Coarse-Graining and Self-Dissimilarity of Complex Networks

Can complex engineered and biological networks be coarse-grained into smaller and more understandable versions in which each node represents an entire pattern in the original network? To address this, we define coarse-graining units (CGU) as connectivity patterns which can serve as the nodes of a coarse-grained network, and present algorithms to detect them. We use this approach to systematically reverse-engineer electronic circuits, forming understandable high-level maps from incomprehensible transistor wiring: first, a coarse-grained version in which each node is a gate made of several transistors is established. Then, the coarse-grained network is itself coarse-grained, resulting in a high-level blueprint in which each node is a circuit-module made of multiple gates. We apply our approach also to a mammalian protein-signaling network, to find a simplified coarse-grained network with three main signaling channels that correspond to cross-interacting MAP-kinase cascades. We find that both biological and electronic networks are 'self-dissimilar', with different network motifs found at each level. The present approach can be used to simplify a wide variety of directed and nondirected, natural and designed networks.Comment: 11 pages, 11 figure

Convex optimization over intersection of simple sets: improved convergence rate guarantees via an exact penalty approach

We consider the problem of minimizing a convex function over the intersection of finitely many simple sets which are easy to project onto. This is an important problem arising in various domains such as machine learning. The main difficulty lies in finding the projection of a point in the intersection of many sets. Existing approaches yield an infeasible point with an iteration-complexity of $O(1/\varepsilon^2)$ for nonsmooth problems with no guarantees on the in-feasibility. By reformulating the problem through exact penalty functions, we derive first-order algorithms which not only guarantees that the distance to the intersection is small but also improve the complexity to $O(1/\varepsilon)$ and $O(1/\sqrt{\varepsilon})$ for smooth functions. For composite and smooth problems, this is achieved through a saddle-point reformulation where the proximal operators required by the primal-dual algorithms can be computed in closed form. We illustrate the benefits of our approach on a graph transduction problem and on graph matching

Explicit Learning Curves for Transduction and Application to Clustering and Compression Algorithms

Inductive learning is based on inferring a general rule from a finite data set and using it to label new data. In transduction one attempts to solve the problem of using a labeled training set to label a set of unlabeled points, which are given to the learner prior to learning. Although transduction seems at the outset to be an easier task than induction, there have not been many provably useful algorithms for transduction. Moreover, the precise relation between induction and transduction has not yet been determined. The main theoretical developments related to transduction were presented by Vapnik more than twenty years ago. One of Vapnik's basic results is a rather tight error bound for transductive classification based on an exact computation of the hypergeometric tail. While tight, this bound is given implicitly via a computational routine. Our first contribution is a somewhat looser but explicit characterization of a slightly extended PAC-Bayesian version of Vapnik's transductive bound. This characterization is obtained using concentration inequalities for the tail of sums of random variables obtained by sampling without replacement. We then derive error bounds for compression schemes such as (transductive) support vector machines and for transduction algorithms based on clustering. The main observation used for deriving these new error bounds and algorithms is that the unlabeled test points, which in the transductive setting are known in advance, can be used in order to construct useful data dependent prior distributions over the hypothesis space

How to Color a French Flag--Biologically Inspired Algorithms for Scale-Invariant Patterning

In the French flag problem, initially uncolored cells on a grid must differentiate to become blue, white or red. The goal is for the cells to color the grid as a French flag, i.e., a three-colored triband, in a distributed manner. To solve a generalized version of the problem in a distributed computational setting, we consider two models: a biologically-inspired version that relies on morphogens (diffusing proteins acting as chemical signals) and a more abstract version based on reliable message passing between cellular agents. Much of developmental biology research has focused on concentration-based approaches using morphogens, since morphogen gradients are thought to be an underlying mechanism in tissue patterning. We show that both our model types easily achieve a French ribbon - a French flag in the 1D case. However, extending the ribbon to the 2D flag in the concentration model is somewhat difficult unless each agent has additional positional information. Assuming that cells are are identical, it is impossible to achieve a French flag or even a close approximation. In contrast, using a message-based approach in the 2D case only requires assuming that agents can be represented as constant size state machines. We hope that our insights may lay some groundwork for what kind of message passing abstractions or guarantees, if any, may be useful in analogy to cells communicating at long and short distances to solve patterning problems. In addition, we hope that our models and findings may be of interest in the design of nano-robots

Modeling Cell-to-Cell Communication Networks Using Response-Time Distributions.

Cell-to-cell communication networks have critical roles in coordinating diverse organismal processes, such as tissue development or immune cell response. However, compared with intracellular signal transduction networks, the function and engineering principles of cell-to-cell communication networks are far less understood. Major complications include: cells are themselves regulated by complex intracellular signaling networks; individual cells are heterogeneous; and output of any one cell can recursively become an additional input signal to other cells. Here, we make use of a framework that treats intracellular signal transduction networks as "black boxes" with characterized input-to-output response relationships. We study simple cell-to-cell communication circuit motifs and find conditions that generate bimodal responses in time, as well as mechanisms for independently controlling synchronization and delay of cell-population responses. We apply our modeling approach to explain otherwise puzzling data on cytokine secretion onset times in T cells. Our approach can be used to predict communication network structure using experimentally accessible input-to-output measurements and without detailed knowledge of intermediate steps