110727
Classification Comparison of Prediction of Solvent Accessibility From Protein Sequences
The prediction of residue solvent accessibility from protein sequences has been studied by various methods. The direct comparison of these methods is impossible due to the variety of datasets used and the difference in structure definition. In this paper we choose 5 classification approaches (decision tree (DT), Support Vector Machine (SVM), Bayesian Statistics (BS), Neural Network (NN) and Multiple Linear Regression (MLR)) for predicting solvent accessibility based on the same dataset and using the same structure definition so that we can directly compare different methods. We evaluate these methods in a cross-validation test on 2148 unique proteins using single sequences and multiple sequences approaches with a cutoff of 20% for two-state definition of solvent accessibility. According to the experiment results, SVM and NN are both the best predictors with accuracy 79%, correlation coefficient 0.59, 2~4% superior to other three methods on multiple sequences prediction. A further test result on a blind test set from Critical Assessment of Techniques for Protein Structure Prediction experiment (CASP5) is consistent with this result. On single sequence prediction, DT, BS and MLR perform about the same at 71~72% with correlation coefficient 0.43. The improvement over the baseline model that use only the identity of target residue is small. Local sequence seems embed very little information on accessibility. Separate training according to protein size improves the prediction when there are sufficiently large dataset available. The consensus prediction combining the 5 approaches is not significantly better than the best single method.
2425436
Cluster Ensemble and Its Applications in Gene Expression Analysis
Huge amount of gene expression data have been generated as a result of the human genomic project. Clustering has been used extensively in mining these gene expression data to find important genetic and biological information. Obtaining high quality clustering results is very challenging because of the inconsistency of the results of different clustering algorithms and noise in the gene expression data. Many clustering algorithms are available and different clustering algorithms may generate different clustering results due to their bias and assumptions. It is a challenging and daunting task for the genomic researchers to choose the best clustering algorithm and generate the best clustering results for their data sets. In this paper, we present a cluster ensemble framework for gene expression analysis to generate high quality and robust clustering results. In our framework, the clustering results of individual clustering algorithm are converted into a distance matrix, these distance matrices are combined and a weighted graph is constructed according to the combined matrix. Then a graph partitioning approach is used to cluster the graph to generate the final clusters. The experiment results indicate that cluster ensemble approach yields better clustering results than the single best clustering algorithm on both synthetic data set and yeast gene expression data set.
14024342
A Semantic Approach for Mining Hidden Links from Complementary and Non-interactive Biomedical Literature
Two complementary and non-interactive literature sets of articles, when they are considered together, can reveal useful information of scientific interest not apparent in either of the two sets alone. Swanson called the existence of such hidden links as undiscovered public knowledge (UPK). The novel connection between Raynaud disease and fish oils was uncovered from complementary and non-interactive biomedical literature by Swanson in 1986. Since then, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manual intervention to reduce the number of possible connections. This paper proposes a semantic-based mining model for undiscovered public knowledge using the biomedical literature. Our method replaces manual ad-hoc pruning by using semantic knowledge from the biomedical ontologies. Using the semantic types and semantic relationships of the biomedical concepts, our prototype system can identify the relevant concepts collected from Medline and generate the novel hypothesis between these concepts. The system successfully replicates Swanson’s two famous discoveries: Raynaud disease/fish oils and migraine/magnesium. Compared with previous approaches such as LSI-based and traditional association rule-based methods, our method generates much fewer but more relevant novel hypotheses, and requires much less human intervention in the discovery procedure
11903789
A semantic-based approach for mining undiscovered public knowledge from biomedical literature
The problem of mining undiscovered public knowledge from biomedical literature was exemplified by Swanson's pioneering work on Raynaud disease/fish-oil discovery in 1986. Since then, there have been many approaches to mine undiscovered public knowledge from biomedical literature. This paper presents a semantic-based approach for mining undiscovered public knowledge from biomedical literature. The method takes advantages of the biomedical ontologies, MeSH and UMLS, as the source of semantic knowledge. A prototype system Biomedical Semantic-based Knowledge Discovery System (Bio-SbKDS) is designed to uncover novel hypothesis/connections hidden in the biomedical literature. Using the semantic types and semantic relations of the biomedical concepts, Bio-SbKDS can identify the relevant concepts collected from Medline and generate the novel hypothesis between these concepts. Bio-SbKDS successfully replicates Dr. Swanson's two famous discoveries: Raynaud disease/fish oil and migraine/magnesium. Compared with previous approaches, our method searches much less articles, generates much less but more relevant novel hypotheses, requires much less human intervention in the discovery procedure.
14227751
Mining undiscovered public knowledge from complementary and non-interactive biomedical literature through semantic pruning
Two complementary and non-interactive literature sets of articles, when they are considered together, can reveal useful information of scientific interest not apparent in either of the two document sets. Swanson called the existence of such knowledge, undiscovered public knowledge (UDPK). This paper proposes a semantic-based mining model for UDPK. Our method replaces manual ad-hoc pruning with using semantic knowledge from the biomedical ontologies. Using the semantic types and semantic relationships of the biomedical concepts, our prototype system can identify the relevant concepts collected from Medline and generate the novel hypothesis between these concepts. The system successfully replicates Swanson's two famous discoveries: Raynaud disease/fish oils and migraine/magnesium. Compared with previous approaches, our methods generate much fewer but more relevant novel hypotheses, and require much less human intervention in the discovery procedure.
6833692
Clustering Large Collection of Biomedical Literature Based on Ontology-Enriched Bipartite Graph Representation and Mutual Refinement Strategy
In this paper we introduce a novel document clustering approach that solves some major problems of traditional document clustering approaches. Instead of depending on traditional vector space model, this approach represents a set of documents as bipartite graphs using domain knowledge in ontology. In this representation, the concepts of the documents are classified according to their relationships with documents that are reflected on the bipartite graph. Using the concept groups, documents are clustered based on the concepts' contribution to each document. Through the mutual-refinement relationship with concept groups and document groups, the two groups are recursively refined. Our experimental results on MEDLINE articles show that our approach outperforms two leading document clustering algorithms: BiSecting K-means and CLUTO. In addition to its decent performance, our approach provides a meaningful explanation for each document cluster by identifying its most contributing concepts, thus helps users to understand and interpret documents and clustering results.
38024133
A Comparative Study on Selection of Cluster Number and Local Subspace Dimension in the Mixture PCA Models
How to determine the number of clusters and the dimensions of local principal subspaces is an important and challenging problem in various applications. Based on a probabilistic model of local PCA, this problem can be solved by one of existing statistical model selection criteria in a two-phase procedure. However, such a two-phase procedure is too time-consuming especially when there is no prior knowledge. The BYY harmony learning has provided a promising mechanism to make automatic model selection in parallel with parameter learning. This paper investigates the BYY harmony learning with automatic model selection on a mixture PCA model in comparison with three typical model selection criteria: AIC, CAIC, and MDL. This comparative study is made by experiments for different model selection tasks on simulated data sets under different conditions. Experiments have shown that automatic model selection by the BYY harmony learning are not only as good as or even better than conventional methods in terms of performances, but also considerably supervisory in terms of much less computational cost.
30531140
A Comparative Study of Several Cluster Number Selection Criteria
The selection of the number of clusters is an important and challenging issue in cluster analysis. In this paper we perform an experimental comparison of several criteria for determining the number of clusters based on Gaussian mixture model. The criteria that we consider include Akaike’s information criterion (AIC), the consistent Akaike’s information criterion (CAIC), the minimum description length (MDL) criterion which formally coincides with the Bayesian inference criterion (BIC), and two model selection methods driven from Bayesian Ying-Yang (BYY) harmony learning: harmony empirical learning criterion (BYY-HEC) and harmony data smoothing criterion (BYY-HDS). We investigate these methods on synthetic data sets of different sample size and the iris data set. The results of experiments illustrate that BYY-HDS has the best overall success rate and obviously outperforms other methods for small sample size. CAIC and MDL tend to underestimate the number of clusters, while AIC and BYY-HEC tend to overestimate the number of clusters especially in the case of small sample size.
12307619
The use of visual search for knowledge gathering in image decision support
This paper presents a new method of knowledge gathering for decision support in image understanding based on information extracted from the dynamics of saccadic eye movements. The framework involves the construction of a generic image feature extraction library, from which the feature extractors that are most relevant to the visual assessment by domain experts are determined automatically through factor analysis. The dynamics of the visual search are analyzed by using the Markov model for providing training information to novices on how and where to look for image features. The validity of the framework has been evaluated in a clinical scenario whereby the pulmonary vascular distribution on Computed Tomography images was assessed by experienced radiologists as a potential indicator of heart failure. The performance of the system has been demonstrated by training four novices to follow the visual assessment behavior of two experienced observers. In all cases, the accuracy of the students improved from near random decision making (33%) to accuracies ranging from 50% to 68%.
2863452
Optimal Polygon Cover Problems and Applications
Polygon cover problems are important in several applied areas, such as material layout, layered manufacturing, radiation therapy and radiosurgery, etc. In this paper, we study three optimal polygon cover problems: monotone polygon cover among obstacles, star-shaped polygon cover among obstacles, and strip cover for trapezoidalized polygons. Based on some interesting geometric observations, we develop efficient algorithms for solving these problems. The complexity bounds of our monotone cover and star-shaped cover algorithms are comparable to those of the previously best known algorithms for simpler cases of the problems without considering obstacles. Our strip cover algorithm improves the quality of the previously best known solutions.
30458595
Finding an Optimal Path without Growing the Tree
In this paper, we study a class of optimal path problems with the following phenomenon: The space complexity of the algorithms for reporting the lengths of single-source optimal paths for these problems is asymptotically smaller than the space complexity of the "standard" treegrowing algorithms for finding actual optimal paths. We present a general and efficient algorithmic paradigm for finding an actual optimal path for such problems without having to grow a single-source optimal path tree. Our paradigm is based on the "marriage-before-conquer" strategy, the prune-and-search technique, and a data structure called clipped trees. The paradigm enables us to compute an actual path for a number of optimal path problems and dynamic programming problems in computational geometry, graph theory, and combinatorial optimization. Our algorithmic solutions improve the space bounds (in certain cases, the time bounds as well) of the previously best known algorithms, and settle some open problems. Our techniques are likely to be applicable to other problems.