Results 1  10
of
25
Graph theory for rulebased modeling of biochemical networks
 Lect. Notes Comput. Sci
, 2006
"... Abstract. We introduce a graphtheoretic formalism suitable for modeling biochemical networks marked by combinatorial complexity, such as signaltransduction systems, in which proteinprotein interactions play a prominent role. This development extends earlier work by allowing for explicit represen ..."
Abstract

Cited by 30 (10 self)
 Add to MetaCart
Abstract. We introduce a graphtheoretic formalism suitable for modeling biochemical networks marked by combinatorial complexity, such as signaltransduction systems, in which proteinprotein interactions play a prominent role. This development extends earlier work by allowing for explicit representation of the connectivity of a protein complex. Within the formalism, typed attributed graphs are used to represent proteins and their functional components, complexes, conformations, and states of posttranslational covalent modification. Graph transformation rules are used to represent proteinprotein interactions and their effects. Each rule defines a generalized reaction, i.e., a class of potential reactions that are logically consistent with knowledge or assumptions about the represented biomolecular interaction. A model is specified by defining 1) molecularentity graphs, which delimit the molecular entities and material components of a system and their possible states, 2) graph transformation rules, and 3) a seed set of graphs representing chemical species, such as the initial species present before introduction of a signal. A reaction network is generated iteratively through application of the graph transformation rules. The rules are first applied to the seed graphs and then to any and all new graphs that subsequently arise as a result of graph transformation. This procedure continues until no new graphs are generated or a specified termination condition is satisfied. The formalism supports the generation of a list of reactions in a system, which can be used to derive different types of physicochemical models, which can be simulated and analyzed in different ways. The processes of generating and simulating the network may be combined so that species are generated only as needed. 1
SelfHealing Networks
"... 3. ForgivingTree WE present two distributed algorithms for selfhealing in networks that are reconfigurable (such as peertopeer networks) in the sense that they can change their topology during an attack. Selfhealing seeks to maintain connectivity and possibly other useful properties in the face ..."
Abstract

Cited by 4 (2 self)
 Add to MetaCart
3. ForgivingTree WE present two distributed algorithms for selfhealing in networks that are reconfigurable (such as peertopeer networks) in the sense that they can change their topology during an attack. Selfhealing seeks to maintain connectivity and possibly other useful properties in the face of repeated attacks by an adversary, that in our model, is assumed to be omniscient. The first algorithm DASH is an algorithm that adds edges only among neighbors of deleted nodes (i.e. localityaware) and provably maintains connectivity and limits the degree increase of any node. Our second algorithm ForgivingTree allows only O(1) degree increase and also limits the diameter increase of the network. It, however, may need to use nodes other than the neighbors of the deleted node for reconstruction. Our approach is orthogonal and complementary to traditional topologybased approaches to defending against attack. ( a) One Deletion.
Typesetting in Hindi, Sanskrit and Persian: A Beginner’s Perspective
"... This paper describes our efforts to produce what is, to our knowledge, the first book typeset totally in an Indian language using LATEX: Chhand Chhand par Kumkum, published by Prabhat Prakashan for Mahatma Gandhi Antarrashtriya ..."
Abstract
 Add to MetaCart
This paper describes our efforts to produce what is, to our knowledge, the first book typeset totally in an Indian language using LATEX: Chhand Chhand par Kumkum, published by Prabhat Prakashan for Mahatma Gandhi Antarrashtriya
The forgiving graph: A distributed data structure for low stretch under adversarial attack
 In Proc. of 28th Symp. on Principles of Distributed Computing (PODC
, 2009
"... We consider the problem of selfhealing in peertopeer networks that are under repeated attack by an omniscient adversary. We assume that, over a sequence of rounds, an adversary either inserts a node with arbitrary connections or deletes an arbitrary node from the network. The network responds to ..."
Abstract

Cited by 12 (2 self)
 Add to MetaCart
We consider the problem of selfhealing in peertopeer networks that are under repeated attack by an omniscient adversary. We assume that, over a sequence of rounds, an adversary either inserts a node with arbitrary connections or deletes an arbitrary node from the network. The network responds to each such change by quick “repairs, ” which consist of adding or deleting a small number of edges. These repairs essentially preserve closeness of nodes after adversarial deletions, without increasing node degrees by too much, in the following sense. At any point in the algorithm, nodes v and w whose distance would have been ℓ in the graph formed by considering only the adversarial insertions (not the adversarial deletions), will be at distance at most ℓ log n in the actual graph, where n is the total number of vertices seen so far. Similarly, at any point, a node v whose degree would have been d in the graph with adversarial insertions only, will have degree at most 3d in the actual graph. Our algorithm is completely distributed and has low latency and bandwidth requirements. 1
Load balanced Scalable Byzantine Agreement through Quorum Building, with Full Information
"... Abstract. We address the problem of designing distributed algorithms for large scale networks that are robust to Byzantine faults. We consider a message passing, full information model: the adversary is malicious, controls a constant fraction of processors, and can view all messages in a round befor ..."
Abstract

Cited by 8 (5 self)
 Add to MetaCart
Abstract. We address the problem of designing distributed algorithms for large scale networks that are robust to Byzantine faults. We consider a message passing, full information model: the adversary is malicious, controls a constant fraction of processors, and can view all messages in a round before sending out its own messages for that round. Furthermore, each bad processor may send an unlimited number of messages. The only constraint on the adversary is that it must choose its corrupt processors at the start, without knowledge of the processors ’ private random bits. A good quorum is a set of O(log n) processors, which contains a majority of good processors. In this paper, we give a synchronous algorithm which uses polylogarithmic time and Õ( √ n) bits of communication per processor to bring all processors to agreement on a collection of n good quorums, solving Byzantine agreement as well. The collection is balanced in that no processor is in more than O(log n) quorums. This yields the first solution to Byzantine agreement which is both scalable and loadbalanced
Picking up the Pieces: SelfHealing in Reconfigurable Networks
"... We consider the problem of selfhealing in networks that are reconfigurable in the sense that they can change their topology during an attack. Our goal is to maintain connectivity in these networks, even in the presence of repeated adversarial node deletion, by carefully adding edges after each atta ..."
Abstract

Cited by 8 (3 self)
 Add to MetaCart
We consider the problem of selfhealing in networks that are reconfigurable in the sense that they can change their topology during an attack. Our goal is to maintain connectivity in these networks, even in the presence of repeated adversarial node deletion, by carefully adding edges after each attack. We present a new algorithm, DASH, that provably ensures that: 1) the network stays connected even if an adversary deletes up to all nodes in the network; and 2) no node ever increases its degree by more than 2 log n, where n is the number of nodes initially in the network. DASH is fully distributed; adds new edges only among neighbors of deleted nodes; and has average latency and bandwidth costs that are at most logarithmic in n. DASH has these properties irrespective of the topology of the initial network, and is thus orthogonal and complementary to traditional topologybased approaches to defending against attack. We also prove lowerbounds showing that DASH is asymptotically optimal in terms of minimizing maximum degree increase over multiple attacks. Finally, we present empirical results on powerlaw graphs that show that DASH performs well in practice, and that it significantly outperforms naive algorithms in reducing maximum degree increase.
January 2012 Research Statement
"... The last decade has seen a surprisingly rich interplay between economics, computer science, and game theory. From the economics side, the emergence of the Internet as a central platform to conduct trade has created new types of markets, mainly onesided auction markets. These electronic markets shar ..."
Abstract
 Add to MetaCart
The last decade has seen a surprisingly rich interplay between economics, computer science, and game theory. From the economics side, the emergence of the Internet as a central platform to conduct trade has created new types of markets, mainly onesided auction markets. These electronic markets share many properties with the more classical auction types, on the one hand, but also exhibit several important structural differences. These differences have motivated many studies, aiming to align classic economic theory with the new electronic environment. From the algorithmic side of computer science, the growth of the Internet has lead to new types of distributed agent systems that are characterized by interactions among computers with different ownership and incentives. Many new algorithmic questions are being asked as a result of this development. In contrast to the traditional assumption in computer science, that computers follow protocols and algorithm specifications, we now ask what happens when the input of the algorithm is kept by independent agents, acting selfishly to maximize their own utility. Game theory offers an elegant connection between these two different views, of classical economy vs. classical algorithmic theory. Using gametheoretic tools, a growing community has begun to study models that integrate these two viewpoints to enable a better understanding of the economic aspects of the Internet era. This community consists of researchers from both economics and computer science, demonstrating a fruitful cooperation between the two disciplines. As a researcher, I belong to this community of algorithmic game theorists. In recent years I have been interested in the following four main research directions, with new results as well as ongoing research and intriguing unsolved questions:
The Forgiving Tree: A SelfHealing Distributed Data Structure
, 802
"... We consider the problem of selfhealing in peertopeer networks that are under repeated attack by an omniscient adversary. We assume that the following process continues for up to n rounds where n is the total number of nodes initially in the network: the adversary deletes an arbitrary node from th ..."
Abstract

Cited by 6 (2 self)
 Add to MetaCart
We consider the problem of selfhealing in peertopeer networks that are under repeated attack by an omniscient adversary. We assume that the following process continues for up to n rounds where n is the total number of nodes initially in the network: the adversary deletes an arbitrary node from the network, then the network responds by quickly adding a small number of new edges. We present a distributed data structure that ensures two key properties. First, the diameter of the network is never more than O(log ∆) times its original diameter, where ∆ is the maximum degree of the network initially. We note that for many peertopeer systems, ∆ is polylogarithmic, so the diameter increase would be a O(log log n) multiplicative factor. Second, the degree of any node never increases by more than 3 over its original degree. Our data structure is fully distributed, has O(1) latency per round and requires each node to send and receive O(1) messages per round. The data structure requires an initial setup phase that has latency equal to the diameter of the original network, and requires, with high probability, each node v to send O(log n) messages along every edge incident to v. Our approach is orthogonal and complementary to traditional topologybased approaches to defending against attack. 1
Composition games for distributed systems: the EU grant games
, 2013
"... We analyze ways by which people decompose into groups in distributed systems. We are interested in systems in which an agent can increase its utility by connecting to other agents, but must also pay a cost that increases with the size of the system. The right balance is achieved by the right size gr ..."
Abstract

Cited by 2 (1 self)
 Add to MetaCart
We analyze ways by which people decompose into groups in distributed systems. We are interested in systems in which an agent can increase its utility by connecting to other agents, but must also pay a cost that increases with the size of the system. The right balance is achieved by the right size group of agents. We formulate and analyze three intuitive and realistic games and show how simple changes in the protocol can drastically improve the price of anarchy of these games. In particular, we identify two important properties for a low price of anarchy: agreement in joining the system, and the possibility of appealing a rejection from a system. We show that the latter property is especially important if there are some preexisting constraints regarding who may collaborate (or communicate) with whom.
Results 1  10
of
25