Physicochemical and Graph Theoretical Descriptors in Developmental Toxicity SAR: A Comparative Study

Abstract

Chemical insults to the developing fetus can lead to growth retardation, malformation, death, and functional deficits. The present study seeks to determine if physicochemical and/or graph theoretical parameters can be used to determine a structure-activity relationship (SAR) for developmental toxicity, and if consistency is observed among the selected features. The biological data utilized consists of a diverse series of compounds evaluated within the Chernoff-Kavlock in vivo mouse assay. Physicochemical parameters calculated correspond to electronic, steric, and transport properties. Graph theoretical parameters calculated include the simple, valence, and kappa indices. Both sets of parameters were independently applied to derive SARs in order to compare the quality of the respective models. Multiple random sampling, without replacement, was utilized to obtain ten training/test partitions. Models were built by linear discriminant analysis, decision trees, and neural networks respectively. Comparisons on identical sets of data were carried out to determine if any of the model building procedures had a significant advantage in terms of predictive performance. Furthermore, comparison of the features selected within and across the model building processes led to the determination of model consistency. Our results indicate that consistent features related to developmental toxicity are observed and that both physicochemical and graph theoretical parameters have equal utility.     

Universal point sets for planar three-trees

For every $n\in \mathbb{N}$, we present a set $S_n$ of $O(n^{3/2}\log n)$ points in the plane such that every planar 3-tree with n vertices has a straight-line embedding in the plane in which the vertices are mapped to a subset of $S_n$. This is the first subquadratic upper bound on the cardinality of universal point sets for planar 3-trees, as well as for the class of 2-trees and serial parallel graphs.     

固体异质结界面结构预测方法及AutoInterface程序实现

预测材料异质结的界面原子结构对于理解界面对性能的影响至关重要. 目前, 从理论上预测材料界面结构仍具有极大挑战, 主要是缺乏普适有效的理论计算方法. 本文介绍了本课题组在异质结界面结构预测方面取得的最新进展. 结合马氏体相变唯象理论、 图论和随机表面行走算法, 提出了界面结构的一种有效预测方法, 可以实现自动化的计算预测. 通过GaP/TiO₂半导体异质结等展示了该方法的有效性和在催化等领域的应用前景.     

Pseudo-orthogonality for graph 1-Laplacian eigenvectors and applications to higher Cheeger constants and data clustering

The data clustering problem consists in dividing a data set into prescribed groups of homogeneous data. This is an NP-hard problem that can be relaxed in the spectral graph theory, where the optimal cuts of a graph are related to the eigenvalues of graph 1-Laplacian. In this paper, we first give new notations to describe the paths, among critical eigenvectors of the graph 1-Laplacian, realizing sets with prescribed genus. We introduce the pseudo-orthogonality to characterize m₃(G), a special eigenvalue for the graph 1-Laplacian. Furthermore, we use it to give an upper bound for the third graph Cheeger constant h₃(G), that is, h₃(G) 6 m₃(G). This is a first step for proving that the k-th Cheeger constant is the minimum of the 1-Laplacian Raylegh quotient among vectors that are pseudo-orthogonal to the vectors realizing the previous k - 1 Cheeger constants. Eventually, we apply these results to give a method and a numerical algorithm to compute m₃(G), based on a generalized inverse power method.     

On the Differential Polynomial of a Graph

We introduce the differential polynomial of a graph. The differential polynomial of a graph G of order n is the polynomial B(G; x) :=∑?(G)k=-nB_k(G) x~(n+k), where B_k(G) denotes the number of vertex subsets of G with differential equal to k. We state some properties of B(G;x) and its coefficients.In particular, we compute the differential polynomial for complete, empty, path, cycle, wheel and double star graphs. We also establish some relationships between B(G; x) and the differential polynomials of graphs which result by removing, adding, and subdividing an edge from G.     

（mg＋k,mf—k）—图中正交于r个不相交子图的边不变的（g,f）—因子

设m,k和r为正整数,且使l≤k＜m.设G是一个具有顶点集合V(G)和边集合E(G)的图,并设g和f是定义在V(G)上的使对每个x∈V(G)有r≤g(x)≤f(x)的整数值函数.设H1,H2,…,Hr是G的r个顶点不相交的子图且|E(Hi)|=k,1≤i≤r.本文证明了每个(mg+k,mf-k)-图有k个边不相交的(g,f)-因子正交于Hi,1≤i≤r.     

The product of the restrained domination numbers of a graph and its complement

Let G=(V,E) be a graph.A set S■V is a restrained dominating set if every vertex in V-S is adjacent to a vertex in S and to a vertex in V-S.The restrained domination number of G,denoted γr(G),is the smallest cardinality of a restrained dominating set of G.In this paper,we show that if G is a graph of order n≥4,then γr(G)γr(G)≤2n.We also characterize the graphs achieving the upper bound.     

论连通图的可重构性

本文我们利用带权核子图的可重构性证明了连通图是可重构的,从而证明了重构猜想为真.     

Differentially expressed genes selection via Laplacian regularized low-rank representation method

With the rapid development of DNA microarray technology and next-generation technology, a large number of genomic data were generated. So how to extract more differentially expressed genes from genomic data has become a matter of urgency. Because Low-Rank Representation (LRR) has the high performance in studying low-dimensional subspace structures, it has attracted a chunk of attention in recent years. However, it does not take into consideration the intrinsic geometric structures in data.In this paper, a new method named Laplacian regularized Low-Rank Representation (LLRR) has been proposed and applied on genomic data, which introduces graph regularization into LRR. By taking full advantages of the graph regularization, LLRR method can capture the intrinsic non-linear geometric information among the data. The LLRR method can decomposes the observation matrix of genomic data into a low rank matrix and a sparse matrix through solving an optimization problem. Because the significant genes can be considered as sparse signals, the differentially expressed genes are viewed as the sparse perturbation signals. Therefore, the differentially expressed genes can be selected according to the sparse matrix. Finally, we use the GO tool to analyze the selected genes and compare the P-values with other methods.The results on the simulation data and two real genomic data illustrate that this method outperforms some other methods: in differentially expressed gene selection.