This work investigates the emergence of oscillations in one of the simplest cellular signaling networks exhibiting oscillations, namely, the dual-site phosphorylation and dephosphorylation network (futile cycle), in which the mechanism for phosphorylation is processive while the one for dephosphorylation is distributive (or vice-versa). The fact that this network yields oscillations was shown recently by Suwanmajo and Krishnan. Our results, which significantly extend their analyses, are as follows. First, in the three-dimensional space of total amounts, the border between systems with a stable versus unstable steady state is a surface defined by the vanishing of a single Hurwitz determinant. Second, this surface consists generically of simple Hopf bifurcations. Next, simulations suggest that when the steady state is unstable, oscillations are the norm. Finally, the emergence of oscillations via a Hopf bifurcation is enabled by the catalytic and association constants of the distributive part of the mechanism: if these rate constants satisfy two inequalities, then the system generically admits a Hopf bifurcation. Our proofs are enabled by the Routh-Hurwitz criterion, a Hopf-bifurcation criterion due to Yang, and a monomial parametrization of steady states.
Our work joins a growing number of works that harness steady-state parametrizations. Such results include criteria for when such parametrizations exist @cite_19 @cite_37 and methods for using them to determine whether a network is multistationary @cite_20 @cite_23 @cite_27 @cite_2 . Going further, steady-state parametrizations can also be used to find a witness to multistationarity or even the precise parameter regions that yield multistationarity @cite_13 @cite_39 . In this work, we use a steady-state parametrization in a novel way: to study oscillations via Hopf bifurcations. (Our approach is similar in spirit to using Clarke's convex parameters together with a Hopf-bifurcation criterion @cite_31 @cite_15 @cite_22 @cite_10 ).
@cite_37 @cite_22 @cite_15 @cite_10 @cite_39 @cite_19 @cite_27 @cite_23 @cite_2 @cite_31 @cite_13 @cite_20
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We study the approximability of multiway partitioning problems, examples of which include Multiway Cut, Node-weighted Multiway Cut, and Hypergraph Multiway Cut. We investigate these problems from the point of view of two possible generalizations: as Min-CSPs, and as Submodular Multiway Partition problems. These two generalizations lead to two natural relaxations that we call respectively the Local Distribution LP, and the Lovasz relaxation. The Local Distribution LP is generally stronger than the Lovasz relaxation, but applicable only to Min-CSP with predicates of constant size. The relaxations coincide in some cases such as Multiway Cut where they are both equivalent to the CKR relaxation. We show that the Lovasz relaxation gives a (2--2 k)-approximation for Submodular Multiway Partition with k terminals, improving a recent 2-approximation [2]. We prove that this factor is optimal in two senses: (1) A (2--2 k -- e)-approximation for Submodular Multiway Partition with k terminals would require exponentially many value queries (in the oracle model), or imply NP = RP (for certain explicit submodular functions). (2) For Hypergraph Multiway Cut and Node-weighted Multiway Cut with k terminals, both special cases of Submodular Multiway Partition, we prove that a (2--2 k -- e)-approximation is NP-hard, assuming the Unique Games Conjecture. Both our hardness results are more general: (1) We show that the notion of symmetry gap, previously used for submodular maximization problems [19, 6], also implies hardness results for submodular minimization problems. (2) Assuming the Unique Games Conjecture, we show that the Local Distribution LP gives an optimal approximation for every Min-CSP that includes the Not-Equal predicate. Finally, we connect the two hardness techniques by proving that the integrality gap of the Local Distribution LP coincides with the symmetry gap of the multilinear relaxation (for a related instance). This shows that the appearance of the same hardness threshold for a Min-CSP and the related submodular minimization problem is not a coincidence. Bifurcation theory is one of the most widely used approaches for analysis of dynamical behaviour of chemical and biochemical reaction networks. Some of the interesting qualitative behaviour that are analyzed are oscillations and bistability (a situation where a system has at least two coexisting stable equilibria). Both phenomena have been identified as central features of many biological and biochemical systems. This paper, using the theory of stoichiometric network analysis (SNA) and notions from algebraic geometry, presents sufficient conditions for a reaction network to display bifurcations associated with these phenomena. The advantage of these conditions is that they impose fewer algebraic conditions on model parameters than conditions associated with standard bifurcation theorems. To derive the new conditions, a coordinate transformation will be made that will guarantee the existence of branches of positive equilibria in the system. This is particularly useful in mathematical biology, where only positive variable values are considered to be meaningful. The first part of the paper will be an extended introduction to SNA and algebraic geometry-related methods which are used in the coordinate transformation and set up of the theorems. In the second part of the paper we will focus on the derivation of bifurcation conditions using SNA and algebraic geometry. Conditions will be derived for three bifurcations: the saddle-node bifurcation, a simple branching point, both linked to bistability, and a simple Hopf bifurcation. The latter is linked to oscillatory behaviour. The conditions derived are sufficient and they extend earlier results from stoichiometric network analysis as can be found in (Aguda and Clarke in J Chem Phys 87:3461-3470, 1987; Clarke and Jiang in J Chem Phys 99:4464-4476, 1993; in J Symb Comput 40:1361-1382, 2005). In these papers some necessary conditions for two of these bifurcations were given. A set of examples will illustrate that algebraic conditions arising from given sufficient bifurcation conditions are not more difficult to interpret nor harder to calculate than those arising from necessary bifurcation conditions. Hence an increasing amount of information is gained at no extra computational cost. The theory can also be used in a second step for a systematic bifurcation analysis of larger reaction networks. Abstract We consider boundary value problems for semilinear hyperbolic systems of the type ∂ t u j + a j ( x , λ ) ∂ x u j + b j ( x , λ , u ) = 0 , x ∈ ( 0 , 1 ) , j = 1 , … , n , with smooth coefficient functions a j and b j such that b j ( x , λ , 0 ) = 0 for all x ∈ [ 0 , 1 ] , λ ∈ R , and j = 1 , … , n . We state conditions for Hopf bifurcation, i.e., for existence, local uniqueness (up to phase shifts), smoothness and smooth dependence on λ of time-periodic solutions bifurcating from the zero stationary solution. Furthermore, we derive a formula which determines the bifurcation direction. The proof is done by means of a Liapunov–Schmidt reduction procedure. For this purpose, Fredholm properties of the linearized system and implicit function theorem techniques are used. Mulmuley [Mul12a] recently gave an explicit version of Noether’s Normalization lemma for ring of invariants of matrices under simultaneous conjugation, under the conjecture that there are deterministic black-box algorithms for polynomial identity testing (PIT). He argued that this gives evidence that constructing such algorithms for PIT is beyond current techniques. In this work, we show this is not the case. That is, we improve Mulmuley’s reduction and correspondingly weaken the conjecture regarding PIT needed to give explicit Noether Normalization. We then observe that the weaker conjecture has recently been nearly settled by the authors ([FS12]), who gave quasipolynomial size hitting sets for the class of read-once oblivious algebraic branching programs (ROABPs). This gives the desired explicit Noether Normalization unconditionally, up to quasipolynomial factors. As a consequence of our proof we give a deterministic parallel polynomial-time algorithm for deciding if two matrix tuples have intersecting orbit closures, under simultaneous conjugation. We also study the strength of conjectures that Mulmuley requires to obtain similar results as ours. We prove that his conjectures are stronger, in the sense that the computational model he needs PIT algorithms for is equivalent to the well-known algebraic branching program (ABP) model, which is provably stronger than the ROABP model. Finally, we consider the depth-3 diagonal circuit model as defined by Saxena [Sax08], as PIT algorithms for this model also have implications in Mulmuley’s work. Previous work (such as [ASS12] and [FS12]) have given quasipolynomial size hitting sets for this model. In this work, we give a much simpler construction of such hitting sets, using techniques of Shpilka and Volkovich [SV09]. We introduce a novel embedding method for knowledge base completion task. Our approach advances state-of-the-art (SOTA) by employing a convolutional neural network (CNN) for the task which can capture global relationships and transitional characteristics. We represent each triple (head entity, relation, tail entity) as a 3-column matrix which is the input for the convolution layer. Different filters having a same shape of 1x3 are operated over the input matrix to produce different feature maps which are then concatenated into a single feature vector. This vector is used to return a score for the triple via a dot product. The returned score is used to predict whether the triple is valid or not. Experiments show that ConvKB achieves better link prediction results than previous SOTA models on two current benchmark datasets WN18RR and FB15k-237. We show an exponential separation between two well-studied models of algebraic computation, namely read-once oblivious algebraic branching programs (ROABPs) and multilinear depth three circuits. In particular we show the following: 1. There exists an explicit n-variate polynomial computable by linear sized multilinear depth three circuits (with only two product gates) such that every ROABP computing it requires 2^ Omega(n) size. 2. Any multilinear depth three circuit computing IMM_ n,d (the iterated matrix multiplication polynomial formed by multiplying d, n * n symbolic matrices) has n^ Omega(d) size. IMM_ n,d can be easily computed by a poly(n,d) sized ROABP. 3. Further, the proof of 2 yields an exponential separation between multilinear depth four and multilinear depth three circuits: There is an explicit n-variate, degree d polynomial computable by a poly(n,d) sized multilinear depth four circuit such that any multilinear depth three circuit computing it has size n^ Omega(d) . This improves upon the quasi-polynomial separation result by Raz and Yehudayoff [2009] between these two models. The hard polynomial in 1 is constructed using a novel application of expander graphs in conjunction with the evaluation dimension measure used previously in Nisan [1991], Raz [2006,2009], Raz and Yehudayoff [2009], and Forbes and Shpilka [2013], while 2 is proved via a new adaptation of the dimension of the partial derivatives measure used by Nisan and Wigderson [1997]. Our lower bounds hold over any field. We consider homogeneous factor models on uniformly sparse graph sequences converging locally to a (unimodular) random tree T, and study the existence of the free energy density ϕ, the limit of the log-partition function divided by the number of vertices n as n tends to infinity. We provide a new interpolation scheme and use it to prove existence of, and to explicitly compute, the quantity ϕ subject to uniqueness of a relevant Gibbs measure for the factor model on T. By way of example we compute ϕ for the independent set (or hard-core) model at low fugacity, for the ferromagnetic Ising model at all parameter values, and for the ferromagnetic Potts model with both weak enough and strong enough interactions. Even beyond uniqueness regimes our interpolation provides useful explicit bounds on ϕ. In the regimes in which we establish existence of the limit, we show that it coincides with the Bethe free energy functional evaluated at a suitable fixed point of the belief propagation (Bethe) recursions on T. In the special case that T has a Galton–Watson law, this formula coincides with the nonrigorous “Bethe prediction” obtained by statistical physicists using the “replica” or “cavity” methods. Thus our work is a rigorous generalization of these heuristic calculations to the broader class of sparse graph sequences converging locally to trees. We also provide a variational characterization for the Bethe prediction in this general setting, which is of independent interest. The objective of this paper is to study the performance of a multicell vector perturbation (MVP) precoding technique under practical situations in a network multiple-input multiple-output (MIMO) scheme employing joint transmission. The conventional perturbation strategy that minimizes the total power is considered, and the power at each base station (BS) is properly scaled to enforce per-BS power constraints. In our scenario, we consider multiple-antenna users and use block diagonalization (BD) as the linear front-end precoder for VP. The sum rate for the MVP in the case of uniformly distributed input and an asymptotic upper bound on the sum rate at high signal-to-noise ratios (SNRs) are derived. In addition, using the asymptotic upper bound on the individual user rates, we propose a proportionally fair (PF) user scheduling algorithm of lower complexity and better performance compared with the benchmark fair semiorthogonal user selection (SUS) algorithm. As opposed to the PF-SUS, the proposed PF scheduling algorithm requires no predefined correlation threshold. Furthermore, we study the impact of backhaul delay on the performance of both VP and BD by deriving bounds on the sum rate. The numerical results show that MVP in the case of perfect channel state information (CSI) outperforms multicell BD. In the presence of a backhaul delay, the performance of MVP significantly degrades, but the upper bound on the sum rate for MVP is still higher than for multicell BD. This paper studies the mutual information improvement attained by rotated multidimensional (multi-D) constellations via a unitary precoder G in Rayleigh fading. At first, based on the symmetric cut-off rate of the N-D signal space, we develop a design criterion with regard to the precoder G. It is then demonstrated that the use of rotated constellations in only a reasonably low dimensional signal space can significantly increase the mutual information in high-rate regimes. Based on parameterizations of unitary matrices, we then construct good unitary precoder G in 4-D signal space using a simple optimization problem, which involves only four real variables and it is applicable to any modulation scheme. To further illustrate the potential of multi-D constellation and to show the practical use of mutual information improvement, we propose a simple yet powerful bit-interleaved coded modulation (BICM) scheme in which a (multi-D) mapping technique employed in a multi-D rotated constellation is concatenated with a short-memory high-rate convolutional code. By using extrinsic information transfer (EXIT) charts, it is shown that the proposed technique provides an exceptionally good error performance. In particular, both EXIT chart analysis and simulation results indicate that a turbo pinch-off and a bit error rate around 10-6 happen at a signal-to-noise ratio that is well below the coded modulation and BICM capacities using traditional signal sets. For example, with code rates ranging from 2 3 to 7 8, the proposed system can operate 0.82 dB-2.93 dB lower than the BICM capacity with QPSK and Gray labeling. The mutual information gain offered by rotated constellations can be therefore utilized to design simple yet near Shannon limit systems in the high-rate regions. This paper proposes a simple method for estimating dense and accurate optical flow field. It revitalizes an early idea of piecewise parametric flow model. A key innovation is that, we fit a flow field piecewise to a variety of parametric models, where the domain of each piece (i.e., each piece's shape, position and size) is determined adaptively, while at the same time maintaining a global inter-piece flow continuity constraint. We achieve this by a multi-model fitting scheme via energy minimization. Our energy takes into account both the piecewise constant model assumption and the flow field continuity constraint, enabling the proposed method to effectively handle both homogeneous motions and complex motions. The experiments on three public optical flow benchmarks (KITTI, MPI Sintel, and Middlebury) show the superiority of our method compared with the state of the art: it achieves top-tier performances on all the three benchmarks. We investigate random interlacements on ℤd, d ≥ 3. This model, recently introduced in [8], corresponds to a Poisson cloud on the space of doubly infinite trajectories modulo time shift tending to infinity at positive and negative infinite times. A nonnegative parameter u measures how many trajectories enter the picture. Our main interest lies in the percolative properties of the vacant set left by random interlacements at level u. We show that for all d ≥ 3 the vacant set at level u percolates when u is small. This solves an open problem of [8], where this fact has only been established when d ≥ 7. It also completes the proof of the nondegeneracy in all dimensions d ≥ 3 of the critical parameter u* of [8]. © 2008 Wiley Periodicals, Inc. Most methods proposed to uncover communities in complex networks rely on their structural properties. Here we introduce the stability of a network partition, a measure of its quality defined in terms of the statistical properties of a dynamical process taking place on the graph. The time-scale of the process acts as an intrinsic parameter that uncovers community structures at different resolutions. The stability extends and unifies standard notions for community detection: modularity and spectral partitioning can be seen as limiting cases of our dynamic measure. Similarly, recently proposed multi-resolution methods correspond to linearisations of the stability at short times. The connection between community detection and Laplacian dynamics enables us to establish dynamically motivated stability measures linked to distinct null models. We apply our method to find multi-scale partitions for different networks and show that the stability can be computed efficiently for large networks with extended versions of current algorithms.