Locally Decodable Codes for Edit Distance

Abstract. Locally decodable codes (LDC) [1,5] are error correcting codes that allow decoding (any) individual symbol of the message, by reading only few symbols of the codeword. Consider an application such as storage solutions for large data, where errors may occur in the disks (or some disks may just crush). In such an application, it is often de-sirable to recover only small portions of the data (have random access). Thus, in such applications, using LDC provides enormous efficiency gains over standard error correcting codes (ECCs), that need to read the en-tire encoded message to learn even a single bit of information. Typically, LDC’s, as well as standard ECC’s decode the encoded messaged if upto some bounded fraction of the symbols had been modified. This corre-sponds to decoding strings of bounded Hamming distance from a valid codeword. An often more realistic metric is the edit distance, measur-ing the shortest sequence of insertions and deletions (indel.) of symbols leading from one word to another. For example, (few) indel. modifica

Thin accretion disc with a corona in a central magnetic field

We study the steady-state structure of an accretion disc with a corona surrounding a central, rotating, magnetized star. We assume that the magneto-rotational instability is the dominant mechanism of angular momentum transport inside the disc and is responsible for producing magnetic tubes above the disc. In our model, a fraction of the dissipated energy inside the disc is transported to the corona via these magnetic tubes. This energy exchange from the disc to the corona which depends on the disc physical properties is modified because of the magnetic interaction between the stellar magnetic field and the accretion disc. According to our fully analytical solutions for such a system, the existence of a corona not only increases the surface density but reduces the temperature of the accretion disc. Also, the presence of a corona enhances the ratio of gas pressure to the total pressure. Our solutions show that when the strength of the magnetic field of the central neutron star is large or the star is rotating fast enough, profiles of the physical variables of the disc significantly modify due to the existence of a corona.Comment: Accepted for publication in Astrophysics & Space Scienc

Evaluating potential effects of solar power facilities on wildlife from an animal behavior perspective

Solar power is a renewable energy source with great potential to help meetincreasing global energy demands and reduce our reliance on fossil fuels.However, research is scarce on how solar facilities affect wildlife. With inputfrom professionals in ecology, conservation, and energy, we conducted aresearch-prioritization process and identified key questions needed to betterunderstand impacts of solar facilities on wildlife. We focused on animalbehavior, which can be used to identify population responses before mortal-ity or other fitness consequences are documented. Behavioral studies canalso offer approaches to understand the mechanisms leading to negativeinteractions (e.g., collision, singeing, avoidance) and provide insight into mit-igating effects. Here, we review how behavioral responses to solar facilities, including perception, movement, habitat use, and interspecific interactionsare priority research areas. Addressing these themes will lead to a morecomprehensive understanding of the effects of solar power on wildlife andguide future mitigatio

Storage and retrieval of individual genomes

Volume: 5541A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. Flexible and efficient data analysis on a such typically huge collection is plausible using suffix trees. However, suffix tree occupies O(N log N) bits, which very soon inhibits in-memory analyses. Recent advances in full-text self-indexing reduce the space of suffix tree to O(N log σ) bits, where σ is the alphabet size. In practice, the space reduction is more than 10-fold, for example on suffix tree of Human Genome. However, this reduction factor remains constant when more sequences are added to the collection. We develop a new family of self-indexes suited for the repetitive sequence collection setting. Their expected space requirement depends only on the length n of the base sequence and the number s of variations in its repeated copies. That is, the space reduction factor is no longer constant, but depends on N / n. We believe the structures developed in this work will provide a fundamental basis for storage and retrieval of individual genomes as they become available due to rapid progress in the sequencing technologies.Peer reviewe

Physics, Topology, Logic and Computation: A Rosetta Stone

In physics, Feynman diagrams are used to reason about quantum processes. In the 1980s, it became clear that underlying these diagrams is a powerful analogy between quantum physics and topology: namely, a linear operator behaves very much like a "cobordism". Similar diagrams can be used to reason about logic, where they represent proofs, and computation, where they represent programs. With the rise of interest in quantum cryptography and quantum computation, it became clear that there is extensive network of analogies between physics, topology, logic and computation. In this expository paper, we make some of these analogies precise using the concept of "closed symmetric monoidal category". We assume no prior knowledge of category theory, proof theory or computer science.Comment: 73 pages, 8 encapsulated postscript figure

Measurement of the Charged Multiplicities in b, c and Light Quark Events from Z0 Decays

Average charged multiplicities have been measured separately in $b$, $c$ and light quark ($u,d,s$) events from $Z^0$ decays measured in the SLD experiment. Impact parameters of charged tracks were used to select enriched samples of $b$ and light quark events, and reconstructed charmed mesons were used to select $c$ quark events. We measured the charged multiplicities: $\bar{n}_{uds} = 20.21 \pm 0.10 (\rm{stat.})\pm 0.22(\rm{syst.})$, $\bar{n}_{c} = 21.28 \pm 0.46(\rm{stat.}) ^{+0.41}_{-0.36}(\rm{syst.})$ $\bar{n}_{b} = 23.14 \pm 0.10(\rm{stat.}) ^{+0.38}_{-0.37}(\rm{syst.})$, from which we derived the differences between the total average charged multiplicities of $c$ or $b$ quark events and light quark events: $\Delta \bar{n}_c = 1.07 \pm 0.47(\rm{stat.})^{+0.36}_{-0.30}(\rm{syst.})$ and $\Delta \bar{n}_b = 2.93 \pm 0.14(\rm{stat.})^{+0.30}_{-0.29}(\rm{syst.})$. We compared these measurements with those at lower center-of-mass energies and with perturbative QCD predictions. These combined results are in agreement with the QCD expectations and disfavor the hypothesis of flavor-independent fragmentation.Comment: 19 pages LaTex, 4 EPS figures, to appear in Physics Letters

Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections

A repetitive sequence collection is one where portions of a base sequence of length n are repeated many times with small variations, forming a collection of total length N. Examples of such collections are version control data and genome sequences of individuals, where the differences can be expressed by lists of basic edit operations. This paper is devoted to studying ways to store massive sets of highly repetitive sequence collections in space-efficient manner so that retrieval of the content as well as queries on the content of the sequences can be provided time-efficiently. We show that the state-of-the-art entropy-bound full-text self-indexes do not yet provide satisfactory space bounds for this specific task. We engineer some new structures that use run-length encoding and give empirical evidence that these structures are superior to the current structures

Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel

A major use of the 1000 Genomes Project (1000GP) data is genotype imputation in genome-wide association studies (GWAS). Here we develop a method to estimate haplotypes from low-coverage sequencing data that can take advantage of single-nucleotide polymorphism (SNP) microarray genotypes on the same samples. First the SNP array data are phased to build a backbone (or 'scaffold') of haplotypes across each chromosome. We then phase the sequence data 'onto' this haplotype scaffold. This approach can take advantage of relatedness between sequenced and non-sequenced samples to improve accuracy. We use this method to create a new 1000GP haplotype reference set for use by the human genetic community. Using a set of validation genotypes at SNP and bi-allelic indels we show that these haplotypes have lower genotype discordance and improved imputation performance into downstream GWAS samples, especially at low-frequency variants. © 2014 Macmillan Publishers Limited. All rights reserved