From human experts to machines: An LLM supported approach to ontology and knowledge graph construction

The conventional process of building Ontologies and Knowledge Graphs (KGs) heavily relies on human domain experts to define entities and relationship types, establish hierarchies, maintain relevance to the domain, fill the ABox (or populate with instances), and ensure data quality (including amongst others accuracy and completeness). On the other hand, Large Language Models (LLMs) have recently gained popularity for their ability to understand and generate human-like natural language, offering promising ways to automate aspects of this process. This work explores the (semi-)automatic construction of KGs facilitated by open-source LLMs. Our pipeline involves formulating competency questions (CQs), developing an ontology (TBox) based on these CQs, constructing KGs using the developed ontology, and evaluating the resultant KG with minimal to no involvement of human experts. We showcase the feasibility of our semi-automated pipeline by creating a KG on deep learning methodologies by exploiting scholarly publications. To evaluate the answers generated via Retrieval-Augmented-Generation (RAG) as well as the KG concepts automatically extracted using LLMs, we design a judge LLM, which rates the generated content based on ground truth. Our findings suggest that employing LLMs could potentially reduce the human effort involved in the construction of KGs, although a human-in-the-loop approach is recommended to evaluate automatically generated KGs.

Concept explainability for plant diseases classification

Plant diseases remain a considerable threat to food security and agricultural sustainability. Rapid and early identification of these diseases has become a significant concern motivating several studies to rely on the increasing global digitalization and the recent advances in computer vision based on deep learning. In fact, plant disease classification based on deep convolutional neural networks has shown impressive performance. However, these methods have yet to be adopted globally due to concerns regarding their robustness, transparency, and the lack of explainability compared with their human experts counterparts. Methods such as saliency-based approaches associating the network output to perturbations of the input pixels have been proposed to give insights into these algorithms. Still, they are not easily comprehensible and not intuitive for human users and are threatened by bias. In this work, we deploy a method called Testing with Concept Activation Vectors (TCAV) that shifts the focus from pixels to user-defined concepts. To the best of our knowledge, our paper is the first to employ this method in the field of plant disease classification. Important concepts such as color, texture and disease related concepts were analyzed. The results suggest that concept-based explanation methods can significantly benefit automated plant disease identification.

Reproducible Domain-Specific Knowledge Graphs in the Life Sciences: a Systematic Literature Review

Knowledge graphs (KGs) are widely used for representing and organizing structured knowledge in diverse domains. However, the creation and upkeep of KGs pose substantial challenges. Developing a KG demands extensive expertise in data modeling, ontology design, and data curation. Furthermore, KGs are dynamic, requiring continuous updates and quality control to ensure accuracy and relevance. These intricacies contribute to the considerable effort required for their development and maintenance. One critical dimension of KGs that warrants attention is reproducibility. The ability to replicate and validate KGs is fundamental for ensuring the trustworthiness and sustainability of the knowledge they represent. Reproducible KGs not only support open science by allowing others to build upon existing knowledge but also enhance transparency and reliability in disseminating information. Despite the growing number of domain-specific KGs, a comprehensive analysis concerning their reproducibility has been lacking. This paper addresses this gap by offering a general overview of domain-specific KGs and comparing them based on various reproducibility criteria. Our study over 19 different domains shows only eight out of 250 domain-specific KGs (3.2%) provide publicly available source code. Among these, only one system could successfully pass our reproducibility assessment (14.3%). These findings highlight the challenges and gaps in achieving reproducibility across domain-specific KGs. Our finding that only 0.4% of published domain-specific KGs are reproducible shows a clear need for further research and a shift in cultural practices.

Machine Learning Pipelines: Provenance, Reproducibility and FAIR Data Principles

Machine learning (ML) is an increasingly important scientific tool supporting decision making and knowledge generation in numerous fields. With this, it also becomes more and more important that the results of ML experiments are reproducible. Unfortunately, that often is not the case. Rather, ML, similar to many other disciplines, faces a reproducibility crisis. In this paper, we describe our goals and initial steps in supporting the end-to-end reproducibility of ML pipelines. We investigate which factors beyond the availability of source code and datasets influence reproducibility of ML experiments. We propose ways to apply FAIR data practices to ML workflows. We present our preliminary results on the role of our tool, ProvBook, in capturing and comparing provenance of ML experiments and their reproducibility using Jupyter Notebooks.

Towards Building Knowledge by Merging Multiple Ontologies with CoMerger: A Partitioning-based Approach

Ontologies are the prime way of organizing data in the Semantic Web. Often, it is necessary to combine several, independently developed ontologies to obtain a knowledge graph fully representing a domain of interest. The complementarity of existing ontologies can be leveraged by merging them. Existing approaches for ontology merging mostly implement a binary merge. However, with the growing number and size of relevant ontologies across domains, scalability becomes a central challenge. A multi-ontology merging technique offers a potential solution to this problem. We present CoMerger, a scalable multiple ontologies merging method. For efficient processing, rather than successively merging complete ontologies pairwise, we group related concepts across ontologies into partitions and merge first within and then across those partitions. The experimental results on well-known datasets confirm the feasibility of our approach and demonstrate its superiority over binary strategies. A prototypical implementation is freely accessible through a live web portal.