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Rate-independent computation in continuous chemical reaction networks 连续化学反应网络中的速率无关计算
Ho-Lin Chen, David Doty, D. Soloveichik
Understanding the algorithmic behaviors that are in principle realizable in a chemical system is necessary for a rigorous understanding of the design principles of biological regulatory networks. Further, advances in synthetic biology herald the time when we'll be able to rationally engineer complex chemical systems, and when idealized formal models will become blueprints for engineering. Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs is not well understood. Here we study the following problem: what functions f : ∪k → ∪ can be computed by a chemical reaction network, in which the CRN eventually produces the correct amount of the "output" ∣ molecule, no matter the rate at which reactions proceed? This captures a previously unexplored, but very natural class of computations: for example, the reaction X1 + X2 → Y can be thought to compute the function y = min(x1, x2). Such a CRN is robust in the sense that it is correct whether its evolution is governed by the standard model of mass-action kinetics, alternatives such as Hill-function or Michaelis-Menten kinetics, or other arbitrary models of chemistry that respect the (fundamentally digital) stoichiometric constraints (what are the reactants and products?). We develop a formal definition of such computation using a novel notion of reachability, and prove that a function is computable in this manner if and only if it is continuous piecewise linear.
理解原则上在化学系统中可实现的算法行为对于严格理解生物调节网络的设计原则是必要的。此外,合成生物学的进步预示着我们将能够合理地设计复杂的化学系统,理想化的正式模型将成为工程的蓝图。在混合良好的溶液中,耦合的化学相互作用通常形式化为化学反应网络(crn)。然而,尽管crn在自然科学中广泛使用,但crn所表现出的计算行为的范围尚未得到很好的理解。这里我们研究以下问题:什么函数f:∪k→∪可以由化学反应网络计算,在这个网络中,无论反应进行的速度如何,CRN最终都会产生正确数量的“输出”∣分子?这捕获了一个以前未开发但非常自然的计算类别:例如,反应X1 + X2→Y可以被认为是计算函数Y = min(X1, X2)。这样的CRN在某种意义上是可靠的,它是正确的,无论它的进化是由质量作用动力学的标准模型,希尔函数或Michaelis-Menten动力学等替代品,还是其他尊重(基本上是数字的)化学计量学约束(什么是反应物和产物?)的任意化学模型控制的。我们利用可达性的新概念给出了这种计算的形式化定义,并证明了一个函数当且仅当它是连续分段线性的,以这种方式可计算。
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引用次数: 50
Coordination mechanisms from (almost) all scheduling policies 来自(几乎)所有调度策略的协调机制
Sayan Bhattacharya, Sungjin Im, Janardhan Kulkarni, Kamesh Munagala
We study the price of anarchy of coordination mechanisms for a scheduling problem where each job j has a weight wj, processing time pij, assignment cost hij, and communication delay (or release date) rij, on machine i. Each machine is free to declare its own scheduling policy. Each job is a selfish agent and selects a machine that minimizes its own disutility, which is equal to its weighted completion time plus its assignment cost. The goal is to minimize the total disutility incurred by all the jobs. Our model is general enough to capture scheduling jobs in a distributed environment with heterogeneous machines (or data centers) that are situated across different locations. Our main result is a characterization of scheduling policies that give a small (robust) Price of Anarchy. More precisely, we show that whenever each machine independently declares any scheduling policy that satisfies a certain bounded stretch condition introduced in this paper, the game induced between the jobs has a small Price of Anarchy. Our characterization is powerful enough to test almost all popular scheduling policies. On the technical side, to derive our results, we use a potential function whose derivative leads to an instantaneous smoothness condition, and linear programming and dual fitting. To the best of our knowledge, this is a novel application of these techniques in the context of coordination mechanisms, and we believe these tools will find more applications in analyzing PoA of games. We also extend our results to the lk-norms and l∞ norm (makespan) objectives.
我们研究了一个调度问题的协调机制的无序代价,其中每个作业j在机器i上具有权重wj、处理时间pij、分配成本hij和通信延迟(或发布日期)rij。每台机器都可以自由声明自己的调度策略。每个作业都是一个自私的智能体,它会选择一台使自身负效用最小化的机器,负效用等于其加权完成时间加上分配成本。目标是最小化所有作业产生的总负效用。我们的模型足够通用,可以捕获分布在不同位置的异构机器(或数据中心)的分布式环境中的调度作业。我们的主要结果是给出一个小的(鲁棒的)无序代价的调度策略的特征。更准确地说,我们证明了当每台机器独立声明满足本文所介绍的某个有界拉伸条件的调度策略时,作业之间诱导的博弈具有较小的无政府价格。我们的描述功能强大到足以测试几乎所有流行的调度策略。在技术方面,为了推导我们的结果,我们使用一个势函数,其导数导致瞬时平滑条件,以及线性规划和对偶拟合。据我们所知,这是这些技术在协调机制背景下的新应用,我们相信这些工具将在分析游戏PoA中找到更多的应用。我们还将结果扩展到lk范数和l∞范数(makespan)目标。
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引用次数: 22
Session details: Session 7: 14:00--14:10 会议详情:会议7:14:00—14:10
S. Irani
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引用次数: 0
Proceedings of the 5th conference on Innovations in theoretical computer science 第五届理论计算机科学创新会议论文集
M. Naor
The papers in this volume were presented at the 5th Innovations in Theoretical Computer Science (ITCS 2014) conference, sponsored by the ACM Special Interest Group on Algorithms and Computation Theory (SIGACT). The conference was held in Princeton, New Jersey, USA, January 11--14, 2014. ITCS (previously known as ICS) seeks to promote research that carries a strong conceptual message, for instance, introducing a new concept or model, opening a new line of inquiry within traditional or cross-interdisciplinary areas, or introducing new techniques or new applications of known techniques). The call for papers welcomed all submissions, whether aligned with current theory of computation research directions or deviating from them. Altogether 116 submissions were received worldwide. Of these the program committee selected 48 papers. The accepted papers cover a wide range of topics in theoretical computer science, including algorithms, complexity, cryptography, learning, data privacy, quantum, physical and biological computing and relations between computing and social sciences. In addition to the selected papers the committee invited Professor Peter Winkler of Dartmouth to give an evening talk and we are grateful for his acceptance. Another evening was devoted to "Graduating Bits" - short talks by recent graduates. The program committee consisted of 24 members (plus the chair): Deeparnab Chakrabarty (Microsoft Research India), Timothy Chan (University of Waterloo), Costis Daskalakis (MIT), Yuval Emek (ETH and Technion), Kousha Etessami (University of Edinburgh), Yuval Filmus (University of Toronto and Simons Institute, Berkeley), Arpita Ghosh (Cornell University), Monika Henzinger (University of Vienna), Sandy Irani (University of California Irvine), Michael nKearns (University of Pennsylvania), Lap Chi Lau (The Chinese University of Hong Kong), Nati Linial (Hebrew University of Jerusalem), Kobbi Nissim (Ben-Gurion University), Rasmus Pagh (IT University of Copenhagen), Shubhangi Saraf (Rutgers University), Ola Svensson (EPFL), Vinod Vaikuntanathan (University of Toronto and MIT), Jan Vondrak (IBM Almaden Research Center), Manfred Warmuth (University of California, Santa Cruz), Daniel Wichs (Northeastern University), Udi Wieder (Microsoft Research SVC), Ryan Williams (Stanford University), Ronald de Wolf (CWI and University of Amsterdam), David Xiao (CNRS and Universite Paris 7). I wish to express my admiration for their hard work of reading, evaluating and debating the merits of the submissions. The many individuals who assisted the reviewing process as subreviewers and extended the expertise of the committee deserve acknowledgments as well.
本卷中的论文在第五届理论计算机科学创新(ITCS 2014)会议上发表,该会议由ACM算法和计算理论特别兴趣小组(SIGACT)主办。会议于2014年1月11日至14日在美国新泽西州普林斯顿举行。ITCS(以前称为ICS)寻求促进具有强烈概念信息的研究,例如,引入新概念或模型,在传统或跨学科领域内开辟新的研究路线,或引入新技术或已知技术的新应用。论文征集欢迎所有的投稿,无论是与当前计算理论研究方向一致还是偏离。全球共收到116份意见书。项目委员会从中选择了48篇论文。接受的论文涵盖了理论计算机科学的广泛主题,包括算法、复杂性、密码学、学习、数据隐私、量子、物理和生物计算以及计算与社会科学之间的关系。除了选定的论文外,委员会还邀请了达特茅斯学院的Peter Winkler教授做晚间演讲,我们对他的接受表示感谢。另一个晚上是“毕业演讲”——由刚毕业的学生做的简短演讲。项目委员会由24名成员(加上主席)组成:Deeparnab Chakrabarty(微软印度研究院)、Timothy Chan(滑铁卢大学)、Costis Daskalakis(麻省理工学院)、Yuval Emek (ETH和Technion)、Kousha Etessami(爱丁堡大学)、Yuval Filmus(多伦多大学和伯克利西蒙斯研究所)、Arpita Ghosh(康奈尔大学)、Monika Henzinger(维也纳大学)、Sandy Irani(加州大学欧文分校)、Michael nKearns(宾夕法尼亚大学)、刘立之(香港中文大学)、Nati Linial(耶路撒冷希伯来大学),Kobbi Nissim(本-古里安大学),Rasmus Pagh(哥本哈根IT大学),Shubhangi Saraf(罗格斯大学),Ola Svensson (EPFL), Vinod Vaikuntanathan(多伦多大学和麻省理工学院),Jan Vondrak (IBM阿尔马登研究中心),Manfred Warmuth(加州大学圣克鲁兹分校),Daniel Wichs(东北大学),Udi Wieder(微软研究院SVC), Ryan Williams(斯坦福大学),罗纳德·德·沃尔夫(CWI和阿姆斯特丹大学),大卫·肖(CNRS和巴黎第七大学)。我对他们辛勤的阅读、评估和辩论所提交作品的优点表示钦佩。作为次级审稿人协助审查过程并扩展委员会专业知识的许多个人也值得感谢。
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引用次数: 11
Session details: Session 3: 14:00--14:10 会议详情:会议3:14:00—14:10
Michael Kearns
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引用次数: 0
Testers and their applications 测试人员及其应用
N. Bshouty
We develop a new notion called tester of a class M of functions f : A → C that maps the elements α ∈ A in the domain A of the function to a finite number (the size of the tester) of elements b1,...,bt in a smaller sub-domain B ⊂ A where the property f(α) ≠ 0 is preserved for all f ∈ M. I.e., for all f ∈ M and - ∈ A if f(α) ≠ 0 then f(bi) ≠ 0 for some i. We use tools from elementary algebra and algebraic function fields to construct testers of almost optimal size in deterministic polynomial time in the size of the tester. We then apply testers to deterministically construct new set of objects with some combinatorial and algebraic properties that can be used to derandomize some algorithms. We show that those new constructions are almost optimal and for many of them meet the union bound of the problem. Constructions include, d-restriction problems, perfect hash, universal sets, cover-free families, separating hash functions, polynomial restriction problems, black box polynomial identity testing for polynomials and circuits over small fields and hitting sets.
我们提出了一个新的概念,称为函数f: a→C的类M的检验者,它将函数的定域a中的元素α∈a映射到元素b1,…的有限个数(检验者的大小)。,bt在更小的子域B∧a中,其中f(α)≠0对所有f∈M和-∈a,如果f(α)≠0,则f(bi)对某些i≠0。我们使用初等代数和代数函数域的工具在测试器大小的确定性多项式时间内构造几乎最优大小的测试器。然后,我们应用测试器确定地构建具有一些组合和代数属性的新对象集,这些属性可用于非随机化一些算法。我们证明了这些新结构几乎是最优的,并且其中许多结构满足问题的并界。构造包括:d-限制问题、完全哈希、泛集、无盖族、分离哈希函数、多项式限制问题、小域上多项式和电路的黑盒多项式恒等式检验和命中集。
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引用次数: 30
Session details: Session 8: 16:00--16:10 会议详情:第8场:16:00—16:10
Yuval Filmus
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引用次数: 0
On the automorphism groups of strongly regular graphs I 关于强正则图的自同构群I
L. Babai
We derive structural constraints on the automorphism groups of strongly regular (s.r.) graphs, giving a surprisingly strong answer to a decades-old problem, with tantalizing implications to testing isomorphism of s.r. graphs, and raising new combinatorial challenges. S.r. graphs, while not believed to be Graph Isomorphism (GI) complete, have long been recognized as hard cases for GI, and, in this author's view, present some of the core difficulties of the general GI problem. Progress on the complexity of testing their isomorphism has been intermittent (Babai 1980, Spielman 1996, BW & CST (STOC'13) and BCSTW (FOCS'13)), and the current best bound is exp(Õ(n1/5)) (n is the number of vertices). Our main result is that if X is a s.r. graph then, with straightforward exceptions, the degree of the largest alternating group involved in the automorphism group Aut(X) (as a quotient of a subgroup) is O((ln n)2ln ln n). (The exceptions admit trivial linear-time GI testing.) The design of isomorphism tests for various classes of structures is intimately connected with the study of the automorphism groups of those structures. We include a brief survey of these connections, starting with an 1869 paper by Jordan on trees. In particular, our result amplifies the potential of Luks's divide-and-conquer methods (1980) to be applicable to testing isomorphism of s.r. graphs in quasipolynomial time. The challenge remains to find a hierarchy of combinatorial substructures through which this potential can be realized. We expect that the generality of our result will help in this regard; the result applies not only to s.r. graphs but to all graphs with strong spectral expansion and with a relatively small number of common neighbors for every pair of vertices. We state a purely mathematical conjecture that could bring us closer to finding the right kind of hierarchy. We also outline the broader GI context, and state conjectures in terms of "primitive coherent configurations." These are generalizations of s.r. graphs, relevant to the general GI problem. Another consequence of the main result is the strongest argument to date against GI-completeness of s.r. graphs: we prove that no polynomial-time categorical reduction of GI to isomorphism of s.r. graphs is possible. All known reductions between isomorphism problems of various classes of structures fit into our notion of "categorical reduction." The proof of the main result is elementary; it is based on known results in spectral graph theory and on a 1987 lemma on permutations by Ákos Seress and the author.
我们推导了强正则图的自同构群上的结构约束,对一个存在了几十年的问题给出了令人惊讶的强有力的答案,对测试强正则图的同构具有诱人的意义,并提出了新的组合挑战。S.r.图,虽然不被认为是图同构(GI)完备的,但长期以来一直被认为是GI的困难案例,并且,在笔者看来,呈现了一般GI问题的一些核心困难。关于测试它们同态的复杂性的进展是断断续续的(Babai 1980, Spielman 1996, BW & CST (STOC'13)和BCSTW (FOCS'13)),目前最好的界是exp(Õ(n1/5)) (n是顶点的数量)。我们的主要结果是,如果X是一个s.r.图,那么,除了简单的例外,自同构群Aut(X)中涉及的最大交替群的程度(作为子群的商)是O((ln n)2ln ln n)。(这些例外允许平凡的线性时间GI检验。)各类结构的同构检验的设计与这些结构的自同构群的研究密切相关。我们从1869年乔丹关于树木的一篇论文开始,对这些联系进行了简要的调查。特别是,我们的结果放大了Luks的分治方法(1980)在拟多项式时间内测试sr图同构的潜力。挑战仍然是找到一个层次的组合子结构,通过它可以实现这种潜力。我们期望我们的结果的普遍性将在这方面有所帮助;这一结果不仅适用于sr图,而且适用于所有具有强谱展开且每对顶点具有相对较少的共同邻居的图。我们陈述一个纯粹的数学猜想,它可以使我们更接近于找到正确的层次结构。我们还概述了更广泛的GI上下文,并根据“原始连贯配置”陈述了猜想。这些是广义广义图的推广,与一般的GI问题相关。主要结果的另一个结果是迄今为止反对s.r.图的GI-完备性的最强有力的论据:我们证明了GI不可能在多项式时间上分类化到s.r.图的同构。所有已知的各种结构的同构问题之间的约简都符合我们的“范畴约简”概念。主要结果的证明是初等的;它是基于谱图理论的已知结果和Ákos Seress和作者1987年关于排列的引理。
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引用次数: 23
Cryptogenography
Joshua Brody, S. K. Jakobsen, Dominik Scheder, P. Winkler
We consider the following cryptographic secret leaking problem. A group of players communicate with the goal of learning (and perhaps revealing) a secret held initially by one of them. Their conversation is monitored by a computationally unlimited eavesdropper, who wants to learn the identity of the secret-holder. Despite the unavailability of key, some protection can be provided to the identity of the secret-holder. We call the study of such communication problems, either from the group's or the eavesdropper's point of view, cryptogenography. We introduce a basic cryptogenography problem and show that two players can force the eavesdropper to missguess the origin of a secret bit with probability 1/3; we complement this with a hardness result showing that they cannot do better than than 3/8. We prove that larger numbers of players can do better than 0.5644, but no group of any size can achieve 0.75.
我们考虑以下的密码秘密泄露问题。一群玩家交流的目标是了解(也许是揭露)最初由其中一人持有的秘密。他们的谈话被一个不受计算限制的窃听者监视,他想知道秘密持有者的身份。尽管无法获得密钥,但可以对秘密持有者的身份提供一定的保护。我们把对这种通信问题的研究,无论是从组织的角度还是从窃听者的角度,称为密码学。我们引入了一个基本的密码学问题,并证明两个玩家可以迫使窃听者以1/3的概率猜错秘密位的来源;我们用硬度结果来补充这一点,表明它们不能超过3/8。我们证明更多的玩家可以做得比0.5644更好,但任何规模的群体都无法达到0.75。
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引用次数: 3
Session details: Session 9: 08:30--08:40 会话详情:会话9:08:30—08:40
D. Wichs
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引用次数: 0
期刊
Proceedings of the 5th conference on Innovations in theoretical computer science
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