31763391
Guest Editors' Introduction to the Special Issue: Machine Learning for Bioinformatics-Part 1
IN recent years, rapid developments in genomics and proteomics have generated a large amount of data. Often, drawing conclusions from these data requires sophisticated computational analyses. Bioinformatics, or computational biology, is the interdisciplinary science of interpreting biological data using information technology and computer science. The importance of this new field of inquiry will grow as we continue to generate and integrate large quantities of genomic, proteomic, and other data. A particularly active area of research in bioinformatics is the application and development of machine learning techniques to biological problems.Analyzing large biological data sets requires making sense of the data by inferring structure or generalizations from the data. Examples of this type of analysis include protein structure prediction, gene classification, cancer classification based onmicroarray data, clustering of gene expression data, statistical modeling of protein-protein interaction, etc. Each of these tasks can be framed as a problem in machine learning. We therefore see a great potential to increase the interaction between machine learning and bioinformatics. This special issue is aimed at facilitating that interaction. We believe that machine learning can provide powerful tools for analyzing, predicting, and understanding data from emerging genomic and proteomic technologies. The papers submitted to this special issue provide strong evidence that this is the case. In total, more than 50 paperswere submitted to the special issue. After extensive reviews and revisions, 13 papers were accepted into the special issue,whichwill bepublished in two parts. The quality and significance of the accepted papers are very high and the papers cover a wide variety of topics. Below,weprovide a summary of the papers published in this journal issue.
9645876
Handling feature interactions in process-planning
Abstract The development of a successful approach to the integration of computer-aided design and computer-aided process-planning will require solutions to several fundamental problems in planning and geometric reasoning. In this article, we consider two such problems, both of which arise from interactions among machinable features. The first problem is that interactions can lead to several alternative interpretations of what the machinable features are. We address this problem by developing an algebra of features. The second problem is that interactions among features can cause problems in optimizing the process plans. For this problem, we have developed a branch-and-bound optimization algorithm with good heuristics to guide the search. This article presents the theory and mathematical framework for both problems and also the details of the implementation and experimental results.
5296157
A Novel Scalable Algorithm for Supervised Subspace Learning
Subspace learning approaches aim to discover important statistical distribution on lower dimensions for high dimensional data. Methods such as principal component analysis (PCA) do not make use of the class information, and linear discriminant analysis (LDA) could not be performed efficiently in a scalable way. In this paper, we propose a novel highly scalable supervised subspace learning algorithm called as supervised Kampong measure (SKM). It assigns data points as close as possible to their corresponding class mean, simultaneously assigns data points to be as far as possible from the other class means in the transformed lower dimensional subspace. Theoretical derivation shows that our algorithm is not limited by the number of classes or the singularity problem faced by LDA. Furthermore, our algorithm can be executed in an incremental manner in which learning is done in an online fashion as data streams are received. Experimental results on several datasets, including a very large text data set RCV1, show the outstanding performance of our proposed algorithm on classification problems as compared to PCA, LDA and a popular feature selection approach, information gain (IG).
11767978
Real-Time Scheduling for Multi-agent Call Center Automation
In a call center, service agents with different capabilities are available for solving incoming customer problems at any time. To supply quick response and better problem solution to customers, it is necessary to schedule customer problems to appropriate service agents efficiently. We developed SANet, a service agent network for call center, which integrates multiple service agents including both software agents and human agents, and employs a broker to schedule customer problems to service agents for better solutions according to their changing capabilities and availability. This paper describes the real-time scheduling method in SANet as well as its architecture. There are two phases in our scheduling method. One is problem-type learning. The broker is trained to learn the problem types and hence can decide the type of incoming problems automatically. The other is the scheduling algorithm based on problem types, capabilities and availability of service agents. We highlight an application in which we apply SANet to a call center problem for a cable-TV company. Finally, we support our claims via experimental results and discuss related works.
13595177
Multiple-Goal Recognition from Low-Level Signals
Researchers and practitioners from both the artificial intelligence and pervasive computing communities have been paying increasing attention to the task of inferring users' high-level goals from low-level sensor readings. A common assumption made by most approaches is that a user either has a single goal in mind, or achieves several goals sequentially. However, in real-world environments, a user often has multiple goals that are concurrently carried out, and a single action can serve as a common step towards multiple goals. In this paper, we formulate the multiple-goal recognition problem and exemplify it in an indoor environment where an RF-based wireless network is available. We propose a goal-recognition algorithm based on a dynamic model set and show how goal models evolve over time based on pre-defined states. Experiments with real data demonstrate that our method can accurately and efficiently recognize multiple interleaving goals in a user's trace.
15099164
A scalable supervised algorithm for dimensionality reduction on streaming data
Algorithms on streaming data have attracted increasing attention in the past decade. Among them, dimensionality reduction algorithms are greatly interesting due to the desirability of real tasks. Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA) are two of the most widely used dimensionality reduction approaches. However, PCA is not optimal for general classification problems because it is unsupervised and ignores valuable label information for classification. On the other hand, the performance of LDA is degraded when encountering limited available low-dimensional spaces and singularity problem. Recently, Maximum Margin Criterion (MMC) was proposed to overcome the shortcomings of PCA and LDA. Nevertheless, the original MMC algorithm could not satisfy the streaming data model to handle large-scale high-dimensional data set. Thus an effective, efficient and scalable approach is needed. In this paper, we propose a supervised incremental dimensionality reduction algorithm and its extension to infer adaptive low-dimensional spaces by optimizing the maximum margin criterion. Experimental results on a synthetic dataset and real datasets demonstrate the superior performance of our proposed algorithm on streaming data.
27730185
Parallel All-Row Preconditioned Interval Linear Solver for Nonlinear Equations on Multiprocessors
Interval Newton methods in conjunction with generalized bisection form the basis of algorithms that find all real roots within a specified X ⊂ Rn of a system of nonlinear equations F(X) = 0 with mathematical certainty, even in finite-precision arithmetic. One of the major computational cost in such methods is solving a correspondent linear interval system. This paper proposes parallel implementations of the all-row preconditioned interval linear solver on two multiprocessor architectures: shared bus multiprocessor and hypercube connected multiprocessor. Efficient parallel algorithms that are specifically tailored for these architectures are presented. The algorithms effectively use the hardware features to minimize communication overheads. Performance evaluation is carried out by means of actual measurements of the algorithms running on real parallel computers. Our numerical results show that data partitioning, data allocation and processor scheduling play important roles in the performance of the parallel computation. In both systems, significant speedup can be obtained by properly overlapping computation and communication.
11786279
Effects of Arbitration Protocols on the Performance of Multiple-Bus Multiprocessors
2566279
PRINS: Optimizing Performance of Reliable Internet Storages
Distributed storage systems employ replicas or erasure code to ensure high reliability and availability of data. Such replicas create great amount of network traffic that negatively impacts storage performance, particularly for distributed storage systems that are geographically dispersed over a wide area network (WAN). This paper presents a performance study of our new data replication methodology that minimizes network traffic for data replications. The idea is to replicate the parity of a data block upon each write operation instead of the data block itself. The data block will be recomputed back at the replica storage site upon receiving the parity. We name the new methodology PRINS (Parity Replication in IP-Network Storages). PRINS trades off highspeed computation for communication that is costly and more likely to be the performance bottleneck for distributed storages. By leveraging the parity computation that exists in common storage systems (RAID), our PRINS does not introduce additional overhead but dramatically reduces network traffic. We have implemented PRINS using iSCSI protocol over a TCP/IP network interconnecting a cluster of PCs as storage nodes. We carried out performance measurements on Oracle database, Postgres database, MySQL database, and Ext2 file system using TPC-C, TPC-W, and Micro benchmarks. Performance measurements show up to 2 orders of magnitudes bandwidth savings of PRINS compared to traditional replicas. A queueing network model is developed to further study network performance for large networks. It is shown that PRINS reduces response time of the distributed storage systems dramatically.
6583750
Building Trust in Online Rating Systems Through Signal Modeling
Online feedback-based rating systems are gaining popularity. Dealing with unfair ratings in such systems has been recognized as an important but difficult problem. This problem is challenging especially when the number of regular ratings is relatively small and the unfair ratings contribute to a significant portion of the overall ratings. In this paper, we propose a novel algorithm to detect the unfair ratings that cannot be effectively prevented by existing state-of-the-art techniques. Our algorithm is particularly effective to detect malicious raters that collaboratively manipulate ratings of one or several products. The main idea of our algorithm is to use an autoregressive signal modeling technique combined with trust-enhanced rating aggregation. We are able to detect and filter out unfair ratings very accurately. Extensive experiments through simulations and real-world data have been performed to validate the proposed algorithm. The experimental results show significant improvements on detecting collaborative unfair raters over existing techniques.
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.