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.
10720584
Graph-Based Semi-Supervised Learning as a Generative Model
This paper proposes and develops a new graph-based semi-supervised learning method. Different from previous graph-based methods that are based on discriminative models, our method is essentially a generative model in that the class conditional probabilities are estimated by graph propagation and the class priors are estimated by linear regression. Experimental results on various datasets show that the proposed method is superior to existing graph-based semi-supervised learning methods, especially when the labeled subset alone proves insufficient to estimate meaningful class priors.
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.
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.
14379760
Protein Quaternary Fold Recognition Using Conditional Graphical Models
Protein fold recognition is a crucial step in inferring biological structure and function. This paper focuses on machine learning methods for predicting quaternary structural folds, which consist of multiple protein chains that form chemical bonds among side chains to reach a structurally stable domain. The complexity associated with modeling the quaternary fold poses major theoretical and computational challenges to current machine learning methods. We propose methods to address these challenges and show how (1) domain knowledge is encoded and utilized to characterize structural properties using segmentation conditional graphical models; and (2) model complexity is handled through efficient inference algorithms. Our model follows a discriminative approach so that any informative features, such as those representative of overlapping or long-range interactions, can be used conveniently. The model is applied to predict two important quaternary folds, the triple β-spirals and double-barrel trimers. Cross-family validation shows that our method outperforms other state-of-the art algorithms.
3183902
An Efficient Implementation of a Drug Candidate Database
The recent advances in laboratory technologies have resulted in a wealth of chemical and biological data. The rapid proliferation of a vast amount of data has led to a set of cheminformatics and bioinformatics applications that manipulate dynamic, heterogeneous, and massive data. An example of such application in the pharmaceutical industry is the computational process involved in the early discovery of lead drug candidates for a given target disease. In this paper, an efficient implementation of a drug candidate database is presented and evaluated. This study shows that high performance data access can be achieved through proper choices of data representation, database schema design, and parallel processing techniques.
9804135
EPNet for Chaotic Time-Series Prediction
EPNet is an evolutionary system for automatic design of artificial neural networks (ANNs) [1, 2, 3]. Unlike most previous methods on evolving ANNs, EPNet puts its emphasis on evolving ANN'S behaviours rather than circuitry. The parsimony of evolved ANNs is encouraged by the sequential application of architectural mutations. In this paper, EP Net is applied to a couple of chaotic time-series prediction problems (i.e., the Mackey-Glass differential equation and the logistic map). The experimental results show that EPNet can produce very compact ANNs with good prediction ability in comparison with other algorithms.
11623191
Mapping component specifications to Enterprise JavaBeans implementations
Component-based software development has become an important approach to building complex software systems. Much research focuses on component specification to achieve the advantages of the component-based approach in theory. Most of this research pays little attention to the mappings from component specifications to component implementations. However, the mappings are important because they determine whether the implementations perform satisfactorily to meet the specifications. After presenting a general approach to component specification and the technology of Enterprise JavaBeans (EJB) component model, this paper presents three approaches to mapping from component specification to EJB implementation. This paper uses a course registration system as an example to demonstrate the ideas. The approaches presented will be helpful to those who are working on the realizations of component systems.
43124802
On the Isomorphisms of Cayley Graphs of Abelian Groups
Let G be a finite group, S a subset of G\{1}, and let Cay (G, S) denote the Cayley digraph of G with respect to S. If, for any subset T of G\{1}, Cay(G, S) ≅ Cay(G, T) implies that Sα = T for some α ∈ Aut(G), then S is called a CI-subset. The group G is called a CIM-group if for any minimal generating subset S of G, S ∪ S-1 is a CI-subset. In this paper, CIM-abelian groups are characterized.
258700
Cervical Cancer Detection Using SVM Based Feature Screening
We present a novel feature screening algorithm by deriving relevance measures from the decision boundary of Support Vector Ma- chines. It alleviates the "independence" assumption of traditional screen- ing methods, e.g. those based on Information Gain and Augmented Vari- ance Ratio, without sacrificing computational efficiency. We applied the proposed method to a bottom-up approach for automatic cervical cancer detection in multispectral microscopic thin PAP smear images. An initial set of around 4,000 multispectral texture features is effectively reduced to a computationally manageable size. The experimental results show significant improvements in pixel-level classification accuracy compared to traditional screening methods.