Enhancing access to the Bibliome: the TREC 2004 Genomics Track

BACKGROUND: The goal of the TREC Genomics Track is to improve information retrieval in the area of genomics by creating test collections that will allow researchers to improve and better understand failures of their systems. The 2004 track included an ad hoc retrieval task, simulating use of a search engine to obtain documents about biomedical topics. This paper describes the Genomics Track of the Text Retrieval Conference (TREC) 2004, a forum for evaluation of IR research systems, where retrieval in the genomics domain has recently begun to be assessed. RESULTS: A total of 27 research groups submitted 47 different runs. The most effective runs, as measured by the primary evaluation measure of mean average precision (MAP), used a combination of domain-specific and general techniques. The best MAP obtained by any run was 0.4075. Techniques that expanded queries with gene name lists as well as words from related articles had the best efficacy. However, many runs performed more poorly than a simple baseline run, indicating that careful selection of system features is essential. CONCLUSION: Various approaches to ad hoc retrieval provide a diversity of efficacy. The TREC Genomics Track and its test collection resources provide tools that allow improvement in information retrieval systems

Using Learning to Rank Approach to Promoting Diversity for Biomedical Information Retrieval with Wikipedia

In most of the traditional information retrieval (IR) models, the independent relevance assumption is taken, which assumes the relevance of a document is independent of other documents. However, the pitfall of this is the high redundancy and low diversity of retrieval result. This has been seen in many scenarios, especially in biomedical IR, where the information need of one query may refer to different aspects. Promoting diversity in IR takes the relationship between documents into account. Unlike previous studies, we tackle this problem in the learning to rank perspective. The main challenges are how to find salient features for biomedical data and how to integrate dynamic features into the ranking model. To address these challenges, Wikipedia is used to detect topics of documents for generating diversity biased features. A combined model is proposed and studied to learn a diversified ranking result. Experiment results show the proposed method outperforms baseline models

Web Page Retrieval by Combining Evidence

The participation of the REINA Research Group in WebCLEF 2005 focused in the monolingual mixed task. Queries or topics are of two types: named and home pages. For both, we first perform a search by thematic contents; for the same query, we do a search in several elements of information from every page (title, some meta tags, anchor text) and then we combine the results. For queries about home pages, we try to detect using a method based in some keywords and their patterns of use. After, a re-rank of the results of the thematic contents retrieval is performed, based on Page-Rank and Centrality coeficients

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.

What Makes a Top-Performing Precision Medicine Search Engine? Tracing Main System Features in a Systematic Way

From 2017 to 2019 the Text REtrieval Conference (TREC) held a challenge task on precision medicine using documents from medical publications (PubMed) and clinical trials. Despite lots of performance measurements carried out in these evaluation campaigns, the scientific community is still pretty unsure about the impact individual system features and their weights have on the overall system performance. In order to overcome this explanatory gap, we first determined optimal feature configurations using the Sequential Model-based Algorithm Configuration (SMAC) program and applied its output to a BM25-based search engine. We then ran an ablation study to systematically assess the individual contributions of relevant system features: BM25 parameters, query type and weighting schema, query expansion, stop word filtering, and keyword boosting. For evaluation, we employed the gold standard data from the three TREC-PM installments to evaluate the effectiveness of different features using the commonly shared infNDCG metric.Comment: Accepted for SIGIR2020, 10 page

Context and Learning in Novelty Detection

We demonstrate the value of using context in a new-information detection system that achieved the highest precision scores at the Text Retrieval Conference's Novelty Track in 2004. In order to determine whether information within a sentence has been seen in material read previously, our system integrates information about the context of the sentence with novel words and named entities within the sentence, and uses a specialized learning algorithm to tune the system parameters

Biomedical Question Answering: A Survey of Approaches and Challenges

Automatic Question Answering (QA) has been successfully applied in various domains such as search engines and chatbots. Biomedical QA (BQA), as an emerging QA task, enables innovative applications to effectively perceive, access and understand complex biomedical knowledge. There have been tremendous developments of BQA in the past two decades, which we classify into 5 distinctive approaches: classic, information retrieval, machine reading comprehension, knowledge base and question entailment approaches. In this survey, we introduce available datasets and representative methods of each BQA approach in detail. Despite the developments, BQA systems are still immature and rarely used in real-life settings. We identify and characterize several key challenges in BQA that might lead to this issue, and discuss some potential future directions to explore.Comment: In submission to ACM Computing Survey

On enhancing the robustness of timeline summarization test collections

Timeline generation systems are a class of algorithms that produce a sequence of time-ordered sentences or text snippets extracted in real-time from high-volume streams of digital documents (e.g. news articles), focusing on retaining relevant and informative content for a particular information need (e.g. topic or event). These systems have a range of uses, such as producing concise overviews of events for end-users (human or artificial agents). To advance the field of automatic timeline generation, robust and reproducible evaluation methodologies are needed. To this end, several evaluation metrics and labeling methodologies have recently been developed - focusing on information nugget or cluster-based ground truth representations, respectively. These methodologies rely on human assessors manually mapping timeline items (e.g. sentences) to an explicit representation of what information a ‘good’ summary should contain. However, while these evaluation methodologies produce reusable ground truth labels, prior works have reported cases where such evaluations fail to accurately estimate the performance of new timeline generation systems due to label incompleteness. In this paper, we first quantify the extent to which the timeline summarization test collections fail to generalize to new summarization systems, then we propose, evaluate and analyze new automatic solutions to this issue. In particular, using a depooling methodology over 19 systems and across three high-volume datasets, we quantify the degree of system ranking error caused by excluding those systems when labeling. We show that when considering lower-effectiveness systems, the test collections are robust (the likelihood of systems being miss-ranked is low). However, we show that the risk of systems being mis-ranked increases as the effectiveness of systems held-out from the pool increases. To reduce the risk of mis-ranking systems, we also propose a range of different automatic ground truth label expansion techniques. Our results show that the proposed expansion techniques can be effective at increasing the robustness of the TREC-TS test collections, as they are able to generate large numbers missing matches with high accuracy, markedly reducing the number of mis-rankings by up to 50%