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BackgroundMetagenomics is limited in its ability to link distinct microbial populations to genetic potential due to a current lack of representative isolate genome sequences. Reference-independent approaches, which exploit for example inherent genomic signatures for the clustering of metagenomic fragments (binning), offer the prospect to resolve and reconstruct population-level genomic complements without the need for prior knowledge.ResultsWe present VizBin, a Java™-based application which offers efficient and intuitive reference-independent visualization of metagenomic datasets from single samples for subsequent human-in-the-loop inspection and binning. The method is based on nonlinear dimension reduction of genomic signatures and exploits the superior pattern recognition capabilities of the human eye-brain system for cluster identification and delineation. We demonstrate the general applicability of VizBin for the analysis of metagenomic sequence data by presenting results from two cellulolytic microbial communities and one human-borne microbial consortium. The superior performance of our application compared to other analogous metagenomic visualization and binning methods is also presented.ConclusionsVizBin can be applied de novo for the visualization and subsequent binning of metagenomic datasets from single samples, and it can be used for the post hoc inspection and refinement of automatically generated bins. Due to its computational efficiency, it can be run on common desktop machines and enables the analysis of complex metagenomic datasets in a matter of minutes. The software implementation is available at https://claczny.github.io/VizBin under the BSD License (four-clause) and runs under Microsoft Windows™, Apple Mac OS X™ (10.7 to 10.10), and Linux.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-014-0066-1) contains supplementary material, which is available to authorized users.

Partially observable Markov decision processes (POMDPs) form an attractive and principled framework for agent planning under uncertainty. Point-based approximate techniques for POMDPs compute a policy based on a finite set of points collected in advance from the agents belief space. We present a randomized point-based value iteration algorithm called Perseus. The algorithm performs approximate value backup stages, ensuring that in each backup stage the value of each point in the belief set is improved; the key observation is that a single backup may improve the value of many belief points. Contrary to other point-based methods, Perseus backs up only a (randomly selected) subset of points in the belief set, sufficient for improving the value of each belief point in the set. We show how the same idea can be extended to dealing with continuous action spaces. Experimental results show the potential of Perseus in large scale POMDP problems

Systemic approaches to the study of a biological cell or tissue rely increasingly on the use of context-specific metabolic network models. The reconstruction of such a model from high-throughput data can routinely involve large numbers of tests under different conditions and extensive parameter tuning, which calls for fast algorithms. We present fastcore, a generic algorithm for reconstructing context-specific metabolic network models from global genome-wide metabolic network models such as Recon X. fastcore takes as input a core set of reactions that are known to be active in the context of interest (e.g., cell or tissue), and it searches for a flux consistent subnetwork of the global network that contains all reactions from the core set and a minimal set of additional reactions. Our key observation is that a minimal consistent reconstruction can be defined via a set of sparse modes of the global network, and fastcore iteratively computes such a set via a series of linear programs. Experiments on liver data demonstrate speedups of several orders of magnitude, and significantly more compact reconstructions, over a rival method. Given its simplicity and its excellent performance, fastcore can form the backbone of many future metabolic network reconstruction algorithms.

Decision-theoretic planning is a popular approach to sequential decision making problems, because it treats uncertainty in sensing and acting in a principled way. In single-agent frameworks like MDPs and POMDPs, planning can be carried out by resorting to Q-value functions: an optimal Q-value function Q* is computed in a recursive manner by dynamic programming, and then an optimal policy is extracted from Q*. In this paper we study whether similar Q-value functions can be defined for decentralized POMDP models (Dec-POMDPs), and how policies can be extracted from such value functions. We define two forms of the optimal Q-value function for Dec-POMDPs: one that gives a normative description as the Q-value function of an optimal pure joint policy and another one that is sequentially rational and thus gives a recipe for computation. This computation, however, is infeasible for all but the smallest problems. Therefore, we analyze various approximate Q-value functions that allow for efficient computation. We describe how they relate, and we prove that they all provide an upper bound to the optimal Q-value function Q*. Finally, unifying some previous approaches for solving Dec-POMDPs, we describe a family of algorithms for extracting policies from such Q-value functions, and perform an experimental evaluation on existing test problems, including a new firefighting benchmark problem