Vector Embeddings by Sequence Similarity and Context for Improved Compression, Similarity Search, Clustering, Organization, and Manipulation of cDNA Libraries
This addresses computational bottlenecks in bioinformatics research involving gene sequence data, though it appears incremental as an application of existing embedding techniques to a specific domain.
The paper tackles the limitations of FASTA/FASTQ files for gene sequence analysis by transforming sequences into vector embeddings, resulting in improved compression, faster similarity searches, and better clustering of cDNA libraries.
This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes, slow processing speeds for mapping and alignment, and contextual dependencies. These challenges significantly hinder investigations and tasks that involve finding similar sequences. The solution lies in transforming sequences into an alternative representation that facilitates easier clustering into similar groups compared to the raw sequences themselves. By assigning a unique vector embedding to each short sequence, it is possible to more efficiently cluster and improve upon compression performance for the string representations of cDNA libraries. Furthermore, through learning alternative coordinate vector embeddings based on the contexts of codon triplets, we can demonstrate clustering based on amino acid properties. Finally, using this sequence embedding method to encode barcodes and cDNA sequences, we can improve the time complexity of the similarity search by coupling vector embeddings with an algorithm that determines the proximity of vectors in Euclidean space; this allows us to perform sequence similarity searches in a quicker and more modular fashion.