Learning Genomic Sequence Representations using Graph Neural Networks
over De Bruijn Graphs
- URL: http://arxiv.org/abs/2312.03865v1
- Date: Wed, 6 Dec 2023 19:23:53 GMT
- Title: Learning Genomic Sequence Representations using Graph Neural Networks
over De Bruijn Graphs
- Authors: Kacper Kapu\'sniak, Manuel Burger, Gunnar R\"atsch, Amir Joudaki
- Abstract summary: Existing techniques often neglect intricate structural details, emphasizing mainly contextual information.
We developed k-mer embeddings that merge contextual and string information by enhancing De Bruijn graphs with structural similarity connections.
Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.
- Score: 1.8024397171920885
- License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
- Abstract: The rapid expansion of genomic sequence data calls for new methods to achieve
robust sequence representations. Existing techniques often neglect intricate
structural details, emphasizing mainly contextual information. To address this,
we developed k-mer embeddings that merge contextual and structural string
information by enhancing De Bruijn graphs with structural similarity
connections. Subsequently, we crafted a self-supervised method based on
Contrastive Learning that employs a heterogeneous Graph Convolutional Network
encoder and constructs positive pairs based on node similarities. Our
embeddings consistently outperform prior techniques for Edit Distance
Approximation and Closest String Retrieval tasks.
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