Related papers: Coding schemes for locally balanced constraints
We study codes that are list-decodable under insertions and deletions. Specifically, we consider the setting where a codeword over some finite alphabet of size $q$ may suffer from $\delta$ fraction of adversarial deletions and $\gamma$…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Locally decodable codes (LDCs) are error-correcting codes $C : \Sigma^k \to \Sigma^n$ that admit a local decoding algorithm that recovers each individual bit of the message by querying only a few bits from a noisy codeword. An important…
Locally decodable channel codes form a special class of error-correcting codes with the property that the decoder is able to reconstruct any bit of the input message from querying only a few bits of a noisy codeword. It is well known that…
Linear integer constraints are one of the most important constraints in combinatorial problems since they are commonly found in many practical applications. Typically, encodings to Boolean satisfiability (SAT) format of conjunctive normal…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The Longest Common Subsequence (LCS) is a fundamental string similarity measure, and computing the LCS of two strings is a classic algorithms question. A textbook dynamic programming algorithm gives an exact algorithm in quadratic time, and…
Deep regression networks are widely used to tackle the problem of predicting a continuous value for a given input. Task-specialized approaches for training regression networks have shown significant improvement over generic approaches, such…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
We consider the problem of binary string reconstruction from the multiset of its substring compositions, i.e., referred to as the substring composition multiset, first introduced and studied by Acharya et al. We introduce a new algorithm…
Motivated by applications in polymer-based data storage we introduced the new problem of characterizing the code rate and designing constant-weight binary $B_2$-sequences. Binary $B_2$-sequences are collections of binary strings of length…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We initiate a study of locally decodable codes with randomized encoding. Standard locally decodable codes are error correcting codes with a deterministic encoding function and a randomized decoding function, such that any desired message…
Deep neural networks are used for a wide range of regression problems. However, there exists a significant gap in accuracy between specialized approaches and generic direct regression in which a network is trained by minimizing the squared…
Constrained codes are used to eliminate error-prone patterns in various practical systems. Recently, we introduced efficient binary symmetric lexicographically-ordered constrained (LOCO) codes and asymmetric LOCO (A-LOCO) codes to increase…
This paper presents and analyzes a novel concatenated coding scheme for enabling error resilience in two distributed storage settings: one being storage using existing regenerating codes and the second being storage using locally repairable…
Composite DNA is a recent novel method to increase the information capacity of DNA-based data storage above the theoretical limit of 2 bits/symbol. In this method, every composite symbol does not store a single DNA nucleotide but a mixture…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is…
This work provides an algebraic framework for source coding with decoder side information and its dual problem, channel coding with encoder side information, showing that nested concatenated codes can achieve the corresponding…