2454583
Temporal rule induction for clinical outcome analysis
Clinical outcomes analysis normally covers a particular time period. The sample under study is constantly changing as patients are censored, leave the study or die. In this paper, we present a novel data mining approach to mine temporal rules that reflect characteristics of outcomes analysis. We apply our temporal rule induction algorithm to a set of cancer patients, clinical records that were prospectively collected for 20 years. We analyse clinical data not only based on the static event, such as local recurrence for survival analysis, but also based on the temporal event with censored data for each time unit. The rules extracted from our temporal rule induction algorithm are compared to results from statistical analysis. The importance of this paper is that this novel temporal rule induction algorithm provides valuable insights for clinical data assessment and complements traditional statistical analysis.
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.
11295819
Biomedical Ontology MeSH Improves Document Clustering Qualify on MEDLINE Articles: A Comparison Study
Document clustering has been used for better document retrieval, document browsing, and text mining. In this paper, we investigate if biomedical ontology MeSH improves the clustering quality for MEDLINE articles. For this investigation, we perform a comprehensive comparison study of various document clustering approaches such as hierarchical clustering methods (single-link, complete-link, and complete link), bisecting K-means, K-means, and suffix tree clustering (STC) in terms of efficiency, effectiveness, and scalability. According to our experiment results, biomedical ontology MeSH significantly enhances clustering quality on biomedical documents. In addition, our results show that decent document clustering approaches, such as bisecting K-means, K-means and STC, gains some benefit from MeSH ontology while hierarchical algorithms showing the poorest clustering quality do not reap the benefit of MeSH ontology
18070841
Ontology-Based Scalable and Portable Information Extraction System to Extract Biological Knowledge from Huge Collection of Biomedical Web Documents
Automated discovery and extraction of biological knowledge from biomedical web documents has become essential because of the enormous amount of biomedical literature published each year. In this paper we present an ontology-based scalable and portable information extraction system to automatically extract biological knowledge from huge collection of online biomedical web documents. Our method integrates ontology-based semantic tagging, information extraction and data mining together, automatically learns the patterns based on a few user seed tuples, and then extract new tuples from the biomedical web documents based on the discovered patterns. A novel system SPIE (Scalable and Portable Information Extraction) is implemented and tested on the PuBMed to find the chromatin protein-protein interaction and the experimental results indicate our approach is very effective in extracting biological knowledge from huge collection of biomedical web documents.
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.
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
19915888
Node merging in Kohonen's self-organizing mapping of fMRI data
In this paper, Kohonen's self-organizing mapping (SOM) is used as a data-driven technique for analyzing functional magnetic resonance imaging (fMRI) data. Upon the completion of an SOM analysis, a cluster merging technique, based on examining the reproducibility of the fMRI data across epochs, is utilized to merge SOM nodes whose feature vectors are sufficiently similar to one another. The resulting 'super nodes' give time course templates of potential interest. These templates can be subsequently used in traditional template-based analysis methods, such as cross-correlation analysis, yielding statistical maps and activation patterns. This technique has been demonstrated on two fMRI datasets obtained from a visually-guided motor paradigm and a visual paradigm, respectively, showing satisfactory results.
206601195
The Role of Discourse Structure and Response Time in Multimodal Communication
In an ongoing project on multimodal communication in humans and agents [1], we investigate the interaction between two linguistic modalities (prosody and dialog structure) and two non-linguistic modalities (eye gaze and facial expressions). The goal is to gain a better understanding of the use of communicative channels in discourse and can subsequently aid the development of more effective animated conversational agents. We studied conversations between humans involved in the Map Task scenario whereby an Instruction Giver (IG) navigates an Instruction Follower (IF) from a starting point to an end point on a map [2].
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.
22875771
ACO-Steiner: Ant Colony Optimization Based Rectilinear Steiner Minimal Tree Algorithm
The rectilinear Steiner minimal tree (RSMT) problem is one of the fundamental problems in physical design, especially in routing, which is known to be NP-complete. This paper presents an algorithm, called ACO-Steiner, for RSMT construction based on ant colony optimization (ACO). An RSMT is constructed with ants' movements in Hanan grid, and then the constraint of Hanan grid is broken to accelerate ants' movements to improve the performance of the algorithm. This algorithm has been implemented on a Sun workstation with Unix operating system and the results have been compared with the fastest exact RSMT algorithm, GeoSteiner 3.1 and a recent heuristic using batched greedy triple construction (BGTC). Experimental results show that ACO-Steiner can get a short running time and keep the high performance. Furthermore, it is also found that the ACO-Steiner can be easily extended to be used to some other problems, such as rectilinear Steiner minimal tree avoiding obstacles, and congestion reduction in global routing.
12292456
The Embodiment of Amodal Symbolic Knowledge Representations
Latent semantic analysis (LSA) is a statistical, corpus-based technique of representing knowledge. It has been successfully used in a variety of applications including intelligent tutoring systems, essay grading and coherence metrics. From its very introduction LSA has been claimed to simulate aspects of human knowledge representation. This amodal symbolic view immediately resulted in a rebuttal from cognitive scientists who argued that LSA can never come close to human knowledge representation, because it lacks embodiment into perceptual experience or action as in human cognition. The ultimate test to determine the embodiment of LSA is to evaluate how well it operates on typical embodied dimensions like spatiality and temporality. The results of such a test would have an impact on theories of meaning and knowledge representation, and would help us in the development of natural language processing modules for applications that use these embodied dimensions. Six Multidimensional Scaling representations are derived from the LSA cosines between spatial and temporal words. Results show that by combining LSA with MDS previously hidden spatial and temporal relations can now be revealed.