Highly Scalable Algorithms for Robust String Barcoding

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size on a well-equipped workstation, and can be easily parallelized to further extend the applicability range to thousands of bacterial size genomes. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem

A Kernelisation Approach for Multiple d-Hitting Set and Its Application in Optimal Multi-Drug Therapeutic Combinations

Therapies consisting of a combination of agents are an attractive proposition, especially in the context of diseases such as cancer, which can manifest with a variety of tumor types in a single case. However uncovering usable drug combinations is expensive both financially and temporally. By employing computational methods to identify candidate combinations with a greater likelihood of success we can avoid these problems, even when the amount of data is prohibitively large. Hitting Set is a combinatorial problem that has useful application across many fields, however as it is NP-complete it is traditionally considered hard to solve exactly. We introduce a more general version of the problem (α,β,d)-Hitting Set, which allows more precise control over how and what the hitting set targets. Employing the framework of Parameterized Complexity we show that despite being NP-complete, the (α,β,d)-Hitting Set problem is fixed-parameter tractable with a kernel of size O(αdkd) when we parameterize by the size k of the hitting set and the maximum number α of the minimum number of hits, and taking the maximum degree d of the target sets as a constant. We demonstrate the application of this problem to multiple drug selection for cancer therapy, showing the flexibility of the problem in tailoring such drug sets. The fixed-parameter tractability result indicates that for low values of the parameters the problem can be solved quickly using exact methods. We also demonstrate that the problem is indeed practical, with computation times on the order of 5 seconds, as compared to previous Hitting Set applications using the same dataset which exhibited times on the order of 1 day, even with relatively relaxed notions for what constitutes a low value for the parameters. Furthermore the existence of a kernelization for (α,β,d)-Hitting Set indicates that the problem is readily scalable to large datasets

Bucket Game with Applications to Set Multicover and Dynamic Page Migration

We present a simple two-person Bucket Game, based on throwing balls into buckets, and we discuss possible players’ strategies. We use these strategies to create an approximation algorithm for a generalization of the well known Set Cover problem, where we need to cover each element by at least k sets. Furthermore, we apply these strategies to construct a randomized algorithm for Dynamic Page Migration problem achieving the optimal competitive ratio against an oblivious adversary

Multiwinner Voting with Fairness Constraints

Multiwinner voting rules are used to select a small representative subset of candidates or items from a larger set given the preferences of voters. However, if candidates have sensitive attributes such as gender or ethnicity (when selecting a committee), or specified types such as political leaning (when selecting a subset of news items), an algorithm that chooses a subset by optimizing a multiwinner voting rule may be unbalanced in its selection -- it may under or over represent a particular gender or political orientation in the examples above. We introduce an algorithmic framework for multiwinner voting problems when there is an additional requirement that the selected subset should be "fair" with respect to a given set of attributes. Our framework provides the flexibility to (1) specify fairness with respect to multiple, non-disjoint attributes (e.g., ethnicity and gender) and (2) specify a score function. We study the computational complexity of this constrained multiwinner voting problem for monotone and submodular score functions and present several approximation algorithms and matching hardness of approximation results for various attribute group structure and types of score functions. We also present simulations that suggest that adding fairness constraints may not affect the scores significantly when compared to the unconstrained case.Comment: The conference version of this paper appears in IJCAI-ECAI 201

Energy Proportionality and Performance in Data Parallel Computing Clusters

Energy consumption in datacenters has recently become a major concern due to the rising operational costs andscalability issues. Recent solutions to this problem propose the principle of energy proportionality, i.e., the amount of energy consumedby the server nodes must be proportional to the amount of work performed. For data parallelism and fault tolerancepurposes, most common file systems used in MapReduce-type clusters maintain a set of replicas for each data block. A coveringset is a group of nodes that together contain at least one replica of the data blocks needed for performing computing tasks. In thiswork, we develop and analyze algorithms to maintain energy proportionality by discovering a covering set that minimizesenergy consumption while placing the remaining nodes in lowpower standby mode. Our algorithms can also discover coveringsets in heterogeneous computing environments. In order to allow more data parallelism, we generalize our algorithms so that itcan discover k-covering sets, i.e., a set of nodes that contain at least k replicas of the data blocks. Our experimental results showthat we can achieve substantial energy saving without significant performance loss in diverse cluster configurations and workingenvironments