Graph based gene/protein prediction and clustering over uncertain medical databases.

Clustering over protein or gene data is now a popular issue in biomedical databases. In general, large sets of gene tags are clustered using high computation techniques over gene or protein distributed data. Most of the traditional clustering techniques are based on subspace, hierarchical and partitioning feature extraction. Various clustering techniques have been proposed in the literature with different cluster measures, but their performance is limited due to spatial noise and uncertainty. In this paper, an improved graph-based clustering technique is proposed for the generation of efficient gene or protein clusters over uncertain and noisy data. The proposed graph-based visualization can effectively identify different types of genes or proteins along with relational attributes. Experimental results show that the proposed graph model more effectively clusters complex gene or protein data when compared with conventional clustering approaches

MeSHLabeler and DeepMeSH: Recent Progress in Large-Scale MeSH Indexing

The US National Library of Medicine (NLM) uses the Medical Subject Headings (MeSH) (seeNote 1 ) to index almost all 24 million citations in MEDLINE, which greatly facilitates the application of biomedical information retrieval and text mining. Large-scale automatic MeSH indexing has two challenging aspects: the MeSH side and citation side. For the MeSH side, each citation is annotated by only 12 (on average) out of all 28, 000 MeSH terms. For the citation side, all existing methods, including Medical Text Indexer (MTI) by NLM, deal with text by bag-of-words, which cannot capture semantic and context-dependent information well. To solve these two challenges, we developed the MeSHLabeler and DeepMeSH. By utilizing “learning to rank” (LTR) framework, MeSHLabeler integrates multiple types of information to solve the challenge in the MeSH side, while DeepMeSH integrates deep semantic representation to solve the challenge in the citation side. MeSHLabeler achieved the first place in both BioASQ2 and BioASQ3, and DeepMeSH achieved the first place in both BioASQ4 and BioASQ5 challenges. DeepMeSH is available at http://datamining-iip.fudan.edu.cn/deepmesh

Concept embedding-based weighting scheme for biomedical text clustering and visualization

Biomedical text clustering is a text mining technique used to provide better document search, browsing, and retrieval in biomedical and clinical text collections. In this research, the document representation based on the concept embedding along with the proposed weighting scheme is explored. The concept embedding is learned through the neural networks to capture the associations between the concepts. The proposed weighting scheme makes use of the concept associations to build document vectors for clustering. We evaluate two types of concept embedding and new weighting scheme for text clustering and visualization on two different biomedical text collections. The returned results demonstrate that the concept embedding along with the new weighting scheme performs better than the baseline tf–idf for clustering and visualization. Based on the internal clustering evaluation metric-Davies–Bouldin index and the visualization, the concept embedding generated from aggregated word embedding can form well-separated clusters, whereas the intact concept embedding can better identify more clusters of specific diseases and gain better F-measure

Multiconstrained gene clustering based on generalized projections

<p>Abstract</p> <p>Background</p> <p>Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontology (GO) annotations and gene network structures. How to integrate multiple pieces of constraints for an optimal clustering solution still remains an unsolved problem.</p> <p>Results</p> <p>We propose a novel multiconstrained gene clustering (MGC) method within the generalized projection onto convex sets (POCS) framework used widely in image reconstruction. Each constraint is formulated as a corresponding set. The generalized projector iteratively projects the clustering solution onto these sets in order to find a consistent solution included in the intersection set that satisfies all constraints. Compared with previous MGC methods, POCS can integrate multiple constraints from different nature without distorting the original constraints. To evaluate the clustering solution, we also propose a new performance measure referred to as Gene Log Likelihood (GLL) that considers genes having more than one function and hence in more than one cluster. Comparative experimental results show that our POCS-based gene clustering method outperforms current state-of-the-art MGC methods.</p> <p>Conclusions</p> <p>The POCS-based MGC method can successfully combine multiple constraints from different nature for gene clustering. Also, the proposed GLL is an effective performance measure for the soft clustering solutions.</p

Investigating text power in predicting semantic similarity

This article presents an empirical evaluation to investigate the distributional semantic power of abstract, body and full-text, as different text levels, in predicting the semantic similarity using a collection of open access articles from PubMed. The semantic similarity is measured based on two criteria namely, linear MeSH terms intersection and hierarchical MeSH terms distance. As such, a random sample of 200 queries and 20000 documents are selected from a test collection built on CITREC open source code. Sim Pack Java Library is used to calculate the textual and semantic similarities. The nDCG value corresponding to two of the semantic similarity criteria is calculated at three precision points. Finally, the nDCG values are compared by using the Friedman test to determine the power of each text level in predicting the semantic similarity. The results showed the effectiveness of the text in representing the semantic similarity in such a way that texts with maximum textual similarity are also shown to be 77% and 67% semantically similar in terms of linear and hierarchical criteria, respectively. Furthermore, the text length is found to be more effective in representing the hierarchical semantic compared to the linear one. Based on the findings, it is concluded that when the subjects are homogenous in the tree of knowledge, abstracts provide effective semantic capabilities, while in heterogeneous milieus, full-texts processing or knowledge bases is needed to acquire IR effectiveness

CITREC: An Evaluation Framework for Citation-Based Similarity Measures based on TREC Genomics and PubMed Central

Citation-based similarity measures such as Bibliographic Coupling and Co-Citation are an integral component of many information retrieval systems. However, comparisons of the strengths and weaknesses of measures are challenging due to the lack of suitable test collections. This paper presents CITREC, an open evaluation framework for citation-based and text-based similarity measures. CITREC prepares the data from the PubMed Central Open Access Subset and the TREC Genomics collection for a citation-based analysis and provides tools necessary for performing evaluations of similarity measures. To account for different evaluation purposes, CITREC implements 35 citation-based and text-based similarity measures, and features two gold standards. The first gold standard uses the Medical Subject Headings (MeSH) thesaurus and the second uses the expert relevance feedback that is part of the TREC Genomics collection to gauge similarity. CITREC additionally offers a system that allows creating user defined gold standards to adapt the evaluation framework to individual information needs and evaluation purposes.ye

Exploração de literatura biomédica usando semântica latente

Mestrado em Engenharia de Computadores e TelemáticaO rápido crescimento de dados disponível na Internet e o facto de se encontrar maioritariamente na forma de texto não estruturado, tem criado sucessivos desafios na recuperação e indexação desta informação. Para além da Internet, também inúmeras bases de dados documentais, de áreas específicas do conhecimento, são confrontadas com este problema. Com a quantidade de informação a crescer tão rapidamente, os métodos tradicionais para indexar e recuperar informação, tornam-se insuficientes face a requisitos cada vez mais exigentes por parte dos utilizadores. Estes problemas levam à necessidade de melhorar os sistemas de recuperação de informação, usando técnicas mais poderosas e eficientes. Um desses métodos designa-se por Latent Semantic Indexing (LSI) e, tem sido sugerido como uma boa solução para modelar e analisar texto não estruturado. O LSI permite revelar a estrutura semântica de um corpus, descobrindo relações entre documentos e termos, mostrando-se uma solução robusta para o melhoramento de sistemas de recuperação de informação, especialmente a identificação de documentos relevantes para a pesquisa de um utilizador. Além disso, o LSI pode ser útil em outras tarefas tais como indexação de documentos e anotação de termos. O principal objectivo deste projeto consistiu no estudo e exploração do LSI na anotação de termos e na estruturação dos resultados de um sistema de recuperação de informação. São apresentados resultados de desempenho destes algoritmos e são igualmente propostas algumas formas para visualizar estes resultados.The rapid increase in the amount of data available on the Internet, and the fact that this is mostly in the form of unstructured text, has brought successive challenges in information indexing and retrieval. Besides the Internet, specific literature databases are also faced with these problems. With the amount of information growing so rapidly, traditional methods for indexing and retrieving information become insufficient for the increasingly stringent requirements from users. These issues lead to the need of improving information retrieval systems using more powerful and efficient techniques. One of those methods is the Latent Semantic Indexing (LSI), which has been suggested as a good solution for modeling and analyzing unstructured text. LSI allows discovering the semantic structure in a corpus, by finding the relations between documents and terms. It is a robust solution for improving information retrieval systems, especially in the identification of relevant documents for a user's query. Besides this, LSI can be useful in other tasks such as document indexing and annotation of terms. The main goal of this project consisted in studying and exploring the LSI process for terms annotations and for structuring the retrieved documents from an information retrieval system. The performance results of these algorithms are presented and, in addition, several new forms of visualizing these results are proposed