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An expanded evaluation of protein function prediction methods shows an improvement in accuracy
(2016)
Background
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.
Results
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.
Conclusions
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.
Bridge-local latency computation is often regarded with caution, as historic efforts with the Credit-Based Shaper (CBS) showed that CBS requires network wide information for tight bounds. Recently, new shaping mechanisms and timed gates were applied to achieve such guarantees nonetheless, but they require support for these new mechanisms in the forwarding devices.
This document presents a per-hop latency bound for individual streams in a class-based network that applies the IEEE 802.1Q strict priority transmission selection algorithm. It is based on self-pacing talkers and uses the accumulated latency fields during the reservation process to provide upper bounds with bridge-local information. The presented delay bound is proven mathematically and then evaluated with respect to its accuracy. It indicates the required information that must be provided for admission control, e.g., implemented by a resource reservation protocol such as IEEE 802.1Qdd. Further, it hints at potential improvements regarding new mechanisms and higher accuracy given more information.
Asynchronous Traffic Shaping enabled bounded latency with low complexity for time sensitive networking without the need for time synchronization. However, its main focus is the guaranteed maximum delay. Jitter-sensitive applications may still be forced towards synchronization. This work proposes traffic damping to reduce end-to-end delay jitter. It discusses its application and shows that both the prerequisites and the guaranteed delay of traffic damping and ATS are very similar. Finally, it presents a brief evaluation of delay jitter in an example topology by means of a simulation and worst case estimation.