Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks

International audienceIncreasing amounts of sequence data are becoming available for a wide range of non-model organisms. Investigating and modelling the metabolic behaviour of those organisms is highly relevant to understand their biology and ecology. As sequences are often incomplete and poorly annotated, draft networks of their metabolism largely suffer from incompleteness. Appropriate gap-filling methods to identify and add missing reactions are therefore required to address this issue. However, current tools rely on phenotypic or taxonomic information, or are very sensitive to the stoichiometric balance of metabolic reactions, especially concerning the co-factors. This type of information is often not available or at least prone to errors for newly-explored organisms. Here we introduce Meneco, a tool dedicated to the topological gap-filling of genome-scale draft metabolic networks. Meneco reformulates gap-filling as a qualitative combinatorial optimization problem, omitting constraints raised by the stoichiometry of a metabolic network considered in other methods, and solves this problem using Answer Set Programming. Run on several artificial test sets gathering 10,800 degraded Escherichia coli networks Meneco was able to efficiently identify essential reactions missing in networks at high degradation rates, outperforming the stoichiometry-based tools in scalability. To demonstrate the utility of Meneco we applied it to two case studies. Its application to recent metabolic networks reconstructed for the brown algal model Ectocarpus siliculosus and an associated bacterium Candidatus Phaeomarinobacter ectocarpi revealed several candidate metabolic pathways for algal-bacterial interactions. Then Meneco was used to reconstruct, from transcriptomic and metabolomic data, the first metabolic network for the microalga Euglena mutabilis. These two case studies show that Meneco is a versatile tool to complete draft genome-scale metabolic networks produced from heterogeneous data, and to suggest relevant reactions that explain the metabolic capacity of a biological system

Tuning the Performance of a Computational Persistent Homology Package

In recent years, persistent homology has become an attractive method for data analysis. It captures topological features, such as connected components, holes, and voids from point cloud data and summarizes the way in which these features appear and disappear in a filtration sequence. In this project, we focus on improving the performanceof Eirene, a computational package for persistent homology. Eirene is a 5000-line open-source software library implemented in the dynamic programming language Julia. We use the Julia profiling tools to identify performance bottlenecks and develop novel methods to manage them, including the parallelization of some time-consuming functions on multicore/manycore hardware. Empirical results show that performance can be greatly improved

Shape Animation with Combined Captured and Simulated Dynamics

We present a novel volumetric animation generation framework to create new types of animations from raw 3D surface or point cloud sequence of captured real performances. The framework considers as input time incoherent 3D observations of a moving shape, and is thus particularly suitable for the output of performance capture platforms. In our system, a suitable virtual representation of the actor is built from real captures that allows seamless combination and simulation with virtual external forces and objects, in which the original captured actor can be reshaped, disassembled or reassembled from user-specified virtual physics. Instead of using the dominant surface-based geometric representation of the capture, which is less suitable for volumetric effects, our pipeline exploits Centroidal Voronoi tessellation decompositions as unified volumetric representation of the real captured actor, which we show can be used seamlessly as a building block for all processing stages, from capture and tracking to virtual physic simulation. The representation makes no human specific assumption and can be used to capture and re-simulate the actor with props or other moving scenery elements. We demonstrate the potential of this pipeline for virtual reanimation of a real captured event with various unprecedented volumetric visual effects, such as volumetric distortion, erosion, morphing, gravity pull, or collisions

PACE Solver Description: Tree Depth with FlowCutter

We describe the FlowCutter submission to the PACE 2020 heuristic tree-depth challenge. The task of the challenge consists of computing an elimination tree of small height for a given graph. At its core our submission uses a nested dissection approach, with FlowCutter as graph bisection algorithm

FastDOG: Fast Discrete Optimization on GPU

We present a massively parallel Lagrange decomposition method for solving 0--1 integer linear programs occurring in structured prediction. We propose a new iterative update scheme for solving the Lagrangean dual and a perturbation technique for decoding primal solutions. For representing subproblems we follow Lange et al. (2021) and use binary decision diagrams (BDDs). Our primal and dual algorithms require little synchronization between subproblems and optimization over BDDs needs only elementary operations without complicated control flow. This allows us to exploit the parallelism offered by GPUs for all components of our method. We present experimental results on combinatorial problems from MAP inference for Markov Random Fields, quadratic assignment and cell tracking for developmental biology. Our highly parallel GPU implementation improves upon the running times of the algorithms from Lange et al. (2021) by up to an order of magnitude. In particular, we come close to or outperform some state-of-the-art specialized heuristics while being problem agnostic. Our implementation is available at https://github.com/LPMP/BDD.Comment: Published at CVPR 2022. Alert before printing: last 10 pages just contains detailed results tabl