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The strength of our predictor was successfully validated on an independent test cohort.
However, our predictor was insensitive to the disease stage and successfully dealt with this issue.
Our predictor was shown to enhance annotation inference for many 'uncharacterized' proteins.
The K562 line was chosen as a negative control as it is a cancer cell line dependent on BCR-Abl expression to test if our predictor was, in fact, recognizing non-specific dependence on any activated kinase.
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In particular, our predictor is based on the fifth algebraic order Adams-Bashforth scheme and our corrector on the sixth algebraic order Adams-Moulton scheme.
Of note, for liposarcomas, we were able to show that our predictor is tracking adipocyte differentiation of MFH irrespective of the myxoid or non-myxoid sub-classification.
Thus, the biological relevance of our predictor is supported by the presence of a significantly high number of predicted substrates in process/pathways related to established roles of Ste20p.
Furthermore, MFH-samples predicted as LIPO (MFH-LIPO) did not cluster exclusively with myxoid or with non-myxoid liposarcomas; rather certain MFH-LIPO clustered with myxoid while other MFH-LIPO clustered with non-myxoid liposarcomas suggesting that our predictor is capturing information associated with adipocyte differentiation irrespective of the myxoid or non-myxoid subclassification (Figure S1).
These results indicated that our predictor is a useful tool to predict RNA-binding proteins.
Our predictor is trained using breakpoints that took place along the human lineage since amniote divergence.
Another characteristic of our predictor is the introduction of a probabilistic model to the outputs.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com