A resource-frugal probabilistic dictionary and applications in (meta)genomics

Genomic and metagenomic fields, generating huge sets of short genomic sequences, brought their own share of high performance problems. To extract relevant pieces of information from the huge data sets generated by current sequencing techniques, one must rely on extremely scalable methods and solutions. Indexing billions of objects is a task considered too expensive while being a fundamental need in this field. In this paper we propose a straightforward indexing structure that scales to billions of element and we propose two direct applications in genomics and metagenomics. We show that our proposal solves problem instances for which no other known solution scales-up. We believe that many tools and applications could benefit from either the fundamental data structure we provide or from the applications developed from this structure.Comment: Submitted to PSC 201

The Road From Classical to Quantum Codes: A Hashing Bound Approaching Design Procedure

Powerful Quantum Error Correction Codes (QECCs) are required for stabilizing and protecting fragile qubits against the undesirable effects of quantum decoherence. Similar to classical codes, hashing bound approaching QECCs may be designed by exploiting a concatenated code structure, which invokes iterative decoding. Therefore, in this paper we provide an extensive step-by-step tutorial for designing EXtrinsic Information Transfer (EXIT) chart aided concatenated quantum codes based on the underlying quantum-to-classical isomorphism. These design lessons are then exemplified in the context of our proposed Quantum Irregular Convolutional Code (QIRCC), which constitutes the outer component of a concatenated quantum code. The proposed QIRCC can be dynamically adapted to match any given inner code using EXIT charts, hence achieving a performance close to the hashing bound. It is demonstrated that our QIRCC-based optimized design is capable of operating within 0.4 dB of the noise limit

Recursive n-gram hashing is pairwise independent, at best

Many applications use sequences of n consecutive symbols (n-grams). Hashing these n-grams can be a performance bottleneck. For more speed, recursive hash families compute hash values by updating previous values. We prove that recursive hash families cannot be more than pairwise independent. While hashing by irreducible polynomials is pairwise independent, our implementations either run in time O(n) or use an exponential amount of memory. As a more scalable alternative, we make hashing by cyclic polynomials pairwise independent by ignoring n-1 bits. Experimentally, we show that hashing by cyclic polynomials is is twice as fast as hashing by irreducible polynomials. We also show that randomized Karp-Rabin hash families are not pairwise independent.Comment: See software at https://github.com/lemire/rollinghashcp

Trading Determinism for Time in Space Bounded Computations

Savitch showed in $1970$ that nondeterministic logspace (NL) is contained in deterministic $\mathcal{O}(\log^2 n)$ space but his algorithm requires quasipolynomial time. The question whether we can have a deterministic algorithm for every problem in NL that requires polylogarithmic space and simultaneously runs in polynomial time was left open. In this paper we give a partial solution to this problem and show that for every language in NL there exists an unambiguous nondeterministic algorithm that requires $\mathcal{O}(\log^2 n)$ space and simultaneously runs in polynomial time.Comment: Accepted in MFCS 201

An Adaptive Entanglement Distillation Scheme Using Quantum Low Density Parity Check Codes

Quantum low density parity check (QLDPC) codes are useful primitives for quantum information processing because they can be encoded and decoded efficiently. Besides, the error correcting capability of a few QLDPC codes exceeds the quantum Gilbert-Varshamov bound. Here, we report a numerical performance analysis of an adaptive entanglement distillation scheme using QLDPC codes. In particular, we find that the expected yield of our adaptive distillation scheme to combat depolarization errors exceed that of Leung and Shor whenever the error probability is less than about 0.07 or greater than about 0.28. This finding illustrates the effectiveness of using QLDPC codes in entanglement distillation.Comment: 12 pages, 6 figure