arXiv subjects

Roman Sokolovskii

Publications and source records attributed to Roman Sokolovskii.

9 recordsLinked to original sources

arXiv2026

SynDe: Syndrome-guided Decoding of Raw Nanopore Reads

Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the basecaller, but such approaches only accommodate a limited number of code classes and incur significant decoding complexity. To overcome these limitations, we propose two algorithms: PrimerSeeker, which efficiently detects primer sequences in raw nanopore sequencing reads, and SynDe, a decoder that operates on the same raw reads and supports any linear error correction code with a low-complexity graphical representation. PrimerSeeker provides primer location estimates close to those of existing approaches while being better suited for real-time primer detection during sequencing. SynDe performs well with convolutional codes augmented with periodic markers, often approaching or exceeding the performance of existing algorithms with a lower time complexity. Remarkably, the confidence scores produced by SynDe reliably identify which of its outputs should be discarded.

cs.IT↗

arXiv2026

Lower Bounds for the Algorithmic Complexity of Learned Indexes

Learned index structures aim to accelerate queries by training machine learning models to approximate the rank function associated with a database attribute. While effective in practice, their theoretical limitations are not fully understood. We present a general framework for proving lower bounds on query time for learned indexes, expressed in terms of their space overhead and parameterized by the model class used for approximation. Our formulation captures a broad family of learned indexes, including most existing designs, as piecewise model-based predictors. We solve the problem of lower bounding query time in two steps: first, we use probabilistic tools to control the effect of sampling when the database attribute is drawn from a probability distribution. Then, we analyze the approximation-theoretic problem of how to optimally represent a cumulative distribution function with approximators from a given model class. Within this framework, we derive lower bounds under a range of modeling and distributional assumptions, paying particular attention to the case of piecewise linear and piecewise constant model classes, which are common in practical implementations. Our analysis shows how tools from approximation theory, such as quantization and Kolmogorov widths, can be leveraged to formalize the space-time tradeoffs inherent to learned index structures. The resulting bounds illuminate core limitations of these methods.

cs.DS↗

arXiv2024

Coding Over Coupon Collector Channels for Combinatorial Motif-Based DNA Storage

Encoding information in combinations of pre-synthesised deoxyribonucleic acid (DNA) strands (referred to as motifs) is an interesting approach to DNA storage that could potentially circumvent the prohibitive costs of nucleotide-by-nucleotide DNA synthesis. Based on our analysis of an empirical data set from HelixWorks, we propose two channel models for this setup (with and without interference) and analyse their fundamental limits. We propose a coding scheme that approaches those limits by leveraging all information available at the output of the channel, in contrast to earlier schemes developed for a similar setup by Preuss et al. We highlight an important connection between channel capacity curves and the fundamental trade-off between synthesis (writing) and sequencing (reading), and offer a way to mitigate an exponential growth in decoding complexity with the size of the motif library.

cs.IT↗

arXiv2024

An End-to-End Coding Scheme for DNA-Based Data Storage With Nanopore-Sequenced Reads

We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are copied a random number of times, and the channel outputs a random selection of $N$ noisy DNA strands. The retrieved DNA reads are prone to strand-dependent insertion, deletion, and substitution (IDS) errors. We construct an index-based concatenated coding scheme consisting of the concatenation of an outer code, an index code, and an inner code. We further propose a low-complexity (linear in $N$) maximum a posteriori probability decoder that takes into account the strand-dependent IDS errors and the randomness of the drawing to infer symbolwise a posteriori probabilities for the outer decoder. We present Monte-Carlo simulations for information-outage probabilities and frame error rates for different channel setups on experimental data. We finally evaluate the overall system performance using the read/write cost trade-off. A powerful combination of tailored channel modeling and soft information processing allows us to achieve excellent performance even with error-prone nanopore-sequenced reads outperforming state-of-the-art schemes.%

cs.IT↗

arXiv2023

Survey of Information Encoding Techniques for DNA

The yearly global production of data is growing exponentially, outpacing the capacity of existing storage media, such as tape and disk, and surpassing our ability to store it. DNA storage - the representation of arbitrary information as sequences of nucleotides - offers a promising storage medium. DNA is nature's information-storage molecule of choice and has a number of key properties: it is extremely dense, offering the theoretical possibility of storing 455 EB/g; it is durable, with a half-life of approximately 520 years that can be increased to thousands of years when DNA is chilled and stored dry; and it is amenable to automated synthesis and sequencing. Furthermore, biochemical processes that act on DNA potentially enable highly parallel data manipulation. Whilst biological information is encoded in DNA via a specific mapping from triplet sequences of nucleotides to amino acids, DNA storage is not limited to a single encoding scheme, and there are many possible ways to map data to chemical sequences of nucleotides for synthesis, storage, retrieval and data manipulation. However, there are several biological, error-tolerance and information-retrieval considerations that an encoding scheme needs to address to be viable. This comprehensive review focuses on comparing existing work done in encoding arbitrary data within DNA in terms of their encoding schemes, methods to address biological constraints and measures to provide error correction. We compare encoding approaches on the overall information density and coverage they achieve, as well as the data-retrieval method they use (i.e., sequential or random access). We also discuss the background and evolution of the encoding schemes.

q-bio.QM↗

arXiv2022

Finite-Length Scaling of SC-LDPC Codes With a Limited Number of Decoding Iterations

We propose four finite-length scaling laws to predict the frame error rate (FER) performance of spatially-coupled low-density parity-check codes under full belief propagation (BP) decoding with a limit on the number of decoding iterations and a scaling law for sliding window decoding, also with limited iterations. The laws for full BP decoding provide a choice between accuracy and computational complexity; a good balance between them is achieved by the law that models the number of decoded bits after a certain number of BP iterations by a time-integrated Ornstein-Uhlenbeck process. This framework is developed further to model sliding window decoding as a race between the integrated Ornstein-Uhlenbeck process and an absorbing barrier that corresponds to the left boundary of the sliding window. The proposed scaling laws yield accurate FER predictions.

cs.IT↗

arXiv2021

On Doped SC-LDPC Codes for Streaming

In streaming applications, doping improves the performance of spatially-coupled low-density parity-check (SC-LDPC) codes by creating reduced-degree check nodes in the coupled chain. We formulate a scaling law to predict the bit and block error rate of periodically-doped semi-infinite SC-LDPC code ensembles streamed over the binary erasure channel under sliding window decoding for a given finite component block length. The scaling law assumes that with some probability doping is equivalent to full termination and triggers two decoding waves; otherwise, decoding performs as if the coupled chain had not been doped at all. We approximate that probability and use the derived scaling laws to predict the error rates of SC-LDPC code ensembles in the presence of doping. The proposed scaling law provides accurate error rate predictions. We further use it to show that in streaming applications periodic doping can yield higher rates than periodic full termination for the same error-correcting performance.

cs.IT↗

arXiv2020

Finite-Length Scaling of Spatially Coupled LDPC Codes Under Window Decoding Over the BEC

We analyze the finite-length performance of spatially coupled low-density parity-check (SC-LDPC) codes under window decoding over the binary erasure channel. In particular, we propose a refinement of the scaling law by Olmos and Urbanke for the frame error rate (FER) of terminated SC-LDPC ensembles under full belief propagation (BP) decoding. The refined scaling law models the decoding process as two independent Ornstein-Uhlenbeck processes, in correspondence to the two decoding waves that propagate toward the center of the coupled chain for terminated SC-LDPC codes. We then extend the proposed scaling law to predict the performance of (terminated) SC-LDPC code ensembles under the more practical sliding window decoding. Finally, we extend this framework to predict the bit error rate (BER) and block error rate (BLER) of SC-LDPC code ensembles. The proposed scaling law yields very accurate predictions of the FER, BLER, and BER for both full BP and window decoding.

cs.IT↗

arXiv2019

A Refined Scaling Law for Spatially Coupled LDPC Codes Over the Binary Erasure Channel

We propose a refined scaling law to predict the finite-length performance in the waterfall region of spatially coupled low-density parity-check codes over the binary erasure channel. In particular, we introduce some improvements to the scaling law proposed by Olmos and Urbanke that result in a better agreement between the predicted and simulated frame error rate. We also show how the scaling law can be extended to predict the bit error rate performance.

cs.IT↗