9,365 research outputs found
Experiments in terabyte searching, genomic retrieval and novelty detection for TREC 2004
In TREC2004, Dublin City University took part in three tracks, Terabyte (in collaboration with University College Dublin), Genomic and Novelty. In this paper we will discuss each track separately and present separate conclusions from this work. In addition, we present a general description of a text retrieval engine that we have developed in the last year to support our experiments into large scale, distributed information retrieval, which underlies all of the track experiments described in this document
Structural term extraction for expansion of template-based genomic queries
This paper describes our experiments run to address the ad hoc task of the TREC 2005 Genomics track. The task topics were expressed with 5 different structures called Generic Topic Templates (GTTs). We hypothesized the presence of GTT-specific structural terms in the free-text fields of documents relevant to a topic instantiated from that same GTT. Our experiments aimed at extracting and selecting candidate structural terms for each GTT. Selected terms were used to expand initial queries and the quality of the term selection was measured by the impact of the expansion on initial search results. The evaluation used the task training topics and the associated relevance information. This paper describes the two term extraction methods used in the experiments and the resulting two runs sent to NIST for evaluation
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
Large-Scale Online Semantic Indexing of Biomedical Articles via an Ensemble of Multi-Label Classification Models
Background: In this paper we present the approaches and methods employed in
order to deal with a large scale multi-label semantic indexing task of
biomedical papers. This work was mainly implemented within the context of the
BioASQ challenge of 2014. Methods: The main contribution of this work is a
multi-label ensemble method that incorporates a McNemar statistical
significance test in order to validate the combination of the constituent
machine learning algorithms. Some secondary contributions include a study on
the temporal aspects of the BioASQ corpus (observations apply also to the
BioASQ's super-set, the PubMed articles collection) and the proper adaptation
of the algorithms used to deal with this challenging classification task.
Results: The ensemble method we developed is compared to other approaches in
experimental scenarios with subsets of the BioASQ corpus giving positive
results. During the BioASQ 2014 challenge we obtained the first place during
the first batch and the third in the two following batches. Our success in the
BioASQ challenge proved that a fully automated machine-learning approach, which
does not implement any heuristics and rule-based approaches, can be highly
competitive and outperform other approaches in similar challenging contexts
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