Bhaskar Dasgupta | University of Illinois at Chicago (original) (raw)

Papers by Bhaskar Dasgupta

Abstract Given a graph of interactions, a module (also called a community or cluster) is a subset... more Abstract Given a graph of interactions, a module (also called a community or cluster) is a subset of nodes whose fitness is a function of the statistical significance of the pairwise interactions of nodes in the module. The topic of this paper is a model-based community finding approach, commonly referred to as modularity clustering, that was originally proposed by Newman [25] and has subsequently been extremely popular in practice (eg, see [1, 20, 28, 30, 32]).

Abstract With improved tools for collecting genetic data from natural and experimental population... more Abstract With improved tools for collecting genetic data from natural and experimental populations, new opportunities arise to study fundamental biological processes, including behavior, mating systems, adaptive trait evolution, and dispersal patterns. Full use of the newly available genetic data often depends upon reconstructing genealogical relationships of individual organisms, such as sibling reconstruction.

Abstract: The understanding of molecular cell biology requires insight into the structure and dyn... more Abstract: The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central goals of systems biology is the unraveling of the as yet poorly characterized complex web of interactions among these components.

Abstract: In this note, we explore a connection between the small-set expansion problem and a pop... more Abstract: In this note, we explore a connection between the small-set expansion problem and a popular community finding approach for social networks, and observe that a sub-exponential time small-set expansion algorithm can be used to provide a sub-exponential time 2-approximation for hard instances of the community finding problem.

Abstract Internet advertising is a sophisticated game in which the many advertisers “play” to opt... more Abstract Internet advertising is a sophisticated game in which the many advertisers “play” to optimize their return on investment. There are many “targets” for the advertisements, and each “target” has a collection of games with a potentially different set of players involved. In this paper, we study the problem of how advertisers allocate their budget across these “targets”. In particular, we focus on formulating their best response strategy as an optimization problem.

Since the discovery of the double helical structure of DNA, the molecular biology field has under... more Since the discovery of the double helical structure of DNA, the molecular biology field has undergone a significant transformation via nucleic acids sequencing to determine genetic information at the most fundamental level. This revolution in biology has created a huge volume of data, estimate by many to grow at an exponential rate, by directly reading DNA sequences. One important reason for this exceptional growth rate of biological data lies in the medical use of such information in the design of therapeutics.

Abstract: Involvements of major financial institutions in the recent financial crisis have genera... more Abstract: Involvements of major financial institutions in the recent financial crisis have generated renewed interests in fragility of global financial networks among economists and regulatory authorities. In particular, one potential vulnerability of the financial networks is the" financial contagion" process in which insolvencies of individual entities propagate through the" web of dependencies" to affect the entire system.

We further investigate and generalize the approximate privacy model recently introduced by Feigen... more We further investigate and generalize the approximate privacy model recently introduced by Feigenbaum et al.(2010)[7]. We explore the privacy properties of a natural class of communication protocols that we refer to as “dissection protocols”. Informally, in a dissection protocol the communicating parties are restricted to answering questions of the form “Is your input between the values α and β (under a pre-defined order over the possible inputs)?”.

The concepts of degeneracy and redundancy are well known in information theory. Loosely speaking,... more The concepts of degeneracy and redundancy are well known in information theory. Loosely speaking, degeneracy refers to structurally different elements performing the same function, whereas redundancy refers to identical elements performing the same function 1. In electronic systems, such measures are* ralbert@ phys. psu. edu; www. phys. psu. edu/∼ ralbert† dasgupta@ cs. uic. edu; www. cs. uic. edu/∼ dasgupta; Author to whom correspondence should be sent.‡ rashmihegde. g@ gmail. com § gsivan2@ uic.

Abstract: Threats on the stability of a financial system may severely affect the functioning of t... more Abstract: Threats on the stability of a financial system may severely affect the functioning of the entire economy, and thus considerable emphasis is placed on the analyzing the cause and effect of such threats. The financial crisis in the current and past decade has shown that one important cause of instability in global markets is the so-called financial contagion, namely the spreadings of instabilities or failures of individual components of the network to other, perhaps healthier, components.

Abstract Circular permutation connects the N and C termini of a protein and concurrently cleaves ... more Abstract Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurrences, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison.

In this paper, we consider approximability issues of the following four problems: triangle packin... more In this paper, we consider approximability issues of the following four problems: triangle packing, full sibling reconstruction, maximum profit coverage and 2-coverage. All of them are generalized or specialized versions of set-cover and have applications in biology ranging from full-sibling reconstructions in wild populations to biomolecular clusterings; however, as this paper shows, their approximability properties differ considerably.

In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model ... more In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model on 3D and 2D lattices [WE Hart, On the computational complexity of sequence design problems, Proceedings of the First Annual International Conference on Computational Molecular Biology 1997, pp. 128–136; EI Shakhnovich, AM Gutin, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl. Acad. Sci. 90 (1993) 7195–7199].

Abstract. We consider two optimization problems with geometric structures. The rst one concerns t... more Abstract. We consider two optimization problems with geometric structures. The rst one concerns the following minimization problem, termed as the rectilinear polygon cover problem:\ Cover certain features of a given rectilinear polygon (possibly with rectilinear holes) with the minimum number of rectangles included in the polygon." Depending upon whether one wants to cover the interior, boundary or corners of the polygon, the problem is termed as the interior, boundary or corner cover problem, respectively.

Over the last few decades, researchers in various fields have witnessed applications of novel com... more Over the last few decades, researchers in various fields have witnessed applications of novel computing models and algorithmic paradigms in many application areas involving biological processes, quantum computing, nanotechnology, social networks and many other such disciplines. Typical characteristics of these application areas include their interdisciplinary nature going beyond previous traditional approaches that were used, and often high-risk high-gain nature of resulting collaborations.

Abstract The rectilinear polygon cover problem is one in which a certain class of features of a r... more Abstract The rectilinear polygon cover problem is one in which a certain class of features of a rectilinear polygon of n vertices has to be covered with the minimum number of rectangles included in the polygon. In particular, one can consider covering the entire interior, the boundary and the set of corners of the polygon. These problems have important applications in, for example, storing images and in the manufacture of integrated circuits. In this paper we consider covering the corners of the polygons, also known as the corner-cover problem.

The modern era of molecular biology began with the discovery of the double helical structure of D... more The modern era of molecular biology began with the discovery of the double helical structure of DNA. Today, sequencing nucleic acids, the determination of genetic information at the most fundamental level, is a major tool of biological research [44]. This revolution in biology has created a huge amount of data at great speed by directly reading DNA sequences. The growth rate of data volume is exponential. For instance, the volume of DNA and protein sequence data is currently doubling every 22 months [32].

For wild populations, the growing development and application of molecular markers, such as micro... more For wild populations, the growing development and application of molecular markers, such as microsatellites, provides new possibilities for establishing kinship and reconstructing pedigrees in species where such information cannot be obtained from field observations alone. Knowledge of kinship in wild or experimental populations of non-model organisms allows the investigation of many fundamental biological phenomena, including mating systems, selection and adaptation, kin selection, and dispersal patterns.

Abstract—With the proliferation of location-based services, mobile devices, and embedded wireless... more Abstract—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 slots. Nevertheless, while engaged in driving, travelers are better suited being guided to an ideal parking slot, than looking at a map and choosing which slot to go to.

Abstract Given a graph of interactions, a module (also called a community or cluster) is a subset... more Abstract Given a graph of interactions, a module (also called a community or cluster) is a subset of nodes whose fitness is a function of the statistical significance of the pairwise interactions of nodes in the module. The topic of this paper is a model-based community finding approach, commonly referred to as modularity clustering, that was originally proposed by Newman [25] and has subsequently been extremely popular in practice (eg, see [1, 20, 28, 30, 32]).

Abstract With improved tools for collecting genetic data from natural and experimental population... more Abstract With improved tools for collecting genetic data from natural and experimental populations, new opportunities arise to study fundamental biological processes, including behavior, mating systems, adaptive trait evolution, and dispersal patterns. Full use of the newly available genetic data often depends upon reconstructing genealogical relationships of individual organisms, such as sibling reconstruction.

Abstract: The understanding of molecular cell biology requires insight into the structure and dyn... more Abstract: The understanding of molecular cell biology requires insight into the structure and dynamics of networks that are made up of thousands of interacting molecules of DNA, RNA, proteins, metabolites, and other components. One of the central goals of systems biology is the unraveling of the as yet poorly characterized complex web of interactions among these components.

Abstract: In this note, we explore a connection between the small-set expansion problem and a pop... more Abstract: In this note, we explore a connection between the small-set expansion problem and a popular community finding approach for social networks, and observe that a sub-exponential time small-set expansion algorithm can be used to provide a sub-exponential time 2-approximation for hard instances of the community finding problem.

Abstract Internet advertising is a sophisticated game in which the many advertisers “play” to opt... more Abstract Internet advertising is a sophisticated game in which the many advertisers “play” to optimize their return on investment. There are many “targets” for the advertisements, and each “target” has a collection of games with a potentially different set of players involved. In this paper, we study the problem of how advertisers allocate their budget across these “targets”. In particular, we focus on formulating their best response strategy as an optimization problem.

Since the discovery of the double helical structure of DNA, the molecular biology field has under... more Since the discovery of the double helical structure of DNA, the molecular biology field has undergone a significant transformation via nucleic acids sequencing to determine genetic information at the most fundamental level. This revolution in biology has created a huge volume of data, estimate by many to grow at an exponential rate, by directly reading DNA sequences. One important reason for this exceptional growth rate of biological data lies in the medical use of such information in the design of therapeutics.

Abstract: Involvements of major financial institutions in the recent financial crisis have genera... more Abstract: Involvements of major financial institutions in the recent financial crisis have generated renewed interests in fragility of global financial networks among economists and regulatory authorities. In particular, one potential vulnerability of the financial networks is the" financial contagion" process in which insolvencies of individual entities propagate through the" web of dependencies" to affect the entire system.

We further investigate and generalize the approximate privacy model recently introduced by Feigen... more We further investigate and generalize the approximate privacy model recently introduced by Feigenbaum et al.(2010)[7]. We explore the privacy properties of a natural class of communication protocols that we refer to as “dissection protocols”. Informally, in a dissection protocol the communicating parties are restricted to answering questions of the form “Is your input between the values α and β (under a pre-defined order over the possible inputs)?”.

The concepts of degeneracy and redundancy are well known in information theory. Loosely speaking,... more The concepts of degeneracy and redundancy are well known in information theory. Loosely speaking, degeneracy refers to structurally different elements performing the same function, whereas redundancy refers to identical elements performing the same function 1. In electronic systems, such measures are* ralbert@ phys. psu. edu; www. phys. psu. edu/∼ ralbert† dasgupta@ cs. uic. edu; www. cs. uic. edu/∼ dasgupta; Author to whom correspondence should be sent.‡ rashmihegde. g@ gmail. com § gsivan2@ uic.

Abstract: Threats on the stability of a financial system may severely affect the functioning of t... more Abstract: Threats on the stability of a financial system may severely affect the functioning of the entire economy, and thus considerable emphasis is placed on the analyzing the cause and effect of such threats. The financial crisis in the current and past decade has shown that one important cause of instability in global markets is the so-called financial contagion, namely the spreadings of instabilities or failures of individual components of the network to other, perhaps healthier, components.

Abstract Circular permutation connects the N and C termini of a protein and concurrently cleaves ... more Abstract Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurrences, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison.

In this paper, we consider approximability issues of the following four problems: triangle packin... more In this paper, we consider approximability issues of the following four problems: triangle packing, full sibling reconstruction, maximum profit coverage and 2-coverage. All of them are generalized or specialized versions of set-cover and have applications in biology ranging from full-sibling reconstructions in wild populations to biomolecular clusterings; however, as this paper shows, their approximability properties differ considerably.

In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model ... more In this paper we investigate the inverse protein folding (IPF) problem under the Canonical model on 3D and 2D lattices [WE Hart, On the computational complexity of sequence design problems, Proceedings of the First Annual International Conference on Computational Molecular Biology 1997, pp. 128–136; EI Shakhnovich, AM Gutin, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl. Acad. Sci. 90 (1993) 7195–7199].

Abstract. We consider two optimization problems with geometric structures. The rst one concerns t... more Abstract. We consider two optimization problems with geometric structures. The rst one concerns the following minimization problem, termed as the rectilinear polygon cover problem:\ Cover certain features of a given rectilinear polygon (possibly with rectilinear holes) with the minimum number of rectangles included in the polygon." Depending upon whether one wants to cover the interior, boundary or corners of the polygon, the problem is termed as the interior, boundary or corner cover problem, respectively.

Over the last few decades, researchers in various fields have witnessed applications of novel com... more Over the last few decades, researchers in various fields have witnessed applications of novel computing models and algorithmic paradigms in many application areas involving biological processes, quantum computing, nanotechnology, social networks and many other such disciplines. Typical characteristics of these application areas include their interdisciplinary nature going beyond previous traditional approaches that were used, and often high-risk high-gain nature of resulting collaborations.

Abstract The rectilinear polygon cover problem is one in which a certain class of features of a r... more Abstract The rectilinear polygon cover problem is one in which a certain class of features of a rectilinear polygon of n vertices has to be covered with the minimum number of rectangles included in the polygon. In particular, one can consider covering the entire interior, the boundary and the set of corners of the polygon. These problems have important applications in, for example, storing images and in the manufacture of integrated circuits. In this paper we consider covering the corners of the polygons, also known as the corner-cover problem.

The modern era of molecular biology began with the discovery of the double helical structure of D... more The modern era of molecular biology began with the discovery of the double helical structure of DNA. Today, sequencing nucleic acids, the determination of genetic information at the most fundamental level, is a major tool of biological research [44]. This revolution in biology has created a huge amount of data at great speed by directly reading DNA sequences. The growth rate of data volume is exponential. For instance, the volume of DNA and protein sequence data is currently doubling every 22 months [32].

For wild populations, the growing development and application of molecular markers, such as micro... more For wild populations, the growing development and application of molecular markers, such as microsatellites, provides new possibilities for establishing kinship and reconstructing pedigrees in species where such information cannot be obtained from field observations alone. Knowledge of kinship in wild or experimental populations of non-model organisms allows the investigation of many fundamental biological phenomena, including mating systems, selection and adaptation, kin selection, and dispersal patterns.

Abstract—With the proliferation of location-based services, mobile devices, and embedded wireless... more Abstract—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 slots. Nevertheless, while engaged in driving, travelers are better suited being guided to an ideal parking slot, than looking at a map and choosing which slot to go to.