Ising Models for Inferring Network Structure From Spike Data

Now that spike trains from many neurons can be recorded simultaneously, there is a need for methods to decode these data to learn about the networks that these neurons are part of. One approach to this problem is to adjust the parameters of a simple model network to make its spike trains resemble the data as much as possible. The connections in the model network can then give us an idea of how the real neurons that generated the data are connected and how they influence each other. In this chapter we describe how to do this for the simplest kind of model: an Ising network. We derive algorithms for finding the best model connection strengths for fitting a given data set, as well as faster approximate algorithms based on mean field theory. We test the performance of these algorithms on data from model networks and experiments.Comment: To appear in "Principles of Neural Coding", edited by Stefano Panzeri and Rodrigo Quian Quirog

Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks

Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental data through computational analysis. However, this task is typically complicated by the enormously large scale of the unknowns in a rather small sample size. Furthermore, when the goal is to study causal relationships within the network, tools capable of overcoming the limitations of correlation networks are required. In this work, we make use of Bayesian Graphical Models to attach this problem and, specifically, we perform a comparative study of different state-of-the-art heuristics, analyzing their performance in inferring the structure of the Bayesian Network from breast cancer data

Impact of lag information on network inference

Extracting useful information from data is a fundamental challenge across disciplines as diverse as climate, neuroscience, genetics, and ecology. In the era of ``big data'', data is ubiquitous, but appropriated methods are needed for gaining reliable information from the data. In this work we consider a complex system, composed by interacting units, and aim at inferring which elements influence each other, directly from the observed data. The only assumption about the structure of the system is that it can be modeled by a network composed by a set of $N$ units connected with $L$ un-weighted and un-directed links, however, the structure of the connections is not known. In this situation the inference of the underlying network is usually done by using interdependency measures, computed from the output signals of the units. We show, using experimental data recorded from randomly coupled electronic R{\"o}ssler chaotic oscillators, that the information of the lag times obtained from bivariate cross-correlation analysis can be useful to gain information about the real connectivity of the system

On the Convexity of Latent Social Network Inference

In many real-world scenarios, it is nearly impossible to collect explicit social network data. In such cases, whole networks must be inferred from underlying observations. Here, we formulate the problem of inferring latent social networks based on network diffusion or disease propagation data. We consider contagions propagating over the edges of an unobserved social network, where we only observe the times when nodes became infected, but not who infected them. Given such node infection times, we then identify the optimal network that best explains the observed data. We present a maximum likelihood approach based on convex programming with a l1-like penalty term that encourages sparsity. Experiments on real and synthetic data reveal that our method near-perfectly recovers the underlying network structure as well as the parameters of the contagion propagation model. Moreover, our approach scales well as it can infer optimal networks of thousands of nodes in a matter of minutes.Comment: NIPS, 201

Estimating Diffusion Network Structures: Recovery Conditions, Sample Complexity & Soft-thresholding Algorithm

Information spreads across social and technological networks, but often the network structures are hidden from us and we only observe the traces left by the diffusion processes, called cascades. Can we recover the hidden network structures from these observed cascades? What kind of cascades and how many cascades do we need? Are there some network structures which are more difficult than others to recover? Can we design efficient inference algorithms with provable guarantees? Despite the increasing availability of cascade data and methods for inferring networks from these data, a thorough theoretical understanding of the above questions remains largely unexplored in the literature. In this paper, we investigate the network structure inference problem for a general family of continuous-time diffusion models using an $l_1$-regularized likelihood maximization framework. We show that, as long as the cascade sampling process satisfies a natural incoherence condition, our framework can recover the correct network structure with high probability if we observe $O(d^3 \log N)$ cascades, where $d$ is the maximum number of parents of a node and $N$ is the total number of nodes. Moreover, we develop a simple and efficient soft-thresholding inference algorithm, which we use to illustrate the consequences of our theoretical results, and show that our framework outperforms other alternatives in practice.Comment: To appear in the 31st International Conference on Machine Learning (ICML), 201

Learning to Discover Sparse Graphical Models

We consider structure discovery of undirected graphical models from observational data. Inferring likely structures from few examples is a complex task often requiring the formulation of priors and sophisticated inference procedures. Popular methods rely on estimating a penalized maximum likelihood of the precision matrix. However, in these approaches structure recovery is an indirect consequence of the data-fit term, the penalty can be difficult to adapt for domain-specific knowledge, and the inference is computationally demanding. By contrast, it may be easier to generate training samples of data that arise from graphs with the desired structure properties. We propose here to leverage this latter source of information as training data to learn a function, parametrized by a neural network that maps empirical covariance matrices to estimated graph structures. Learning this function brings two benefits: it implicitly models the desired structure or sparsity properties to form suitable priors, and it can be tailored to the specific problem of edge structure discovery, rather than maximizing data likelihood. Applying this framework, we find our learnable graph-discovery method trained on synthetic data generalizes well: identifying relevant edges in both synthetic and real data, completely unknown at training time. We find that on genetics, brain imaging, and simulation data we obtain performance generally superior to analytical methods