Petr Knoth

Wojciech Kusa, Petr Knoth, Allan Hanbury

Keeping up with research and finding related work is still a time-consuming task for academics. Researchers sift through thousands of studies to identify a few relevant ones. Automation techniques can help by increasing the efficiency and effectiveness of this task. To this end, we developed CRUISE-Screening, a web-based application for conducting living literature reviews - a type of literature review that is continuously updated to reflect the latest research in a particular field. CRUISE-Screening is connected to several search engines via an API, which allows for updating the search results periodically. Moreover, it can facilitate the process of screening for relevant publications by using text classification and question answering models. CRUISE-Screening can be used both by researchers conducting literature reviews and by those working on automating the citation screening process to validate their algorithms. The application is open-source: https://github.com/ProjectDoSSIER/cruise-screening, and a demo is available under this URL: https://citation-screening.ec.tuwien.ac.at. We discuss the limitations of our tool in Appendix A.

Mike Thelwall, Kayvan Kousha, Mahshid Abdoli et al.

National research evaluation initiatives and incentive schemes have previously chosen between simplistic quantitative indicators and time-consuming peer review, sometimes supported by bibliometrics. Here we assess whether artificial intelligence (AI) could provide a third alternative, estimating article quality using more multiple bibliometric and metadata inputs. We investigated this using provisional three-level REF2021 peer review scores for 84,966 articles submitted to the UK Research Excellence Framework 2021, matching a Scopus record 2014-18 and with a substantial abstract. We found that accuracy is highest in the medical and physical sciences Units of Assessment (UoAs) and economics, reaching 42% above the baseline (72% overall) in the best case. This is based on 1000 bibliometric inputs and half of the articles used for training in each UoA. Prediction accuracies above the baseline for the social science, mathematics, engineering, arts, and humanities UoAs were much lower or close to zero. The Random Forest Classifier (standard or ordinal) and Extreme Gradient Boosting Classifier algorithms performed best from the 32 tested. Accuracy was lower if UoAs were merged or replaced by Scopus broad categories. We increased accuracy with an active learning strategy and by selecting articles with higher prediction probabilities, as estimated by the algorithms, but this substantially reduced the number of scores predicted.

David Pride, Matteo Cancellieri, Petr Knoth

In this paper, we present CORE-GPT, a novel question-answering platform that combines GPT-based language models and more than 32 million full-text open access scientific articles from CORE. We first demonstrate that GPT3.5 and GPT4 cannot be relied upon to provide references or citations for generated text. We then introduce CORE-GPT which delivers evidence-based answers to questions, along with citations and links to the cited papers, greatly increasing the trustworthiness of the answers and reducing the risk of hallucinations. CORE-GPT's performance was evaluated on a dataset of 100 questions covering the top 20 scientific domains in CORE, resulting in 100 answers and links to 500 relevant articles. The quality of the provided answers and and relevance of the links were assessed by two annotators. Our results demonstrate that CORE-GPT can produce comprehensive and trustworthy answers across the majority of scientific domains, complete with links to genuine, relevant scientific articles.

Abdel Aziz Taha, Leonhard Hennig, Petr Knoth

One of the most common problems preventing the application of prediction models in the real world is lack of generalization: The accuracy of models, measured in the benchmark does repeat itself on future data, e.g. in the settings of real business. There is relatively little methods exist that estimate the confidence of prediction models. In this paper, we propose novel methods that, given a neural network classification model, estimate uncertainty of particular predictions generated by this model. Furthermore, we propose a method that, given a model and a confidence level, calculates a threshold that separates prediction generated by this model into two subsets, one of them meets the given confidence level. In contrast to other methods, the proposed methods do not require any changes on existing neural networks, because they simply build on the output logit layer of a common neural network. In particular, the methods infer the confidence of a particular prediction based on the distribution of the logit values corresponding to this prediction. The proposed methods constitute a tool that is recommended for filtering predictions in the process of knowledge extraction, e.g. based on web scrapping, where predictions subsets are identified that maximize the precision on cost of the recall, which is less important due to the availability of data. The method has been tested on different tasks including relation extraction, named entity recognition and image classification to show the significant increase of accuracy achieved.

Wojciech Kusa, Óscar E. Mendoza, Petr Knoth et al.

Clinical trials (CTs) often fail due to inadequate patient recruitment. This paper tackles the challenges of CT retrieval by presenting an approach that addresses the patient-to-trials paradigm. Our approach involves two key components in a pipeline-based model: (i) a data enrichment technique for enhancing both queries and documents during the first retrieval stage, and (ii) a novel re-ranking schema that uses a Transformer network in a setup adapted to this task by leveraging the structure of the CT documents. We use named entity recognition and negation detection in both patient description and the eligibility section of CTs. We further classify patient descriptions and CT eligibility criteria into current, past, and family medical conditions. This extracted information is used to boost the importance of disease and drug mentions in both query and index for lexical retrieval. Furthermore, we propose a two-step training schema for the Transformer network used to re-rank the results from the lexical retrieval. The first step focuses on matching patient information with the descriptive sections of trials, while the second step aims to determine eligibility by matching patient information with the criteria section. Our findings indicate that the inclusion criteria section of the CT has a great influence on the relevance score in lexical models, and that the enrichment techniques for queries and documents improve the retrieval of relevant trials. The re-ranking strategy, based on our training schema, consistently enhances CT retrieval and shows improved performance by 15\% in terms of precision at retrieving eligible trials. The results of our experiments suggest the benefit of making use of extracted entities. Moreover, our proposed re-ranking schema shows promising effectiveness compared to larger neural models, even with limited training data.

Wojciech Kusa, Oscar E. Mendoza, Matthias Samwald et al.

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

João Gonçalves, Sonia de Jager, Petr Knoth et al.

This intermediate technical report introduces the SHARE family of base models and the MIRROR user interface. The SHARE models are the first causal language models fully pretrained by and for the social sciences and humanities (SSH). Their performance in modelling SSH texts is close to that of general purpose models (Phi-4) which use 100 times more tokens, as shown by our custom SSH Cloze benchmark. The MIRROR user interface is designed for reviewing text inputs from the SSH disciplines while preserving critical engagement. By prototyping a generative AI interface that does not generate any text, we propose a way to harness the capabilities of the SHARE models without compromising the integrity of SSH principles and norms.

Petr Knoth, Laurent Romary, Patrice Lopez et al.

A key issue hindering discoverability, attribution and reusability of open research software is that its existence often remains hidden within the manuscript of research papers. For these resources to become first-class bibliographic records, they first need to be identified and subsequently registered with persistent identifiers (PIDs) to be made FAIR (Findable, Accessible, Interoperable and Reusable). To this day, much open research software fails to meet FAIR principles and software resources are mostly not explicitly linked from the manuscripts that introduced them or used them. SoFAIR is a 2-year international project (2024-2025) which proposes a solution to the above problem realised over the content available through the global network of open repositories. SoFAIR will extend the capabilities of widely used open scholarly infrastructures (CORE, Software Heritage, HAL) and tools (GROBID) operated by the consortium partners, delivering and deploying an effective solution for the management of the research software lifecycle, including: 1) ML-assisted identification of research software assets from within the manuscripts of scholarly papers, 2) validation of the identified assets by authors, 3) registration of software assets with PIDs and their archival.

Wojciech Kusa, Allan Hanbury, Petr Knoth

In the process of Systematic Literature Review, citation screening is estimated to be one of the most time-consuming steps. Multiple approaches to automate it using various machine learning techniques have been proposed. The first research papers that apply deep neural networks to this problem were published in the last two years. In this work, we conduct a replicability study of the first two deep learning papers for citation screening and evaluate their performance on 23 publicly available datasets. While we succeeded in replicating the results of one of the papers, we were unable to replicate the results of the other. We summarise the challenges involved in the replication, including difficulties in obtaining the datasets to match the experimental setup of the original papers and problems with executing the original source code. Motivated by this experience, we subsequently present a simpler model based on averaging word embeddings that outperforms one of the models on 18 out of 23 datasets and is, on average, 72 times faster than the second replicated approach. Finally, we measure the training time and the invariance of the models when exposed to a variety of input features and random initialisations, demonstrating differences in the robustness of these approaches.

Joeran Beel, Andrew Collins, Oliver Kopp et al.

We introduce the first 'living lab' for scholarly recommender systems. This lab allows recommender-system researchers to conduct online evaluations of their novel algorithms for scholarly recommendations, i.e., recommendations for research papers, citations, conferences, research grants, etc. Recommendations are delivered through the living lab's API to platforms such as reference management software and digital libraries. The living lab is built on top of the recommender-system as-a-service Mr. DLib. Current partners are the reference management software JabRef and the CORE research team. We present the architecture of Mr. DLib's living lab as well as usage statistics on the first sixteen months of operating it. During this time, 1,826,643 recommendations were delivered with an average click-through rate of 0.21%.

Petr Knoth, Lucas Anastasiou, Aristotelis Charalampous et al.

In this paper, we argue why and how the integration of recommender systems for research can enhance the functionality and user experience in repositories. We present the latest technical innovations in the CORE Recommender, which provides research article recommendations across the global network of repositories and journals. The CORE Recommender has been recently redeveloped and released into production in the CORE system and has also been deployed in several third-party repositories. We explain the design choices of this unique system and the evaluation processes we have in place to continue raising the quality of the provided recommendations. By drawing on our experience, we discuss the main challenges in offering a state-of-the-art recommender solution for repositories. We highlight two of the key limitations of the current repository infrastructure with respect to developing research recommender systems: 1) the lack of a standardised protocol and capabilities for exposing anonymised user-interaction logs, which represent critically important input data for recommender systems based on collaborative filtering and 2) the lack of a voluntary global sign-on capability in repositories, which would enable the creation of personalised recommendation and notification solutions based on past user interactions.

Drahomira Herrmannova, Petr Knoth

With the growing amount of published research, automatic evaluation of scholarly publications is becoming an important task. In this paper we address this problem and present a simple and transparent approach for evaluating the importance of scholarly publications. Our method has been ranked among the top performers in the WSDM Cup 2016 Challenge. The first part of this paper describes our method. In the second part we present potential improvements to the method and analyse the evaluation setup which was provided during the challenge. Finally, we discuss future challenges in automatic evaluation of papers including the use of full-texts based evaluation methods.