Epiphany Quiz

Besides the human cell lines, what species' cell lines were used for training/testing the model?

• Guinea Pigs

• Bears

• Mice

• Tigers

What is the resolution of the epigenomic tracks used as inputs to Epiphany?

• 100bp

• 150bp

• 200bp

• 100kbp

• To weight the losses coming from the SVM

• To generate the loss using L1/L2 Norm

• To generate the loss using AUC and softmax

• To weight the losses from the respective loss functions.

Which normalization method produced the highest correlation between ground truth and predicted contact matrices, and between ground truth and predicted insulation scores?

• ICE

• HiC-DC+ Z-scores

• HiC-DC+ obs/exp counts

• KR

Masking which epigenomic input track resulted in Epiphany performing just as well as it did with all input tracks?

• DNase I

• H3K27me3

• CTCF

• H3K27ac

At which of the following tasks did the MSE model outperform the MSE+GAN model?

• Constructing high perceptual quality HiC matrices

• Predicting 3D structural changes from epigenomic perturbation

• Predicting significant interactions at high genomic distances

• Reducing blurriness in predicted matrices

What is the purpose of the insulation score?

• For evaluating the similarity of HiC matricies

• For finding topological domains

• For featurizing epigenomic tracks

• For quantifying the long range dependencies

Which model is based on the Basenji architecture base?

• Epiphany

• DeepC

• ConvMHSA

• Akita

What are the downsides of using the full sequence as input?

• Expensive with respect to compute time (i.e. CPU/GPU time)

• Expensive with respect to space complexity (i.e. RAM usage)

• Excludes cell-type specific information

• Makes it harder for the model to learn the contextual relationships within the sequence.

Outside the context of this paper, what is a(n) Epiphany?

• The annual ritual where Brown and Harvard students engage in a heated debate to decide which campus has the better selection of mystical unicorn stables.

• An extension of the python "pip" package manager

• The phenomenon where aliens visit Earth, bestow profound wisdom upon us, and then challenge humans to interstellar dance-offs to determine the fate of the universe.

• A sudden realization that changes someones world view