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Theoretical Limits of Language Model Alignment $f$-Divergence Regularized RLHF: Two Tales of Sampling and Unified Analyses A Unified Measure-Theoretic View of Diffusion, Score-Based, and Flow Matching Generative Models When Can Voting Help, Hurt, or Change Course? Exact Structure of Binary Test-Time Aggregation When Semantic Communication Meets Queueing: Cross-Layer Latency and Task Fidelity Optimization Convexity in Disguise: A Theoretical Framework for Nonconvex Low-Rank Matrix Estimation Conditional Diffusion Under Linear Constraints: Langevin Mixing and Information-Theoretic Guarantees Sharp Capacity Thresholds in Linear Associative Memory: From Winner-Take-All to Listwise Retrieval Expert Routing for Communication-Efficient MoE via Finite Expert Banks Contextual Memory-Enhanced Source Coding for Low-SNR Communications Realizable Bayes-Consistency for General Metric Losses Leveraging Code Automorphisms for Improved Syndrome-Based Neural Decoding A Hierarchical Sampling Framework for bounding the Generalization Error of Federated Learning Dueling DDQN-Based Adaptive Multi-Objective Handover Optimization for LEO Satellite Networks The Causal Description Gap: Information-Theoretic Separations Across Pearl's Hierarchy Optimization of CV-QKD Under Practical Constraints Benchmarking Wireless Representations: High-Dimensional vs. Compressed Embeddings for Efficiency and Robustness Real-Time Text Transmission via LLM-Based Entropy Coding over Fixed-Rate Channels SwiftChannel: Algorithm-Hardware Co-Design for Deep Learning-Based 5G Channel Estimation Evolving Token Communication with Parametric Memory Network Remote Action Generation: Remote Control with Minimal Communication The (Marginal) Value of a Search Ad: An Online Causal Framework for Repeated Second-price Auctions Stabilizing Private LASSO under Heterogeneous Covariates via Anisotropic Objective Perturbation Linear-Readout Floors and Threshold Recovery in Computation in Superposition Soft Graph Diffusion Transformer for MIMO Detection Hierarchical Federated Learning for Networked AI: From Communication Saving to Architecture-Aware Design Exponential families from a single KL identity MIFair: A Mutual-Information Framework for Intersectionality and Multiclass Fairness Diffusion-OAMP for Joint Image Compression and Wireless Transmission Decoupled Descent: Exact Test Error Tracking Via Approximate Message Passing
Permutation Recovery Problem against Deletion Errors for ...
Shubhransh Singhvi, Charchit Gupta, Avital Boruchovsky, Yuval Go · 2024-03-23 · via cs.IT updates on arXiv.org

Owing to its immense storage density and durability, DNA has emerged as a promising storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules called data blocks that are stored in an unordered way. To handle the unordered nature of DNA data storage systems, a unique address is typically prepended to each data block to form a DNA strand. However, DNA storage systems are prone to errors and generate multiple noisy copies of each strand called DNA reads. Thus, we study the permutation recovery problem against deletions errors for DNA data storage. The permutation recovery problem for DNA data storage requires one to reconstruct the addresses or in other words to uniquely identify the noisy reads. By successfully reconstructing the addresses, one can essentially determine the correct order of the data blocks, effectively solving the clustering problem. We first show that we can almost surely identify all the noisy reads under certain mild assumptions. We then propose a permutation recovery procedure and analyze its complexity.