Search

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., Comment: This paper is currently in submission with Intelligent Systems with Applications Journal Technology-Assisted Review Systems Special issue and is under peer review. arXiv admin note: text overlap with arXiv:2112.00277

The Simons Observatory (SO) is a ground-based cosmic microwave background survey experiment that consists of three 0.5 m small-aperture telescopes and one 6 m large-aperture telescope, sited at an elevation of 5200 m in the Atacama Desert in Chile. SO will study the polarization and temperature anisotropies of the Cosmic Microwave Background (CMB). The observatory will require well-understood telescope pointing and scanning. Good antenna control will allow us to execute the scan strategy devised to optimize sensitivity to our scientific goals, calibrate the system with celestial targets, and make maps. To achieve this, we integrate the data acquisition and control of the telescopes' Antenna Control Units (ACUs) within the software framework of the SO Observatory Control System (OCS). We present here the current status of the software integration for the ACUs, as well as measurements of the Small Aperture Telescope platforms' responsiveness to software commanding in the factory, plans for in situ measurements, and prospects for implementation on the Large Aperture Telescope., Comment: 20 pages, 8 figures, paper 12190-170 for "Proc. SPIE 12190 Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy XI"

Pseudo-Relevance Feedback (PRF) assumes that the top results retrieved by a first-stage ranker are relevant to the original query and uses them to improve the query representation for a second round of retrieval. This assumption however is often not correct: some or even all of the feedback documents may be irrelevant. Indeed, the effectiveness of PRF methods may well depend on the quality of the feedback signal and thus on the effectiveness of the first-stage ranker. This aspect however has received little attention before. In this paper we control the quality of the feedback signal and measure its impact on a range of PRF methods, including traditional bag-of-words methods (Rocchio), and dense vector-based methods (learnt and not learnt). Our results show the important role the quality of the feedback signal plays on the effectiveness of PRF methods. Importantly, and surprisingly, our analysis reveals that not all PRF methods are the same when dealing with feedback signals of varying quality. These findings are critical to gain a better understanding of the PRF methods and of which and when they should be used, depending on the feedback signal quality, and set the basis for future research in this area., Comment: Accepted at SIGIR 2022

In a paper recently published in this journal, van Marle et al. (van Marle et al., 2022) introduce an interesting new data set for land use and land cover change CO2 emissions (LULCC) that they use to study whether a trend is present in the airborne fraction (AF), defined as the fraction of CO2 emissions remaining in the atmosphere. Testing the hypothesis of a trend in the AF has attracted much attention, with the overall consensus that no statistical evidence is found for a trend in the data (Knorr, 2009; Gloor et al., 2010; Raupach et al., 2014; Bennedsen et al., 2019). In their paper, van Marle et al. analyze the AF as implied by three different LULCC emissions time series (GCP, H&N, and their new data series). In a Monte Carlo simulation study based on their new LULCC emissions data, van Marle et al. find evidence of a declining trend in the AF. In this note, we argue that the statistical analysis presented in van Marle et al. can be improved in several respects. Specifically, the Monte Carlo study presented in van Marle et al. is not conducive to determine whether there is a trend in the AF. Further, we re-examine the evidence for a trend in the AF by using a variety of different statistical tests. The statistical evidence for an uninterrupted (positive or negative) trend in the airborne fraction remains mixed at best. When allowing for a break in the trend, there is some evidence for upward trends in both subsamples.

Medical systematic review query formulation is a highly complex task done by trained information specialists. Complexity comes from the reliance on lengthy Boolean queries, which express a detailed research question. To aid query formulation, information specialists use a set of exemplar documents, called `seed studies', prior to query formulation. Seed studies help verify the effectiveness of a query prior to the full assessment of retrieved studies. Beyond this use of seeds, specific IR methods can exploit seed studies for guiding both automatic query formulation and new retrieval models. One major limitation of work to date is that these methods exploit `pseudo seed studies' through retrospective use of included studies (i.e., relevance assessments). However, we show pseudo seed studies are not representative of real seed studies used by information specialists. Hence, we provide a test collection with real world seed studies used to assist with the formulation of queries. To support our collection, we provide an analysis, previously not possible, on how seed studies impact retrieval and perform several experiments using seed-study based methods to compare the effectiveness of using seed studies versus pseudo seed studies. We make our test collection and the results of all of our experiments and analysis available at http://github.com/ielab/sysrev-seed-collection, Comment: Accepted and To be appeared in SIGIR 2022 proceeding

These are the proceedings of the first teacher training of the Erasmus+ project No. 2020-1-PT01-KA203-078646 -- Sustrainable. The full title of this project is Promoting Sustainability as a Fundamental Driver in Software Development Training and Education and the interested reader may know more about it at: https://sustrainable.github.io The flagship contribution is the organization of two summer schools on sustainable software production. The first summer school is moved due to the Corona pandemic. It is now scheduled for July 2022 in Rijeka, Croatia. This summer school will consist of lectures and practical work for master and PhD students in the area of computing science and closely related fields. There will be contributions from Plovdiv University, University of Ko\v{s}ice, University of Coimbra, University of Minho, E\"otv\"os Lor\'and University, University of Rijeka, Radboud University Nijmegen, University of Pula, University of Amsterdam and Babe\c{s}-Bolyai University. To prepare and streamline this summer school, the consortium organized a teacher training in Nijmegen, the Netherlands. This was an event of five full days on November 1-5, 2022 organized by Ingrid Berenbroek, Mart Lubbers and Pieter Koopman on the campus of the Radboud University Nijmegen, The Netherlands. Sustainability is one of the themes within the strategy of the Radboud University called `A Significant Impact', see https://www.ru.nl/sustainability/organisation/radboud-sustainable/. Sustainability plays an important role in education, research, and management. The contributions were reviewed and give a good overview of what can be expected from the summer school. Based on these papers and the very positive and constructive atmosphere, we expect a high quality and pleasant summer school. We are looking forward to contributing to a sustainable future., Comment: 96 pages and 16 figures, editors: Pieter Koopman, Mart Lubbers, Jo\~ao Paulo Fernandes

We present a parallel algorithm for the fast Fourier transform (FFT) in higher dimensions. This algorithm generalizes the cyclic-to-cyclic one-dimensional parallel algorithm to a cyclic-to-cyclic multidimensional parallel algorithm while retaining the property of needing only a single all-to-all communication step. This is under the constraint that we use at most $\sqrt{N}$ processors for an FFT on an array with a total of $N$ elements, irrespective of the dimension $d$ or the shape of the array. The only assumption we make is that $N$ is sufficiently composite. Our algorithm starts and ends in the same data distribution. We present our multidimensional implementation FFTU which utilizes the sequential FFTW program for its local FFTs, and which can handle any dimension $d$. We obtain experimental results for $d\leq 5$ using MPI on up to 4096 cores of the supercomputer Snellius, comparing FFTU with the parallel FFTW program and with PFFT and heFFTe. These results show that FFTU is competitive with the state of the art and that it allows one to use a larger number of processors, while keeping communication limited to a single all-to-all operation. For arrays of size $1024^3$ and $64^5$, FFTU achieves a speedup of a factor 149 and 176, respectively, on 4096 processors., Comment: 23 pages, 3 figures. The new version has mainly added results in section 4.2 for the package heFFT, following referee comments. Furthermore, small linguistic changes have been made to render the arXiv version identical in text to the final published journal version

This Snowmass 2021 White Paper describes the Cosmic Microwave Background Stage 4 project CMB-S4, which is designed to cross critical thresholds in our understanding of the origin and evolution of the Universe, from the highest energies at the dawn of time through the growth of structure to the present day. We provide an overview of the science case, the technical design, and project plan., Comment: Contribution to Snowmass 2021. arXiv admin note: substantial text overlap with arXiv:1908.01062, arXiv:1907.04473

Automatically generating a report from a patient's Chest X-Rays (CXRs) is a promising solution to reducing clinical workload and improving patient care. However, current CXR report generators -- which are predominantly encoder-to-decoder models -- lack the diagnostic accuracy to be deployed in a clinical setting. To improve CXR report generation, we investigate warm starting the encoder and decoder with recent open-source computer vision and natural language processing checkpoints, such as the Vision Transformer (ViT) and PubMedBERT. To this end, each checkpoint is evaluated on the MIMIC-CXR and IU X-Ray datasets. Our experimental investigation demonstrates that the Convolutional vision Transformer (CvT) ImageNet-21K and the Distilled Generative Pre-trained Transformer 2 (DistilGPT2) checkpoints are best for warm starting the encoder and decoder, respectively. Compared to the state-of-the-art ($\mathcal{M}^2$ Transformer Progressive), CvT2DistilGPT2 attained an improvement of 8.3\% for CE F-1, 1.8\% for BLEU-4, 1.6\% for ROUGE-L, and 1.0\% for METEOR. The reports generated by CvT2DistilGPT2 have a higher similarity to radiologist reports than previous approaches. This indicates that leveraging warm starting improves CXR report generation. Code and checkpoints for CvT2DistilGPT2 are available at https://github.com/aehrc/cvt2distilgpt2.

Finding concepts in large clinical ontologies can be challenging when queries use different vocabularies. A search algorithm that overcomes this problem is useful in applications such as concept normalisation and ontology matching, where concepts can be referred to in different ways, using different synonyms. In this paper, we present a deep learning based approach to build a semantic search system for large clinical ontologies. We propose a Triplet-BERT model and a method that generates training data directly from the ontologies. The model is evaluated using five real benchmark data sets and the results show that our approach achieves high results on both free text to concept and concept to concept searching tasks, and outperforms all baseline methods.