DNA Data Storage IDS Trellises for Multi-Trace Error Correction
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current DNA data storage systems face challenges in reducing errors during encoding and decoding operations, particularly due to insertion-deletion-substitution (IDS) errors, despite the use of outer and inner codes, and there is a need for improved error correction mechanisms.
Innovation Solution
The implementation of IDS trellises for multiple traces, modeled as finite state machines, which independently construct trellises for each noisy DNA sequence and use forward-backward algorithms to compute posterior marginal probabilities, allowing for progressive decoding and error correction by aggregating beliefs across multiple traces.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If outer codes and inner codes are used for error correction in DNA data storage, then error mitigation is improved, but device complexity increases
Solution Approach 1:
The patent divides the error correction task into two distinct segments: outer codes that handle missing or under-sampled DNA sequences by synthesizing redundant sequences, and inner codes that detect and correct errors within individual DNA strands by introducing redundant bases. This segmentation allows each code type to specialize in specific error types, improving overall reliability while managing complexity through functional separation.
Solution Approach 2:
The patent introduces an intermediary mapping layer between the binary data and DNA sequences that incorporates both outer and inner code structures. This intermediary layer translates binary data into DNA sequences with built-in redundancy mechanisms, allowing error correction to occur at multiple levels without requiring complex post-processing of the raw DNA data.
2Manufacturing precision
If redundant bases are introduced in inner codes to correct errors within a single DNA strand, then manufacturing precision is improved, but loss of information increases due to reduced data density
Solution Approach 1:
The patent applies local quality by introducing redundant bases only in specific locations within the DNA sequence rather than uniformly throughout. The inner code structure strategically places redundant bases at positions where they can maximize error detection capability while minimizing impact on overall data density. This localized approach allows high precision error correction where needed while preserving data storage efficiency in other regions.
Solution Approach 2:
The patent changes the parameter of base redundancy ratio dynamically based on the specific requirements of the data being stored and the expected error rates. By adjusting the proportion of redundant bases in the inner code structure, the system can optimize the balance between error correction capability and data storage density for different application scenarios.
Data Source
AI summary
Techniques for achieving reductions in cost of encoding and decoding operations used in DNA data storage systems to facilitate reducing errors in those encoding and decoding operations while accounting for a code structure used during the encoding and decoding by constructing and using insertion-deletion-substitution (IDS) trellises for multiple traces are disclosed. A DNA sequencing channel is used to randomly sample and sequence DNA strands to generate noisy traces. Multiple trellises are independently constructed for each respective noisy trace. A forward-backward algorithm is run on each trellis to compute posterior marginal probabilities for vertices included in each trellises. An estimate of the data message sequence is then computed.