Topological exploration of artificial neuronal network dynamics

One of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and statistical mechanics to describe the spatiotemporal structure of such network dynamics. Our novel approach employs tools from algebraic topology to characterize the global properties of network structure and dynamics. We propose a method based on persistent homology to automatically classify network dynamics using topological features of spaces built from various spike-train distances. We investigate the efficacy of our method by simulating activity in three small artificial neural networks with different sets of parameters, giving rise to dynamics that can be classified into four regimes. We then compute three measures of spike train similarity and use persistent homology to extract topological features that are fundamentally different from those used in traditional methods. Our results show that a machine learning classifier trained on these features can accurately predict the regime of the network it was trained on and also generalize to other networks that were not presented during training. Moreover, we demonstrate that using features extracted from multiple spike-train distances systematically improves the performance of our method

When Does a Mixture of Products Contain a Product of Mixtures?

We derive relations between theoretical properties of restricted Boltzmann machines (RBMs), popular machine learning models which form the building blocks of deep learning models, and several natural notions from discrete mathematics and convex geometry. We give implications and equivalences relating RBM-representable probability distributions, perfectly reconstructible inputs, Hamming modes, zonotopes and zonosets, point configurations in hyperplane arrangements, linear threshold codes, and multi-covering numbers of hypercubes. As a motivating application, we prove results on the relative representational power of mixtures of product distributions and products of mixtures of pairs of product distributions (RBMs) that formally justify widely held intuitions about distributed representations. In particular, we show that a mixture of products requiring an exponentially larger number of parameters is needed to represent the probability distributions which can be obtained as products of mixtures.Comment: 32 pages, 6 figures, 2 table

Secret Sharing Schemes with a large number of players from Toric Varieties

A general theory for constructing linear secret sharing schemes over a finite field \Fq from toric varieties is introduced. The number of players can be as large as $(q-1)^r-1$ for $r\geq 1$. We present general methods for obtaining the reconstruction and privacy thresholds as well as conditions for multiplication on the associated secret sharing schemes. In particular we apply the method on certain toric surfaces. The main results are ideal linear secret sharing schemes where the number of players can be as large as $(q-1)^2-1$. We determine bounds for the reconstruction and privacy thresholds and conditions for strong multiplication using the cohomology and the intersection theory on toric surfaces.Comment: 15 pages, 4 figures. arXiv admin note: text overlap with arXiv:1203.454

On the Connectivity of Unions of Random Graphs

Graph-theoretic tools and techniques have seen wide use in the multi-agent systems literature, and the unpredictable nature of some multi-agent communications has been successfully modeled using random communication graphs. Across both network control and network optimization, a common assumption is that the union of agents' communication graphs is connected across any finite interval of some prescribed length, and some convergence results explicitly depend upon this length. Despite the prevalence of this assumption and the prevalence of random graphs in studying multi-agent systems, to the best of our knowledge, there has not been a study dedicated to determining how many random graphs must be in a union before it is connected. To address this point, this paper solves two related problems. The first bounds the number of random graphs required in a union before its expected algebraic connectivity exceeds the minimum needed for connectedness. The second bounds the probability that a union of random graphs is connected. The random graph model used is the Erd\H{o}s-R\'enyi model, and, in solving these problems, we also bound the expectation and variance of the algebraic connectivity of unions of such graphs. Numerical results for several use cases are given to supplement the theoretical developments made.Comment: 16 pages, 3 tables; accepted to 2017 IEEE Conference on Decision and Control (CDC

Inferring Biologically Relevant Models: Nested Canalyzing Functions

Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast