RankAggreg, an R package for weighted rank aggregation

<p>Abstract</p> <p>Background</p> <p>Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that allows one to objectively perform the necessary aggregation. With the rapid growth of high-throughput genomic and proteomic studies, the potential utility of rank aggregation in the context of meta-analysis becomes even more apparent. One of the major strengths of rank-based aggregation is the ability to combine lists coming from different sources and platforms, for example different microarray chips, which may or may not be directly comparable otherwise.</p> <p>Results</p> <p>The <it>RankAggreg </it>package provides two methods for combining the ordered lists: the Cross-Entropy method and the Genetic Algorithm. Two examples of rank aggregation using the package are given in the manuscript: one in the context of clustering based on gene expression, and the other one in the context of meta-analysis of prostate cancer microarray experiments.</p> <p>Conclusion</p> <p>The two examples described in the manuscript clearly show the utility of the <it>RankAggreg </it>package in the current bioinformatics context where ordered lists are routinely produced as a result of modern high-throughput technologies.</p

Probabilistic methods in the analysis of protein interaction networks

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Application of the Markov Chain Method in a Health Portal Recommendation System

This study produced a recommendation system that can effectively recommend items on a health portal. Toward this aim, a transaction log that records users’ traversal activities on the Medical College of Wisconsin’s HealthLink, a health portal with a subject directory, was utilized and investigated. This study proposed a mixed-method that included the transaction log analysis method, the Markov chain analysis method, and the inferential analysis method. The transaction log analysis method was applied to extract users’ traversal activities from the log. The Markov chain analysis method was adopted to model users’ traversal activities and then generate recommendation lists for topics, articles, and Q&A items on the health portal. The inferential analysis method was applied to test whether there are any correlations between recommendation lists generated by the proposed recommendation system and recommendation lists ranked by experts. The topics selected for this study are Infections, the Heart, and Cancer. These three topics were the three most viewed topics in the portal. The findings of this study revealed the consistency between the recommendation lists generated from the proposed system and the lists ranked by experts. At the topic level, two topic recommendation lists generated from the proposed system were consistent with the lists ranked by experts, while one topic recommendation list was highly consistent with the list ranked by experts. At the article level, one article recommendation list generated from the proposed system was consistent with the list ranked by experts, while 14 article recommendation lists were highly consistent with the lists ranked by experts. At the Q&A item level, three Q&A item recommendation lists generated from the proposed system were consistent with the lists ranked by experts, while 12 Q&A item recommendation lists were highly consistent with the lists ranked by experts. The findings demonstrated the significance of users’ traversal data extracted from the transaction log. The methodology applied in this study proposed a systematic approach to generating the recommendation systems for other similar portals. The outcomes of this study can facilitate users’ navigation, and provide a new method for building a recommendation system that recommends items at three levels: the topic level, the article level, and the Q&A item level

Enhanced web-based summary generation for search.

After a user types in a search query on a major search engine, they are presented with a number of search results. Each search result is made up of a title, brief text summary and a URL. It is then the user\u27s job to select documents for further review. Our research aims to improve the accuracy of users selecting relevant documents by improving the way these web pages are summarized. Improvements in accuracy will lead to time improvements and user experience improvements. We propose ReClose, a system for generating web document summaries. ReClose generates summary content through combining summarization techniques from query-biased and query-independent summary generation. Query-biased summaries generally provide query terms in context. Query-independent summaries focus on summarizing documents as a whole. Combining these summary techniques led to a 10% improvement in user decision making over Google generated summaries. Color-coded ReClose summaries provide keyword usage depth at a glance and also alert users to topic departures. Color-coding further enhanced ReClose results and led to a 20% improvement in user decision making over Google generated summaries. Many online documents include structure and multimedia of various forms such as tables, lists, forms and images. We propose to include this structure in web page summaries. We found that the expert user was insignificantly slowed in decision making while the majority of average users made decisions more quickly using summaries including structure without any decrease in decision accuracy. We additionally extended ReClose for use in summarizing large numbers of tweets in tracking flu outbreaks in social media. The resulting summaries have variable length and are effective at summarizing flu related trends. Users of the system obtained an accuracy of 0.86 labeling multi-tweet summaries. This showed that the basis of ReClose is effective outside of web documents and that variable length summaries can be more effective than fixed length. Overall the ReClose system provides unique summaries that contain more informative content than current search engines produce, highlight the results in a more meaningful way, and add structure when meaningful. The applications of ReClose extend far beyond search and have been demonstrated in summarizing pools of tweets

Network Approaches to the Study of Genomic Variation in Cancer

Advances in genomic sequencing technologies opened the door for a wider study of cancer etiology. By analyzing datasets with thousands of exomes (or genomes), researchers gained a better understanding of the genomic alterations that confer a selective advantage towards cancerous growth. A predominant narrative in the field has been based on a dichotomy of alterations that confer a strong selective advantage, called cancer drivers, and the bulk of other alterations assumed to have a neutral effect, called passengers. Yet, a series of studies questioned this narrative and assigned potential roles to passengers, be it in terms of facilitating tumorigenesis or countering the effect of drivers. Consequently, the passenger mutational landscape received a higher level of attention in attempt to prioritize the possible effects of its alterations and to identify new therapeutic targets. In this dissertation, we introduce interpretable network approaches to the study of genomic variation in cancer. We rely on two types of networks, namely functional biological networks and artificial neural nets. In the first chapter, we describe a propagation method that prioritizes 230 infrequently mutated genes with respect to their potential contribution to cancer development. In the second chapter, we further transcend the driver-passenger dichotomy and demonstrate a gradient of cancer relevance across human genes. In the last two chapters, we present methods that simplify neural network models to render them more interpretable with a focus on functional genomic applications in cancer and beyond

ConSus : a decision support tool for the procurement of sustainable social housing

Abstract unavailable please refer to PD

Study of some aspects of managerial communication

This research is concerned with factors which improve or inhibit effective communication between managers in organisations.An appraisal of the literature is carried out and a framework of the main variables affecting effective communication is suggested. This framework is tested within seven operating companies and the results discussed. Of particular interest is the finding that an individual manager's career achievement is related to the accuracy with which he communicates with his superior. The study also isolates factors affecting this accuracy and shows for example that when subordinates trust their superiors more accurate communication results, while strong desires for promotion reduce accuracy. These secondary variables are then examined to indicate how individual managers and organisations as a whole might improve their communicating effectiveness.Finally suggestions are made to develop the methods used in the present study and to point out areas which seem worthy of future research

Filtering News from Document Streams: Evaluation Aspects and Modeled Stream Utility

Events like hurricanes, earthquakes, or accidents can impact a large number of people. Not only are people in the immediate vicinity of the event affected, but concerns about their well-being are shared by the local government and well-wishers across the world. The latest information about news events could be of use to government and aid agencies in order to make informed decisions on providing necessary support, security and relief. The general public avails of news updates via dedicated news feeds or broadcasts, and lately, via social media services like Facebook or Twitter. Retrieving the latest information about newsworthy events from the world-wide web is thus of importance to a large section of society. As new content on a multitude of topics is continuously being published on the web, specific event related information needs to be filtered from the resulting stream of documents. We present in this thesis, a user-centric evaluation measure for evaluating systems that filter news related information from document streams. Our proposed evaluation measure, Modeled Stream Utility (MSU), models users accessing information from a stream of sentences produced by a news update filtering system. The user model allows for simulating a large number of users with different characteristic stream browsing behavior. Through simulation, MSU estimates the utility of a system for an average user browsing a stream of sentences. Our results show that system performance is sensitive to a user population's stream browsing behavior and that existing evaluation metrics correspond to very specific types of user behavior. To evaluate systems that filter sentences from a document stream, we need a set of judged sentences. This judged set is a subset of all the sentences returned by all systems, and is typically constructed by pooling together the highest quality sentences, as determined by respective system assigned scores for each sentence. Sentences in the pool are manually assessed and the resulting set of judged sentences is then used to compute system performance metrics. In this thesis, we investigate the effect of including duplicates of judged sentences, into the judged set, on system performance evaluation. We also develop an alternative pooling methodology, that given the MSU user model, selects sentences for pooling based on the probability of a sentences being read by modeled users. Our research lays the foundation for interesting future work for utilizing user-models in different aspects of evaluation of stream filtering systems. The MSU measure enables incorporation of different user models. Furthermore, the applicability of MSU could be extended through calibration based on user behavior

Statistics for Learning Genetics

This study investigated the knowledge and skills that biology students may need to help them understand statistics/mathematics as it applies to genetics. The data are based on analyses of current representative genetics texts, practicing genetics professors' perspectives, and more directly, students' perceptions of, and performance in, doing statistically-based genetics problems. This issue is at the emerging edge of modern college-level genetics instruction, and this study attempts to identify key theoretical components for creating a specialized biological statistics curriculum. The goal of this curriculum will be to prepare biology students with the skills for assimilating quantitatively-based genetic processes, increasingly at the forefront of modern genetics. To fulfill this, two college level classes at two universities were surveyed. One university was located in the northeastern US and the other in the West Indies. There was a sample size of 42 students and a supplementary interview was administered to a select 9 students. Interviews were also administered to professors in the field in order to gain insight into the teaching of statistics in genetics. Key findings indicated that students had very little to no background in statistics (55%). Although students did perform well on exams with 60% of the population receiving an A or B grade, 77% of them did not offer good explanations on a probability question associated with the normal distribution provided in the survey. The scope and presentation of the applicable statistics/mathematics in some of the most used textbooks in genetics teaching, as well as genetics syllabi used by instructors do not help the issue. It was found that the text books, often times, either did not give effective explanations for students, or completely left out certain topics. The omission of certain statistical/mathematical oriented topics was seen to be also true with the genetics syllabi reviewed for this study. Nonetheless, although the necessity for infusing these quantitative subjects with genetics and, overall, the biological sciences is growing (topics including synthetic biology, molecular systems biology and phylogenetics) there remains little time in the semester to be dedicated to the consolidation of learning and understanding