| 1. |
- Pepic, I., et al.
(författare)
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Early detection of sepsis using artificial intelligence : a scoping review protocol
- 2021
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Ingår i: Systematic Reviews. - : Springer Nature. - 2046-4053. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Sepsis is a life-threatening organ dysfunction caused by a dysregulated host response to infection. To decrease the high case fatality rates and morbidity for sepsis and septic shock, there is a need to increase the accuracy of early detection of suspected sepsis in prehospital and emergency department settings. This may be achieved by developing risk prediction decision support systems based on artificial intelligence.Methods: The overall aim of this scoping review is to summarize the literature on existing methods for early detection of sepsis using artificial intelligence. The review will be performed using the framework formulated by Arksey and O’Malley and further developed by Levac and colleagues. To identify primary studies and reviews that are suitable to answer our research questions, a comprehensive literature collection will be compiled by searching several sources. Constrictions regarding time and language will have to be implemented. Therefore, only studies published between 1 January 1990 and 31 December 2020 will be taken into consideration, and foreign language publications will not be considered, i.e., only papers with full text in English will be included. Databases/web search engines that will be used are PubMed, Web of Science Platform, Scopus, IEEE Xplore, Google Scholar, Cochrane Library, and ACM Digital Library. Furthermore, clinical studies that have completed patient recruitment and reported results found in the database ClinicalTrials.gov will be considered. The term artificial intelligence is viewed broadly, and a wide range of machine learning and mathematical models suitable as base for decision support will be evaluated. Two members of the team will test the framework on a sample of included studies to ensure that the coding framework is suitable and can be consistently applied. Analysis of collected data will provide a descriptive summary and thematic analysis. The reported results will convey knowledge about the state of current research and innovation for using artificial intelligence to detect sepsis in early phases of the medical care chain.Ethics and dissemination: The methodology used here is based on the use of publicly available information and does not need ethical approval. It aims at aiding further research towards digital solutions for disease detection and health innovation. Results will be extracted into a review report for submission to a peer-reviewed scientific journal. Results will be shared with relevant local and national authorities and disseminated in additional appropriate formats such as conferences, lectures, and press releases.
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| 2. |
- Buongermino Pereira, Mariana, 1982, et al.
(författare)
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A comprehensive survey of integron-associated genes present in metagenomes
- 2020
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 21:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundIntegrons are genomic elements that mediate horizontal gene transfer by inserting and removing genetic material using site-specific recombination. Integrons are commonly found in bacterial genomes, where they maintain a large and diverse set of genes that plays an important role in adaptation and evolution. Previous studies have started to characterize the wide range of biological functions present in integrons. However, the efforts have so far mainly been limited to genomes from cultivable bacteria and amplicons generated by PCR, thus targeting only a small part of the total integron diversity. Metagenomic data, generated by direct sequencing of environmental and clinical samples, provides a more holistic and unbiased analysis of integron-associated genes. However, the fragmented nature of metagenomic data has previously made such analysis highly challenging.ResultsHere, we present a systematic survey of integron-associated genes in metagenomic data. The analysis was based on a newly developed computational method where integron-associated genes were identified by detecting their associated recombination sites. By processing contiguous sequences assembled from more than 10 terabases of metagenomic data, we were able to identify 13,397 unique integron-associated genes. Metagenomes from marine microbial communities had the highest occurrence of integron-associated genes with levels more than 100-fold higher than in the human microbiome. The identified genes had a large functional diversity spanning over several functional classes. Genes associated with defense mechanisms and mobility facilitators were most overrepresented and more than five times as common in integrons compared to other bacterial genes. As many as two thirds of the genes were found to encode proteins of unknown function. Less than 1% of the genes were associated with antibiotic resistance, of which several were novel, previously undescribed, resistance gene variants.ConclusionsOur results highlight the large functional diversity maintained by integrons present in unculturable bacteria and significantly expands the number of described integron-associated genes.
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| 3. |
- Imberg, Henrik, 1991, et al.
(författare)
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Optimal sampling in unbiased active learning
- 2020
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Ingår i: Proceedings of Machine Learning Research. - 2640-3498. ; 108, s. 559-569
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Konferensbidrag (refereegranskat)abstract
- A common belief in unbiased active learning is that, in order to capture the most informative instances, the sampling probabilities should be proportional to the uncertainty of the class labels. We argue that this produces suboptimal predictions and present sampling schemes for unbiased pool-based active learning that minimise the actual prediction error, and demonstrate a better predictive performance than competing methods on a number of benchmark datasets. In contrast, both probabilistic and deterministic uncertainty sampling performed worse than simple random sampling on some of the datasets.
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| 4. |
- Imberg, Henrik, 1991, et al.
(författare)
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Optimal subsampling designs
- 2023
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Subsampling is commonly used to overcome computational and economical bottlenecks in the analysis of finite populations and massive datasets. Existing methods are often limited in scope and use optimality criteria (e.g., A-optimality) with well-known deficiencies, such as lack of invariance to the measurement-scale of the data and parameterisation of the model. A unified theory of optimal subsampling design is still lacking. We present a theory of optimal design for general data subsampling problems, including finite population inference, parametric density estimation, and regression modelling. Our theory encompasses and generalises most existing methods in the field of optimal subdata selection based on unequal probability sampling and inverse probability weighting. We derive optimality conditions for a general class of optimality criteria, and present corresponding algorithms for finding optimal sampling schemes under Poisson and multinomial sampling designs. We present a novel class of transformation- and parameterisation-invariant linear optimality criteria which enjoy the best of two worlds: the computational tractability of A-optimality and invariance properties similar to D-optimality. The methodology is illustrated on an application in the traffic safety domain. In our experiments, the proposed invariant linear optimality criteria achieve 92-99% D-efficiency with 90-95% lower computational demand. In contrast, the A-optimality criterion has only 46% and 60% D-efficiency on two of the examples.
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