Clustering by soft-constraint affinity propagation: Applications to gene-expression data

Motivation: Similarity-measure based clustering is a crucial problem appearing throughout scientific data analysis. Recently, a powerful new algorithm called Affinity Propagation (AP) based on message-passing techniques was proposed by Frey and Dueck \cite{Frey07}. In AP, each cluster is identified by a common exemplar all other data points of the same cluster refer to, and exemplars have to refer to themselves. Albeit its proved power, AP in its present form suffers from a number of drawbacks. The hard constraint of having exactly one exemplar per cluster restricts AP to classes of regularly shaped clusters, and leads to suboptimal performance, {\it e.g.}, in analyzing gene expression data. Results: This limitation can be overcome by relaxing the AP hard constraints. A new parameter controls the importance of the constraints compared to the aim of maximizing the overall similarity, and allows to interpolate between the simple case where each data point selects its closest neighbor as an exemplar and the original AP. The resulting soft-constraint affinity propagation (SCAP) becomes more informative, accurate and leads to more stable clustering. Even though a new {\it a priori} free-parameter is introduced, the overall dependence of the algorithm on external tuning is reduced, as robustness is increased and an optimal strategy for parameter selection emerges more naturally. SCAP is tested on biological benchmark data, including in particular microarray data related to various cancer types. We show that the algorithm efficiently unveils the hierarchical cluster structure present in the data sets. Further on, it allows to extract sparse gene expression signatures for each cluster.Comment: 11 pages, supplementary material: http://isiosf.isi.it/~weigt/scap_supplement.pd

Efficient classification using parallel and scalable compressed model and Its application on intrusion detection

In order to achieve high efficiency of classification in intrusion detection, a compressed model is proposed in this paper which combines horizontal compression with vertical compression. OneR is utilized as horizontal com-pression for attribute reduction, and affinity propagation is employed as vertical compression to select small representative exemplars from large training data. As to be able to computationally compress the larger volume of training data with scalability, MapReduce based parallelization approach is then implemented and evaluated for each step of the model compression process abovementioned, on which common but efficient classification methods can be directly used. Experimental application study on two publicly available datasets of intrusion detection, KDD99 and CMDC2012, demonstrates that the classification using the compressed model proposed can effectively speed up the detection procedure at up to 184 times, most importantly at the cost of a minimal accuracy difference with less than 1% on average

Distributed Clustering in Cognitive Radio Ad Hoc Networks Using Soft-Constraint Affinity Propagation

Absence of network infrastructure and heterogeneous spectrum availability in cognitive radio ad hoc networks (CRAHNs) necessitate the self-organization of cognitive radio users (CRs) for efficient spectrum coordination. The cluster-based structure is known to be effective in both guaranteeing system performance and reducing communication overhead in variable network environment. In this paper, we propose a distributed clustering algorithm based on soft-constraint affinity propagation message passing model (DCSCAP). Without dependence on predefined common control channel (CCC), DCSCAP relies on the distributed message passing among CRs through their available channels, making the algorithm applicable for large scale networks. Different from original soft-constraint affinity propagation algorithm, the maximal iterations of message passing is controlled to a relatively small number to accommodate to the dynamic environment of CRAHNs. Based on the accumulated evidence for clustering from the message passing process, clusters are formed with the objective of grouping the CRs with similar spectrum availability into smaller number of clusters while guaranteeing at least one CCC in each cluster. Extensive simulation results demonstrate the preference of DCSCAP compared with existing algorithms in both efficiency and robustness of the clusters

Distributed Low-rank Subspace Segmentation

Vision problems ranging from image clustering to motion segmentation to semi-supervised learning can naturally be framed as subspace segmentation problems, in which one aims to recover multiple low-dimensional subspaces from noisy and corrupted input data. Low-Rank Representation (LRR), a convex formulation of the subspace segmentation problem, is provably and empirically accurate on small problems but does not scale to the massive sizes of modern vision datasets. Moreover, past work aimed at scaling up low-rank matrix factorization is not applicable to LRR given its non-decomposable constraints. In this work, we propose a novel divide-and-conquer algorithm for large-scale subspace segmentation that can cope with LRR's non-decomposable constraints and maintains LRR's strong recovery guarantees. This has immediate implications for the scalability of subspace segmentation, which we demonstrate on a benchmark face recognition dataset and in simulations. We then introduce novel applications of LRR-based subspace segmentation to large-scale semi-supervised learning for multimedia event detection, concept detection, and image tagging. In each case, we obtain state-of-the-art results and order-of-magnitude speed ups

Cortical spatio-temporal dimensionality reduction for visual grouping

The visual systems of many mammals, including humans, is able to integrate the geometric information of visual stimuli and to perform cognitive tasks already at the first stages of the cortical processing. This is thought to be the result of a combination of mechanisms, which include feature extraction at single cell level and geometric processing by means of cells connectivity. We present a geometric model of such connectivities in the space of detected features associated to spatio-temporal visual stimuli, and show how they can be used to obtain low-level object segmentation. The main idea is that of defining a spectral clustering procedure with anisotropic affinities over datasets consisting of embeddings of the visual stimuli into higher dimensional spaces. Neural plausibility of the proposed arguments will be discussed

Multi-view constrained clustering with an incomplete mapping between views

Multi-view learning algorithms typically assume a complete bipartite mapping between the different views in order to exchange information during the learning process. However, many applications provide only a partial mapping between the views, creating a challenge for current methods. To address this problem, we propose a multi-view algorithm based on constrained clustering that can operate with an incomplete mapping. Given a set of pairwise constraints in each view, our approach propagates these constraints using a local similarity measure to those instances that can be mapped to the other views, allowing the propagated constraints to be transferred across views via the partial mapping. It uses co-EM to iteratively estimate the propagation within each view based on the current clustering model, transfer the constraints across views, and then update the clustering model. By alternating the learning process between views, this approach produces a unified clustering model that is consistent with all views. We show that this approach significantly improves clustering performance over several other methods for transferring constraints and allows multi-view clustering to be reliably applied when given a limited mapping between the views. Our evaluation reveals that the propagated constraints have high precision with respect to the true clusters in the data, explaining their benefit to clustering performance in both single- and multi-view learning scenarios