Systematic reviews are comprehensive literature reviews that address highly focused research questions and represent the highest form of evidence in medicine. A critical step in this process is the development of complex Boolean queries to retrieve relevant literature. Given the difficulty of manually constructing these queries, recent efforts have explored Large Language Models (LLMs) to assist in their formulation. One of the first studies,Wang et al., investigated ChatGPT for this task, followed by Staudinger et al., which evaluated multiple LLMs in a reproducibility study. However, the latter overlooked several key aspects of the original work, including (i) validation of generated queries, (ii) output formatting constraints, and (iii) selection of examples for chain-of-thought (Guided) prompting. As a result, its findings diverged significantly from the original study. In this work, we systematically reproduce both studies while addressing these overlooked factors. Our results show that query effectiveness varies significantly across models and prompt designs, with guided query formulation benefiting from well-chosen seed studies. Overall, prompt design and model selection are key drivers of successful query formulation. Our findings provide a clearer understanding of LLMs' potential in Boolean query generation and highlight the importance of model- and prompt-specific optimisations. The complex nature of systematic reviews adds to challenges in both developing and reproducing methods but also highlights the importance of reproducibility studies in this domain.

Deep learning underpins most of the currently advanced natural language processing (NLP) tasks such as textual classification, neural machine translation (NMT), abstractive summarization and question-answering (QA). However, the robustness of the models, particularly QA models, against adversarial attacks is a critical concern that remains insufficiently explored. This paper introduces QA-Attack (Question Answering Attack), a novel word-level adversarial strategy that fools QA models. Our attention-based attack exploits the customized attention mechanism and deletion ranking strategy to identify and target specific words within contextual passages. It creates deceptive inputs by carefully choosing and substituting synonyms, preserving grammatical integrity while misleading the model to produce incorrect responses. Our approach demonstrates versatility across various question types, particularly when dealing with extensive long textual inputs. Extensive experiments on multiple benchmark datasets demonstrate that QA-Attack successfully deceives baseline QA models and surpasses existing adversarial techniques regarding success rate, semantics changes, BLEU score, fluency and grammar error rate.

Screening prioritisation in medical systematic reviews aims to rank the set of documents retrieved by complex Boolean queries. Prioritising the most important documents ensures that subsequent review steps can be carried out more efficiently and effectively. The current state of the art uses the final title of the review as a query to rank the documents using BERT-based neural rankers. However, the final title is only formulated at the end of the review process, which makes this approach impractical as it relies on ex post facto information. At the time of screening, only a rough working title is available, with which the BERT-based ranker performs significantly worse than with the final title. In this paper, we explore alternative sources of queries for prioritising screening, such as the Boolean query used to retrieve the documents to be screened and queries generated by instruction-based generative large-scale language models such as ChatGPT and Alpaca. Our best approach is not only viable based on the information available at the time of screening, but also has similar effectiveness to the final title.

Systematic reviews are comprehensive reviews of the literature for a highly focused research question. These reviews are often treated as the highest form of evidence in evidence-based medicine, and are the key strategy to answer research questions in the medical field. To create a high-quality systematic review, complex Boolean queries are often constructed to retrieve studies for the review topic. However, it often takes a long time for systematic review researchers to construct a high quality systematic review Boolean query, and often the resulting queries are far from effective. Poor queries may lead to biased or invalid reviews, because they missed to retrieve key evidence, or to extensive increase in review costs, because they retrieved too many irrelevant studies. Recent advances in Transformer-based generative models have shown great potential to effectively follow instructions from users and generate answers based on the instructions being made. In this paper, we investigate the effectiveness of the latest of such models, ChatGPT, in generating effective Boolean queries for systematic review literature search. Through a number of extensive experiments on standard test collections for the task, we find that ChatGPT is capable of generating queries that lead to high search precision, although trading-off this for recall. Overall, our study demonstrates the potential of ChatGPT in generating effective Boolean queries for systematic review literature search. The ability of ChatGPT to follow complex instructions and generate queries with high precision makes it a valuable tool for researchers conducting systematic reviews, particularly for rapid reviews where time is a constraint and often trading-off higher precision for lower recall is acceptable.

Boolean query construction is often critical for medical systematic review literature search. To create an effective Boolean query, systematic review researchers typically spend weeks coming up with effective query terms and combinations. One challenge to creating an effective systematic review Boolean query is the selection of effective MeSH Terms to include in the query. In our previous work, we created neural MeSH term suggestion methods and compared them to state-of-the-art MeSH term suggestion methods. We found neural MeSH term suggestion methods to be highly effective. In this demonstration, we build upon our previous work by creating (1) a Web-based MeSH term suggestion prototype system that allows users to obtain suggestions from a number of underlying methods and (2) a Python library that implements ours and others' MeSH term suggestion methods and that is aimed at researchers who want to further investigate, create or deploy such type of methods. We describe the architecture of the web-based system and how to use it for the MeSH term suggestion task. For the Python library, we describe how the library can be used for advancing further research and experimentation, and we validate the results of the methods contained in the library on standard datasets. Our web-based prototype system is available at http://ielab-mesh-suggest.uqcloud.net, while our Python library is at https://github.com/ielab/meshsuggestlib.

High-quality medical systematic reviews require comprehensive literature searches to ensure the recommendations and outcomes are sufficiently reliable. Indeed, searching for relevant medical literature is a key phase in constructing systematic reviews and often involves domain (medical researchers) and search (information specialists) experts in developing the search queries. Queries in this context are highly complex, based on Boolean logic, include free-text terms and index terms from standardised terminologies (e.g., the Medical Subject Headings (MeSH) thesaurus), and are difficult and time-consuming to build. The use of MeSH terms, in particular, has been shown to improve the quality of the search results. However, identifying the correct MeSH terms to include in a query is difficult: information experts are often unfamiliar with the MeSH database and unsure about the appropriateness of MeSH terms for a query. Naturally, the full value of the MeSH terminology is often not fully exploited. This article investigates methods to suggest MeSH terms based on an initial Boolean query that includes only free-text terms. In this context, we devise lexical and pre-trained language models based methods. These methods promise to automatically identify highly effective MeSH terms for inclusion in a systematic review query. Our study contributes an empirical evaluation of several MeSH term suggestion methods. We further contribute an extensive analysis of MeSH term suggestions for each method and how these suggestions impact the effectiveness of Boolean queries.

Full-Text Search is one of those tools people use every day without realizing it. If you ever googled "golang coverage report" or tried to find "indoor wireless camera" on an e-commerce website, you used some kind of full-text search. Full-Text Search (FTS) is a technique for searching text in a collection of documents. A document can refer to a web page, a newspaper article, an email message, or any structured text. Today we are going to build our own FTS engine.

Pandas offers some methods to get information of a data structure: info, index, columns, axes, where you can see the memory usage of the data, information about the axes such as the data types involved, and the number of not-null values. To make a boolean query, you need to pass the DataFrame a True/False Series whose index aligns with the DataFrame being queried's index. Merging is another way of combining DataFrames, but unlike concat it combines them looking for matching values in columns of said DataFrames (you can merge by index too). The main method to perform merging in Pandas is merge which lives both in the main pandas namespace and in the DataFrame namespace (unlike concat).

Here at Tryolabs we love Python almost as much as we love machine learning problems. These kind of problems always involve working with large amounts of data which is key to understand before applying any machine learning technique. To understand the data, we need to manipulate it, clean it, make calculations and see how variables behave independently, and how they relate to one another. At this post will show how we have been doing this lately. Up next you'll find an overview of Pandas, a Python library which is old but gold and a must-know if you're attempting to do any work with data while living in the Python world, and a glance of Seaborn, a Python library for making statistical visualizations. From our experience, they complement each other really well, and are worth learning together. We hope this post serves as a first guide for diving into them and kickstart your data handling & visualization journey.

In this paper we model the problem of data linkage in Linked Data as a reasoning problem on possibly decentralized data. We describe a novel import-by-query algorithm that alternates steps of sub-query rewriting and of tailored querying the Linked Data cloud in order to import data as specific as possible for inferring or contradicting given target same-as facts. Experiments conducted on a real-world dataset have demonstrated the feasibility of this approach and its usefulness in practice for data linkage and disambiguation.