Exact(6)
To assess the biological relevance of imbalance predictions, we used electrophoretic mobility shift assays to functionally test for predicted allelic differences in CREB1 binding in the GM12878 lymphoblast cell line.
This suggests that errors may exist in the complete genotype data leading to false negative imbalance predictions.
Overall, we found that for all alignments, imbalance predictions were accurately replicated using incomplete genotypes at sites where both alleles were used in the alignment.
The lack of a comprehensive catalog of experimentally validated sites with functional allelic differences limits our ability to evaluate allelic imbalance predictions.
We experimentally detected differential protein binding at six of nine tested imbalance predictions from AA-ALIGNER for CREB1 (Cyclic-AMP Responsive Element Binding protein 1) binding in GM12878 ChIP-seq data, including imbalances at two disease-associated loci.
We created an allelic imbalance detection pipeline, AA-ALIGNER, to remove reference mapping biases influencing allelic imbalance detection and evaluate accuracy of allelic imbalance predictions in the absence of complete genotype data.
Similar(54)
The above analyses assume that imbalances detected using complete genotypes are the most accurate for comparing the effects of reduced information and parameter settings, but they do not address the functional accuracy of the imbalance prediction.
Note that if the model is trained with uniform weights, our features can achieve a higher (R^{2}=0.47) and mean absolute error of 9.3 years, but at the expense of imbalance in predictions with higher error for less frequent ages.
More concretely, the previous paper presented a classification analysis process of imbalance data prediction based on Apache Hadoop [39], Hive [65] and Mahout [56].
Former works have stressed the dramatic effect of class imbalance on link prediction problems in social networks, especially in mobile phone networks ([11, 20]).
Our results indicate that including any amount of genotype information, or both alleles at common variants, significantly increases accuracy of imbalance detection compared to predictions when complete genotypes are known.
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