Unifying Amplitude and Phase Analysis: A Compositional Data Approach to Functional Multivariate Mixed-Effects Modeling of Mandarin Chinese

Mandarin Chinese is characterized by being a tonal language; the pitch (or $F_0$) of its utterances carries considerable linguistic information. However, speech samples from different individuals are subject to changes in amplitude and phase which must be accounted for in any analysis which attempts to provide a linguistically meaningful description of the language. A joint model for amplitude, phase and duration is presented which combines elements from Functional Data Analysis, Compositional Data Analysis and Linear Mixed Effects Models. By decomposing functions via a functional principal component analysis, and connecting registration functions to compositional data analysis, a joint multivariate mixed effect model can be formulated which gives insights into the relationship between the different modes of variation as well as their dependence on linguistic and non-linguistic covariates. The model is applied to the COSPRO-1 data set, a comprehensive database of spoken Taiwanese Mandarin, containing approximately 50 thousand phonetically diverse sample $F_0$ contours (syllables), and reveals that phonetic information is jointly carried by both amplitude and phase variation.Comment: 49 pages, 13 figures, small changes to discussio

ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.

BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster

Many-to-Many Graph Matching: a Continuous Relaxation Approach

Graphs provide an efficient tool for object representation in various computer vision applications. Once graph-based representations are constructed, an important question is how to compare graphs. This problem is often formulated as a graph matching problem where one seeks a mapping between vertices of two graphs which optimally aligns their structure. In the classical formulation of graph matching, only one-to-one correspondences between vertices are considered. However, in many applications, graphs cannot be matched perfectly and it is more interesting to consider many-to-many correspondences where clusters of vertices in one graph are matched to clusters of vertices in the other graph. In this paper, we formulate the many-to-many graph matching problem as a discrete optimization problem and propose an approximate algorithm based on a continuous relaxation of the combinatorial problem. We compare our method with other existing methods on several benchmark computer vision datasets.Comment: 1

WarpNet: Weakly Supervised Matching for Single-view Reconstruction

We present an approach to matching images of objects in fine-grained datasets without using part annotations, with an application to the challenging problem of weakly supervised single-view reconstruction. This is in contrast to prior works that require part annotations, since matching objects across class and pose variations is challenging with appearance features alone. We overcome this challenge through a novel deep learning architecture, WarpNet, that aligns an object in one image with a different object in another. We exploit the structure of the fine-grained dataset to create artificial data for training this network in an unsupervised-discriminative learning approach. The output of the network acts as a spatial prior that allows generalization at test time to match real images across variations in appearance, viewpoint and articulation. On the CUB-200-2011 dataset of bird categories, we improve the AP over an appearance-only network by 13.6%. We further demonstrate that our WarpNet matches, together with the structure of fine-grained datasets, allow single-view reconstructions with quality comparable to using annotated point correspondences.Comment: to appear in IEEE Conference on Computer Vision and Pattern Recognition (CVPR) 201