310 research outputs found
Recommended from our members
Deduplication of Scholarly Documents using Locality Sensitive Hashing and Word Embeddings
Deduplication is the task of identifying near and exact duplicate data items in a collection. In this paper, we present a novel method for deduplication of scholarly documents. We develop a hybrid model which uses structural similarity (locality sensitive hashing) and meaning representation (word embeddings) of document texts to determine (near) duplicates. Our collection constitutes a subset of multidisciplinary scholarly documents aggregated from research repositories. We identify several issues causing data inaccuracies in such collections and motivate the need for deduplication. In lack of existing dataset suitable for study of deduplication of scholarly documents, we create a ground truth dataset of 100K scholarly documents and conduct a series of experiments to empirically establish optimal values for the parameters of our deduplication method. Experimental evaluation shows that our method achieves a macro F1-score of 0.90. We productionise our method as a publicly accessible web API service serving deduplication of scholarly documents in real time
Efficient, Dependable Storage of Human Genome Sequencing Data
A compreensão do genoma humano impacta várias áreas da vida. Os dados oriundos do genoma humano são enormes pois existem milhões de amostras a espera de serem sequenciadas e cada genoma humano sequenciado pode ocupar centenas de gigabytes de espaço de armazenamento. Os genomas humanos são crÃticos porque são extremamente valiosos para a investigação e porque podem fornecer informações delicadas sobre o estado de saúde dos indivÃduos, identificar os seus dadores ou até mesmo revelar informações sobre os parentes destes. O tamanho e a criticidade destes genomas, para além da quantidade de dados produzidos por instituições médicas e de ciências da vida, exigem que os sistemas informáticos sejam escaláveis, ao mesmo tempo que sejam seguros, confiáveis, auditáveis e com custos acessÃveis. As infraestruturas de armazenamento existentes são tão caras que não nos permitem ignorar a eficiência de custos no armazenamento de genomas humanos, assim como em geral estas não possuem o conhecimento e os mecanismos adequados para proteger a privacidade dos dadores de amostras biológicas. Esta tese propõe um sistema de armazenamento de genomas humanos eficiente, seguro e auditável para instituições médicas e de ciências da vida. Ele aprimora os ecossistemas de armazenamento tradicionais com técnicas de privacidade, redução do tamanho dos dados e auditabilidade a fim de permitir o uso eficiente e confiável de infraestruturas públicas de computação em nuvem para armazenar genomas humanos. As contribuições desta tese incluem (1) um estudo sobre a sensibilidade à privacidade dos genomas humanos; (2) um método para detetar sistematicamente as porções dos genomas que são sensÃveis à privacidade; (3) algoritmos de redução do tamanho de dados, especializados para dados de genomas sequenciados; (4) um esquema de auditoria independente para armazenamento disperso e seguro de dados; e (5) um fluxo de armazenamento completo que obtém garantias razoáveis de proteção, segurança e confiabilidade a custos modestos (por exemplo, menos de 1/Genome/Year) by integrating the proposed mechanisms with appropriate storage configurations
Exploring the evolution of research topics during the COVID-19 pandemic
The COVID-19 pandemic has changed the research agendas of most scientific
communities, resulting in an overwhelming production of research articles in a
variety of domains, including medicine, virology, epidemiology, economy,
psychology, and so on. Several open-access corpora and literature hubs were
established; among them, the COVID-19 Open Research Dataset (CORD-19) has
systematically gathered scientific contributions for 2.5 years, by collecting
and indexing over one million articles. Here, we present the CORD-19 Topic
Visualizer (CORToViz), a method and associated visualization tool for
inspecting the CORD-19 textual corpus of scientific abstracts. Our method is
based upon a careful selection of up-to-date technologies (including large
language models), resulting in an architecture for clustering articles along
orthogonal dimensions and extraction techniques for temporal topic mining.
Topic inspection is supported by an interactive dashboard, providing fast,
one-click visualization of topic contents as word clouds and topic trends as
time series, equipped with easy-to-drive statistical testing for analyzing the
significance of topic emergence along arbitrarily selected time windows. The
processes of data preparation and results visualization are completely general
and virtually applicable to any corpus of textual documents - thus suited for
effective adaptation to other contexts.Comment: 16 pages, 6 figures, 1 tabl
CIDACS-RL: a novel indexing search and scoring-based record linkage system for huge datasets with high accuracy and scalability
Background: Record linkage is the process of identifying and combining records about the same individual from two or more different datasets. While there are many open source and commercial data linkage tools, the volume and complexity of currently available datasets for linkage pose a huge challenge; hence, designing an efficient linkage tool with reasonable accuracy and scalability is required. Methods: We developed CIDACS-RL (Centre for Data and Knowledge Integration for Health – Record Linkage), a novel iterative deterministic record linkage algorithm based on a combination of indexing search and scoring algorithms (provided by Apache Lucene). We described how the algorithm works and compared its performance with four open source linkage tools (AtyImo, Febrl, FRIL and RecLink) in terms of sensitivity and positive predictive value using gold standard dataset. We also evaluated its accuracy and scalability using a case-study and its scalability and execution time using a simulated cohort in serial (single core) and multi-core (eight core) computation settings. Results: Overall, CIDACS-RL algorithm had a superior performance: positive predictive value (99.93% versus AtyImo 99.30%, RecLink 99.5%, Febrl 98.86%, and FRIL 96.17%) and sensitivity (99.87% versus AtyImo 98.91%, RecLink 73.75%, Febrl 90.58%, and FRIL 74.66%). In the case study, using a ROC curve to choose the most appropriate cut-off value (0.896), the obtained metrics were: sensitivity = 92.5% (95% CI 92.07–92.99), specificity = 93.5% (95% CI 93.08–93.8) and area under the curve (AUC) = 97% (95% CI 96.97–97.35). The multi-core computation was about four times faster (150 seconds) than the serial setting (550 seconds) when using a dataset of 20 million records. Conclusion: CIDACS-RL algorithm is an innovative linkage tool for huge datasets, with higher accuracy, improved scalability, and substantially shorter execution time compared to other existing linkage tools. In addition, CIDACS-RL can be deployed on standard computers without the need for high-speed processors and distributed infrastructures
- …