A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to both include biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer and the model-based search was more accurate than keyword search; it moreover recovered biologically meaningful relationships that are not straightforwardly visible from annotations, for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

We propose a novel method for maximum likelihood-based parameter inference in nonlinear and/or non-Gaussian state space models. The method is an iterative procedure with three steps. At each iteration a particle filter is used to estimate the value of the log-likelihood function at the current parameter iterate. Using these log-likelihood estimates, a surrogate objective function is created by utilizing a Gaussian process model. Finally, we use a heuristic procedure to obtain a revised parameter iterate, providing an automatic trade-off between exploration and exploitation of the surrogate model. The method is profiled on two state space models with good performance both considering accuracy and computational cost.

We describe Venture, an interactive virtual machine for probabilistic programming that aims to be sufficiently expressive, extensible, and efficient for general-purpose use. Like Church, probabilistic models and inference problems in Venture are specified via a Turing-complete, higher-order probabilistic language descended from Lisp. Unlike Church, Venture also provides a compositional language for custom inference strategies built out of scalable exact and approximate techniques. We also describe four key aspects of Venture's implementation that build on ideas from probabilistic graphical models. First, we describe the stochastic procedure interface (SPI) that specifies and encapsulates primitive random variables. The SPI supports custom control flow, higher-order probabilistic procedures, partially exchangeable sequences and ``likelihood-free'' stochastic simulators. It also supports external models that do inference over latent variables hidden from Venture. Second, we describe probabilistic execution traces (PETs), which represent execution histories of Venture programs. PETs capture conditional dependencies, existential dependencies and exchangeable coupling. Third, we describe partitions of execution histories called scaffolds that factor global inference problems into coherent sub-problems. Finally, we describe a family of stochastic regeneration algorithms for efficiently modifying PET fragments contained within scaffolds. Stochastic regeneration linear runtime scaling in cases where many previous approaches scaled quadratically. We show how to use stochastic regeneration and the SPI to implement general-purpose inference strategies such as Metropolis-Hastings, Gibbs sampling, and blocked proposals based on particle Markov chain Monte Carlo and mean-field variational inference techniques.

The fundamental step in measuring the robustness of a system is the synthesis of the so called Process Map.This is generally based on the user raw data material.Process Maps are of fundamental importance towards the understanding of the nature of a system in that they indicate which variables are causally related and which are particularly important.This paper represent the system Map or business structure map to understand business criteria studying the various aspects of the company.The business structure map or knowledge map or Process map are used to increase the growth of the company by giving some useful measures according to the business criteria.This paper also deals with the different company strategy to reduce the risk factors.Process Map is helpful for building such knowledge successfully.Making decisions from such map in a highly complex situation requires more knowledge and resources.

We present a general framework for accelerating a large class of widely used Markov chain Monte Carlo (MCMC) algorithms. Our approach exploits fast, iterative approximations to the target density to speculatively evaluate many potential future steps of the chain in parallel. The approach can accelerate computation of the target distribution of a Bayesian inference problem, without compromising exactness, by exploiting subsets of data. It takes advantage of whatever parallel resources are available, but produces results exactly equivalent to standard serial execution. In the initial burn-in phase of chain evaluation, it achieves speedup over serial evaluation that is close to linear in the number of available cores.

Discovering and characterizing the large-scale topological features in empirical networks are crucial steps in understanding how complex systems function. However, most existing methods used to obtain the modular structure of networks suffer from serious problems, such as being oblivious to the statistical evidence supporting the discovered patterns, which results in the inability to separate actual structure from noise. In addition to this, one also observes a resolution limit on the size of communities, where smaller but well-defined clusters are not detectable when the network becomes large. This phenomenon occurs not only for the very popular approach of modularity optimization, which lacks built-in statistical validation, but also for more principled methods based on statistical inference and model selection, which do incorporate statistical validation in a formally correct way. Here we construct a nested generative model that, through a complete description of the entire network hierarchy at multiple scales, is capable of avoiding this limitation, and enables the detection of modular structure at levels far beyond those possible with current approaches. Even with this increased resolution, the method is based on the principle of parsimony, and is capable of separating signal from noise, and thus will not lead to the identification of spurious modules even on sparse networks. Furthermore, it fully generalizes other approaches in that it is not restricted to purely assortative mixing patterns, directed or undirected graphs, and ad hoc hierarchical structures such as binary trees. Despite its general character, the approach is tractable, and can be combined with advanced techniques of community detection to yield an efficient algorithm that scales well for very large networks.

Markov chain Monte Carlo (MCMC) is a popular and successful general-purpose tool for Bayesian inference. However, MCMC cannot be practically applied to large data sets because of the prohibitive cost of evaluating every likelihood term at every iteration. Here we present Firefly Monte Carlo (FlyMC) an auxiliary variable MCMC algorithm that only queries the likelihoods of a potentially small subset of the data at each iteration yet simulates from the exact posterior distribution, in contrast to recent proposals that are approximate even in the asymptotic limit. FlyMC is compatible with a wide variety of modern MCMC algorithms, and only requires a lower bound on the per-datum likelihood factors. In experiments, we find that FlyMC generates samples from the posterior more than an order of magnitude faster than regular MCMC, opening up MCMC methods to larger datasets than were previously considered feasible.

Communication costs, resulting from synchronization requirements during learning, can greatly slow down many parallel machine learning algorithms. In this paper, we present a parallel Markov chain Monte Carlo (MCMC) algorithm in which subsets of data are processed independently, with very little communication. First, we arbitrarily partition data onto multiple machines. Then, on each machine, any classical MCMC method (e.g., Gibbs sampling) may be used to draw samples from a posterior distribution given the data subset. Finally, the samples from each machine are combined to form samples from the full posterior. This embarrassingly parallel algorithm allows each machine to act independently on a subset of the data (without communication) until the final combination stage. We prove that our algorithm generates asymptotically exact samples and empirically demonstrate its ability to parallelize burn-in and sampling in several models.

Nodes in real world networks often have class labels, or underlying attributes, that are related to the way in which they connect to other nodes. Sometimes this relationship is simple, for instance nodes of the same class are may be more likely to be connected. In other cases, however, this is not true, and the way that nodes link in a network exhibits a different, more complex relationship to their attributes. Here, we consider networks in which we know how the nodes are connected, but we do not know the class labels of the nodes or how class labels relate to the network links. We wish to identify the best subset of nodes to label in order to learn this relationship between node attributes and network links. We can then use this discovered relationship to accurately predict the class labels of the rest of the network nodes. We present a model that identifies groups of nodes with similar link patterns, which we call network roles, using a generative blockmodel. The model then predicts labels by learning the mapping from network roles to class labels using a maximum margin classifier. We choose a subset of nodes to label according to an iterative margin-based active learning strategy. By integrating the discovery of network roles with the classifier optimisation, the active learning process can adapt the network roles to better represent the network for node classification. We demonstrate the model by exploring a selection of real world networks, including a marine food web and a network of English words. We show that, in contrast to other network classifiers, this model achieves good classification accuracy for a range of networks with different relationships between class labels and network links.

Scientific practice typically involves repeatedly studying a system, each time trying to unravel a different perspective. In each study, the scientist may take measurements under different experimental conditions (interventions, manipulations, perturbations) and measure different sets of quantities (variables). The result is a collection of heterogeneous data sets coming from different data distributions. In this work, we present algorithm COmbINE, which accepts a collection of data sets over overlapping variable sets under different experimental conditions; COmbINE then outputs a summary of all causal models indicating the invariant and variant structural characteristics of all models that simultaneously fit all of the input data sets. COmbINE converts estimated dependencies and independencies in the data into path constraints on the data-generating causal model and encodes them as a SAT instance. The algorithm is sound and complete in the sample limit. To account for conflicting constraints arising from statistical errors, we introduce a general method for sorting constraints in order of confidence, computed as a function of their corresponding p-values. In our empirical evaluation, COmbINE outperforms in terms of efficiency the only pre-existing similar algorithm; the latter additionally admits feedback cycles, but does not admit conflicting constraints which hinders the applicability on real data. As a proof-of-concept, COmbINE is employed to co-analyze 4 real, mass-cytometry data sets measuring phosphorylated protein concentrations of overlapping protein sets under 3 different interventions.