Objective and automated protocols for the evaluation of biomedical search engines using No Title Evaluation protocols

<p>Abstract</p> <p>Background</p> <p>The evaluation of information retrieval techniques has traditionally relied on human judges to determine which documents are relevant to a query and which are not. This protocol is used in the Text Retrieval Evaluation Conference (TREC), organized annually for the past 15 years, to support the unbiased evaluation of novel information retrieval approaches. The TREC Genomics Track has recently been introduced to measure the performance of information retrieval for biomedical applications.</p> <p>Results</p> <p>We describe two protocols for evaluating biomedical information retrieval techniques without human relevance judgments. We call these protocols No Title Evaluation (NT Evaluation). The first protocol measures performance for focused searches, where only one relevant document exists for each query. The second protocol measures performance for queries expected to have potentially many relevant documents per query (high-recall searches). Both protocols take advantage of the clear separation of titles and abstracts found in Medline. We compare the performance obtained with these evaluation protocols to results obtained by reusing the relevance judgments produced in the 2004 and 2005 TREC Genomics Track and observe significant correlations between performance rankings generated by our approach and TREC. Spearman's correlation coefficients in the range of 0.79–0.92 are observed comparing bpref measured with NT Evaluation or with TREC evaluations. For comparison, coefficients in the range 0.86–0.94 can be observed when evaluating the same set of methods with data from two independent TREC Genomics Track evaluations. We discuss the advantages of NT Evaluation over the TRels and the data fusion evaluation protocols introduced recently.</p> <p>Conclusion</p> <p>Our results suggest that the NT Evaluation protocols described here could be used to optimize some search engine parameters before human evaluation. Further research is needed to determine if NT Evaluation or variants of these protocols can fully substitute for human evaluations.</p

Concept-based query expansion for retrieving gene related publications from MEDLINE

<p>Abstract</p> <p>Background</p> <p>Advances in biotechnology and in high-throughput methods for gene analysis have contributed to an exponential increase in the number of scientific publications in these fields of study. While much of the data and results described in these articles are entered and annotated in the various existing biomedical databases, the scientific literature is still the major source of information. There is, therefore, a growing need for text mining and information retrieval tools to help researchers find the relevant articles for their study. To tackle this, several tools have been proposed to provide alternative solutions for specific user requests.</p> <p>Results</p> <p>This paper presents QuExT, a new PubMed-based document retrieval and prioritization tool that, from a given list of genes, searches for the most relevant results from the literature. QuExT follows a concept-oriented query expansion methodology to find documents containing concepts related to the genes in the user input, such as protein and pathway names. The retrieved documents are ranked according to user-definable weights assigned to each concept class. By changing these weights, users can modify the ranking of the results in order to focus on documents dealing with a specific concept. The method's performance was evaluated using data from the 2004 TREC genomics track, producing a mean average precision of 0.425, with an average of 4.8 and 31.3 relevant documents within the top 10 and 100 retrieved abstracts, respectively.</p> <p>Conclusions</p> <p>QuExT implements a concept-based query expansion scheme that leverages gene-related information available on a variety of biological resources. The main advantage of the system is to give the user control over the ranking of the results by means of a simple weighting scheme. Using this approach, researchers can effortlessly explore the literature regarding a group of genes and focus on the different aspects relating to these genes.</p

Search beyond traditional probabilistic information retrieval

"This thesis focuses on search beyond probabilistic information retrieval. Three ap- proached are proposed beyond the traditional probabilistic modelling. First, term associ- ation is deeply examined. Term association considers the term dependency using a factor analysis based model, instead of treating each term independently. Latent factors, con- sidered the same as the hidden variables of ""eliteness"" introduced by Robertson et al. to gain understanding of the relation among term occurrences and relevance, are measured by the dependencies and occurrences of term sequences and subsequences. Second, an entity-based ranking approach is proposed in an entity system named ""EntityCube"" which has been released by Microsoft for public use. A summarization page is given to summarize the entity information over multiple documents such that the truly relevant entities can be highly possibly searched from multiple documents through integrating the local relevance contributed by proximity and the global enhancer by topic model. Third, multi-source fusion sets up a meta-search engine to combine the ""knowledge"" from different sources. Meta-features, distilled as high-level categories, are deployed to diversify the baselines. Three modified fusion methods are employed, which are re- ciprocal, CombMNZ and CombSUM with three expanded versions. Through extensive experiments on the standard large-scale TREC Genomics data sets, the TREC HARD data sets and the Microsoft EntityCube Web collections, the proposed extended models beyond probabilistic information retrieval show their effectiveness and superiority.

Adaptation of machine translation for multilingual information retrieval in the medical domain

Objective. We investigate machine translation (MT) of user search queries in the context of cross-lingual information retrieval (IR) in the medical domain. The main focus is on techniques to adapt MT to increase translation quality; however, we also explore MT adaptation to improve eectiveness of cross-lingual IR. Methods and Data. Our MT system is Moses, a state-of-the-art phrase-based statistical machine translation system. The IR system is based on the BM25 retrieval model implemented in the Lucene search engine. The MT techniques employed in this work include in-domain training and tuning, intelligent training data selection, optimization of phrase table configuration, compound splitting, and exploiting synonyms as translation variants. The IR methods include morphological normalization and using multiple translation variants for query expansion. The experiments are performed and thoroughly evaluated on three language pairs: Czech–English, German–English, and French–English. MT quality is evaluated on data sets created within the Khresmoi project and IR eectiveness is tested on the CLEF eHealth 2013 data sets. Results. The search query translation results achieved in our experiments are outstanding – our systems outperform not only our strong baselines, but also Google Translate and Microsoft Bing Translator in direct comparison carried out on all the language pairs. The baseline BLEU scores increased from 26.59 to 41.45 for Czech–English, from 23.03 to 40.82 for German–English, and from 32.67 to 40.82 for French–English. This is a 55% improvement on average. In terms of the IR performance on this particular test collection, a significant improvement over the baseline is achieved only for French–English. For Czech–English and German–English, the increased MT quality does not lead to better IR results. Conclusions. Most of the MT techniques employed in our experiments improve MT of medical search queries. Especially the intelligent training data selection proves to be very successful for domain adaptation of MT. Certain improvements are also obtained from German compound splitting on the source language side. Translation quality, however, does not appear to correlate with the IR performance – better translation does not necessarily yield better retrieval. We discuss in detail the contribution of the individual techniques and state-of-the-art features and provide future research directions

Learning to select for information retrieval

The effective ranking of documents in search engines is based on various document features, such as the frequency of the query terms in each document, the length, or the authoritativeness of each document. In order to obtain a better retrieval performance, instead of using a single or a few features, there is a growing trend to create a ranking function by applying a learning to rank technique on a large set of features. Learning to rank techniques aim to generate an effective document ranking function by combining a large number of document features. Different ranking functions can be generated by using different learning to rank techniques or on different document feature sets. While the generated ranking function may be uniformly applied to all queries, several studies have shown that different ranking functions favour different queries, and that the retrieval performance can be significantly enhanced if an appropriate ranking function is selected for each individual query. This thesis proposes Learning to Select (LTS), a novel framework that selectively applies an appropriate ranking function on a per-query basis, regardless of the given query's type and the number of candidate ranking functions. In the learning to select framework, the effectiveness of a ranking function for an unseen query is estimated from the available neighbouring training queries. The proposed framework employs a classification technique (e.g. k-nearest neighbour) to identify neighbouring training queries for an unseen query by using a query feature. In particular, a divergence measure (e.g. Jensen-Shannon), which determines the extent to which a document ranking function alters the scores of an initial ranking of documents for a given query, is proposed for use as a query feature. The ranking function which performs the best on the identified training query set is then chosen for the unseen query. The proposed framework is thoroughly evaluated on two different TREC retrieval tasks (namely, Web search and adhoc search tasks) and on two large standard LETOR feature sets, which contain as many as 64 document features, deriving conclusions concerning the key components of LTS, namely the query feature and the identification of neighbouring queries components. Two different types of experiments are conducted. The first one is to select an appropriate ranking function from a number of candidate ranking functions. The second one is to select multiple appropriate document features from a number of candidate document features, for building a ranking function. Experimental results show that our proposed LTS framework is effective in both selecting an appropriate ranking function and selecting multiple appropriate document features, on a per-query basis. In addition, the retrieval performance is further enhanced when increasing the number of candidates, suggesting the robustness of the learning to select framework. This thesis also demonstrates how the LTS framework can be deployed to other search applications. These applications include the selective integration of a query independent feature into a document weighting scheme (e.g. BM25), the selective estimation of the relative importance of different query aspects in a search diversification task (the goal of the task is to retrieve a ranked list of documents that provides a maximum coverage for a given query, while avoiding excessive redundancy), and the selective application of an appropriate resource for expanding and enriching a given query for document search within an enterprise. The effectiveness of the LTS framework is observed across these search applications, and on different collections, including a large scale Web collection that contains over 50 million documents. This suggests the generality of the proposed learning to select framework. The main contributions of this thesis are the introduction of the LTS framework and the proposed use of divergence measures as query features for identifying similar queries. In addition, this thesis draws insights from a large set of experiments, involving four different standard collections, four different search tasks and large document feature sets. This illustrates the effectiveness, robustness and generality of the LTS framework in tackling various retrieval applications

Making a Better Query: Find Good Feedback Documents and Terms via Semantic Associations

When people search, they always input several keywords as an input query. While current information retrieval (IR) systems are based on term matching, documents will not be considered as relevant if they do not have the exact terms as in the query. However, it is common that these documents are relevant if they contain terms semantically similar to the query. To retrieve these documents, a classic way is to expand the original query with more related terms. Pseudo relevance feedback (PRF) has proven to be effective to expand origin queries and improve the performance of IR. It assumes the top k ranked documents obtained through the first round retrieval are relevant as feedback documents, and expand the original queries with feedback terms selected from these feedback documents. However, applying PRF for query expansion must be very carefully. Wrongly added terms can bring noisy information and hurt the overall search experiences extensively. The assumption of feedback documents is too strong to be completely true. To avoid noise import and make significant improvements simultaneously, we solve the significant problem through four ways in this dissertation. Firstly, we assume the proximity information among terms as term semantic associations and utilize them to seek new relevant terms. Next, to obtain good and robust performance for PRF via adapting topic information, we propose a new concept named topic space and present three models based on it. Topics obtained through topic modeling do help identify how relevant a feedback document is. Weights of candidate terms in these more relevant feedback documents will be boosted and have higher probabilities to be chosen. Furthermore, we apply machine learning methods to classify which feedback documents are effective for PRF. To solve the problem of lack-of-training-data for the application of machine learning methods in PRF, we improve a traditional co-training method and take the quality of classifiers into account. Finally, we present a new probabilistic framework to integrate existing effective methods like semantic associations as components for further research. All the work has been tested on public datasets and proven to be effective and efficient