A Combinatorial Perspective on Random Access Efficiency for DNA Storage
Bibliographic record
Abstract
We investigate the fundamental limits of the recently proposedrandom access coverage depth problemfor DNA data storage. Under this paradigm, it is assumed that the user information consists ofkinformation strands, which are encoded intonstrands via a generator matrixG. During the sequencing process, the strands are read uniformly at random, as each strand is available in a large number of copies. In this context, the random access coverage depth problem refers to the expected number of reads (i.e., sequenced strands) required to decode a specific information strand requested by the user. This problem heavily depends on the generator matrixG, and besides computing the expectation for different choices ofG, the goal is to construct matrices that minimize the maximum expectation over all possible requested information strands, denoted byTmax(G). In this paper, we introduce new techniques to investigate the random access coverage depth problem, capturing its combinatorial nature and identifying the structural properties of generator matrices that are advantageous. We establish two general formulas to determineTmax(G) for arbitrary generator matrices. The first formula depends on the linear dependencies between columns ofG, whereas the second formula takes into account recovery sets and their intersection structure. We also introduce the concept ofrecovery balanced codesand provide three sufficient conditions for a code to be recovery balanced. These conditions can be used to computeTmax(G) for various families of codes, such as MDS, simplex, Hamming, and binary Reed-Muller codes. Additionally, we study the performance of modified systematic MDS and simplex matrices, showing that the best results forTmax(G) are achieved with a specific combination of encoded strands and replication of the information strands.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.008 | 0.048 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.005 |
| Scholarly communication | 0.008 | 0.018 |
| Open science | 0.006 | 0.004 |
| Research integrity | 0.003 | 0.005 |
| Insufficient payload (model declined to judge) | 0.017 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".