Gerbil: A Fast and Memory-Efficient kk-mer Counter with GPU-Support

A basic task in bioinformatics is the counting of $k$-mers in genome strings. The $k$-mer counting problem is to build a histogram of all substrings of length $k$ in a given genome sequence. We present the open source $k$-mer counting software Gerbil that has been designed for the efficient counting of $k$-mers for $k\geq32$. Given the technology trend towards long reads of next-generation sequencers, support for large $k$ becomes increasingly important. While existing $k$-mer counting tools suffer from excessive memory resource consumption or degrading performance for large $k$, Gerbil is able to efficiently support large $k$ without much loss of performance. Our software implements a two-disk approach. In the first step, DNA reads are loaded from disk and distributed to temporary files that are stored at a working disk. In a second step, the temporary files are read again, split into $k$-mers and counted via a hash table approach. In addition, Gerbil can optionally use GPUs to accelerate the counting step. For large $k$, we outperform state-of-the-art open source $k$-mer counting tools for large genome data sets.Comment: A short version of this paper will appear in the proceedings of WABI 201

Who is going to save us now? Bureaucrats, Politicians and Risky Tasks

The paper compares the policy choices regarding risk-transfer against low-probability-high-loss events between elected and appointed public officials. Empirical evidence using data on U.S. municipality-level shows that appointed city managers are more likely to adopt federal risk-transfer regimes. It is argued that the variation in the level of insurance activity emerges from the different incentive schemes each government form is facing. Controlling for spatial dependencies further shows that the participation decision in the insurance program significantly depends on the decision of neighboring communities.Politicians, bureaucrats, decision making under uncertainty, flood insurance, spatial econometrics

Trip-Based Public Transit Routing

We study the problem of computing all Pareto-optimal journeys in a public transit network regarding the two criteria of arrival time and number of transfers taken. We take a novel approach, focusing on trips and transfers between them, allowing fine-grained modeling. Our experiments on the metropolitan network of London show that the algorithm computes full 24-hour profiles in 70 ms after a preprocessing phase of 30 s, allowing fast queries in dynamic scenarios.Comment: Minor corrections, no substantial changes. To be presented at ESA 201

How to Attack the NP-complete Dag Realization Problem in Practice

We study the following fundamental realization problem of directed acyclic graphs (dags). Given a sequence S:=(a_1,b_1),...,(a_n, b_n) with a_i, b_i in Z_0^+, does there exist a dag (no parallel arcs allowed) with labeled vertex set V:= {v_1,...,v_n} such that for all v_i in V indegree and outdegree of v_i match exactly the given numbers a_i and b_i, respectively? Recently this decision problem has been shown to be NP-complete by Nichterlein (2011). However, we can show that several important classes of sequences are efficiently solvable. In previous work (Berger and Mueller-Hannemann, FCT2011), we have proved that yes-instances always have a special kind of topological order which allows us to reduce the number of possible topological orderings in most cases drastically. This leads to an exact exponential-time algorithm which significantly improves upon a straightforward approach. Moreover, a combination of this exponential-time algorithm with a special strategy gives a linear-time algorithm. Interestingly, in systematic experiments we observed that we could solve a huge majority of all instances by the linear-time heuristic. This motivates us to develop characteristics like dag density and "distance to provably easy sequences" which can give us an indicator how easy or difficult a given sequence can be realized. Furthermore, we propose a randomized algorithm which exploits our structural insight on topological sortings and uses a number of reduction rules. We observe that it clearly outperforms all other variants and behaves surprisingly well for almost all instances. Another striking observation is that our simple linear-time algorithm solves a set of real-world instances from different domains, namely ordered binary decision diagrams (OBDDs), train and flight schedules, as well as instances derived from food-web networks without any exception.Comment: 20 pages, 11 figures, extended abstract to appear in Proceedings of SEA 201

Charity hazard - A real hazard to natural disaster insurance

After the flooding in 2002 European governments provided billions of Euros of financial assistance to their citizens. Although there is no doubt that solidarity and some sort of assistance is reasonable, the question arises why these damages were not sufficiently insured. One explanation why individuals reject to obtain insurance cover against natural hazards is that they anticipate governmental and private aid. This problem became to be known as "charity hazard". The present paper gives an economic analysis of the institutional arrangements on the market for natural disaster insurances focusing on imperfections caused by governmental financial relief. It provides a theoretical explanation why charity hazard is a problem on the market for natural disaster insurances, in the way that it acts as an obstacle for the proper diffusion and therefore the establishment of natural hazard insurances. This paper provides a review of the scientific discussion on charity hazard, provides a theoretical analysis and points out the existing empirical problems regarding this issue.natural hazard insurance, market failure, governmental assistance

Accelerating Wilson Fermion Matrix Inversions by Means of the Stabilized Biconjugate Gradient Algorithm

The stabilized biconjugate gradient algorithm BiCGStab recently presented by van der Vorst is applied to the inversion of the lattice fermion operator in the Wilson formulation of lattice Quantum Chromodynamics. Its computational efficiency is tested in a comparative study against the conjugate gradient and minimal residual methods. Both for quenched gauge configurations at beta= 6.0 and gauge configurations with dynamical fermions at beta=5.4, we find BiCGStab to be superior to the other methods. BiCGStab turns out to be particularly useful in the chiral regime of small quark masses.Comment: 25 pages, WUB 94-1

Reducing the first-order Doppler shift in a Sagnac interferometer

4p(5)p[1/2](0) transition in Kr at lambda = 212 nm. The achieved precision of 6 x 10(-10) is limited by the characteristics of the laser system. (c) 2007 Optical Society of America

Argotario: Computational Argumentation Meets Serious Games

An important skill in critical thinking and argumentation is the ability to spot and recognize fallacies. Fallacious arguments, omnipresent in argumentative discourse, can be deceptive, manipulative, or simply leading to `wrong moves' in a discussion. Despite their importance, argumentation scholars and NLP researchers with focus on argumentation quality have not yet investigated fallacies empirically. The nonexistence of resources dealing with fallacious argumentation calls for scalable approaches to data acquisition and annotation, for which the serious games methodology offers an appealing, yet unexplored, alternative. We present Argotario, a serious game that deals with fallacies in everyday argumentation. Argotario is a multilingual, open-source, platform-independent application with strong educational aspects, accessible at www.argotario.net.Comment: EMNLP 2017 demo paper. Source codes: https://github.com/UKPLab/argotari