arXiv subjects

Momiao Xiong

Publications and source records attributed to Momiao Xiong.

22 records · Page 2Linked to original sources

arXiv2013

An Efficient Sufficient Dimension Reduction Method for Identifying Genetic Variants of Clinical Significance

Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomic variants of clinical utility which will provide information for optimal wellness and interference strategies. Traditional paradigm for identifying variants of clinical validity is to test association of the variants. However, significantly associated genetic variants may or may not be usefulness for diagnosis and prognosis of diseases. Alternative to association studies for finding genetic variants of predictive utility is to systematically search variants that contain sufficient information for phenotype prediction. To achieve this, we introduce concepts of sufficient dimension reduction and coordinate hypothesis which project the original high dimensional data to very low dimensional space while preserving all information on response phenotypes. We then formulate clinically significant genetic variant discovery problem into sparse SDR problem and develop algorithms that can select significant genetic variants from up to or even ten millions of predictors with the aid of dividing SDR for whole genome into a number of subSDR problems defined for genomic regions. The sparse SDR is in turn formulated as sparse optimal scoring problem, but with penalty which can remove row vectors from the basis matrix. To speed up computation, we develop the modified alternating direction method for multipliers to solve the sparse optimal scoring problem which can easily be implemented in parallel. To illustrate its application, the proposed method is applied to simulation data and the NHLBI's Exome Sequencing Project dataset

q-bio.GN↗

arXiv2008

Network Quotients: Structural Skeletons of Complex Systems

A defining feature of many large empirical networks is their intrinsic complexity. However, many networks also contain a large degree of structural repetition. An immediate question then arises: can we characterize essential network complexity while excluding structural redundancy? In this article we utilize inherent network symmetry to collapse all redundant information from a network, resulting in a coarse-graining which we show to carry the essential structural information of the `parent' network. In the context of algebraic combinatorics, this coarse-graining is known as the \emph{quotient}. We systematically explore the theoretical properties of network quotients and summarize key statistics of a variety of `real-world' quotients with respect to those of their parent networks. In particular, we find that quotients can be substantially smaller than their parent networks yet typically preserve various key functional properties such as complexity (heterogeneity and hubs vertices) and communication (diameter and mean geodesic distance), suggesting that quotients constitute the essential structural skeleton of their parent network. We summarize with a discussion of potential uses of quotients in analysis of biological regulatory networks and ways in which using quotients can reduce the computational complexity of network algorithms.

physics.soc-ph↗

arXiv2007

Symmetry based Structure Entropy of Complex Networks

Precisely quantifying the heterogeneity or disorder of a network system is very important and desired in studies of behavior and function of the network system. Although many degree-based entropies have been proposed to measure the heterogeneity of real networks, heterogeneity implicated in the structure of networks can not be precisely quantified yet. Hence, we propose a new structure entropy based on automorphism partition to precisely quantify the structural heterogeneity of networks. Analysis of extreme cases shows that entropy based on automorphism partition can quantify the structural heterogeneity of networks more precisely than degree-based entropy. We also summarized symmetry and heterogeneity statistics of many real networks, finding that real networks are indeed more heterogenous in the view of automorphism partition than what have been depicted under the measurement of degree based entropies; and that structural heterogeneity is strongly negatively correlated to symmetry of real networks.

physics.soc-ph↗

arXiv2007

Emergence of Symmetry in Complex Networks

Many real networks have been found to have a rich degree of symmetry, which is a very important structural property of complex network, yet has been rarely studied so far. And where does symmetry comes from has not been explained. To explore the mechanism underlying symmetry of the networks, we studied statistics of certain local symmetric motifs, such as symmetric bicliques and generalized symmetric bicliques, which contribute to local symmetry of networks. We found that symmetry of complex networks is a consequence of similar linkage pattern, which means that nodes with similar degree tend to share similar linkage targets. A improved version of BA model integrating similar linkage pattern successfully reproduces the symmetry of real networks, indicating that similar linkage pattern is the underlying ingredient that responsible for the emergence of the symmetry in complex networks.

physics.soc-ph↗