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Background The Australian hospital-acquired complication (HAC) policy was introduced to facilitate negative funding adjustments in Australian hospitals using ICD-10-AM codes.Objective The aim of this study was to determine the positive predictive value (PPV) of the ICD-10-AM codes in the HAC framework to detect hospital-acquired pneumonia in patients with cancer and to describe any change in PPV before and after implementation of an electronic medical record (EMR) at our centre.Method A retrospective case review of all coded pneumonia episodes at the Peter MacCallum Cancer Centre in Melbourne, Australia spanning two time periods (01 July 2015 to 30 June 2017 [pre-EMR period] and 01 September 2020 to 28 February 2021 [EMR period]) was performed to determine the proportion of events satisfying standardised surveillance definitions.Results HAC-coded pneumonia occurred in 3.66% (n= 151) of 41,260 separations during the study period. Of the 151 coded pneumonia separations, 27 satisfied consensus surveillance criteria, corresponding to an overall PPV of 0.18 (95% CI: 0.12, 0.25). The PPV was approximately three times higher following EMR implementation (0.34 [95% CI: 0.19, 0.53] versus 0.13 [95% CI: 0.08, 0.21]; p= .013).Conclusion The current HAC definition is a poor-to-moderate classifier for hospital-acquired pneumonia in patients with cancer and, therefore, may not accurately reflect hospital-level quality improvement. Implementation of an EMR did enhance case detection, and future refinements to administratively coded data in support of robust monitoring frameworks should focus on EMR systems.Implications Although ICD-10-AM data are readily available in Australian healthcare settings, these data are not sufficient for monitoring and reporting of hospital-acquired pneumonia in haematology-oncology patients.

A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.