DNA Data Reconstruction Trellises for IDS Error Correction
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Existing DNA data storage systems face significant challenges in reducing errors due to insertion, deletion, and substitution (IDS) errors, which current outer and inner codes have not adequately addressed, leading to inefficiencies in encoding and decoding operations.
Innovation Solution
The use of trellis-based reconstruction algorithms and inner codes that model the DNA sequencing channel as a finite state machine, allowing for the construction of independent trellises for multiple noisy traces, and employing a forward-backward algorithm to compute posterior marginal probabilities and iteratively refine the data message sequence estimation, leveraging redundancy within DNA sequences.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If outer codes and inner codes are used to mitigate IDS errors in DNA data storage, then error detection and correction capability is improved, but encoding and decoding complexity increases
Solution Approach 1:
The patent segments the error correction task by separating outer codes (for recovering lost DNA sequences) from inner codes (for correcting errors within individual strands). This segmentation allows each code type to be optimized independently, reducing overall system complexity while maintaining comprehensive error protection.
Solution Approach 2:
The patent introduces trellis-based reconstruction algorithms as an intermediary layer between the DNA sequencing channel and the outer/inner codes. This intermediary processes noisy traces to reconstruct original DNA sequences before error correction, simplifying the burden on traditional error correction codes and reducing their complexity requirements.
2Reliability
If redundant bases are introduced in inner codes to correct errors within a single DNA strand, then error correction capability is improved, but storage density decreases
Solution Approach 1:
The patent applies partial redundancy by introducing redundant bases only in specific positions within DNA strands where error correction is most needed, rather than uniformly across all positions. This selective approach provides sufficient error correction capability while minimizing the impact on storage density.
Solution Approach 2:
The patent implements local quality by varying the redundancy structure at different positions within the DNA strand. Inner codes are designed with position-dependent redundancy patterns that provide enhanced error correction where synthesis and sequencing errors are most likely to occur, while maintaining higher information density in less error-prone regions.
3Reliability
If multiple DNA strands are synthesized and sequenced to recover data, then error mitigation through redundancy is improved, but the number of sequencing operations and computational processing increases
Solution Approach 1:
The patent performs preliminary action by constructing trellis models and computing forward-backward probabilities before final data reconstruction. This pre-processing of multiple noisy traces allows the system to identify and correct errors early in the decoding process, reducing the need for extensive re-sequencing and iterative processing.
Solution Approach 2:
The patent implements feedback mechanisms through the forward-backward algorithm, where decoding results from multiple strands are fed back into the trellis model to refine probability estimates. This feedback loop enables the system to progressively improve reconstruction accuracy without requiring a linear increase in the number of sequencing operations.
Data Source
Figure 1A
Figure 1B
Figure 1C
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.