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Farzad Farnoud

Publications and source records attributed to Farzad Farnoud.

At least 19 recordsLinked to original sources
arXiv2026

An Additive Approximation Scheme for Generating Dyadic Codings for the Outputs of an LLM

We study the problem of approximating a discrete probability distribution, such as the next-token distribution of a large language model, by a dyadic distribution induced by a binary tree under encoding rate constraints. The objective is to partition the support of the distribution and assign dyadic probabilities to minimize total variation distance while achieving a prescribed rate. We formulate this task as a tree-based partitioning problem and develop a polynomial-time additive approximation scheme for the rate-constrained setting in the constant-rate regime. Our results provide provable guarantees for near-optimal dyadic approximations and, as an application, yield a principled framework for LLM-based steganography, where the rate maps to bits of hidden information embedded per token and the total variation bound controls statistical detectability.

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arXiv2025

Constructing Low-Redundancy Codes via Distributed Graph Coloring

We present a general framework for constructing error-correcting codes using distributed graph coloring under the LOCAL model. Building on the correspondence between independent sets in the confusion graph and valid codes, we show that the color of a single vertex - consistent with a global proper coloring - can be computed in polynomial time using a modified version of Linial's coloring algorithm, leading to efficient encoding and decoding. Our results include: i) uniquely decodable code constructions for a constant number of errors of any type with redundancy twice the Gilbert-Varshamov bound; ii) list-decodable codes via a proposed extension of graph coloring, namely, hypergraph labeling; iii) an incremental synchronization scheme with reduced average-case communication when the edit distance is not precisely known; and iv) the first asymptotically optimal codes (up to a factor of 8) for correcting bursts of unbounded-length edits. Compared to syndrome compression, our approach is more flexible and generalizable, does not rely on a good base code, and achieves improved redundancy across a range of parameters.

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arXiv2025

Asymptotically Optimal Codes Correcting One Substring Edit

The substring edit error is the operation of replacing a substring $u$ of $x$ with another string $v$, where the lengths of $u$ and $v$ are bounded by a given constant $k$. It encompasses localized insertions, deletions, and substitutions within a window. Codes correcting one substring edit have redundancy at least $\log n+k$. In this paper, we construct codes correcting one substring edit with redundancy $\log n+O(\log \log n)$, which is asymptotically optimal.

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arXiv2024

Variance-Aware Regret Bounds for Stochastic Contextual Dueling Bandits

Dueling bandits is a prominent framework for decision-making involving preferential feedback, a valuable feature that fits various applications involving human interaction, such as ranking, information retrieval, and recommendation systems. While substantial efforts have been made to minimize the cumulative regret in dueling bandits, a notable gap in the current research is the absence of regret bounds that account for the inherent uncertainty in pairwise comparisons between the dueling arms. Intuitively, greater uncertainty suggests a higher level of difficulty in the problem. To bridge this gap, this paper studies the problem of contextual dueling bandits, where the binary comparison of dueling arms is generated from a generalized linear model (GLM). We propose a new SupLinUCB-type algorithm that enjoys computational efficiency and a variance-aware regret bound $\tilde O\big(d\sqrt{\sum_{t=1}^Tσ_t^2} + d\big)$, where $σ_t$ is the variance of the pairwise comparison in round $t$, $d$ is the dimension of the context vectors, and $T$ is the time horizon. Our regret bound naturally aligns with the intuitive expectation in scenarios where the comparison is deterministic, the algorithm only suffers from an $\tilde O(d)$ regret. We perform empirical experiments on synthetic data to confirm the advantage of our method over previous variance-agnostic algorithms.

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arXiv2023

Borda Regret Minimization for Generalized Linear Dueling Bandits

Dueling bandits are widely used to model preferential feedback prevalent in many applications such as recommendation systems and ranking. In this paper, we study the Borda regret minimization problem for dueling bandits, which aims to identify the item with the highest Borda score while minimizing the cumulative regret. We propose a rich class of generalized linear dueling bandit models, which cover many existing models. We first prove a regret lower bound of order $Ω(d^{2/3} T^{2/3})$ for the Borda regret minimization problem, where $d$ is the dimension of contextual vectors and $T$ is the time horizon. To attain this lower bound, we propose an explore-then-commit type algorithm for the stochastic setting, which has a nearly matching regret upper bound $\tilde{O}(d^{2/3} T^{2/3})$. We also propose an EXP3-type algorithm for the adversarial linear setting, where the underlying model parameter can change at each round. Our algorithm achieves an $\tilde{O}(d^{2/3} T^{2/3})$ regret, which is also optimal. Empirical evaluations on both synthetic data and a simulated real-world environment are conducted to corroborate our theoretical analysis.

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arXiv2022

Non-binary Codes for Correcting a Burst of at Most t Deletions

The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in non-binary sequences. We first propose a non-binary code correcting a burst of at most 2 deletions for $q$-ary alphabets. Afterwards, we extend this result to the case where the length of the burst can be at most $t$ where $t$ is a constant. Finally, we consider the setup where the sequences that are transmitted are permutations. The proposed codes are the largest known for their respective parameter regimes.

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arXiv2022

Low-redundancy codes for correcting multiple short-duplication and edit errors

Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions, duplications, and substitutions may arise in DNA at different stages of data storage and retrieval. The current paper constructs error-correcting codes for simultaneously correcting short (tandem) duplications and at most $p$ edits, where a short duplication generates a copy of a substring with length $\leq 3$ and inserts the copy following the original substring, and an edit is a substitution, deletion, or insertion. Compared to the state-of-the-art codes for duplications only, the proposed codes correct up to $p$ edits (in addition to duplications) at the additional cost of roughly $8p(\log_q n)(1+o(1))$ symbols of redundancy, thus achieving the same asymptotic rate, where $q\ge 4$ is the alphabet size and $p$ is a constant. Furthermore, the time complexities of both the encoding and decoding processes are polynomial when $p$ is a constant with respect to the code length.

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arXiv2022

Data Deduplication with Random Substitutions

Data deduplication saves storage space by identifying and removing repeats in the data stream. Compared with traditional compression methods, data deduplication schemes are more time efficient and are thus widely used in large scale storage systems. In this paper, we provide an information-theoretic analysis on the performance of deduplication algorithms on data streams in which repeats are not exact. We introduce a source model in which probabilistic substitutions are considered. More precisely, each symbol in a repeated string is substituted with a given edit probability. Deduplication algorithms in both the fixed-length scheme and the variable-length scheme are studied. The fixed-length deduplication algorithm is shown to be unsuitable for the proposed source model as it does not take into account the edit probability. Two modifications are proposed and shown to have performances within a constant factor of optimal with the knowledge of source model parameters. We also study the conventional variable-length deduplication algorithm and show that as source entropy becomes smaller, the size of the compressed string vanishes relative to the length of the uncompressed string, leading to high compression ratios.

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arXiv2021

Adaptive Sampling for Heterogeneous Rank Aggregation from Noisy Pairwise Comparisons

In heterogeneous rank aggregation problems, users often exhibit various accuracy levels when comparing pairs of items. Thus a uniform querying strategy over users may not be optimal. To address this issue, we propose an elimination-based active sampling strategy, which estimates the ranking of items via noisy pairwise comparisons from users and improves the users' average accuracy by maintaining an active set of users. We prove that our algorithm can return the true ranking of items with high probability. We also provide a sample complexity bound for the proposed algorithm which is better than that of non-active strategies in the literature. Experiments are provided to show the empirical advantage of the proposed methods over the state-of-the-art baselines.

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arXiv2020

Error-correcting Codes for Short Tandem Duplication and Substitution Errors

Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging task. This paper aims to address simultaneously correcting two types of errors, namely, short tandem duplication and substitution errors. We focus on tandem repeats of length at most 3 and design codes for correcting an arbitrary number of duplication errors and one substitution error. Because a substituted symbol can be duplicated many times (as part of substrings of various lengths), a single substitution can affect an unbounded substring of the retrieved word. However, we show that with appropriate preprocessing, the effect may be limited to a substring of finite length, thus making efficient error-correction possible. We construct a code for correcting the aforementioned errors and provide lower bounds for its rate. Compared to optimal codes correcting only duplication errors, numerical results show that the asymptotic cost of protecting against an additional substitution is only 0.003 bits/symbol when the alphabet has size 4, an important case corresponding to data storage in DNA.

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arXiv2020

Error-correcting Codes for Noisy Duplication Channels

Because of its high data density and longevity, DNA is emerging as a promising candidate for satisfying increasing data storage needs. Compared to conventional storage media, however, data stored in DNA is subject to a wider range of errors resulting from various processes involved in the data storage pipeline. In this paper, we consider correcting duplication errors for both exact and noisy tandem duplications of a given length k. An exact duplication inserts a copy of a substring of length k of the sequence immediately after that substring, e.g., ACGT to ACGACGT, where k = 3, while a noisy duplication inserts a copy suffering from substitution noise, e.g., ACGT to ACGATGT. Specifically, we design codes that can correct any number of exact duplication and one noisy duplication errors, where in the noisy duplication case the copy is at Hamming distance 1 from the original. Our constructions rely upon recovering the duplication root of the stored codeword. We characterize the ways in which duplication errors manifest in the root of affected sequences and design efficient codes for correcting these error patterns. We show that the proposed construction is asymptotically optimal, in the sense that it has the same asymptotic rate as optimal codes correcting exact duplications only.

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arXiv2020

Single-Error Detection and Correction for Duplication and Substitution Channels

Motivated by mutation processes occurring in in-vivo DNA-storage applications, a channel that mutates stored strings by duplicating substrings as well as substituting symbols is studied. Two models of such a channel are considered: one in which the substitutions occur only within the duplicated substrings, and one in which the location of substitutions is unrestricted. Both error-detecting and error-correcting codes are constructed, which can handle correctly any number of tandem duplications of a fixed length $k$, and at most a single substitution occurring at any time during the mutation process.

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arXiv2020

Coding for Optimized Writing Rate in DNA Storage

A method for encoding information in DNA sequences is described. The method is based on the precision-resolution framework, and is aimed to work in conjunction with a recently suggested terminator-free template independent DNA synthesis method. The suggested method optimizes the amount of information bits per synthesis time unit, namely, the writing rate. Additionally, the encoding scheme studied here takes into account the existence of multiple copies of the DNA sequence, which are independently distorted. Finally, quantizers for various run-length distributions are designed.

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arXiv2019

Rank Aggregation via Heterogeneous Thurstone Preference Models

We propose the Heterogeneous Thurstone Model (HTM) for aggregating ranked data, which can take the accuracy levels of different users into account. By allowing different noise distributions, the proposed HTM model maintains the generality of Thurstone's original framework, and as such, also extends the Bradley-Terry-Luce (BTL) model for pairwise comparisons to heterogeneous populations of users. Under this framework, we also propose a rank aggregation algorithm based on alternating gradient descent to estimate the underlying item scores and accuracy levels of different users simultaneously from noisy pairwise comparisons. We theoretically prove that the proposed algorithm converges linearly up to a statistical error which matches that of the state-of-the-art method for the single-user BTL model. We evaluate the proposed HTM model and algorithm on both synthetic and real data, demonstrating that it outperforms existing methods.

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arXiv2018

Evolution of $k$-mer Frequencies and Entropy in Duplication and Substitution Mutation Systems

Genomic evolution can be viewed as string-editing processes driven by mutations. An understanding of the statistical properties resulting from these mutation processes is of value in a variety of tasks related to biological sequence data, e.g., estimation of model parameters and compression. At the same time, due to the complexity of these processes, designing tractable stochastic models and analyzing them are challenging. In this paper, we study two kinds of systems, each representing a set of mutations. In the first system, tandem duplications and substitution mutations are allowed and in the other, interspersed duplications. We provide stochastic models and, via stochastic approximation, study the evolution of substring frequencies for these two systems separately. Specifically, we show that $k$-mer frequencies converge almost surely and determine the limit set. Furthermore, we present a method for finding upper bounds on entropy for such systems.

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arXiv2018

Reconciling Similar Sets of Data

In this work, we consider the problem of synchronizing two sets of data where the size of the symmetric difference between the sets is small and, in addition, the elements in the symmetric difference are related through the Hamming distance metric. Upper and lower bounds are derived on the minimum amount of information exchange. Furthermore, explicit encoding and decoding algorithms are provided for many cases.

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arXiv2018

The Capacity of Some Pólya String Models

We study random string-duplication systems, which we call Pólya string models. These are motivated by DNA storage in living organisms, and certain random mutation processes that affect their genome. Unlike previous works that study the combinatorial capacity of string-duplication systems, or various string statistics, this work provides exact capacity or bounds on it, for several probabilistic models. In particular, we study the capacity of noisy string-duplication systems, including the tandem-duplication, end-duplication, and interspersed-duplication systems. Interesting connections are drawn between some systems and the signature of random permutations, as well as to the beta distribution common in population genetics.

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