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Register a new userIntroducing Information Retrieval for Biomedical Informatics Students
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Added by
Sanya Bathla Taneja
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Introducing biomedical informatics (BMI) students to natural language processing (NLP) requires balancing technical depth with practical know-how to address application-focused needs. We developed a set of three activities introducing introductory BMI students to information retrieval with NLP, covering document representation strategies and language models from TF-IDF to BERT. These activities provide students with hands-on experience targeted towards common use cases, and introduce fundamental components of NLP workflows for a wide variety of applications.
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As a crucial role in cross-language information retrieval (CLIR), query translation has three main challenges: 1) the adequacy of translation; 2) the lack of in-domain parallel training data; and 3) the requisite of low latency. To this end, existing CLIR systems mainly exploit statistical-based machine translation (SMT) rather than the advanced neural machine translation (NMT), limiting the further improvements on both translation and retrieval quality. In this paper, we investigate how to exploit neural query translation model into CLIR system. Specifically, we propose a novel data augmentation method that extracts query translation pairs according to user clickthrough data, thus to alleviate the problem of domain-adaptation in NMT. Then, we introduce an asynchronous strategy which is able to leverage the advantages of the real-time in SMT and the veracity in NMT. Experimental results reveal that the proposed approach yields better retrieval quality than strong baselines and can be well applied into a real-world CLIR system, i.e. Aliexpress e-Commerce search engine. Readers can examine and test their cases on our website: https://aliexpress.com .
Dense retrieval has shown great success in passage ranking in English. However, its effectiveness in document retrieval for non-English languages remains unexplored due to the limitation in training resources. In this work, we explore different transfer techniques for document ranking from English annotations to multiple non-English languages. Our experiments on the test collections in six languages (Chinese, Arabic, French, Hindi, Bengali, Spanish) from diverse language families reveal that zero-shot model-based transfer using mBERT improves the search quality in non-English mono-lingual retrieval. Also, we find that weakly-supervised target language transfer yields competitive performances against the generation-based target language transfer that requires external translators and query generators.
This study considers the task of machine reading at scale (MRS) wherein, given a question, a system first performs the information retrieval (IR) task of finding relevant passages in a knowledge source and then carries out the reading comprehension (RC) task of extracting an answer span from the passages. Previous MRS studies, in which the IR component was trained without considering answer spans, struggled to accurately find a small number of relevant passages from a large set of passages. In this paper, we propose a simple and effective approach that incorporates the IR and RC tasks by using supervised multi-task learning in order that the IR component can be trained by considering answer spans. Experimental results on the standard benchmark, answering SQuAD questions using the full Wikipedia as the knowledge source, showed that our model achieved state-of-the-art performance. Moreover, we thoroughly evaluated the individual contributions of our model components with our new Japanese dataset and SQuAD. The results showed significant improvements in the IR task and provided a new perspective on IR for RC: it is effective to teach which part of the passage answers the question rather than to give only a relevance score to the whole passage.
Query translation (QT) is a key component in cross-lingual information retrieval system (CLIR). With the help of deep learning, neural machine translation (NMT) has shown promising results on various tasks. However, NMT is generally trained with large-scale out-of-domain data rather than in-domain query translation pairs. Besides, the translation model lacks a mechanism at the inference time to guarantee the generated words to match the search index. The two shortages of QT result in readable texts for human but inadequate candidates for the downstream retrieval task. In this paper, we propose a novel approach to alleviate these problems by limiting the open target vocabulary search space of QT to a set of important words mined from search index database. The constraint translation candidates are employed at both of training and inference time, thus guiding the translation model to learn and generate well performing target queries. The proposed methods are exploited and examined in a real-word CLIR system--Aliexpress e-Commerce search engine. Experimental results demonstrate that our approach yields better performance on both translation quality and retrieval accuracy than the strong NMT baseline.
Dense retrieval methods have shown great promise over sparse retrieval methods in a range of NLP problems. Among them, dense phrase retrieval-the most fine-grained retrieval unit-is appealing because phrases can be directly used as the output for question answering and slot filling tasks. In this work, we follow the intuition that retrieving phrases naturally entails retrieving larger text blocks and study whether phrase retrieval can serve as the basis for coarse-level retrieval including passages and documents. We first observe that a dense phrase-retrieval system, without any retraining, already achieves better passage retrieval accuracy (+3-5% in top-5 accuracy) compared to passage retrievers, which also helps achieve superior end-to-end QA performance with fewer passages. Then, we provide an interpretation for why phrase-level supervision helps learn better fine-grained entailment compared to passage-level supervision, and also show that phrase retrieval can be improved to achieve competitive performance in document-retrieval tasks such as entity linking and knowledge-grounded dialogue. Finally, we demonstrate how phrase filtering and vector quantization can reduce the size of our index by 4-10x, making dense phrase retrieval a practical and versatile solution in multi-granularity retrieval.
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