Coding over Sets for DNA Storage

In this paper, we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where data is represented by an unordered set of $M$ sequences, each of length $L$. Errors within that model are losses of whole sequences and point errors inside the sequences, such as substitutions, insertions and deletions. We propose code constructions which can correct these errors with efficient encoders and decoders. By deriving upper bounds on the cardinalities of these codes using sphere packing arguments, we show that many of our codes are close to optimal.Comment: 5 page

Homological Product Codes

Quantum codes with low-weight stabilizers known as LDPC codes have been actively studied recently due to their simple syndrome readout circuits and potential applications in fault-tolerant quantum computing. However, all families of quantum LDPC codes known to this date suffer from a poor distance scaling limited by the square-root of the code length. This is in a sharp contrast with the classical case where good families of LDPC codes are known that combine constant encoding rate and linear distance. Here we propose the first family of good quantum codes with low-weight stabilizers. The new codes have a constant encoding rate, linear distance, and stabilizers acting on at most $\sqrt{n}$ qubits, where $n$ is the code length. For comparison, all previously known families of good quantum codes have stabilizers of linear weight. Our proof combines two techniques: randomized constructions of good quantum codes and the homological product operation from algebraic topology. We conjecture that similar methods can produce good stabilizer codes with stabilizer weight $n^a$ for any $a>0$. Finally, we apply the homological product to construct new small codes with low-weight stabilizers.Comment: 49 page

Enhanced Feedback Iterative Decoding of Sparse Quantum Codes

Decoding sparse quantum codes can be accomplished by syndrome-based decoding using a belief propagation (BP) algorithm.We significantly improve this decoding scheme by developing a new feedback adjustment strategy for the standard BP algorithm. In our feedback procedure, we exploit much of the information from stabilizers, not just the syndrome but also the values of the frustrated checks on individual qubits of the code and the channel model. Furthermore we show that our decoding algorithm is superior to belief propagation algorithms using only the syndrome in the feedback procedure for all cases of the depolarizing channel. Our algorithm does not increase the measurement overhead compared to the previous method, as the extra information comes for free from the requisite stabilizer measurements.Comment: 10 pages, 11 figures, Second version, To be appeared in IEEE Transactions on Information Theor

A single-photon sampling architecture for solid-state imaging

Advances in solid-state technology have enabled the development of silicon photomultiplier sensor arrays capable of sensing individual photons. Combined with high-frequency time-to-digital converters (TDCs), this technology opens up the prospect of sensors capable of recording with high accuracy both the time and location of each detected photon. Such a capability could lead to significant improvements in imaging accuracy, especially for applications operating with low photon fluxes such as LiDAR and positron emission tomography. The demands placed on on-chip readout circuitry imposes stringent trade-offs between fill factor and spatio-temporal resolution, causing many contemporary designs to severely underutilize the technology's full potential. Concentrating on the low photon flux setting, this paper leverages results from group testing and proposes an architecture for a highly efficient readout of pixels using only a small number of TDCs, thereby also reducing both cost and power consumption. The design relies on a multiplexing technique based on binary interconnection matrices. We provide optimized instances of these matrices for various sensor parameters and give explicit upper and lower bounds on the number of TDCs required to uniquely decode a given maximum number of simultaneous photon arrivals. To illustrate the strength of the proposed architecture, we note a typical digitization result of a 120x120 photodiode sensor on a 30um x 30um pitch with a 40ps time resolution and an estimated fill factor of approximately 70%, using only 161 TDCs. The design guarantees registration and unique recovery of up to 4 simultaneous photon arrivals using a fast decoding algorithm. In a series of realistic simulations of scintillation events in clinical positron emission tomography the design was able to recover the spatio-temporal location of 98.6% of all photons that caused pixel firings.Comment: 24 pages, 3 figures, 5 table

Problems on q-Analogs in Coding Theory

The interest in $q$-analogs of codes and designs has been increased in the last few years as a consequence of their new application in error-correction for random network coding. There are many interesting theoretical, algebraic, and combinatorial coding problems concerning these q-analogs which remained unsolved. The first goal of this paper is to make a short summary of the large amount of research which was done in the area mainly in the last few years and to provide most of the relevant references. The second goal of this paper is to present one hundred open questions and problems for future research, whose solution will advance the knowledge in this area. The third goal of this paper is to present and start some directions in solving some of these problems.Comment: arXiv admin note: text overlap with arXiv:0805.3528 by other author

Universal fault-tolerant gates on concatenated stabilizer codes

It is an oft-cited fact that no quantum code can support a set of fault-tolerant logical gates that is both universal and transversal. This no-go theorem is generally responsible for the interest in alternative universality constructions including magic state distillation. Widely overlooked, however, is the possibility of non-transversal, yet still fault-tolerant, gates that work directly on small quantum codes. Here we demonstrate precisely the existence of such gates. In particular, we show how the limits of non-transversality can be overcome by performing rounds of intermediate error-correction to create logical gates on stabilizer codes that use no ancillas other than those required for syndrome measurement. Moreover, the logical gates we construct, the most prominent examples being Toffoli and controlled-controlled-Z, often complete universal gate sets on their codes. We detail such universal constructions for the smallest quantum codes, the 5-qubit and 7-qubit codes, and then proceed to generalize the approach. One remarkable result of this generalization is that any nondegenerate stabilizer code with a complete set of fault-tolerant single-qubit Clifford gates has a universal set of fault-tolerant gates. Another is the interaction of logical qubits across different stabilizer codes, which, for instance, implies a broadly applicable method of code switching.Comment: 18 pages + 5 pages appendix, 12 figure