5241796
Finding Biclusters by Random Projections
Given a matrix X composed of symbols, a bicluster is a submatrix of X obtained by removing some of the rows and some of the columns of X in such a way that each row of what is left reads the same string. In this paper, we are concerned with the problem of finding the bicluster with the largest area in a large matrix X. The problem is first proved to be NP-complete. We present a fast and efficient randomized algorithm that discovers the largest bicluster by random projections. A detailed probabilistic analysis of the algorithm and an asymptotic study of the statistical significance of the solutions are given. We report results of extensive simulations on synthetic data.
1859019
A parallel algorithm for clustering protein-protein interaction networks
The increasing availability of interaction graphs requires new resource-efficient tools capable of extracting valuable biological knowledge from these networks. In this paper we report on a novel parallel implementation of Girvan and Newman's clustering algorithm that is capable of running on clusters of computers. Our parallel implementation achieves almost linear speed-up up to 32 processors and allows us to run this computationally intensive algorithm on large protein-protein interaction networks. Preliminary experiments show that the algorithm has very high accuracy in identifying functional related protein modules.
32009068
Finding biclusters by random projections
Given a matrix X composed of symbols, a bicluster is a submatrix of X obtained by removing some of the rows and some of the columns of X in such a way that each row of what is left reads the same string. In this paper, we are concerned with the problem of finding the bicluster with the largest area in a large matrix X. The problem is first proved to be NP-complete. We present a fast and efficient randomized algorithm that discovers the largest bicluster by random projections. A detailed probabilistic analysis of the algorithm and an asymptotic study of the statistical significance of the solutions are given. We report results of extensive simulations on synthetic data.
18229979
A Compression-Boosting Transform for Two-Dimensional Data
We introduce a novel invertible transform for two- dimensional data which has the objective of reordering the matrix so it will improve its (lossless) compression at later stages. The transform requires to solve a computationally hard problem for which a randomized algorithm is used. The inverse transform is fast and can be implemented in linear time in the size of the matrix. Preliminary experimental results show that the reordering improves the compressibility of digital images.
1414068
Theory and Algorithms for Plan Merging
Abstract Merging operators in a plan can yield significant savings in the cost to execute a plan. This paper provides a formal theory for plan merging and presents both optimal and efficient heuristic algorithms for finding minimum cost merged plans. The optimal plan merging algorithm applies a dynamic programming method to handle multiple linear plans and is extended to partially ordered plans in a novel way. Furthermore, with worst-case and average-case complexity analysis and empirical tests, we demonstrate that efficient and well-behaved approximation algorithms are applicable for optimizing plans with large sizes.
7531376
Deriving a Stationary Dynamic Bayesian Network from a Logic Program with Recursive Loops
Recursive loops in a logic program present a challenging problem to the PLP framework. On the one hand, they loop forever so that the PLP backward-chaining inferences would never stop. On the other hand, they generate cyclic influences, which are disallowed in Bayesian networks. Therefore, in existing PLP approaches logic programs with recursive loops are considered to be problematic and thus are excluded. In this paper, we propose an approach that makes use of recursive loops to build a stationary dynamic Bayesian network. Our work stems from an observation that recursive loops in a logic program imply a time sequence and thus can be used to model a stationary dynamic Bayesian network without using explicit time parameters. We introduce a Bayesian knowledge base with logic clauses of the form A ← A1,...,Al, true, Context, Types, which naturally represents the knowledge that the Ais have direct influences on A in the context Context under the type constraints Types. We then use the well-founded model of a logic program to define the direct influence relation and apply SLG-resolution to compute the space of random variables together with their parental connections. We introduce a novel notion of influence clauses, based on which a declarative semantics for a Bayesian knowledge base is established and algorithms for building a two-slice dynamic Bayesian network from a logic program are developed.
17999609
A Data Cube Model for Prediction-Based Web Prefetching
Reducing the web latency is one of the primary concerns of Internet research. Web caching and web prefetching are two effective techniques to latency reduction. A primary method for intelligent prefetching is to rank potential web documents based on prediction models that are trained on the past web server and proxy server log data, and to prefetch the highly ranked objects. For this method to work well, the prediction model must be updated constantly, and different queries must be answered efficiently. In this paper we present a data-cube model to represent Web access sessions for data mining for supporting the prediction model construction. The cube model organizes session data into three dimensions. With the data cube in place, we apply efficient data mining algorithms for clustering and correlation analysis. As a result of the analysis, the web page clusters can then be used to guide the prefetching system. In this paper, we propose an integrated web-caching and web-prefetching model, where the issues of prefetching aggressiveness, replacement policy and increased network traffic are addressed together in an integrated framework. The core of our integrated solution is a prediction model based on statistical correlation between web objects. This model can be frequently updated by querying the data cube of web server logs. This integrated data cube and prediction based prefetching framework represents a first such effort in our knowledge.
2850409
A Framework for Automatic Problem Decomposition in Planning
An intelligent problem solver must be able to decompose a complex problem into simpler parts. A decomposition algorithm would not only be beneficial for traditional subgoal-oriented planning systems but also support distributed, multi-agent planners. In this paper, we present an algorithm for automatic problem decomposition. Given a domain description with a number of objects to be manipulated, our method constructs subspaces complete with subproblem descriptions and operators, and solves the subproblems concurrently. The solutions in individual subspaces are combined using a constraint satisfaction algorithm. The effectiveness of the approach is guaranteed by our careful analysis of the interactions among different subspaces. The results presented in this paper support parallel, distributed and multi-agent planning systems.
6653256
Domain-constrained semi-supervised mining of tracking models in sensor networks
Accurate localization of mobile objects is a major research problem in sensor networks and an important data mining application. Specifically, the localization problem is to determine the location of a client device accurately given the radio signal strength values received at the client device from multiple beacon sensors or access points. Conventional data mining and machine learning methods can be applied to solve this problem. However, all of them require large amounts of labeled training data, which can be quite expensive. In this paper, we propose a probabilistic semi supervised learning approach to reduce the calibration effort and increase the tracking accuracy. Our method is based on semi-supervised conditional random fields which can enhance the learned model from a small set of training data with abundant unlabeled data effectively. To make our method more efficient, we exploit a Generalized EM algorithm coupled with domain constraints. We validate our method through extensive experiments in a real sensor network using Crossbow MICA2 sensors. The results demonstrate the advantages of methods compared to other state-of-the-art object-tracking algorithms.