Soft Information Generation for DNA Storage LDPC Decoding
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Solution Overview
Problem
DNA-based storage systems are prone to errors during synthesis, storage, and sequencing, limiting their reliability compared to traditional electronic storage systems, as they cannot utilize soft bits for error correction.
Innovation Solution
Generating and updating soft information by comparing multiple copies of DNA sequences to determine bit error rates and log likelihood ratios, which are then used to enhance the accuracy and efficiency of low-density parity-check (LDPC) codes in DNA-based storage systems.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Reliability
If multiple copies of DNA strings are generated and majority rule is applied for error correction, then error correction capability is improved, but system complexity and processing overhead increase
Solution Approach 1:
The patent pre-calculates and stores soft information (log-likelihood ratios) during the DNA sequencing and consensus generation phase. This preliminary computation of reliability metrics allows the LDPC decoder to efficiently utilize soft bits without requiring complex real-time calculations, thus improving error correction while managing system complexity
Solution Approach 2:
The patent introduces soft information (log-likelihood ratios) as an intermediary between the DNA consensus generation and LDPC decoding processes. This intermediary carries reliability information that bridges the gap between hard consensus bits and soft-bit LDPC decoding, enabling improved error correction without directly increasing the complexity of either the consensus generation or decoding processes
2Measurement precision
If soft bit information is generated and used in LDPC decoders, then decoding accuracy and efficiency are improved, but computational requirements and processing time increase
Solution Approach 1:
The patent computes soft information (log-likelihood ratios) in advance during the DNA sequencing and consensus generation phase, storing these pre-computed values for use during decoding. This preliminary computation avoids the need for time-consuming real-time calculations during the actual decoding process, thereby maintaining high decoding accuracy while reducing processing time
Solution Approach 2:
The system generates its own soft information internally during the consensus generation process, using the same DNA sequence data without requiring external or additional computational resources. This self-service approach to soft information generation provides accurate soft bits for LDPC decoding without adding external processing overhead
Data Source
AI summary
A DNA-based storage system generates soft information that increases an efficiency and/or a reliability of a low-density parity-check (LDPC) decoder of the DNA-based storage system. The soft information is generated by comparing corresponding DNA segments of multiple copies of a DNA sequence to determine a ratio of DNA symbols in agreement in each of the DNA segments and/or whether a length of each of the DNA segments are the same. The ratio of symbols in agreement and/or the length information may be used to determine a bit error rate (BER) of a particular DNA segment. The BER of each DNA segment may then be used to determine soft information, or a log likelihood ratio (LLR), associated with that particular DNA segment.