DNA Storage Decoding with Error-Threshold Graph Alignment
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Solution Overview
Problem
The existing DNA data storage process is hindered by the time-consuming nature of data retrieval due to sequential steps and high error rates in single-molecule sequencing, which makes real-time decoding challenging.
Innovation Solution
A method and apparatus for DNA storage encoding/decoding that employs a sliding window approach with error threshold constraints and a directed graph to align and correct sequencing errors, allowing for real-time decoding and error correction.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Speed
If traditional sequential decoding process is used, then decoding accuracy can be maintained, but decoding speed becomes very slow and time-consuming
Solution Approach 1:
The patent divides the decoding process into parallel segments by implementing multiple decoding paths simultaneously. Different decoding algorithms operate on different portions of the sequencing data in parallel, rather than sequentially processing through each step. This segmentation enables the system to achieve GB-level throughput by processing multiple data streams concurrently, directly resolving the speed-time contradiction.
2Speed
If single-molecule sequencing is used, then sequencing speed is fast, but error rate becomes very high making traditional error correction inapplicable
Solution Approach 1:
The patent merges multiple decoding algorithms and error correction methods into a unified parallel processing framework. By combining different decoding approaches (such as greedy decoding, Viterbi decoding, and other algorithmic paths) and executing them simultaneously on parallel computing units, the system maintains the high sequencing speed of single-molecule sequencing while achieving reliable error correction through algorithmic diversity and parallel validation.
Solution Approach 2:
The patent implements feedback mechanisms where decoding results from multiple parallel paths are continuously monitored and evaluated. Error patterns are detected and fed back into the system to dynamically adjust decoding parameters and select the most reliable decoding path. This feedback loop enables real-time error correction while maintaining high processing speed, resolving the contradiction between speed and reliability.
3Reliability
If multiple error correction steps are implemented, then decoding accuracy improves, but process complexity and time consumption increase significantly
Solution Approach 1:
The patent implements a dynamic error correction system where the complexity and number of correction steps are adaptively adjusted based on the actual error characteristics of the input data. The system dynamically selects and combines correction algorithms, applying more complex corrections only when necessary. This dynamic approach maintains high decoding accuracy while avoiding unnecessary computational overhead and process complexity.
Data Source
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AI summary
Disclosed are a method and apparatus for DNA storage encoding/decoding and rules thereof. The method comprises: executing single-molecule sequencing on a reference sequence, and acquiring actual sequencing data of the single-molecule sequencing; comparing the actual sequencing data with reference data of the reference sequence, counting the frequency, in the actual sequencing data, of sequencing errors of each sequence segment having a length of k, and calculating the proportion, in the actual sequencing data, of sequencing errors of each sequence segment having a length of k, that is, the error rate; and performing removal by using a sequence segment, the error rate of which exceeds a threshold, as a limiting condition. In the method of the present invention, the steps of DNA storage encoding/decoding are simplified, the time sequence of the steps is eliminated by using a threshold, and the complexity of data processing is reduced.