Improving average ranking precision in user searches for biomedical research datasets

Availability of research datasets is keystone for health and life science study reproducibility and scientific progress. Due to the heterogeneity and complexity of these data, a main challenge to be overcome by research data management systems is to provide users with the best answers for their search queries. In the context of the 2016 bioCADDIE Dataset Retrieval Challenge, we investigate a novel ranking pipeline to improve the search of datasets used in biomedical experiments. Our system comprises a query expansion model based on word embeddings, a similarity measure algorithm that takes into consideration the relevance of the query terms, and a dataset categorisation method that boosts the rank of datasets matching query constraints. The system was evaluated using a corpus with 800k datasets and 21 annotated user queries. Our system provides competitive results when compared to the other challenge participants. In the official run, it achieved the highest infAP among the participants, being +22.3% higher than the median infAP of the participant's best submissions. Overall, it is ranked at top 2 if an aggregated metric using the best official measures per participant is considered. The query expansion method showed positive impact on the system's performance increasing our baseline up to +5.0% and +3.4% for the infAP and infNDCG metrics, respectively. Our similarity measure algorithm seems to be robust, in particular compared to Divergence From Randomness framework, having smaller performance variations under different training conditions. Finally, the result categorization did not have significant impact on the system's performance. We believe that our solution could be used to enhance biomedical dataset management systems. In particular, the use of data driven query expansion methods could be an alternative to the complexity of biomedical terminologies

Comparison of Balancing Techniques for Multimedia IR over Imbalanced Datasets

A promising method to improve the performance of information retrieval systems is to approach retrieval tasks as a supervised classification problem. Previous user interactions, e.g. gathered from a thorough log file analysis, can be used to train classifiers which aim to inference relevance of retrieved documents based on user interactions. A problem in this approach is, however, the large imbalance ratio between relevant and non-relevant documents in the collection. In standard test collection as used in academic evaluation frameworks such as TREC, non-relevant documents outnumber relevant documents by far. In this work, we address this imbalance problem in the multimedia domain. We focus on the logs of two multimedia user studies which are highly imbalanced. We compare a naiinodotve solution of randomly deleting documents belonging to the majority class with various balancing algorithms coming from different fields: data classification and text classification. Our experiments indicate that all algorithms improve the classification performance of just deleting at random from the dominant class

MBT: A Memory-Based Part of Speech Tagger-Generator

We introduce a memory-based approach to part of speech tagging. Memory-based learning is a form of supervised learning based on similarity-based reasoning. The part of speech tag of a word in a particular context is extrapolated from the most similar cases held in memory. Supervised learning approaches are useful when a tagged corpus is available as an example of the desired output of the tagger. Based on such a corpus, the tagger-generator automatically builds a tagger which is able to tag new text the same way, diminishing development time for the construction of a tagger considerably. Memory-based tagging shares this advantage with other statistical or machine learning approaches. Additional advantages specific to a memory-based approach include (i) the relatively small tagged corpus size sufficient for training, (ii) incremental learning, (iii) explanation capabilities, (iv) flexible integration of information in case representations, (v) its non-parametric nature, (vi) reasonably good results on unknown words without morphological analysis, and (vii) fast learning and tagging. In this paper we show that a large-scale application of the memory-based approach is feasible: we obtain a tagging accuracy that is on a par with that of known statistical approaches, and with attractive space and time complexity properties when using {\em IGTree}, a tree-based formalism for indexing and searching huge case bases.} The use of IGTree has as additional advantage that optimal context size for disambiguation is dynamically computed.Comment: 14 pages, 2 Postscript figure

Socializing the Semantic Gap: A Comparative Survey on Image Tag Assignment, Refinement and Retrieval

Where previous reviews on content-based image retrieval emphasize on what can be seen in an image to bridge the semantic gap, this survey considers what people tag about an image. A comprehensive treatise of three closely linked problems, i.e., image tag assignment, refinement, and tag-based image retrieval is presented. While existing works vary in terms of their targeted tasks and methodology, they rely on the key functionality of tag relevance, i.e. estimating the relevance of a specific tag with respect to the visual content of a given image and its social context. By analyzing what information a specific method exploits to construct its tag relevance function and how such information is exploited, this paper introduces a taxonomy to structure the growing literature, understand the ingredients of the main works, clarify their connections and difference, and recognize their merits and limitations. For a head-to-head comparison between the state-of-the-art, a new experimental protocol is presented, with training sets containing 10k, 100k and 1m images and an evaluation on three test sets, contributed by various research groups. Eleven representative works are implemented and evaluated. Putting all this together, the survey aims to provide an overview of the past and foster progress for the near future.Comment: to appear in ACM Computing Survey

Topic-dependent sentiment analysis of financial blogs

While most work in sentiment analysis in the financial domain has focused on the use of content from traditional finance news, in this work we concentrate on more subjective sources of information, blogs. We aim to automatically determine the sentiment of financial bloggers towards companies and their stocks. To do this we develop a corpus of financial blogs, annotated with polarity of sentiment with respect to a number of companies. We conduct an analysis of the annotated corpus, from which we show there is a significant level of topic shift within this collection, and also illustrate the difficulty that human annotators have when annotating certain sentiment categories. To deal with the problem of topic shift within blog articles, we propose text extraction techniques to create topic-specific sub-documents, which we use to train a sentiment classifier. We show that such approaches provide a substantial improvement over full documentclassification and that word-based approaches perform better than sentence-based or paragraph-based approaches