Structured Sequence Modeling with Graph Convolutional Recurrent Networks

This paper introduces Graph Convolutional Recurrent Network (GCRN), a deep learning model able to predict structured sequences of data. Precisely, GCRN is a generalization of classical recurrent neural networks (RNN) to data structured by an arbitrary graph. Such structured sequences can represent series of frames in videos, spatio-temporal measurements on a network of sensors, or random walks on a vocabulary graph for natural language modeling. The proposed model combines convolutional neural networks (CNN) on graphs to identify spatial structures and RNN to find dynamic patterns. We study two possible architectures of GCRN, and apply the models to two practical problems: predicting moving MNIST data, and modeling natural language with the Penn Treebank dataset. Experiments show that exploiting simultaneously graph spatial and dynamic information about data can improve both precision and learning speed

The Topology ToolKit

This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the topological analysis of scalar data, including: critical points, integral lines, persistence diagrams, persistence curves, merge trees, contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots, Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due to a tight integration with ParaView. It is also easily accessible to developers through a variety of bindings (Python, VTK/C++) for fast prototyping or through direct, dependence-free, C++, to ease integration into pre-existing complex systems. While developing TTK, we faced several algorithmic and software engineering challenges, which we document in this paper. In particular, we present an algorithm for the construction of a discrete gradient that complies to the critical points extracted in the piecewise-linear setting. This algorithm guarantees a combinatorial consistency across the topological abstractions supported by TTK, and importantly, a unified implementation of topological data simplification for multi-scale exploration and analysis. We also present a cached triangulation data structure, that supports time efficient and generic traversals, which self-adjusts its memory usage on demand for input simplicial meshes and which implicitly emulates a triangulation for regular grids with no memory overhead. Finally, we describe an original software architecture, which guarantees memory efficient and direct accesses to TTK features, while still allowing for researchers powerful and easy bindings and extensions. TTK is open source (BSD license) and its code, online documentation and video tutorials are available on TTK's website

Segmentation of Unstructured Datasets

Datasets generated by computer simulations and experiments in Computational Fluid Dynamics tend to be extremely large and complex. It is difficult to visualize these datasets using standard techniques like Volume Rendering and Ray Casting. Object Segmentation provides a technique to extract and quantify regions of interest within these massive datasets. This thesis explores basic algorithms to extract coherent amorphous regions from two-dimensional and three-dimensional scalar unstructured grids. The techniques are applied to datasets from Computational Fluid Dynamics and from Finite Element Analysis

Scientific visualizations

Visualizations for three different categories of problems are presented: measurements of object parameters as they vary over time, constructing surfaces from unorganized sets of points, and representing the internal structure of volumes using isosurfaces. Problem backgrounds are discussed as well as the operational details of each visualization. Visualizations were written with ease of use in mind for Spiegel, a programmable visualization environment

Compiling global name-space programs for distributed execution

Distributed memory machines do not provide hardware support for a global address space. Thus programmers are forced to partition the data across the memories of the architecture and use explicit message passing to communicate data between processors. The compiler support required to allow programmers to express their algorithms using a global name-space is examined. A general method is presented for analysis of a high level source program and along with its translation to a set of independently executing tasks communicating via messages. If the compiler has enough information, this translation can be carried out at compile-time. Otherwise run-time code is generated to implement the required data movement. The analysis required in both situations is described and the performance of the generated code on the Intel iPSC/2 is presented

Phase behavior and morphology of multicomponent liquid mixtures

Multicomponent systems are ubiquitous in nature and industry. While the physics of few-component liquid mixtures (i.e., binary and ternary ones) is well-understood and routinely taught in undergraduate courses, the thermodynamic and kinetic properties of $N$-component mixtures with $N>3$ have remained relatively unexplored. An example of such a mixture is provided by the intracellular fluid, in which protein-rich droplets phase separate into distinct membraneless organelles. In this work, we investigate equilibrium phase behavior and morphology of $N$-component liquid mixtures within the Flory-Huggins theory of regular solutions. In order to determine the number of coexisting phases and their compositions, we developed a new algorithm for constructing complete phase diagrams, based on numerical convexification of the discretized free energy landscape. Together with a Cahn-Hilliard approach for kinetics, we employ this method to study mixtures with $N=4$ and $5$ components. We report on both the coarsening behavior of such systems, as well as the resulting morphologies in three spatial dimensions. We discuss how the number of coexisting phases and their compositions can be extracted with Principal Component Analysis (PCA) and K-Means clustering algorithms. Finally, we discuss how one can reverse engineer the interaction parameters and volume fractions of components in order to achieve a range of desired packing structures, such as nested `Russian dolls' and encapsulated Janus droplets.Comment: 16 pages, 11 figures + hyperlinks to 7 video

Mining Point Cloud Local Structures by Kernel Correlation and Graph Pooling

Unlike on images, semantic learning on 3D point clouds using a deep network is challenging due to the naturally unordered data structure. Among existing works, PointNet has achieved promising results by directly learning on point sets. However, it does not take full advantage of a point's local neighborhood that contains fine-grained structural information which turns out to be helpful towards better semantic learning. In this regard, we present two new operations to improve PointNet with a more efficient exploitation of local structures. The first one focuses on local 3D geometric structures. In analogy to a convolution kernel for images, we define a point-set kernel as a set of learnable 3D points that jointly respond to a set of neighboring data points according to their geometric affinities measured by kernel correlation, adapted from a similar technique for point cloud registration. The second one exploits local high-dimensional feature structures by recursive feature aggregation on a nearest-neighbor-graph computed from 3D positions. Experiments show that our network can efficiently capture local information and robustly achieve better performances on major datasets. Our code is available at http://www.merl.com/research/license#KCNetComment: Accepted in CVPR'18. *indicates equal contributio

A Distributed-Memory Randomized Structured Multifrontal Method for Sparse Direct Solutions

We design a distributed-memory randomized structured multifrontal solver for large sparse matrices. Two layers of hierarchical tree parallelism are used. A sequence of innovative parallel methods are developed for randomized structured frontal matrix operations, structured update matrix computation, skinny extend-add operation, selected entry extraction from structured matrices, etc. Several strategies are proposed to reuse computations and reduce communications. Unlike an earlier parallel structured multifrontal method that still involves large dense intermediate matrices, our parallel solver performs the major operations in terms of skinny matrices and fully structured forms. It thus significantly enhances the efficiency and scalability. Systematic communication cost analysis shows that the numbers of words are reduced by factors of about $O(\sqrt{n}/r)$ in two dimensions and about $O(n^{2/3}/r)$ in three dimensions, where $n$ is the matrix size and $r$ is an off-diagonal numerical rank bound of the intermediate frontal matrices. The efficiency and parallel performance are demonstrated with the solution of some large discretized PDEs in two and three dimensions. Nice scalability and significant savings in the cost and memory can be observed from the weak and strong scaling tests, especially for some 3D problems discretized on unstructured meshes