GRASS: Generative Recursive Autoencoders for Shape Structures

We introduce a novel neural network architecture for encoding and synthesis of 3D shapes, particularly their structures. Our key insight is that 3D shapes are effectively characterized by their hierarchical organization of parts, which reflects fundamental intra-shape relationships such as adjacency and symmetry. We develop a recursive neural net (RvNN) based autoencoder to map a flat, unlabeled, arbitrary part layout to a compact code. The code effectively captures hierarchical structures of man-made 3D objects of varying structural complexities despite being fixed-dimensional: an associated decoder maps a code back to a full hierarchy. The learned bidirectional mapping is further tuned using an adversarial setup to yield a generative model of plausible structures, from which novel structures can be sampled. Finally, our structure synthesis framework is augmented by a second trained module that produces fine-grained part geometry, conditioned on global and local structural context, leading to a full generative pipeline for 3D shapes. We demonstrate that without supervision, our network learns meaningful structural hierarchies adhering to perceptual grouping principles, produces compact codes which enable applications such as shape classification and partial matching, and supports shape synthesis and interpolation with significant variations in topology and geometry.Comment: Corresponding author: Kai Xu ([email protected]

Pattern vectors from algebraic graph theory

Graphstructures have proven computationally cumbersome for pattern analysis. The reason for this is that, before graphs can be converted to pattern vectors, correspondences must be established between the nodes of structures which are potentially of different size. To overcome this problem, in this paper, we turn to the spectral decomposition of the Laplacian matrix. We show how the elements of the spectral matrix for the Laplacian can be used to construct symmetric polynomials that are permutation invariants. The coefficients of these polynomials can be used as graph features which can be encoded in a vectorial manner. We extend this representation to graphs in which there are unary attributes on the nodes and binary attributes on the edges by using the spectral decomposition of a Hermitian property matrix that can be viewed as a complex analogue of the Laplacian. To embed the graphs in a pattern space, we explore whether the vectors of invariants can be embedded in a low- dimensional space using a number of alternative strategies, including principal components analysis ( PCA), multidimensional scaling ( MDS), and locality preserving projection ( LPP). Experimentally, we demonstrate that the embeddings result in well- defined graph clusters. Our experiments with the spectral representation involve both synthetic and real- world data. The experiments with synthetic data demonstrate that the distances between spectral feature vectors can be used to discriminate between graphs on the basis of their structure. The real- world experiments show that the method can be used to locate clusters of graphs

Incorporating peak grouping information for alignment of multiple liquid chromatography-mass spectrometry datasets

Motivation: The combination of liquid chromatography and mass spectrometry (LC/MS) has been widely used for large-scale comparative studies in systems biology, including proteomics, glycomics and metabolomics. In almost all experimental design, it is necessary to compare chromatograms across biological or technical replicates and across sample groups. Central to this is the peak alignment step, which is one of the most important but challenging preprocessing steps. Existing alignment tools do not take into account the structural dependencies between related peaks that co-elute and are derived from the same metabolite or peptide. We propose a direct matching peak alignment method for LC/MS data that incorporates related peaks information (within each LC/MS run) and investigate its effect on alignment performance (across runs). The groupings of related peaks necessary for our method can be obtained from any peak clustering method and are built into a pairwise peak similarity score function. The similarity score matrix produced is used by an approximation algorithm for the weighted matching problem to produce the actual alignment result.<p></p> Results: We demonstrate that related peak information can improve alignment performance. The performance is evaluated on a set of benchmark datasets, where our method performs competitively compared to other popular alignment tools.<p></p> Availability: The proposed alignment method has been implemented as a stand-alone application in Python, available for download at http://github.com/joewandy/peak-grouping-alignment.<p></p&gt

Graph edit distance from spectral seriation

This paper is concerned with computing graph edit distance. One of the criticisms that can be leveled at existing methods for computing graph edit distance is that they lack some of the formality and rigor of the computation of string edit distance. Hence, our aim is to convert graphs to string sequences so that string matching techniques can be used. To do this, we use a graph spectral seriation method to convert the adjacency matrix into a string or sequence order. We show how the serial ordering can be established using the leading eigenvector of the graph adjacency matrix. We pose the problem of graph-matching as a maximum a posteriori probability (MAP) alignment of the seriation sequences for pairs of graphs. This treatment leads to an expression in which the edit cost is the negative logarithm of the a posteriori sequence alignment probability. We compute the edit distance by finding the sequence of string edit operations which minimizes the cost of the path traversing the edit lattice. The edit costs are determined by the components of the leading eigenvectors of the adjacency matrix and by the edge densities of the graphs being matched. We demonstrate the utility of the edit distance on a number of graph clustering problems

Data-Driven Shape Analysis and Processing

Data-driven methods play an increasingly important role in discovering geometric, structural, and semantic relationships between 3D shapes in collections, and applying this analysis to support intelligent modeling, editing, and visualization of geometric data. In contrast to traditional approaches, a key feature of data-driven approaches is that they aggregate information from a collection of shapes to improve the analysis and processing of individual shapes. In addition, they are able to learn models that reason about properties and relationships of shapes without relying on hard-coded rules or explicitly programmed instructions. We provide an overview of the main concepts and components of these techniques, and discuss their application to shape classification, segmentation, matching, reconstruction, modeling and exploration, as well as scene analysis and synthesis, through reviewing the literature and relating the existing works with both qualitative and numerical comparisons. We conclude our report with ideas that can inspire future research in data-driven shape analysis and processing.Comment: 10 pages, 19 figure

Digital Image Access & Retrieval

The 33th Annual Clinic on Library Applications of Data Processing, held at the University of Illinois at Urbana-Champaign in March of 1996, addressed the theme of "Digital Image Access & Retrieval." The papers from this conference cover a wide range of topics concerning digital imaging technology for visual resource collections. Papers covered three general areas: (1) systems, planning, and implementation; (2) automatic and semi-automatic indexing; and (3) preservation with the bulk of the conference focusing on indexing and retrieval.published or submitted for publicatio

Acetylcholine neuromodulation in normal and abnormal learning and memory: vigilance control in waking, sleep, autism, amnesia, and Alzheimer's disease

This article provides a unified mechanistic neural explanation of how learning, recognition, and cognition break down during Alzheimer's disease, medial temporal amnesia, and autism. It also clarifies whey there are often sleep disturbances during these disorders. A key mechanism is how acetylcholine modules vigilance control in cortical layer

3D Object Discovery and Modeling Using Single RGB-D Images Containing Multiple Object Instances

Unsupervised object modeling is important in robotics, especially for handling a large set of objects. We present a method for unsupervised 3D object discovery, reconstruction, and localization that exploits multiple instances of an identical object contained in a single RGB-D image. The proposed method does not rely on segmentation, scene knowledge, or user input, and thus is easily scalable. Our method aims to find recurrent patterns in a single RGB-D image by utilizing appearance and geometry of the salient regions. We extract keypoints and match them in pairs based on their descriptors. We then generate triplets of the keypoints matching with each other using several geometric criteria to minimize false matches. The relative poses of the matched triplets are computed and clustered to discover sets of triplet pairs with similar relative poses. Triplets belonging to the same set are likely to belong to the same object and are used to construct an initial object model. Detection of remaining instances with the initial object model using RANSAC allows to further expand and refine the model. The automatically generated object models are both compact and descriptive. We show quantitative and qualitative results on RGB-D images with various objects including some from the Amazon Picking Challenge. We also demonstrate the use of our method in an object picking scenario with a robotic arm