Biomedical subjects

Songde Ma

Publications and source records attributed to Songde Ma.

6 recordsLinked to original sources

PubMed2006

Exploring candidate genes for human brain diseases from a brain-specific gene network.

It is believed that large numbers of genes are involved in common human brain diseases. Here, we propose a novel computational strategy for simultaneously identifying multiple candidate genes for genetic human brain diseases from a brain-specific gene network-level perspective. By integrating diverse genomic and proteomic datasets based on Bayesian statistical model, we built a large-scale human brain-specific gene network. Based on this network and minor prior knowledge of a specific brain disease, we can effectively identify multiple candidate genes for this disease. When four known Alzheimer's disease genes were used as the prior knowledge, among the top 46 high-scoring genes that we have found, 37 were previously reported to be associated with Alzheimer's disease. And the higher score a gene has, the more likely this gene is a disease-related one. The results suggest that the proposed method is effective, convenient, and applicable in the future genetic studies.

Alzheimer Disease↗

PubMed2006

Face recognition using kernel scatter-difference-based discriminant analysis.

There are two fundamental problems with the Fisher linear discriminant analysis for face recognition. One is the singularity problem of the within-class scatter matrix due to small training sample size. The other is that it cannot efficiently describe complex nonlinear variations of face images because of its linear property. In this letter, a kernel scatter-difference-based discriminant analysis is proposed to overcome these two problems. We first use the nonlinear kernel trick to map the input data into an implicit feature space F. Then a scatter-difference-based discriminant rule is defined to analyze the data in F. The proposed method can not only produce nonlinear discriminant features but also avoid the singularity problem of the within-class scatter matrix. Extensive experiments show encouraging recognition performance of the new algorithm.

Discriminant Analysis↗

PubMed2005

Parametric reconstruction of generalized cylinders from limb edges.

The three-dimensional (3-D) reconstruction of generalized cylinders (GCs) is an important research field in computer vision. One of the main difficulties is that some contour features in images cannot be reconstructed by traditional stereovision because they do not correspond to reflectance discontinuities of surface in space. In this paper, we present a novel, parametric approach for the 3-D reconstruction of circular generalized cylinders (CGCs) only from the limb edges of CGCs in two images. Instead of exploiting the invariant and quasiinvariant properties of some specific subclasses of GCs in projections, our reconstruction is achieved by some general assumptions on GCs, and can, therefore, be applied to a broader subclass of GCs. In order to improve robustness, we perform the extraction and labeling of the limb edge interactively, and estimate the epipolar geometry between two images by an optimal algorithm. Then, for different types of GCs, three kinds of symmetries (parallel symmetry, skew symmetry, and local smooth symmetry) are employed to compute the symmetry of limb edges. The surface points corresponding to limb edges in images are reconstructed by integrating the recovered epipolar geometry and the properties induced from the assumptions that we make on the GCs. Finally, a homography-based method is exploited to further refine the 3-D description of the GC with a coplanar curved axis.

Algorithms↗

PubMed2004

Characterizing the dynamic connectivity between genes by variable parameter regression and Kalman filtering based on temporal gene expression data.

MOTIVATION: One popular method for analyzing functional connectivity between genes is to cluster genes with similar expression profiles. The most popular metrics measuring the similarity (or dissimilarity) among genes include Pearson's correlation, linear regression coefficient and Euclidean distance. As these metrics only give some constant values, they can only depict a stationary connectivity between genes. However, the functional connectivity between genes usually changes with time. Here, we introduce a novel insight for characterizing the relationship between genes and find out a proper mathematical model, variable parameter regression and Kalman filtering to model it. RESULTS: We applied our algorithm to some simulated data and two pairs of real gene expression data. The changes of connectivity in simulated data are closely identical with the truth and the results of two pairs of gene expression data show that our method has successfully demonstrated the dynamic connectivity between genes. CONTACT: jiangtz@nlpr.ia.ac.cn.

Computer Simulation↗

PubMed2004

A combinational feature selection and ensemble neural network method for classification of gene expression data.

BACKGROUND: Microarray experiments are becoming a powerful tool for clinical diagnosis, as they have the potential to discover gene expression patterns that are characteristic for a particular disease. To date, this problem has received most attention in the context of cancer research, especially in tumor classification. Various feature selection methods and classifier design strategies also have been generally used and compared. However, most published articles on tumor classification have applied a certain technique to a certain dataset, and recently several researchers compared these techniques based on several public datasets. But, it has been verified that differently selected features reflect different aspects of the dataset and some selected features can obtain better solutions on some certain problems. At the same time, faced with a large amount of microarray data with little knowledge, it is difficult to find the intrinsic characteristics using traditional methods. In this paper, we attempt to introduce a combinational feature selection method in conjunction with ensemble neural networks to generally improve the accuracy and robustness of sample classification. RESULTS: We validate our new method on several recent publicly available datasets both with predictive accuracy of testing samples and through cross validation. Compared with the best performance of other current methods, remarkably improved results can be obtained using our new strategy on a wide range of different datasets. CONCLUSIONS: Thus, we conclude that our methods can obtain more information in microarray data to get more accurate classification and also can help to extract the latent marker genes of the diseases for better diagnosis and treatment.

Acute Disease↗

PubMed2004

Esub8: a novel tool to predict protein subcellular localizations in eukaryotic organisms.

BACKGROUND: Subcellular localization of a new protein sequence is very important and fruitful for understanding its function. As the number of new genomes has dramatically increased over recent years, a reliable and efficient system to predict protein subcellular location is urgently needed. RESULTS: Esub8 was developed to predict protein subcellular localizations for eukaryotic proteins based on amino acid composition. In this research, the proteins are classified into the following eight groups: chloroplast, cytoplasm, extracellular, Golgi apparatus, lysosome, mitochondria, nucleus and peroxisome. We know subcellular localization is a typical classification problem; consequently, a one-against-one (1-v-1) multi-class support vector machine was introduced to construct the classifier. Unlike previous methods, ours considers the order information of protein sequences by a different method. Our method is tested in three subcellular localization predictions for prokaryotic proteins and four subcellular localization predictions for eukaryotic proteins on Reinhardt's dataset. The results are then compared to several other methods. The total prediction accuracies of two tests are both 100% by a self-consistency test, and are 92.9% and 84.14% by the jackknife test, respectively. Esub8 also provides excellent results: the total prediction accuracies are 100% by a self-consistency test and 87% by the jackknife test. CONCLUSIONS: Our method represents a different approach for predicting protein subcellular localization and achieved a satisfactory result; furthermore, we believe Esub8 will be a useful tool for predicting protein subcellular localizations in eukaryotic organisms.

Computational Biology↗