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Large expert-curated database for benchmarking document similarity detection in biomedical literature search

#artificialintelligence

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations.


Named Entity Recognition for Electronic Health Records: A Comparison of Rule-based and Machine Learning Approaches

arXiv.org Artificial Intelligence

This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning systems for the task of NER on brain imaging reports with a focus on records from patients with stroke. We explore the strengths and weaknesses of each approach, develop rules and train on a common dataset, and evaluate each system's performance on common test sets of Scottish radiology reports from two sources (brain imaging reports in ESS -- Edinburgh Stroke Study data collected by NHS Lothian as well as radiology reports created in NHS Tayside). Our comparison shows that a hand-crafted system is the most accurate way to automatically label EHR, but machine learning approaches can provide a feasible alternative where resources for a manual system are not readily available.


NeuroQuery: comprehensive meta-analysis of human brain mapping

arXiv.org Machine Learning

Reaching a global view of brain organization requires assembling evidence on widely different mental processes and mechanisms. The variety of human neuroscience concepts and terminology poses a fundamental challenge to relating brain imaging results across the scientific literature. Existing meta-analysis methods perform statistical tests on sets of publications associated with a particular concept. Thus, large-scale meta-analyses only tackle single terms that occur frequently. We propose a new paradigm, focusing on prediction rather than inference. Our multivariate model predicts the spatial distribution of neurological observations, given text describing an experiment, cognitive process, or disease. This approach handles text of arbitrary length and terms that are too rare for standard meta-analysis. We capture the relationships and neural correlates of 7 547 neuroscience terms across 13 459 neuroimaging publications. The resulting meta-analytic tool, neuroquery.org, can ground hypothesis generation and data-analysis priors on a comprehensive view of published findings on the brain.


PathVQA: 30000+ Questions for Medical Visual Question Answering

arXiv.org Artificial Intelligence

Is it possible to develop an "AI Pathologist" to pass the board-certified examination of the American Board of Pathology? To achieve this goal, the first step is to create a visual question answering (VQA) dataset where the AI agent is presented with a pathology image together with a question and is asked to give the correct answer. Our work makes the first attempt to build such a dataset. Different from creating general-domain VQA datasets where the images are widely accessible and there are many crowdsourcing workers available and capable of generating question-answer pairs, developing a medical VQA dataset is much more challenging. First, due to privacy concerns, pathology images are usually not publicly available. Second, only well-trained pathologists can understand pathology images, but they barely have time to help create datasets for AI research. To address these challenges, we resort to pathology textbooks and online digital libraries. We develop a semi-automated pipeline to extract pathology images and captions from textbooks and generate question-answer pairs from captions using natural language processing. We collect 32,799 open-ended questions from 4,998 pathology images where each question is manually checked to ensure correctness. To our best knowledge, this is the first dataset for pathology VQA. Our dataset will be released publicly to promote research in medical VQA.