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.
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.
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.
14257785
Comparison of probabilistic combination methods for protein secondary structure prediction
MOTIVATION
Protein secondary structure prediction is an important step towards understanding how proteins fold in three dimensions. Recent analysis by information theory indicates that the correlation between neighboring secondary structures are much stronger than that of neighboring amino acids. In this article, we focus on the combination problem for sequences, i.e. combining the scores or assignments from single or multiple prediction systems under the constraint of a whole sequence, as a target for improvement in protein secondary structure prediction.


RESULTS
We apply several graphical chain models to solve the combination problem and show that they are consistently more effective than the traditional window-based methods. In particular, conditional random fields (CRFs) moderately improve the predictions for helices and, more importantly, for beta sheets, which are the major bottleneck for protein secondary structure prediction.
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.
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.
6732585
Systematic Derivation of Incremental Programs
A systematic approach is given for deriving incremental programs from non-incremental programs written in a standard functional programming language. We exploit a number of program analysis and transformation techniques and domain-specific knowledge, centered around effective utilization of caching, in order to provide a degree of incrementality not otherwise achievable by a generic incremental evaluator.
30454395
Flag Guided Integration of Multiple Registered Range Images
Integration of multiple registered range images finds applications in numerous areas. While most existing integration algorithms detect corresponding points between neighbouring views based on interpoint distances, we define in this paper corresponding area for each point and then carry out geometrical, rigidity, and orientation tests for the same purpose, not only reflecting the scanning nature of sampling resolution, but also the geometry of object surface. To more accurately fuse corresponding points, while most existing algorithms consider the confidence of points, we consider an accumulative fusion scheme of confidences, reflecting the number of times of observation. The fused points are finally triangulated using the improved Delaunay triangulation method, guaranteeing a watertight surface. A comparative study based on real images shows that the proposed algorithm is accurate and efficient and is able to compensate both the accumulative registration errors and imaging noise
6898492
Using Conditional Random Fields for Sentence Boundary Detection in Speech
Sentence boundary detection in speech is important for enriching speech recognition output, making it easier for humans to read and downstream modules to process. In previous work, we have developed hidden Markov model (HMM) and maximum entropy (Maxent) classifiers that integrate textual and prosodic knowledge sources for detecting sentence boundaries. In this paper, we evaluate the use of a conditional random field (CRF) for this task and relate results with this model to our prior work. We evaluate across two corpora (conversational telephone speech and broadcast news speech) on both human transcriptions and speech recognition output. In general, our CRF model yields a lower error rate than the HMM and Maxent models on the NIST sentence boundary detection task in speech, although it is interesting to note that the best results are achieved by three-way voting among the classifiers. This probably occurs because each model has different strengths and weaknesses for modeling the knowledge sources.
11844078
Customized Benchmark Generation Using MDA
This paper describes an approach for generating customized benchmark applications from a software architecture description using a Model Driven Architecture (MDA) approach. The benchmark generation and performance data capture tool implementation is based on widely used open source MDA frameworks. The business logic of the benchmark application is modeled in UML and generated by taking advantage of the existing generation "cartridges" so that the current component technology can be exploited in the benchmark. This greatly reduces the effort and expertise needed for benchmarking with complex component technology. We have also extended the MDA framework to model and generate a load testing suite and automatic performance measurement infrastructure. The approach complements current model-based performance prediction and analysis methods by generating the benchmark application from the same application architecture that the performance models are derived from. This provides the potential for tightly integrating runtime performance measurement with model-based prediction either for model validation or improving model prediction accuracy. We illustrate the approach using a case study based on EJB component technology.