Generalising sequence models for epigenome predictions with tissue and
  assay embeddings
Jacob Deasy Ron Schwessinger Ferran Gonzalez Stephen Young Kim Branson
Sequence modelling approaches for epigenetic profile prediction have recently
expanded in terms of sequence length, model size, and profile diversity.
However, current models cannot infer on many experimentally feasible tissue and
assay pairs due to poor usage of contextual information, limiting $\textit{in
silico}$ understanding of regulatory genomics. We demonstrate that strong
correlation can be achieved across a large range of experimental conditions by
integrating tissue and assay embeddings into a Contextualised Genomic Network
(CGN). In contrast to previous approaches, we enhance long-range sequence
embeddings with contextual information in the input space, rather than
expanding the output space. We exhibit the efficacy of our approach across a
broad set of epigenetic profiles and provide the first insights into the effect
of genetic variants on epigenetic sequence model training. Our general approach
to context integration exceeds state of the art in multiple settings while
employing a more rigorous validation procedure.