Long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes is essential in order to uncover the functional role of individual RNA transcripts, especially for unannotated and sparsely discovered RNA sequences with no known interactions. Recently, sequence-based deep learning and network embedding methods are gaining traction as high-performing and flexible approaches that can either predict RNA-RNA interactions from a sequence or infer likely/missing interactions from patterns that may exist in the network topology. However, the majority of these current methods have several limitations, e.g., the inability to perform inductive predictions, to distinguish the directionality of interactions, or to integrate various sequence, interaction, expression, and genomic annotation datasets. We proposed a novel deep learning-based framework, rna2rna, which learns from RNA sequences to produce a low-dimensional embedding that preserves the proximities in both the interactions topology and the functional affinity topology. In this proposed embedding space, we have designated a two-part "source and target contexts" to capture the receptive fields of each RNA transcript, while encapsulating the heterogenous crosstalk interactions between lncRNAs and miRNAs. The proximity between RNAs in this embedding space also uncovers the second-order relationships that allow to accurately infer a novel directed interaction or functional similarity between any two RNA sequences. From experimental results, our method exhibits superior performance in measured AUPR rates compared to state-of-art approaches at predicting missing interactions in different RNA-RNA interaction databases. Additional results suggest that our proposed framework can capture a manifold for heterogeneous RNA sequences to discover novel functional annotations. functional interaction mechanisms, lncRNAs are known to act as miRNA decoys, derepress gene expression by competing with miRNAs for shared mRNA targets, or directly regulate gene expression. 1 Determining the biological functions of the individual lncRNAs remains a challenge as most of these RNA transcripts are currently unannotated, and their known interactions are sparse. Recent advances in RNA sequencing (RNA-Seq), deep sequencing (CLIP-seq, LIGR-Seq), and computational methods allow for an unprecedented analysis of such transcripts and have enabled researchers to generate large-scale interaction and functional annotation databases. However, the interaction networks generated from such data are often scant and incomplete in the number of lncRNAs covered. Furthermore, although a large number of lncRNAs have been identified, only a few hundreds have had functional and molecular mechanisms determined to date, as observed in as lncRNAdb. 2 In other avenues, a growing number of lncRNAs are being assigned biological f...