9255277
A New Pairwise Ensemble Approach for Text Classification
Text classification, whether by topic or genre, is an important task that contributes to text extraction, retrieval, summarization and question answering. In this paper we present a new pairwise ensemble approach, which uses pairwise Support Vector Machine (SVM) classifiers as base classifiers and "input-dependent latent variable" method for model combination. This new approach better captures the characteristics of genre classification, including its heterogeneous nature. Our experiments on two multi-genre collections and one topic-based classification datasets show that the pairwise ensemble method outperforms both boosting, which has been demonstrated as a powerful ensemble approach, and Error-Correcting Output Codes (ECOC), which applies pairwise-like classifiers for multiclass classification problems.
389729
Predicting protein folds with structural repeats using a chain graph model
Protein fold recognition is a key step towards inferring the tertiary structures from amino-acid sequences. Complex folds such as those consisting of interacting structural repeats are prevalent in proteins involved in a wide spectrum of biological functions. However, extant approaches often perform inadequately due to their inability to capture long-range interactions between structural units and to handle low sequence similarities across proteins (under 25% identity). In this paper, we propose a chain graph model built on a causally connected series of segmentation conditional random fields (SCRFs) to address these issues. Specifically, the SCRF model captures long-range interactions within recurring structural units and the Bayesian network backbone decomposes cross-repeat interactions into locally computable modules consisting of repeat-specific SCRFs and a model for sequence motifs. We applied this model to predict β-helices and leucine-rich repeats, and found it significantly outperforms extant methods in predictive accuracy and/or computational efficiency.
12839905
Context sensitive vocabulary and its application in protein secondary structure prediction
Protein secondary structure prediction is an important step towards understanding the relation between protein sequence and structure. However, most current prediction methods use features difficult for biologists to interpret. In this paper, we present a new method that applies information retrieval techniques to solve the problem:we extract a context sensitive biological vocabulary for protein sequences and apply text classification methods to predict protein secondary structure. Experimental results show that our method performs comparably to the state-of-art methods. Furthermore, the context sensitive vocabularies can serve as a useful tool to discover meaningful regular expression patterns for protein structures.
619505
Semi-Supervised Learning of Attribute-Value Pairs from Product Descriptions
We describe an approach to extract attribute-value pairs from product descriptions. This allows us to represent products as sets of such attribute-value pairs to augment product databases. Such a representation is useful for a variety of tasks where treating a product as a set of attribute-value pairs is more useful than as an atomic entity. Examples of such applications include product recommendations, product comparison, and demand forecasting. We formulate the extraction as a classification problem and use a semi-supervised algorithm (co-EM) along with (Naive Bayes). The extraction system requires very little initial user supervision: using unlabeled data, we automatically extract an initial seed list that serves as training data for the supervised and semi-supervised classification algorithms. Finally, the extracted attributes and values are linked to form pairs using dependency information and co-location scores. We present promising results on product descriptions in two categories of sporting goods.
5651676
Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition
Protein fold recognition is an important step towards understanding protein three-dimensional structures and their functions. A conditional graphical model, i.e. segmentation conditional random fields (SCRFs), is proposed to solve the problem. In contrast to traditional graphical models such as hidden markov model (HMM), SCRFs follow a discriminative approach. It has the flexibility to include overlapping or long-range interaction features over the whole sequence, as well as global optimally solutions for the parameters. On the other hand, the segmentation setting in SCRFs makes its graphical structures intuitively similar to the protein 3-D structures and more importantly, provides a framework to model the long-range interactions directly. 
 
Our model is applied to predict the parallel β-helix fold, an important fold in bacterial infection of plants and binding of antigens. The cross-family validation shows that SCRFs not only can score all known β-helices higher than non β-helices in Protein Data Bank, but also demonstrate more success in locating each rung in the known β-helix proteins than BetaWrap, a state-of-the-art algorithm for predicting β-helix fold, and HMMER, a general motif detection algorithm based on HMM. Applying our prediction model to Uniprot database, we hypothesize previously unknown β-helices.
3096549
Kernel conditional random fields: representation and clique selection
Kernel conditional random fields (KCRFs) are introduced as a framework for discriminative modeling of graph-structured data. A representer theorem for conditional graphical models is given which shows how kernel conditional random fields arise from risk minimization procedures defined using Mercer kernels on labeled graphs. A procedure for greedily selecting cliques in the dual representation is then proposed, which allows sparse representations. By incorporating kernels and implicit feature spaces into conditional graphical models, the framework enables semi-supervised learning algorithms for structured data through the use of graph kernels. The framework and clique selection methods are demonstrated in synthetic data experiments, and are also applied to the problem of protein secondary structure prediction.
8217950
Evolutionary ensembles with negative correlation learning
Based on negative correlation learning and evolutionary learning, this paper presents evolutionary ensembles with negative correlation learning (EENCL) to address the issues of automatic determination of the number of individual neural networks (NNs) in an ensemble and the exploitation of the interaction between individual NN design and combination. The idea of EENCL is to encourage different individual NNs in the ensemble to learn different parts or aspects of the training data so that the ensemble can learn better the entire training data. The cooperation and specialization among different individual NNs are considered during the individual NN design. This provides an opportunity for different NNs to interact with each other and to specialize. Experiments on two real-world problems demonstrate that EENCL can produce NN ensembles with good generalization ability.
5645902
On designing incentive-compatible routing and forwarding protocols in wireless ad-hoc networks: an integrated approach using game theoretical and cryptographic techniques
In many applications, wireless ad-hoc networks are formed by devices belonging to independent users. Therefore, a challenging problem is how to provide incentives to stimulate cooperation. In this paper, we study ad-hoc games---the routing and packet forwarding games in wireless ad-hoc networks. Unlike previous work which focuses either on routing or on forwarding, this paper investigates both routing and forwarding. We first uncover an impossibility result---there does not exist a protocol such that following the protocol to always forward others' traffic is a dominant action. Then we define a novel solution concept called cooperation-optimal protocols. We present Corsac, a cooperation-optimal protocol consisting of a routing protocol and a forwarding protocol. The routing protocol of Corsac integrates VCG with a novel cryptographic technique to address the challenge in wireless ad-hoc networks that a link's cost (ie, its type) is determined by two nodes together. Corsac also applies efficient cryptographic techniques to design a forwarding protocol to enforce the routing decision, such that fulfilling the routing decision is the optimal action of each node in the sense that it brings the maximum utility to the node. Additionally, we extend our framework to a practical radio propagation model where a transmission is successful with a probability. We evaluate our protocols using simulations. Our evaluations demonstrate that our protocols provide incentives for nodes to forward packets.
903407
On integrating fluid models with packet simulation
Fluid models have been shown to he efficient and accurate in modelling large IP networks. However, unlike packet models, it is difficult to extract packet-level information from them. In this paper, we present a hybrid simulation method that maintains the performance advantage of fluid models while providing detailed packet level information for selected packet traffic flows. We propose two models to account for the interaction between background TCP traffic in a fluid network and foreground packet traffic of interest. The first assumes that the packet traffic poses a negligible load on the fluid network whereas the second accounts for the added load by transforming the packet traffic into fluid flows and solving the resulting enhanced fluid model. The first of these yields an efficient one pass solution algorithm whereas the second requires an additional pass to account for the packet traffic load. We establish the correctness of both approaches and present their implementation within ns-2. Comparisons between the hybrid models and a classical packet simulation show the two pass approach to be quite accurate and computationally efficient.
20456243
Energy-Efficient Cooperative Image Processing in Video Sensor Networks
Different from conventional sensor networks, video sensor networks are distinctly characterized by their immense information and directional sensing models. In this paper, we propose an innovative, systematic method for image processing in video sensor networks in order to reduce the workload for individual sensors. Given the severe resource constraints on individual sensor nodes, our approach is to employ the redundancy among sensor nodes by partitioning the sensing task among highly correlated sensors. For an object of interest, each sensor only needs to capture and deliver a fraction of the scene of interests and these partial images can be fused at the sink to reconstruct a composite image. In particular, we detail how the sensing task can be partitioned among the sensors and propose an image fusion algorithms based on epipolar line constraint to fuse the received partial images at the sink. The experimental results show that our approach can achieve satisfactory results and we give detailed discussions on the effects of different system parameters.
14931870
SVM decision boundary based discriminative subspace induction
We study the problem of linear dimension reduction for classification, with a focus on sufficient dimension reduction, i.e., finding subspaces without loss of discrimination power. First, we formulate the concept of sufficient subspace for classification in parallel terms as for regression. Then we present a new method to estimate the smallest sufficient subspace based on an improvement of decision boundary analysis (DBA). The main idea is to combine DBA with support vector machines (SVM) to overcome the inherent difficulty of DBA in small sample size situations while keeping DBA's estimation simplicity. The compact representation of SVM boundary results in a significant gain in both speed and accuracy over previous DBA implementations. Alternatively, this technique can be viewed as a way to reduce the run-time complexity of SVM itself. Comparative experiments on one simulated and four real-world benchmark datasets highlight the superior performance of the proposed approach.