and empirically evaluate the runtime and approximation quality of our approach.