Bipartite graph partitioning and data clustering

Many data types arising from data mining applications can be modeled as bipartite graphs, examples include terms and documents in a text corpus, customers and purchasing items in market basket analysis and reviewers and movies in a movie recommender system. In this paper, we propose a new data clustering method based on partitioning the underlying bipartite graph. The partition is constructed by minimizing a normalized sum of edge weights between unmatched pairs of vertices of the bipartite graph. We show that an approximate solution to the minimization problem can be obtained by computing a partial singular value decomposition (SVD) of the associated edge weight matrix of the bipartite graph. We point out the connection of our clustering algorithm to correspondence analysis used in multivariate analysis. We also briefly discuss the issue of assigning data objects to multiple clusters. In the experimental results, we apply our clustering algorithm to the problem of document clustering to illustrate its effectiveness and efficiency.Comment: Proceedings of ACM CIKM 2001, the Tenth International Conference on Information and Knowledge Management, 200

Order independent structural alignment of circularly permuted proteins

Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because current detection methods can miss many occurances, mistaking random repeats as circular permutation. Here we develop a method for detecting circularly permuted proteins from structural comparison. Sequence order independent alignment of protein structures can be regarded as a special case of the maximum-weight independent set problem, which is known to be computationally hard. We develop an efficient approximation algorithm by repeatedly solving relaxations of an appropriate intermediate integer programming formulation, we show that the approximation ratio is much better then the theoretical worst case ratio of $r = 1/4$. Circularly permuted proteins reported in literature can be identified rapidly with our method, while they escape the detection by publicly available servers for structural alignment.Comment: 5 pages, 3 figures, Accepted by IEEE-EMBS 2004 Conference Proceeding

Adaptive Nonparametric Image Parsing

In this paper, we present an adaptive nonparametric solution to the image parsing task, namely annotating each image pixel with its corresponding category label. For a given test image, first, a locality-aware retrieval set is extracted from the training data based on super-pixel matching similarities, which are augmented with feature extraction for better differentiation of local super-pixels. Then, the category of each super-pixel is initialized by the majority vote of the $k$-nearest-neighbor super-pixels in the retrieval set. Instead of fixing $k$ as in traditional non-parametric approaches, here we propose a novel adaptive nonparametric approach which determines the sample-specific k for each test image. In particular, $k$ is adaptively set to be the number of the fewest nearest super-pixels which the images in the retrieval set can use to get the best category prediction. Finally, the initial super-pixel labels are further refined by contextual smoothing. Extensive experiments on challenging datasets demonstrate the superiority of the new solution over other state-of-the-art nonparametric solutions.Comment: 11 page

Memetic Multilevel Hypergraph Partitioning

Hypergraph partitioning has a wide range of important applications such as VLSI design or scientific computing. With focus on solution quality, we develop the first multilevel memetic algorithm to tackle the problem. Key components of our contribution are new effective multilevel recombination and mutation operations that provide a large amount of diversity. We perform a wide range of experiments on a benchmark set containing instances from application areas such VLSI, SAT solving, social networks, and scientific computing. Compared to the state-of-the-art hypergraph partitioning tools hMetis, PaToH, and KaHyPar, our new algorithm computes the best result on almost all instances

An Agent-Based Algorithm exploiting Multiple Local Dissimilarities for Clusters Mining and Knowledge Discovery

We propose a multi-agent algorithm able to automatically discover relevant regularities in a given dataset, determining at the same time the set of configurations of the adopted parametric dissimilarity measure yielding compact and separated clusters. Each agent operates independently by performing a Markovian random walk on a suitable weighted graph representation of the input dataset. Such a weighted graph representation is induced by the specific parameter configuration of the dissimilarity measure adopted by the agent, which searches and takes decisions autonomously for one cluster at a time. Results show that the algorithm is able to discover parameter configurations that yield a consistent and interpretable collection of clusters. Moreover, we demonstrate that our algorithm shows comparable performances with other similar state-of-the-art algorithms when facing specific clustering problems

Multiclass Data Segmentation using Diffuse Interface Methods on Graphs

We present two graph-based algorithms for multiclass segmentation of high-dimensional data. The algorithms use a diffuse interface model based on the Ginzburg-Landau functional, related to total variation compressed sensing and image processing. A multiclass extension is introduced using the Gibbs simplex, with the functional's double-well potential modified to handle the multiclass case. The first algorithm minimizes the functional using a convex splitting numerical scheme. The second algorithm is a uses a graph adaptation of the classical numerical Merriman-Bence-Osher (MBO) scheme, which alternates between diffusion and thresholding. We demonstrate the performance of both algorithms experimentally on synthetic data, grayscale and color images, and several benchmark data sets such as MNIST, COIL and WebKB. We also make use of fast numerical solvers for finding the eigenvectors and eigenvalues of the graph Laplacian, and take advantage of the sparsity of the matrix. Experiments indicate that the results are competitive with or better than the current state-of-the-art multiclass segmentation algorithms.Comment: 14 page