Efficiently Correcting Matrix Products

We study the problem of efficiently correcting an erroneous product of two $n\times n$ matrices over a ring. Among other things, we provide a randomized algorithm for correcting a matrix product with at most $k$ erroneous entries running in $\tilde{O}(n^2+kn)$ time and a deterministic $\tilde{O}(kn^2)$-time algorithm for this problem (where the notation $\tilde{O}$ suppresses polylogarithmic terms in $n$ and $k$).Comment: Fixed invalid reference to figure in v

Wear Minimization for Cuckoo Hashing: How Not to Throw a Lot of Eggs into One Basket

We study wear-leveling techniques for cuckoo hashing, showing that it is possible to achieve a memory wear bound of $\log\log n+O(1)$ after the insertion of $n$ items into a table of size $Cn$ for a suitable constant $C$ using cuckoo hashing. Moreover, we study our cuckoo hashing method empirically, showing that it significantly improves on the memory wear performance for classic cuckoo hashing and linear probing in practice.Comment: 13 pages, 1 table, 7 figures; to appear at the 13th Symposium on Experimental Algorithms (SEA 2014

Efficient counting of k-mers in DNA sequences using a bloom filter

<p>Abstract</p> <p>Background</p> <p>Counting <it>k</it>-mers (substrings of length <it>k </it>in DNA sequence data) is an essential component of many methods in bioinformatics, including for genome and transcriptome assembly, for metagenomic sequencing, and for error correction of sequence reads. Although simple in principle, counting <it>k</it>-mers in large modern sequence data sets can easily overwhelm the memory capacity of standard computers. In current data sets, a large fraction-often more than 50%-of the storage capacity may be spent on storing <it>k</it>-mers that contain sequencing errors and which are typically observed only a single time in the data. These singleton <it>k</it>-mers are uninformative for many algorithms without some kind of error correction.</p> <p>Results</p> <p>We present a new method that identifies all the <it>k</it>-mers that occur more than once in a DNA sequence data set. Our method does this using a Bloom filter, a probabilistic data structure that stores all the observed <it>k</it>-mers implicitly in memory with greatly reduced memory requirements. We then make a second sweep through the data to provide exact counts of all nonunique <it>k</it>-mers. For example data sets, we report up to 50% savings in memory usage compared to current software, with modest costs in computational speed. This approach may reduce memory requirements for any algorithm that starts by counting <it>k</it>-mers in sequence data with errors.</p> <p>Conclusions</p> <p>A reference implementation for this methodology, BFCounter, is written in C++ and is GPL licensed. It is available for free download at <url>http://pritch.bsd.uchicago.edu/bfcounter.html</url></p

Fashioning Entitlements: A Comparative Law and Economic Analysis of the Judicial Role in Environmental Centralization in the U.S. and Europe

This paper identifies and evaluates, from an economic point of view, the role of the judiciary the steady shift of environmental regulatory authority to higher, more centralized levels of government in both the U.S. and Europe. We supply both a positive analysis of how the decisions made by judges have affected the incentives of both private and public actors to pollute the natural environment, and normative answers to the question of whether judges have acted so as to create incentives that move levels of pollution in an efficient direction, toward their optimal, cost-minimizing (or net-benefit-maximizing) levels. Highlights of the analysis include the following points: 1) Industrial-era local (state or national) legislation awarding entitlements to pollute was almost certainly inefficient due to a fundamental economic obstacle faced by those who suffer harm from the over-pollution of publicly owned natural resources: the inability to monetize and credibly commit to repay the future economic value of reducing pollution. 2) When industrial era pollution spilled across state lines in the US, the federal courts, in particular the Supreme Court, fashioned a federal common law of interstate nuisance that set up essentially the same sort of blurry, uncertain entitlements to pollute or be free of pollution that had been created by the state courts in resolving local pollution disputes. We argue that for the typical pollution problem, a legal regime of blurry interstate entitlements - with neither jurisdiction having a clear right either to pollute or be free of pollution from the other - is likely to generate efficient incentives for interjursidictional bargaining, even despite the public choice problems besetting majority-rule government. Interestingly, a very similar system of de facto entitlements arose and often stimulated interjursidictional bargaining in Europe as well as in the U.S. 3) The US federal courts have generally interpreted the federal environmental statutes in ways that give clear primacy to federal regulators. Through such judicial interpretation, state and local regulators face a continuing risk of having their decisions overridden by federal regulators. This reduces the incentives for regulatory innovation at the state and local level. Judicial authorization of federal overrides has thus weakened the economic rationale for cooperative federalism suggested by economic models of principal-agent relationships. As a result of the principle of attribution, there is less risk in Europe that (like in the US) courts would enlarge the federal purview and thereby limit the powers of the Member States. Despite this principle, the power of the European bureaucracy (that is, the European Commission) has steadily increased and led to a steady shift of environmental regulatory competencies to the European level. This shift is only sometimes normatively desirable, and yet there is little that the ECJ can or will do to slow it

Lectin-Dependent Enhancement of Ebola Virus Infection via Soluble and Transmembrane C-type Lectin Receptors

Mannose-binding lectin (MBL) is a key soluble effector of the innate immune system that recognizes pathogen-specific surface glycans. Surprisingly, low-producing MBL genetic variants that may predispose children and immunocompromised individuals to infectious diseases are more common than would be expected in human populations. Since certain immune defense molecules, such as immunoglobulins, can be exploited by invasive pathogens, we hypothesized that MBL might also enhance infections in some circumstances. Consequently, the low and intermediate MBL levels commonly found in human populations might be the result of balancing selection. Using model infection systems with pseudotyped and authentic glycosylated viruses, we demonstrated that MBL indeed enhances infection of Ebola, Hendra, Nipah and West Nile viruses in low complement conditions. Mechanistic studies with Ebola virus (EBOV) glycoprotein pseudotyped lentiviruses confirmed that MBL binds to N-linked glycan epitopes on viral surfaces in a specific manner via the MBL carbohydrate recognition domain, which is necessary for enhanced infection. MBL mediates lipid-raft-dependent macropinocytosis of EBOV via a pathway that appears to require less actin or early endosomal processing compared with the filovirus canonical endocytic pathway. Using a validated RNA interference screen, we identified C1QBP (gC1qR) as a candidate surface receptor that mediates MBL-dependent enhancement of EBOV infection. We also identified dectin-2 (CLEC6A) as a potentially novel candidate attachment factor for EBOV. Our findings support the concept of an innate immune haplotype that represents critical interactions between MBL and complement component C4 genes and that may modify susceptibility or resistance to certain glycosylated pathogens. Therefore, higher levels of native or exogenous MBL could be deleterious in the setting of relative hypocomplementemia which can occur genetically or because of immunodepletion during active infections. Our findings confirm our hypothesis that the pressure of infectious diseases may have contributed in part to evolutionary selection of MBL mutant haplotypes

Linking-Based Revocation for Group Signatures: A Pragmatic Approach for Efficient Revocation Checks

Group signature schemes (GSS) represent an important privacy-enhancing technology. However, their practical applicability is restricted due to inefficiencies of existing membership revocation mechanisms that often place a too large computational burden and communication overhead on the involved parties. Moreover, it seems that the general belief (or unwritten law) of avoiding online authorities by all means artificially and unnecessarily restricts the efficiency and practicality of revocation mechanisms in GSSs. While a mindset of preventing online authorities might have been appropriate more than 10 years ago, today the availability of highly reliable cloud computing infrastructures could be used to solve open challenges. More specifically, in order to overcome the inefficiencies of existing revocation mechanisms, we propose an alternative approach denoted as linking-based revocation (LBR) which is based on the concept of controllable linkability. The novelty of LBR is its transparency for signers and verifiers that spares additional computations as well as updates. We therefore introduce dedicated revocation authorities (RAs) that can be contacted for efficient (constant time) revocation checks. In order to protect these RAs and to reduce the trust in involved online authorities, we additionally introduce distributed controllable linkability. Using latter, RAs cooperate with multiple authorities to compute the required linking information, thus reducing the required trust. Besides efficiency, an appealing benefit of LBR is its generic applicability to pairing-based GSSs secure in the BSZ model as well as GSSs with controllable linkability. This includes the XSGS scheme, and the GSSs proposed by Hwang et al., one of which has been standardized in the recent ISO 20008-2 standard