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Moreover, we demonstrated clusDCA's ability to identify putatively associated genes for newly created GO labels without any annotations, which suggests that our method can be used to improve poorly annotated labels and thus takes a significant step towards more comprehensive understanding of gene or protein function in various organisms.
For example, we consider the yaw pose annotated labels right and left to be extreme and the labels slightly right and slightly left to be neutral.
However, DCA also suffers from overfitting for sparsely annotated labels when predicting GO labels for a larger human interactome, if we want to train label-wise classifiers for all labels.
Because labels that are similar to each other in the ontology graph are co-localized in the label vector space, classifiers for sparsely annotated labels will now favor genes associated with other similar labels in the neighborhood.
For DCA, we tested only the kNN version, because the SVM version seriously suffers from overfitting for sparsely annotated labels and also does not scale to the human dataset.
There are 1,583,882 images with valid annotated labels for gross tonnage.
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Although based on DCA, clusDCA is a substantial advance, as evidenced by its superior performance over DCA, as well as GeneMANIA and HC, on sparsely annotated GO labels, while maintaining a comparable performance on labels with many genes.
The major idea of clusDCA is to leverage similarity between functional labels in addition to similarity between genes to prevent overfitting of sparsely annotated GO labels.
Thus, in the experiment, only one person annotated the labels.
Each photo was annotated with labels, legends, and text explaining what the specimen was, how it was observed (whole or mounted on a microscope slide), what type of sectioning was used (whole mount, cross section, longitudinal section), and whether it was observed with a dissecting or compound microscope (and at what total magnification).
These histology sections are annotated with labels detailing the various anatomical structures that can be identified at each stage.
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