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
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.
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
40136335
On Rearrangeability of Multirate Clos Networks
Chung and Ross [SIAM J. Comput., 20 (1991), pp. 726--736] conjectured that the multirate three-stage Clos network C(n,2n-1,r) is rearrangeable in the general discrete bandwidth case; i.e., each connection has a weight chosen from a given finite set {p1, p2,. . .,pk} where $1 \geq p_1 > p_2 > \cdots > p_k > 0$ and pi is an integer multiple of pi, denoted by $p_k \mid p_i$, for $1 \leq i \leq k-1$. In this paper, we prove that multirate three-stage Clos network C(n,2n-1,r) is rearrangeable when each connection has a weight chosen from a given finite set {p1, p2,. . .,pk} where $1 \geq p_1 > p_2 > \cdots > p_{h} > 1/2 \geq p_{h+1} > \cdots > p_k > 0$ and ph+2 | ph+1,ph+3 |ph+2,. . . ,pk | ph+1. We also prove that C(n,2n-1,r) is two-rate rearrangeable and $C(n, \lceil \frac{7n}{3} \rceil, r)$ is three-rate rearrangeable.
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%.
26341684
Automatic Cluster Number Determination via BYY Harmony Learning
Selection of the number of clusters is a crucial problem in clustering. Conventionally, it was effected via cost function based criteria such as AIC and MDL. In this paper we empirically investigate automatic selection of the number of clusters via BYY harmony empirical learning. Results of experiments show that the true number of clusters can be automatically obtained during BYY harmony empirical learning. It is superior to conventional methods in that it needs much less computational cost.
37056316
Learning about the Ethical Treatment of Human Subjects in Experiments on a Web Facility with a Conversational Agent and ITS Components
The Human Use Regulatory Affairs Advisor (HURAA) is a web-based help facility that provides training on the ethical use of human subjects in research, and that serves as an information retrieval system on ethical policies. The content for HURAA is derived from United States Federal agency documents and regulations. HURAA has a number of components that go beyond conventional page-turning or hypertext systems, including (1) an animated conversational agent that serves as a navigational guide for the web facility, (2) an enhanced multimedia introduction, (3) lessons with case-based and explanation-based reasoning, and (4) document retrieval through natural language queries or a Point & Query facility. The effectiveness of HURAA was tested on a small sample of participants (N = 18) who were assigned to either the full HURAA version or a conventional computer-based training version.
16662300
A comparative investigation on subspace dimension determination
It is well-known that constrained Hebbian self-organization on multiple linear neural units leads to the same k-dimensional subspace spanned by the first k principal components. Not only the batch PCA algorithm has been widely applied in various fields since 1930s, but also a variety of adaptive algorithms have been proposed in the past two decades. However, most studies assume a known dimension k or determine it heuristically, though there exist a number of model selection criteria in the literature of statistics. Recently, criteria have also been obtained under the framework of Bayesian Ying-Yang (BYY) harmony learning. This paper further investigates the BYY criteria in comparison with existing typical criteria, including Akaike's information criterion (AIC), the consistent Akaike's information criterion (CAIC), the Bayesian inference criterion (BIC), and the cross-validation (CV) criterion. This comparative study is made via experiments not only on simulated data sets of different sample sizes, noise variances, data space dimensions, and subspace dimensions, but also on two real data sets from air pollution problem and sport track records, respectively. Experiments have shown that BIC outperforms AIC, CAIC, and CV while the BYY criteria are either comparable with or better than BIC. Therefore, BYY harmony learning is a more preferred tool for subspace dimension determination by further considering that the appropriate subspace dimension k can be automatically determined during implementing BYY harmony learning for the principal subspace while the selection of subspace dimension k by BIC, AIC, CAIC, and CV has to be made at the second stage based on a set of candidate subspaces with different dimensions which have to be obtained at the first stage of learning.