Generic Strategies for Chemical Space Exploration

Computational approaches to exploring "chemical universes", i.e., very large sets, potentially infinite sets of compounds that can be constructed by a prescribed collection of reaction mechanisms, in practice suffer from a combinatorial explosion. It quickly becomes impossible to test, for all pairs of compounds in a rapidly growing network, whether they can react with each other. More sophisticated and efficient strategies are therefore required to construct very large chemical reaction networks. Undirected labeled graphs and graph rewriting are natural models of chemical compounds and chemical reactions. Borrowing the idea of partial evaluation from functional programming, we introduce partial applications of rewrite rules. Binding substrate to rules increases the number of rules but drastically prunes the substrate sets to which it might match, resulting in dramatically reduced resource requirements. At the same time, exploration strategies can be guided, e.g. based on restrictions on the product molecules to avoid the explicit enumeration of very unlikely compounds. To this end we introduce here a generic framework for the specification of exploration strategies in graph-rewriting systems. Using key examples of complex chemical networks from sugar chemistry and the realm of metabolic networks we demonstrate the feasibility of a high-level strategy framework. The ideas presented here can not only be used for a strategy-based chemical space exploration that has close correspondence of experimental results, but are much more general. In particular, the framework can be used to emulate higher-level transformation models such as illustrated in a small puzzle game

Deep Functional Maps: Structured Prediction for Dense Shape Correspondence

We introduce a new framework for learning dense correspondence between deformable 3D shapes. Existing learning based approaches model shape correspondence as a labelling problem, where each point of a query shape receives a label identifying a point on some reference domain; the correspondence is then constructed a posteriori by composing the label predictions of two input shapes. We propose a paradigm shift and design a structured prediction model in the space of functional maps, linear operators that provide a compact representation of the correspondence. We model the learning process via a deep residual network which takes dense descriptor fields defined on two shapes as input, and outputs a soft map between the two given objects. The resulting correspondence is shown to be accurate on several challenging benchmarks comprising multiple categories, synthetic models, real scans with acquisition artifacts, topological noise, and partiality.Comment: Accepted for publication at ICCV 201

Learning shape correspondence with anisotropic convolutional neural networks

Establishing correspondence between shapes is a fundamental problem in geometry processing, arising in a wide variety of applications. The problem is especially difficult in the setting of non-isometric deformations, as well as in the presence of topological noise and missing parts, mainly due to the limited capability to model such deformations axiomatically. Several recent works showed that invariance to complex shape transformations can be learned from examples. In this paper, we introduce an intrinsic convolutional neural network architecture based on anisotropic diffusion kernels, which we term Anisotropic Convolutional Neural Network (ACNN). In our construction, we generalize convolutions to non-Euclidean domains by constructing a set of oriented anisotropic diffusion kernels, creating in this way a local intrinsic polar representation of the data (`patch'), which is then correlated with a filter. Several cascades of such filters, linear, and non-linear operators are stacked to form a deep neural network whose parameters are learned by minimizing a task-specific cost. We use ACNNs to effectively learn intrinsic dense correspondences between deformable shapes in very challenging settings, achieving state-of-the-art results on some of the most difficult recent correspondence benchmarks

Localized Manifold Harmonics for Spectral Shape Analysis

The use of Laplacian eigenfunctions is ubiquitous in a wide range of computer graphics and geometry processing applications. In particular, Laplacian eigenbases allow generalizing the classical Fourier analysis to manifolds. A key drawback of such bases is their inherently global nature, as the Laplacian eigenfunctions carry geometric and topological structure of the entire manifold. In this paper, we introduce a new framework for local spectral shape analysis. We show how to efficiently construct localized orthogonal bases by solving an optimization problem that in turn can be posed as the eigendecomposition of a new operator obtained by a modification of the standard Laplacian. We study the theoretical and computational aspects of the proposed framework and showcase our new construction on the classical problems of shape approximation and correspondence. We obtain significant improvement compared to classical Laplacian eigenbases as well as other alternatives for constructing localized bases

Point-wise Map Recovery and Refinement from Functional Correspondence

Since their introduction in the shape analysis community, functional maps have met with considerable success due to their ability to compactly represent dense correspondences between deformable shapes, with applications ranging from shape matching and image segmentation, to exploration of large shape collections. Despite the numerous advantages of such representation, however, the problem of converting a given functional map back to a point-to-point map has received a surprisingly limited interest. In this paper we analyze the general problem of point-wise map recovery from arbitrary functional maps. In doing so, we rule out many of the assumptions required by the currently established approach -- most notably, the limiting requirement of the input shapes being nearly-isometric. We devise an efficient recovery process based on a simple probabilistic model. Experiments confirm that this approach achieves remarkable accuracy improvements in very challenging cases