Uniform sampling of steady states in metabolic networks: heterogeneous scales and rounding

The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case of inferring the feasible steady states in models of metabolic networks, since they can show heterogeneous time scales . In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient hit-and-run (HR) Markov Chain Monte Carlo. In this way the uniformity of the sampling of the convex space of interest is rigorously guaranteed, at odds with non markovian methods. We analyze and compare three rounding methods in order to sample the feasible steady states of metabolic networks of three models of growing size up to genomic scale. The first is based on principal component analysis (PCA), the second on linear programming (LP) and finally we employ the lovasz ellipsoid method (LEM). Our results show that a rounding procedure is mandatory for the application of the HR in these inference problem and suggest that a combination of LEM or LP with a subsequent PCA perform the best. We finally compare the distributions of the HR with that of two heuristics based on the Artificially Centered hit-and-run (ACHR), gpSampler and optGpSampler. They show a good agreement with the results of the HR for the small network, while on genome scale models present inconsistencies.Comment: Replacement with major revision

Attention and Anticipation in Fast Visual-Inertial Navigation

We study a Visual-Inertial Navigation (VIN) problem in which a robot needs to estimate its state using an on-board camera and an inertial sensor, without any prior knowledge of the external environment. We consider the case in which the robot can allocate limited resources to VIN, due to tight computational constraints. Therefore, we answer the following question: under limited resources, what are the most relevant visual cues to maximize the performance of visual-inertial navigation? Our approach has four key ingredients. First, it is task-driven, in that the selection of the visual cues is guided by a metric quantifying the VIN performance. Second, it exploits the notion of anticipation, since it uses a simplified model for forward-simulation of robot dynamics, predicting the utility of a set of visual cues over a future time horizon. Third, it is efficient and easy to implement, since it leads to a greedy algorithm for the selection of the most relevant visual cues. Fourth, it provides formal performance guarantees: we leverage submodularity to prove that the greedy selection cannot be far from the optimal (combinatorial) selection. Simulations and real experiments on agile drones show that our approach ensures state-of-the-art VIN performance while maintaining a lean processing time. In the easy scenarios, our approach outperforms appearance-based feature selection in terms of localization errors. In the most challenging scenarios, it enables accurate visual-inertial navigation while appearance-based feature selection fails to track robot's motion during aggressive maneuvers.Comment: 20 pages, 7 figures, 2 table

Structured Prediction Problem Archive

Structured prediction problems are one of the fundamental tools in machinelearning. In order to facilitate algorithm development for their numericalsolution, we collect in one place a large number of datasets in easy to readformats for a diverse set of problem classes. We provide archival links todatasets, description of the considered problems and problem formats, and ashort summary of problem characteristics including size, number of instancesetc. For reference we also give a non-exhaustive selection of algorithmsproposed in the literature for their solution. We hope that this centralrepository will make benchmarking and comparison to established works easier.We welcome submission of interesting new datasets and algorithms for inclusionin our archive.<br