links for 2010-​​07-​​30

  • “Strat­egy changes are an essen­tial part of evo­lu­tion­ary games. Here we intro­duce a sim­ple rule that, depend­ing on the value of a sin­gle para­me­ter $w$, influ­ences the selec­tion of play­ers that are con­sid­ered as poten­tial sources of the new strat­egy. For pos­i­tive $w$ play­ers with high pay­offs will be con­sid­ered more likely, while for neg­a­tive $w$ the oppo­site holds. Set­ting $w$ equal to zero returns the fre­quently adopted ran­dom selec­tion of the oppo­nent. We find that increas­ing the prob­a­bil­ity of adopt­ing the strat­egy from the fittest player within reach, i.e. set­ting $w$ pos­i­tive, pro­motes the evo­lu­tion of coop­er­a­tion. The robust­ness of this obser­va­tion is tested against dif­fer­ent lev­els of uncer­tainty in the strat­egy adop­tion process and for dif­fer­ent inter­ac­tion net­work. Since the evo­lu­tion to wide­spread defec­tion is tightly asso­ci­ated with coop­er­a­tors hav­ing a lower fit­ness than defec­tors, the fact that pos­i­tive val­ues of $w$ facil­i­tate coop­er­a­tion is quite surprising. …”
  • “In this work we study a weak Prisoner’s Dilemma game in which both strate­gies and update rules are sub­jected to evo­lu­tion­ary pres­sure. Inter­ac­tions among agents are spec­i­fied by com­plex topolo­gies, and we con­sider both homo­ge­neous and het­ero­ge­neous sit­u­a­tions. We con­sider deter­min­is­tic and sto­chas­tic update rules for the strate­gies, which in turn may con­sider sin­gle links or full con­text when select­ing agents to copy from. Our results indi­cate that the co-​​evolutionary process pre­serves het­ero­ge­neous net­works as a suit­able frame­work for the emer­gence of coop­er­a­tion. Fur­ther­more, on those net­works, the update rule lead­ing to a larger frac­tion of coop­er­a­tion, repli­ca­tor dynam­ics, is selected dur­ing co-evolution.…We con­clude that for a vari­ety of topolo­gies, the fact that the dynam­ics coe­volves with the strate­gies leads in gen­eral to more coop­er­a­tion in the weak Prisoner’s Dilemma game.”
  • “Dynam­ics of evo­lu­tion­ary games strongly depend on under­ly­ing net­works. We study the coevo­lu­tion­ary prisoner’s dilemma in which play­ers change their local net­works as well as strate­gies (i.e., coop­er­ate or defect). This topic has been increas­ingly explored by many researchers. On the basis of active link­ing dynam­ics [J. M. Pacheco et al., J. Theor. Biol. 243, 437 (2006), J. M. Pacheco et al., Phys. Rev. Lett. 97, 258103 (2006)], we show that coop­er­a­tion is enhanced fairly robustly. In par­tic­u­lar, coop­er­a­tion evolves when the pay­off of the player is nor­mal­ized by the num­ber of neigh­bors; this is not the case in the evo­lu­tion­ary prisoner’s dilemma on sta­tic networks.”
  • “Bio­log­i­cal net­works of inter­act­ing agents exhibit sim­i­lar topo­log­i­cal prop­er­ties for a wide range of scales, from cel­lu­lar to eco­log­i­cal lev­els, sug­gest­ing the exis­tence of a com­mon evo­lu­tion­ary ori­gin. A gen­eral evo­lu­tion­ary mech­a­nism based on global sta­bil­ity has been pro­posed recently [J I Per­otti, O V Bil­loni, F A Tamarit, D R Chialvo, S A Can­nas, Phys. Rev. Lett. 103, 108701 (2009)]. This mech­a­nism is incor­po­rated into a model of a grow­ing net­work of inter­act­ing agents in which each new agent’s mem­ber­ship in the net­work is deter­mined by the agent’s effect on the network’s global sta­bil­ity. We show that, out of this sta­bil­ity con­straint, sev­eral topo­log­i­cal prop­er­ties observed in bio­log­i­cal net­works emerge in a self orga­nized man­ner. The influ­ence of the sta­bil­ity selec­tion mech­a­nism on the dynam­ics asso­ci­ated to the result­ing net­work is ana­lyzed as well.”
  • “How do liv­ing cells achieve suf­fi­cient abun­dances of func­tional pro­tein com­plexes while min­i­miz­ing promis­cu­ous non-​​functional inter­ac­tions between their pro­teins? Here we study this prob­lem using a first-​​principle model of the cell whose phe­no­typic traits are directly deter­mined from its genome through bio­phys­i­cal prop­er­ties of pro­tein struc­tures and bind­ing inter­ac­tions in crowded cel­lu­lar envi­ron­ment. The model cell includes three inde­pen­dent path­ways, whose topolo­gies of PPI sub­net­works are dif­fer­ent, but whose func­tional con­cen­tra­tions equally con­tribute to cell’s fit­ness. The model cells evolve through geno­typic muta­tions and phe­no­typic pro­tein copy num­ber vari­a­tions. We found a strong rela­tion­ship between evolved physical-​​chemical prop­er­ties of pro­tein inter­ac­tions and their abun­dances due to a “frus­tra­tion” effect: strength­en­ing of func­tional inter­ac­tions brings about hydropho­bic sur­faces, which make pro­teins prone to promis­cu­ous binding.…”
  • “We intro­duce the het­ero­ge­neous voter model (HVM), in which each agent has its own intrin­sic rate to change state, reflec­tive of the het­ero­gene­ity of real peo­ple, and the par­ti­san voter model (PVM), in which each agent has an innate and fixed pref­er­ence for one of two pos­si­ble opin­ion states. For the HVM, the time until con­sen­sus is reached is much longer than in the clas­sic voter model. For the PVM in the mean-​​field limit, a pop­u­la­tion evolves to a “self­ish” state, where each agent tends to be aligned with its inter­nal pref­er­ence. For finite pop­u­la­tions, dis­crete fluc­tu­a­tions ulti­mately lead to con­sen­sus being reached in a time that scales expo­nen­tially with pop­u­la­tion size.”

links for 2010-​​07-​​29

  • “We con­sider the prob­lem of sched­ul­ing in mul­ti­hop wire­less net­works sub­ject to inter­fer­ence con­straints. We con­sider a graph based rep­re­sen­ta­tion of wire­less net­works, where sched­uled links adhere to the K-​​hop link inter­fer­ence model. We develop a dis­trib­uted greedy heuris­tic for this sched­ul­ing prob­lem. Fur­ther, we show that this dis­trib­uted greedy heuris­tic com­putes the exact same sched­ule as the cen­tral­ized greedy heuristic.”
  • “…Here we study the quan­ti­ta­tive rela­tion between adap­tive response and back­ground com­pen­sa­tion within a mod­el­ing frame­work. In con­trast to the com­monly held view, we show that any par­tic­u­lar type of adap­tive response is nei­ther suf­fi­cient nor nec­es­sary for adap­tive enlarge­ment of dynamic range. In par­tic­u­lar a pre­cise adap­tive response, where sys­tem activ­ity is main­tained at a con­stant level at steady state, does not ensure a large dynamic range nei­ther in input sig­nal nor in sys­tem out­put. A gen­eral mech­a­nism for input dynamic range enlarge­ment comes about from the activity-​​dependent mod­u­la­tion of pro­tein respon­sive­ness by mul­ti­ple bio­chem­i­cal mod­i­fi­ca­tion, regard­less of the type of adap­tive response it induces. There­fore hier­ar­chi­cal bio­chem­i­cal processes such as methy­la­tion and phos­pho­ry­la­tion are nat­ural can­di­dates to induce this prop­erty in sig­nalling systems.”
  • “Many mod­els of mar­ket dynam­ics make use of the idea of wealth exchanges among eco­nomic agents. A sim­ple anal­ogy com­pares the wealth in a soci­ety with the energy in a phys­i­cal sys­tem, and the trade between agents to the energy exchange between mol­e­cules dur­ing col­li­sions. How­ever, while in phys­i­cal sys­tems the equipar­ti­tion of energy is valid, in most exchange mod­els for eco­nomic mar­kets the sys­tem con­verges to a very unequal “con­densed” state, where one or a few agents con­cen­trate all the wealth of the soci­ety and the wide major­ity of agents shares zero or a very tiny frac­tion of the wealth. Here we present an exchange model where the goal is not only to avoid con­den­sa­tion but also to reduce the inequal­ity; to carry out this objec­tive the choice of inter­act­ing agents is not at ran­dom, but fol­lows an extremal dynam­ics reg­u­lated by the wealth of the agent.…”
  • “One direc­tion for future research would be to investi– gate to what extent these coun­terex­am­ples are spe­cial. For exam­ple, are all shapes which repel a point charge sim­i­lar to the hemi­sphere geom­e­try dis­cussed here, or are there com­pletely dif­fer­ent kinds of geome­tries with this prop­erty? More specif­i­cally, is it pos­si­ble to achieve re– pul­sion with a con­vex metal­lic object? One can ask sim– ilar ques­tions about Casimir repul­sion. There are many open ques­tions here—we have only just begun to under– stand these coun­ter­in­tu­itive geo­met­ric effects.”
  • “Rotor-​​router net­works are dis­crete ana­logues of con­tin­u­ous lin­ear sys­tems such as elec­tri­cal cir­cuits; they are also deter– min­is­tic ana­logues of sto­chas­tic sys­tems such as ran­dom walk processes. These analo­gies per­mit one to design rotor-​​router net­works to com­pute numer­i­cal quan­ti­ties asso­ci­ated with lin– ear and/​or sto­chas­tic sys­tems. These dis­trib­uted com­pu­ta­tions can behave sta­bly even in the pres­ence of sig­nif­i­cant disruption.”
  • “Behavior-​​Driven Devel­op­ment (BDD) is a spec­i­fi­ca­tion tech­nique that auto­mat­i­cally cer­ti­fies that all func­tional require­ments are treated prop­erly by source code, through the con­nec­tion of the tex­tual descrip­tion of these require­ments to auto­mated tests. Given that in some areas, in spe­cial Enter­prise Infor­ma­tion Sys­tems, require­ments are iden­ti­fied by Busi­ness Process Mod­el­ing — which uses graph­i­cal nota­tions of the under­ly­ing busi­ness processes, this paper aims to pro­vide a map­ping from the basic con­structs that form the most com­mon BPM lan­guages to Behav­ior Dri­ven Devel­op­ment constructs.”
  • “The study of net­works has grown into a sub­stan­tial inter­dis­ci­pli­nary endeavor across the nat­ural, social, and infor­ma­tion sci­ences. Yet there have been very few attempts to inves­ti­gate the inter­re­lat­ed­ness of the dif­fer­ent classes of net­works stud­ied by dif­fer­ent dis­ci­plines. Here, we intro­duced a frame­work to estab­lish a tax­on­omy of net­works from var­i­ous ori­gins. The pro­vi­sion of this fam­ily tree not only helps under­stand the kin­ship of net­works, but also facil­i­tates the trans­fer of empir­i­cal analy­sis, the­o­ret­i­cal mod­el­ing, and con­cep­tual devel­op­ments across dis­ci­pli­nary bound­aries. The frame­work is based on prob­ing the meso­scopic prop­er­ties of net­works, an impor­tant source of het­ero­gene­ity for their struc­ture and func­tion. Using our method, we com­puted a tax­on­omy for 752 indi­vid­ual net­works and a sep­a­rate tax­on­omy for 12 net­work classes. We also com­puted three within-​​class tax­onomies for polit­i­cal, fun­gal, and finan­cial net­works, and found them to be insight­ful in each case.”
  • “…The h index is com­pared with the Degree cen­tral­ity (a local mea­sure), the Between­ness and Eigen­vec­tor cen­tral­i­ties (two non-​​local mea­sures) in the case of a bio­log­i­cal net­work (Yeast inter­ac­tion protein-​​protein net­work) and a lin­guis­tic net­work (Moby The­saurus II). In both net­works, the Hirsch index has poor cor­re­la­tion with Between­ness cen­tral­ity but cor­re­lates well with Eigen­vec­tor cen­tral­ity, spe­cially for the more impor­tant nodes that are rel­e­vant for rank­ing pur­poses, say in Search Engine Opti­miza­tion. In the the­saurus net­work, the h index seems even to out­per­form the Eigen­vec­tor cen­tral­ity mea­sure as eval­u­ated by sim­ple lin­guis­tic criteria.”
  • “Despite the avail­abil­ity of very detailed data on finan­cial mar­ket, agent-​​based mod­el­ing is hin­dered by the lack of infor­ma­tion about real trader behav­ior. This makes it impos­si­ble to val­i­date agent-​​based mod­els, which are thus reverse-​​engineering attempts. This work is a con­tri­bu­tion to the build­ing of a set of styl­ized facts about the traders them­selves. Using the client data­base of Swis­squote Bank SA, the largest on-​​line Swiss bro­ker, we find empir­i­cal rela­tion­ships between turnover, account val­ues and the num­ber of assets in which a trader is invested. A the­ory based on sim­ple mean-​​variance port­fo­lio opti­miza­tion that cru­cially includes vari­able trans­ac­tion costs is able to repro­duce faith­fully the observed behav­iors. We finally argue that our results bring into light the col­lec­tive abil­ity of a pop­u­la­tion to con­struct a mean-​​variance port­fo­lio that takes into account the struc­ture of trans­ac­tion costs.”
  • “We con­sider the prob­lem of para­me­ter esti­ma­tion for a sys­tem of ordi­nary dif­fer­en­tial equa­tions from noisy obser­va­tions on a solu­tion of the sys­tem. In case the sys­tem is non­lin­ear, as it typ­i­cally is in prac­ti­cal appli­ca­tions, an ana­lytic solu­tion to it usu­ally does not exist. Con­se­quently, straight­for­ward esti­ma­tion meth­ods like the ordi­nary least squares method depend on repet­i­tive use of numer­i­cal inte­gra­tion in order to deter­mine the solu­tion of the sys­tem for each of the para­me­ter val­ues con­sid­ered, and to find sub­se­quently the para­me­ter esti­mate that min­imises the objec­tive func­tion. This induces a huge com­pu­ta­tional load to such esti­ma­tion meth­ods. We pro­pose an esti­ma­tor that is defined as a min­imiser of an appro­pri­ate dis­tance between a non­para­met­ri­cally esti­mated deriv­a­tive of the solu­tion and the right-​​hand side of the sys­tem applied to a non­para­met­ri­cally esti­mated solution.…”
  • “We present designs of 2D isotropic, dis­or­dered pho­tonic mate­ri­als of arbi­trary size with com­plete band gaps block­ing all direc­tions and polar­iza­tions. The designs with the largest gaps are obtained by a con­strained opti­miza­tion method that starts from a hype­r­uni­form dis­or­dered point pat­tern, an array of points whose num­ber vari­ance within a spher­i­cal sam­pling win­dow grows more slowly than the vol­ume. We argue that hype­r­uni­for­mity, com­bined with uni­form local topol­ogy and short-​​range geo­met­ric order, can explain how com­plete pho­tonic band gaps are pos­si­ble with­out long-​​range trans­la­tional order. We note the ram­i­fi­ca­tions for elec­tronic and phononic band gaps in dis­or­dered materials.”
  • “Sys­tems whose orga­ni­za­tion dis­plays causal asym­me­try con­straints, from evo­lu­tion­ary trees to river basins or trans­port net­works, can be often described in terms of directed paths (causal flows) on a dis­crete state space. Such a set of paths defines a feed-​​forward, acyclic net­work. A key prob­lem asso­ci­ated with these sys­tems involves char­ac­ter­iz­ing their intrin­sic degree of path reversibil­ity: given an end node in the graph, what is the uncer­tainty of recov­er­ing the process back­wards until the ori­gin? Here we pro­pose a novel con­cept, \textit{topological reversibil­ity}, which rig­or­ously weigths such uncer­tainty in path depen­dency quan­ti­fied as the min­i­mum amount of infor­ma­tion required to suc­cess­fully revert a causal path.…”
  • “In this paper, a para­met­ric level set method for recon­struc­tion of obsta­cles in gen­eral inverse prob­lems is con­sid­ered. Gen­eral evo­lu­tion equa­tions for the recon­struc­tion of unknown obsta­cles are derived in terms of the under­ly­ing level set para­me­ters. We show that using the appro­pri­ate form of para­me­ter­iz­ing the level set func­tion results a sig­nif­i­cantly lower dimen­sional prob­lem, which bypasses many dif­fi­cul­ties with tra­di­tional level set meth­ods, such as reg­u­lar­iza­tion, re-​​initialization and use of signed dis­tance function.…”
  • “… The aim is to find effi­cient decom­po­si­tions that simul­ta­ne­ously min­i­mize the irra­di­a­tion time, the car­di­nal­ity of the decom­po­si­tion and the setup-​​time to con­fig­ure the multi-​​leaf col­li­ma­tor at each step of the decom­po­si­tion. We pro­pose for this NP-​​hard mul­ti­ob­jec­tive com­bi­na­to­r­ial prob­lem a heuris­tic, based on the adap­ta­tion of the two-​​phase Pareto local search. Exper­i­ments are car­ried out on dif­fer­ent size instances and the results are reported.”
  • “The knap­sack prob­lem (KP) and its mul­ti­di­men­sional ver­sion (MKP) are basic prob­lems in com­bi­na­to­r­ial opti­miza­tion. In this paper we con­sider their mul­ti­ob­jec­tive exten­sion (MOKP and MOMKP), for which the aim is to obtain or to approx­i­mate the set of effi­cient solu­tions. In a first step, we clas­sify and describe briefly the exist­ing works, that are essen­tially based on the use of meta­heuris­tics. In a sec­ond step, we pro­pose the adap­ta­tion of the two-​​phase Pareto local search (2PPLS) to the res­o­lu­tion of the MOMKP. With this aim, we use a very-​​large scale neigh­bor­hood (VLSN) in the sec­ond phase of the method, that is the Pareto local search. We com­pare our results to state-​​of-​​the-​​art results and we show that we obtain results never reached before by heuris­tics, for the biob­jec­tive instances. Finally we con­sider the exten­sion to three-​​objective instances.”
  • “We con­sider the prob­lem of com­put­ing a response curve for binary cel­lu­lar automata — that is, the curve describ­ing the depen­dence of the den­sity of ones after many iter­a­tions of the rule on the ini­tial den­sity of ones. We demon­strate how this prob­lem could be approached using rule 130 as an exam­ple. For this rule, preim­age sets of finite strings exhibit rec­og­niz­able pat­terns, and it is there­fore pos­si­ble to com­pute both car­di­nal­i­ties of preim­ages of cer­tain finite strings and prob­a­bil­i­ties of occur­rence of these strings in a con­fig­u­ra­tion obtained by iter­at­ing a ran­dom ini­tial con­fig­u­ra­tion $n$ times. Response curves can be rig­or­ously cal­cu­lated in both one– and two-​​dimensional ver­sions of CA rule 130. We also dis­cuss a spe­cial case of totally dis­or­dered ini­tial con­fig­u­ra­tions, that is, ran­dom con­fig­u­ra­tions where the den­sity of ones and zeros are equal to 12.”
  • “This paper presents a new numer­i­cal approach to the study of non-​​periodicity in sig­nals, which can com­ple­ment the max­i­mal Lya­punov expo­nent method for deter­min­ing chaos tran­si­tions of a given dynam­i­cal sys­tem. The pro­posed tech­nique is based on the con­tin­u­ous wavelet trans­form and the wavelet mul­tires­o­lu­tion analy­sis. A new para­me­ter, the \textit{scale index}, is intro­duced and inter­preted as a mea­sure of the degree of the signal’s non-​​periodicity. This method­ol­ogy is suc­cess­fully applied to three clas­si­cal dynam­i­cal sys­tems: the Bonhoeffer-​​van der Pol oscil­la­tor, the logis­tic map, and the Henon map.”

links for 2010-​​07-​​28

links for 2010-​​07-​​26

links for 2010-​​07-​​25