To study the ways in which compounds can induce adverse effects, toxicologists have been constructing Adverse Outcome Pathways (AOPs). An AOP can be considered as a pragmatic tool to capture and visualize mechanisms underlying different types of toxicity inflicted by any kind of stressor, and describes the interactions between key entities that lead to the adverse outcome on multiple biological levels of organization. The construction or optimization of an AOP is a labor intensive process, which currently depends on the manual search, collection, reviewing and synthesis of available scientific literature. This process could however be largely facilitated using Natural Language Processing (NLP) to extract information contained in scientific literature in a systematic, objective, and rapid manner that would lead to greater accuracy and reproducibility. This would support researchers to invest their expertise in the substantive assessment of the AOPs by replacing the time spent on evidence gathering by a critical review of the data extracted by NLP. As case examples, we selected two frequent adversities observed in the liver: namely, cholestasis and steatosis denoting accumulation of bile and lipid, respectively. We used deep learning language models to recognize entities of interest in text and establish causal relationships between them. We demonstrate how an NLP pipeline combining Named Entity Recognition and a simple rules-based relationship extraction model helps screen compounds related to liver adversities in the literature, but also extract mechanistic information for how such adversities develop, from the molecular to the organismal level. Finally, we provide some perspectives opened by the recent progress in Large Language Models and how these could be used in the future. We propose this work brings two main contributions: 1) a proof-of-concept that NLP can support the extraction of information from text for modern toxicology and 2) a template open-source model for recognition of toxicological entities and extraction of their relationships. All resources are openly accessible via GitHub (https://github.com/ontox-project/en-tox).
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Adverse Outcome Pathways (AOPs) are conceptual frameworks that tie an initial perturbation (molecular initiat- ing event) to a phenotypic toxicological manifestation (adverse outcome), through a series of steps (key events). They provide therefore a standardized way to map and organize toxicological mechanistic information. As such, AOPs inform on key events underlying toxicity, thus supporting the development of New Approach Methodologies (NAMs), which aim to reduce the use of animal testing for toxicology purposes. However, the establishment of a novel AOP relies on the gathering of multiple streams of evidence and infor- mation, from available literature to knowledge databases. Often, this information is in the form of free text, also called unstructured text, which is not immediately digestible by a computer. This information is thus both tedious and increasingly time-consuming to process manually with the growing volume of data available. The advance- ment of machine learning provides alternative solutions to this challenge. To extract and organize information from relevant sources, it seems valuable to employ deep learning Natural Language Processing techniques. We review here some of the recent progress in the NLP field, and show how these techniques have already demonstrated value in the biomedical and toxicology areas. We also propose an approach to efficiently and reliably extract and combine relevant toxicological information from text. This data can be used to map underlying mechanisms that lead to toxicological effects and start building quantitative models, in particular AOPs, ultimately allowing animal-free human-based hazard and risk assessment.
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Objective:Acknowledging study limitations in a scientific publication is a crucial element in scientific transparency and progress. However, limitation reporting is often inadequate. Natural language processing (NLP) methods could support automated reporting checks, improving research transparency. In this study, our objective was to develop a dataset and NLP methods to detect and categorize self-acknowledged limitations (e.g., sample size, blinding) reported in randomized controlled trial (RCT) publications.Methods:We created a data model of limitation types in RCT studies and annotated a corpus of 200 full-text RCT publications using this data model. We fine-tuned BERT-based sentence classification models to recognize the limitation sentences and their types. To address the small size of the annotated corpus, we experimented with data augmentation approaches, including Easy Data Augmentation (EDA) and Prompt-Based Data Augmentation (PromDA). We applied the best-performing model to a set of about 12K RCT publications to characterize self-acknowledged limitations at larger scale.Results:Our data model consists of 15 categories and 24 sub-categories (e.g., Population and its sub-category DiagnosticCriteria). We annotated 1090 instances of limitation types in 952 sentences (4.8 limitation sentences and 5.5 limitation types per article). A fine-tuned PubMedBERT model for limitation sentence classification improved upon our earlier model by about 1.5 absolute percentage points in F1 score (0.821 vs. 0.8) with statistical significance (). Our best-performing limitation type classification model, PubMedBERT fine-tuning with PromDA (Output View), achieved an F1 score of 0.7, improving upon the vanilla PubMedBERT model by 2.7 percentage points, with statistical significance ().Conclusion:The model could support automated screening tools which can be used by journals to draw the authors’ attention to reporting issues. Automatic extraction of limitations from RCT publications could benefit peer review and evidence synthesis, and support advanced methods to search and aggregate the evidence from the clinical trial literature.
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A considerable amount of literature has been published on Corporate Reputation, Branding and Brand Image. These studies are extensive and focus particularly on questionnaires and statistical analysis. Although extensive research has been carried out, no single study was found which attempted to predict corporate reputation performance based on data collected from media sources. To perform this task, a biLSTM Neural Network extended with attention mechanism was utilized. The advantages of this architecture are that it obtains excellent performance for NLP tasks. The state-of-the-art designed model achieves highly competitive results, F1 scores around 72%, accuracy of 92% and loss around 20%.
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Artikel in Memorad: Kunstmatige Intelligentie (Artificial Intelligence of kortweg AI) heeft de laatste jaren de radiologiewereld ingrijpend veranderd. Ook het werk van Medische Beeldvormings - en Bestralingsdeskundigen (MBB'ers) verandert hierdoor sterk.
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De maat is vol: jonge mensen spijbelen voor het klimaat. Maar de ecologische crisis is een crisis in ons denken, en daarmee ook een crisis in ons onderwijs. Het aangaan van de grote ecologische en economische uitdagingen is niet geholpen met ‘oud denken’. Ze vragen om mensen die minder atomistisch en meer ecologisch kunnen denken over hoe zaken elkaar beïnvloeden en met elkaar verbonden zijn. Leren kritisch te denken is niet genoeg. Ontwerpgericht leren denken en samen nieuwe kennis construeren, is cruciaal. Velen zien leren als een neurologisch of cognitief informatieverwerkingsproces. Leren is vooral een psychologisch proces waarbij kennis in-ter-actie ontstaat. In de rede wordt deze stelling conceptueel besproken en onderbouwd met semantische, sociale netwerkanalyses van student-interacties. De rede eindigt met handreikingen voor studenten en docenten voor responsief en kennisconstruerend leren.
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Developing a framework that integrates Advanced Language Models into the qualitative research process.Qualitative research, vital for understanding complex phenomena, is often limited by labour-intensive data collection, transcription, and analysis processes. This hinders scalability, accessibility, and efficiency in both academic and industry contexts. As a result, insights are often delayed or incomplete, impacting decision-making, policy development, and innovation. The lack of tools to enhance accuracy and reduce human error exacerbates these challenges, particularly for projects requiring large datasets or quick iterations. Addressing these inefficiencies through AI-driven solutions like AIDA can empower researchers, enhance outcomes, and make qualitative research more inclusive, impactful, and efficient.The AIDA project enhances qualitative research by integrating AI technologies to streamline transcription, coding, and analysis processes. This innovation enables researchers to analyse larger datasets with greater efficiency and accuracy, providing faster and more comprehensive insights. By reducing manual effort and human error, AIDA empowers organisations to make informed decisions and implement evidence-based policies more effectively. Its scalability supports diverse societal and industry applications, from healthcare to market research, fostering innovation and addressing complex challenges. Ultimately, AIDA contributes to improving research quality, accessibility, and societal relevance, driving advancements across multiple sectors.
This study provides a comprehensive analysis of the AI-related skills and roles needed to bridge the AI skills gap in Europe. Using a mixed-method research approach, this study investigated the most in-demand AI expertise areas and roles by surveying 409 organizations in Europe, analyzing 2,563 AI-related job advertisements, and conducting 24 focus group sessions with 145 industry and policy experts. The findings underscore the importance of both general technical skills in AI related to big data, machine learning and deep learning, cyber and data security, large language models as well as AI soft skills such as problemsolving and effective communication. This study sets the foundation for future research directions, emphasizing the importance of upskilling initiatives and the evolving nature of AI skills demand, contributing to an EU-wide strategy for future AI skills development.
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The main goal of this study was to investigate if a computational analyses of text data from the National Student Survey (NSS) can add value to the existing, manual analysis. The results showed the computational analysis of the texts from the open questions of the NSS contain information which enriches the results of standard quantitative analysis of the NSS.
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Preprint submitted to Information Processing & Management Tags are a convenient way to label resources on the web. An interesting question is whether one can determine the semantic meaning of tags in the absence of some predefined formal structure like a thesaurus. Many authors have used the usage data for tags to find their emergent semantics. Here, we argue that the semantics of tags can be captured by comparing the contexts in which tags appear. We give an approach to operationalizing this idea by defining what we call paradigmatic similarity: computing co-occurrence distributions of tags with tags in the same context, and comparing tags using information theoretic similarity measures of these distributions, mostly the Jensen-Shannon divergence. In experiments with three different tagged data collections we study its behavior and compare it to other distance measures. For some tasks, like terminology mapping or clustering, the paradigmatic similarity seems to give better results than similarity measures based on the co-occurrence of the documents or other resources that the tags are associated to. We argue that paradigmatic similarity, is superior to other distance measures, if agreement on topics (as opposed to style, register or language etc.), is the most important criterion, and the main differences between the tagged elements in the data set correspond to different topics
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