Bhaskar DasGupta

Parking slot assignment games

With the proliferation of location-based services, mobile devices, and embedded wireless sensors, more and more applications are being developed to improve the efficiency of the transportation system. In particular, new applications are arising to help vehicles locate open parking spaces. Nevertheless, while engaged in driving, travelers are better suited being guided to a particular and ideal parking slot, than looking at a map and choosing which spot to go to. Then the question of how an application should choose this ideal parking spot becomes relevant. Vehicular parking can be viewed as vehicles (players) competing for parking slots (resources with different costs). Based on this competition, we present a game-theoretic framework to analyze parking situations. We introduce and analyze Parking Slot Assignment Games (Psag) in complete and incomplete information contexts. For both models we present algorithms for individual players to choose parking spaces ideally. To evaluate the more realistic incomplete information Psag, simulations were performed to test the performance of various proposed algorithms.

Multi-phase Algorithms for Throughput Maximization for Real-Time Scheduling

We consider the problem of off-line throughput maximization for job scheduling on one or more machines, where each job has a release time, a deadline and a profit. Most of the versions of the problem discussed here were already treated by Bar-Noy et al. (Proc. 31st ACM STOC, 1999, pp. 622–631; http://www.eng.tau.ac.il/∼amotz/). Our main contribution is to provide algorithms that do not use linear programming, are simple and much faster than the corresponding ones proposed in Bar-Noy et al. (ibid., 1999), while either having the same quality of approximation or improving it. More precisely, compared to the results of in Bar-Noy et al. (ibid., 1999), our pseudo-polynomial algorithm for multiple unrelated machines and all of our strongly-polynomial algorithms have better performance ratios, all of our algorithms run much faster, are combinatorial in nature and avoid linear programming. Finally, we show that algorithms with better performance ratios than 2 are possible if the stretch factors of the jobs are bounded; a straightforward consequence of this result is an improvement of the ratio of an optimal solution of the integer programming formulation of the JISP2 problem (see Spieksma, Journal of Scheduling, vol. 2, pp. 215–227, 1999) to its linear programming relaxation.

NET-SYNTHESIS

UNLABELLED We present a software for combined synthesis, inference and simplification of signal transduction networks. The main idea of our method lies in representing observed indirect causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. We illustrate the biological usability of our software by applying it to a previously published signal transduction network and by using it to synthesize and simplify a novel network corresponding to activation-induced cell death in large granular lymphocyte leukemia. AVAILABILITY NET-SYNTHESIS is freely downloadable from http://www.cs.uic.edu/~dasgupta/network-synthesis/

Motif discoveries in unaligned molecular sequences using self-organizing neural networks

In this paper, we study the problem of motif discoveries in unaligned DNA and protein sequences. The problem of motif identification in DNA and protein sequences has been studied for many years in the literature. Major hurdles at this point include computational complexity and reliability of the search algorithms. We propose a self-organizing neural network structure for solving the problem of motif identification in DNA and protein sequences. Our network contains several layers, with each layer performing classifications at different levels. The top layer divides the input space into a small number of regions and the bottom layer classifies all input patterns into motifs and nonmotif patterns. Depending on the number of input patterns to be classified, several layers between the top layer and the bottom layer are needed to perform intermediate classifications. We maintain a low computational complexity through the use of the layered structure so that each patterns classification is performed with respect to a small subspace of the whole input space. Our self-organizing neural network will grow as needed (e.g., when more motif patterns are classified). It will give the same amount of attention to each input pattern and will not omit any potential motif patterns. Finally, simulation results show that our algorithm outperforms existing algorithms in certain aspects. In particular, simulation results show that our algorithm can identify motifs with more mutations than existing algorithms. Our algorithm works well for long DNA sequences as well.

A novel method for signal transduction network inference from indirect experimental evidence.

In this paper, we introduce a new method of combined synthesis and inference of biological signal transduction networks. A main idea of our method lies in representing observed causal relationships as network paths and using techniques from combinatorial optimization to find the sparsest graph consistent with all experimental observations. Our contributions are twofold: (a) We formalize our approach, study its computational complexity and prove new results for exact and approximate solutions of the computationally hard transitive reduction substep of the approach (Sections 2 and 5). (b) We validate the biological usability of our approach by successfully applying it to a previously published signal transduction network by Li et al. (2006) and show that our algorithm for the transitive reduction substep performs well on graphs with a structure similar to those observed in transcriptional regulatory and signal transduction networks.

Efficient Approximation Algorithms for Tiling and Packing Problems with Rectangles

We provide improved approximation algorithms for several rectangle tiling and packing problems (RTILE, DRTILE, and d-RPACK) studied in the literature. Most of our algorithms are highly efficient since their running times are near-linear in the sparse input size rather than in the domain size. In addition, we improve the best known approximation ratios.

Improvements in throughout maximization for real-time scheduling

We consider the problem of off-line throughput maximization for job scheduling on one or more machines, where each job has a release time, a deadline and a profit. Most of the versions of the problem discussed here were already treated by Bar-Noy et al.(Proc. 31st ACM STOC, 622-631, 1999). Our main contribution is to provide algorithms that do not use linear programming, are simple and much faster than the corresponding ones proposed in Bar-Noy et al., while either having the same quality of approximation or improving it. More precisely, compared to the results of in Bar-Noy et al., our pseudo-polynomial algorithm for multiple unrelated machines and all of our strongly-polynomial algorithms have better performance ratios, all of our algorithms run much faster, are combinatorial in nature and avoid linear programming. Finally, we show that algorithms with better performance ratios than 2 are possible if the stretch factors of the jobs are bounded.

DNA-BAR: distinguisher selection for DNA barcoding

DNA-BAR is a software package for selecting DNA probes (henceforth referred to as distinguishers) that can be used in genomic-based identification of microorganisms. Given the genomic sequences of the microorganisms, DNA-BAR finds a near-minimum number of distinguishers yielding a distinct hybridization pattern for each microorganism. Selected distinguishers satisfy user specified bounds on length, melting temperature and GC content, as well as redundancy and cross-hybridization constraints.

KINALYZER, a computer program for reconstructing sibling groups

A software suite KINALYZER reconstructs full‐sibling groups without parental information using data from codominant marker loci such as microsatellites. KINALYZER utilizes a new algorithm for sibling reconstruction in diploid organisms based on combinatorial optimization. KINALYZER makes use of a Minimum 2‐Allele Set Cover approach based on Mendelian inheritance rules and finds the smallest number of sibling groups that contain all the individuals in the sample. Also available is a ‘Greedy Consensus’ approach that reconstructs sibgroups using subsets of loci and finds the consensus of the partial solutions. Unlike likelihood methods for sibling reconstruction, KINALYZER does not require information about population allele frequencies and it makes no assumptions regarding the mating system of the species. KINALYZER is freely available as a web‐based service.

Pricing of parking for congestion reduction

The proliferation of mobile devices, location-based services and embedded wireless sensors has given rise to applications that seek to improve the efficiency of the transportation system. In particular, new applications are already available that help travelers to find parking in urban settings by conveying the parking slot availability near the desired destinations of travelers on their mobile devices. In this paper we present two notions of parking choice: the optimal and the equilibrium. The equilibrium describes the behavior of individual, selfish agents in a system. We will show how a pricing authority can use the parking availability information to set prices that entice drivers to choose parking in the optimal way, the way that minimizes total driving distance by the vehicles and is then better for the transportation system (by reducing congestion) and for the environment. We will present two pricing schemes that perform this task. Furthermore, through simulations we show the potential congestion improvements that can be obtained through the use of these schemes.