15435799
Structural and temporal analysis of the blogosphere through community factorization
The blogosphere has unique structural and temporal properties since blogs are typically used as communication media among human individuals. In this paper, we propose a novel technique that captures the structure and temporal dynamics of blog communities. In our framework, a community is a set of blogs that communicate with each other triggered by some events (such as a news article). The community is represented by its structure and temporal dynamics: a community graph indicates how often one blog communicates with another, and a community intensity indicates the activity level of the community that varies over time. Our method, community factorization, extracts such communities from the blogosphere, where the communication among blogs is observed as a set of subgraphs (i.e., threads of discussion). This community extraction is formulated as a factorization problem in the framework of constrained optimization, in which the objective is to best explain the observed interactions in the blogosphere over time. We further provide a scalable algorithm for computing solutions to the constrained optimization problems. Extensive experimental studies on both synthetic and real blog data demonstrate that our technique is able to discover meaningful communities that are not detectable by traditional methods.
1527832
Document clustering with cluster refinement and model selection capabilities
In this paper, we propose a document clustering method that strives to achieve: (1) a high accuracy of document clustering, and (2) the capability of estimating the number of clusters in the document corpus (i.e. the model selection capability). To accurately cluster the given document corpus, we employ a richer feature set to represent each document, and use the Gaussian Mixture Model (GMM) together with the Expectation-Maximization (EM) algorithm to conduct an initial document clustering. From this initial result, we identify a set of discriminative featuresfor each cluster, and refine the initially obtained document clusters by voting on the cluster label of each document using this discriminative feature set. This self-refinement process of discriminative feature identification and cluster label voting is iteratively applied until the convergence of document clusters. On the other hand, the model selection capability is achieved by introducing randomness in the cluster initialization stage, and then discovering a value C for the number of clusters N by which running the document clustering process for a fixed number of times yields sufficiently similar results. Performance evaluations exhibit clear superiority of the proposed method with its improved document clustering and model selection accuracies. The evaluations also demonstrate how each feature as well as the cluster refinement process contribute to the document clustering accuracy.
15097946
Algorithms for clustering high dimensional and distributed data
Clustering is the problem of identifying the distribution of patterns and intrinsic correlations in large data sets by partitioning the data points into similarity classes. The clustering problem has been widely studied in machine learning, databases, and statistics. This paper studies the problem of clustering high dimensional data. The paper proposes an algorithm called the CoFD algorithm, which is a non-distance based clustering algorithm for high dimensional spaces. Based on the Maximum Likelihood Principle, CoFD attempts to optimize its parameter settings to maximize the likelihood between data points and the model generated by the parameters. The distributed versions of the problem, called the D-CoFD algorithms, are also proposed. Experimental results on both synthetic and real data sets show the efficiency and effectiveness of CoFD and D-CoFD algorithms.
8864863
Integrating Features from Different Sources for Music Information Retrieval
Efficient and intelligent music information retrieval is a very important topic of the 21st century. With the ultimate goal of building personal music information retrieval systems, this paper studies the problem of identifying "similar" artists using both lyrics and acoustic data. In this paper, we present a clustering algorithm that integrates features from both sources to perform bimodal learning. The algorithm is tested on a data set consisting of 570 songs from 53 albums of 41 artists using artist similarity provided by All Music Guide. Experimental results show that the accuracy of artist similarity classifiers can be significantly improved and that artist similarity can be efficiently identified.
9813108
CoFD : An Algorithm for Non-distance Based Clustering in High Dimensional Spaces
The clustering problem, which aims at identifying the distribution of patterns and intrinsic correlations in large data sets by partitioning the data points into similarity clusters, has been widely studied. Traditional clustering algorithms use distance functions to measure similarity and are not suitable for high dimensional spaces. In this paper, we propose CoFD algorithm, which is a non-distance based clustering algorithm for high dimensional spaces. Based on the maximum likelihood principle, CoFD is to optimize parameters to maximize the likelihood between data points and the model generated by the parameters. Experimental results on both synthetic data sets and a real data set show the efficiency and effectiveness of CoFD.
37613840
Improving medical/biological data classification performance by wavelet preprocessing
Many real-world datasets contain noise which could degrade the performances of learning algorithms. Motivated from the success of wavelet denoising techniques in image data, we explore a general solution to alleviate the effect of noisy data by wavelet preprocessing for medical/biological data classification. Our experiments are divided into two categories: one is of different classification algorithms on a specific database, and the other is of a specific classification algorithm (decision tree) on different databases. The experiment results show that the wavelet denoising of noisy data is able to improve the accuracies of those classification methods, if the localities of the attributes are strong enough.
7249026
Cloth representation by shape from shading with shading primitives
Cloth is a complex visual pattern with flexible 3D shape and illumination variations. Computing the 3D shape of cloth from a single image is of great interest to both computer graphics and vision researches. However, the acquisition of 3D cloth shape by shape from shading (SFS) is still a challenge. In this paper, we present a two-layer generative model for representing both the 2D cloth image and the 3D cloth surface. The first layer represents all the folds on cloth, which are called "shading primitives" in (Haddon and Forsyth, 1998), and thus captures the overall "skeleton structures" of cloth. We learn a number of typical 3D fold primitives using some training images obtained through photometric stereo. The 3D fold primitives yield a dictionary of 2D shading primitives/or cloth images. The second layer represents non-fold parts with very smooth (often flat) surface or shading, which interpolates the primitives in the first layer with a smoothness prior like conventional SFS. Then we present an algorithm called "cloth sketching" to find all the shading primitives on cloth image and simultaneously recover their 3D shape by fitting to the 3D fold primitives. Our sketch representation can be viewed as a 2-layer Markov random field (MRF), and it introduces some prior knowledge on the folds and has lower dimension and is more robust than the traditional shape-fmm-shading representation which assumes a MRF model on pixels. We show a number of experiments with satisfactory results in comparison to previous work.
11176389
Incorporating visual knowledge representation in stereo reconstruction
In this paper, we present a two-layer generative model that incorporates generic middle-level visual knowledge for dense stereo reconstruction. The visual knowledge is represented by a dictionary of surface primitives including various categories of boundary discontinuities and junctions in parametric form. Given a stereo pair, we first compute a primal sketch representation which decomposes the image into a structural part for object boundaries and high intensity contrast represented by a 2D sketch graph, and a structure less part represented by Markov random field on pixels. Then we label the sketch graph and compute the 3D sketch (like a wire-frame) by fitting the primitive dictionary to the sketch graph. The surfaces between the 3D sketches are filled in by computing the depth of the MRP model on the structureless part. These two levels interact closely since the MRF is used to propagate information between the primitives, and at the same time, the primitives act as boundary conditions for the MRF. The two processes maximize a Bayesian posterior probability jointly. We propose an MCMC algorithm that simultaneously infers the 3D primitive types and parameters and estimates the depth of the scene. Our experiments show that this representation can infer the depth map with sharp boundaries and junctions for textureless images, curve objects and free-form shapes.
6739132
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules
MOTIVATION
Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules.


RESULTS
We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.
17718282
A Stochastic Algorithm for 3D Scene Segmentation and Reconstruction
In this paper, we present a stochastic algorithm by effective Markov chain Monte Carlo (MCMC) for segmenting and reconstructing 3D scenes. The objective is to segment a range image and its associated reflectance map into a number of surfaces which fit to various 3D surface models and have homogeneous reflectance (material) properties. In comparison to previous work on range image segmentation, the paper makes the following contributions. Firstly, it is aimed at generic natural scenes, indoor and outdoor, which are often much complexer than most of the existing experiments in the "polyhedra world". Natural scenes require the algorithm to automatically deal with multiple types (families) of surface models which compete to explain the data. Secondly, it integrates the range image with the reflectance map. The latter provides material properties and is especially useful for surface of high specularity, such as glass, metal, ceramics. Thirdly, the algorithm is designed by reversible jump and diffusion Markov chain dynamics and thus achieves globally optimal solutions under the Bayesian statistical framework. Thus it realizes the cue integration and multiple model switching. Fourthly, it adopts two techniques to improve the speed of the Markov chain search: One is a coarse-to-fine strategy and the other are data driven techniques such as edge detection and clustering. The data driven methods provide important information for narrowing the search spaces in a probabilistic fashion. We apply the algorithm to two data sets and the experiments demonstrate robust and satisfactory results on both. Based on the segmentation results, we extend the reconstruction of surfaces behind occlusions to fill in the occluded parts.
14172606
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature
MOTIVATION
The importance of chemical compounds has been emphasized more in molecular biology, and 'chemical genomics' has attracted a great deal of attention in recent years. Thus an important issue in current molecular biology is to identify biological-related chemical compounds (more specifically, drugs) and genes. Co-occurrence of biological entities in the literature is a simple, comprehensive and popular technique to find the association of these entities. Our focus is to mine implicit 'chemical compound and gene' relations from the co-occurrence in the literature.


RESULTS
We propose a probabilistic model, called the mixture aspect model (MAM), and an algorithm for estimating its parameters to efficiently handle different types of co-occurrence datasets at once. We examined the performance of our approach not only by a cross-validation using the data generated from the MEDLINE records but also by a test using an independent human-curated dataset of the relationships between chemical compounds and genes in the ChEBI database. We performed experimentation on three different types of co-occurrence datasets (i.e. compound-gene, gene-gene and compound-compound co-occurrences) in both cases. Experimental results have shown that MAM trained by all datasets outperformed any simple model trained by other combinations of datasets with the difference being statistically significant in all cases. In particular, we found that incorporating compound-compound co-occurrences is the most effective in improving the predictive performance. We finally computed the likelihoods of all unknown compound-gene (more specifically, drug-gene) pairs using our approach and selected the top 20 pairs according to the likelihoods. We validated them from biological, medical and pharmaceutical viewpoints.