ArticlePloS one2021
Optical pattern generator for efficient bio-data encoding in a photonic sequence comparison architecture.
Article in PloS one, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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Who cites it
2 citing papers in PubMed.
- HELIOS: High-speed sequence alignment in optics.PLoS computational biology · 2022Article
- WalkIm: Compact image-based encoding for high-performance classification of biological sequences using simple tuning-free CNNs.PloS one · 2022Article
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Authors and funding
3 authors.
Funding
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Abstract
In this study, optical technology is considered as SA issues' solution with the potential ability to increase the speed, overcome memory-limitation, reduce power consumption, and increase output accuracy. So we examine the effect of bio-data encoding and the creation of input images on the pattern-recognition error-rate at the output of optical Vander-lugt correlator. Moreover, we present a genetic algorithm-based coding approach, named as GAC, to minimize output noises of cross-correlating data. As a case study, we adopt the proposed coding approach within a correlation-based optical architecture for counting k-mers in a DNA string. As verified by the simulations on Salmonella whole-genome, we can improve sensitivity and speed more than 86% and 81%, respectively, compared to BLAST by using coding set generated by GAC method fed to the proposed optical correlator system. Moreover, we present a comprehensive report on the impact of 1D and 2D cross-correlation approaches, as-well-as various coding parameters on the output noise, which motivate the system designers to customize the coding sets within the optical setup.
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Registered trials
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