MAP: Medial Axis Based Geometric Routing in Sensor Networks

One of the challenging tasks in the deployment of dense wireless networks (like sensor networks) is in devising a routing scheme for node to node communication. Important consideration includes scalability, routing complexity, the length of the communication paths and the load sharing of the routes. In this paper, we show that a compact and expressive abstraction of network connectivity by the medial axis enables efficient and localized routing. We propose MAP, a Medial Axis based naming and routing Protocol that does not require locations, makes routing decisions locally, and achieves good load balancing. In its preprocessing phase, MAP constructs the medial axis of the sensor field, defined as the set of nodes with at least two closest boundary nodes. The medial axis of the network captures both the complex geometry and non-trivial topology of the sensor field. It can be represented compactly by a graph whose size is comparable with the complexity of the geometric features (e.g., the number of holes). Each node is then given a name related to its position with respect to the medial axis. The routing scheme is derived through local decisions based on the names of the source and destination nodes and guarantees delivery with reasonable and natural routes. We show by both theoretical analysis and simulations that our medial axis based geometric routing scheme is scalable, produces short routes, achieves excellent load balancing, and is very robust to variations in the network model

Formal Verification of Input-Output Mappings of Tree Ensembles

Recent advances in machine learning and artificial intelligence are now being considered in safety-critical autonomous systems where software defects may cause severe harm to humans and the environment. Design organizations in these domains are currently unable to provide convincing arguments that their systems are safe to operate when machine learning algorithms are used to implement their software. In this paper, we present an efficient method to extract equivalence classes from decision trees and tree ensembles, and to formally verify that their input-output mappings comply with requirements. The idea is that, given that safety requirements can be traced to desirable properties on system input-output patterns, we can use positive verification outcomes in safety arguments. This paper presents the implementation of the method in the tool VoTE (Verifier of Tree Ensembles), and evaluates its scalability on two case studies presented in current literature. We demonstrate that our method is practical for tree ensembles trained on low-dimensional data with up to 25 decision trees and tree depths of up to 20. Our work also studies the limitations of the method with high-dimensional data and preliminarily investigates the trade-off between large number of trees and time taken for verification

Parametric shortest-path algorithms via tropical geometry

We study parameterized versions of classical algorithms for computing shortest-path trees. This is most easily expressed in terms of tropical geometry. Applications include shortest paths in traffic networks with variable link travel times.Comment: 24 pages and 8 figure

Greedy Algorithms for Steiner Forest

In the Steiner Forest problem, we are given terminal pairs $\{s_i, t_i\}$, and need to find the cheapest subgraph which connects each of the terminal pairs together. In 1991, Agrawal, Klein, and Ravi, and Goemans and Williamson gave primal-dual constant-factor approximation algorithms for this problem; until now, the only constant-factor approximations we know are via linear programming relaxations. We consider the following greedy algorithm: Given terminal pairs in a metric space, call a terminal "active" if its distance to its partner is non-zero. Pick the two closest active terminals (say $s_i, t_j$), set the distance between them to zero, and buy a path connecting them. Recompute the metric, and repeat. Our main result is that this algorithm is a constant-factor approximation. We also use this algorithm to give new, simpler constructions of cost-sharing schemes for Steiner forest. In particular, the first "group-strict" cost-shares for this problem implies a very simple combinatorial sampling-based algorithm for stochastic Steiner forest

A multiple layer model to compare RNA secondary structures

International audienceWe formally introduce a new data structure, called MiGaL for ``Multiple Graph Layers'', that is composed of various graphs linked together by relations of abstraction/refinement. The new structure is useful for representing information that can be described at different levels of abstraction, each level corresponding to a graph. We then propose an algorithm for comparing two MiGaLs. The algorithm performs a step-by-step comparison starting with the most ``abstract'' level. The result of the comparison at a given step is communicated to the next step using a special colouring scheme. MiGaLs represent a very natural model for comparing RNA secondary structures that may be seen at different levels of detail, going from the sequence of nucleotides, single or paired with another to participate in a helix, to the network of multiple loops that is believed to represent the most conserved part of RNAs having similar function. We therefore show how to use MiGaLs to very efficiently compare two RNAs of any size at different levels of detail

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

This work introduces a number of algebraic topology approaches, such as multicomponent persistent homology, multi-level persistent homology and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. Multicomponent persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for chemical and biological problems. Extensive numerical experiments involving more than 4,000 protein-ligand complexes from the PDBBind database and near 100,000 ligands and decoys in the DUD database are performed to test respectively the scoring power and the virtual screening power of the proposed topological approaches. It is demonstrated that the present approaches outperform the modern machine learning based methods in protein-ligand binding affinity predictions and ligand-decoy discrimination