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Improving Biomedical Information Retrieval with Neural Retrievers [article]

Man Luo, Arindam Mitra, Tejas Gokhale, Chitta Baral
2022 arXiv   pre-print
In this paper, we seek to improve information retrieval (IR) using neural retrievers (NR) in the biomedical domain, and achieve this goal using a three-pronged approach.  ...  First, to tackle the relative lack of data in the biomedical domain, we propose a template-based question generation method that can be leveraged to train neural retriever models.  ...  Unfortunately, these improvements on standard NLP datasets are not observed in the biomedical domain with neural retrievers.  ... 
arXiv:2201.07745v1 fatcat:u4x346mylvhjbcuvezdgkitkky

Deep fusion of multiple term-similarity measures for biomedical passage retrieval

Andrés Rosso-Mateus, Manuel Montes-y-Gómez, Paolo Rosso, Fabio A. González
2020 Journal of Intelligent & Fuzzy Systems  
This paper presents a novel approach for biomedical passage retrieval which is able to combine different information sources using a similarity matrix fusion strategy based on a convolutional neural network  ...  However, closed domains also offer some advantages such as the availability of specialized structured information sources, e.g. ontologies and thesauri, that could be used to improve retrieval performance  ...  In this paper, we present a novel method for biomedical passage retrieval. The model has the ability to combine different information sources.  ... 
doi:10.3233/jifs-179887 fatcat:3sqkyjvkhjbt3im5airrunbcfi

Feature Weighting in Finding Feedback Documents for Query Expansion in Biomedical Document Retrieval

Jainisha Sankhavara
2020 SN Computer Science  
Finding good feedback documents for query expansion is a well-known problem in the field of information retrieval.  ...  This paper describes a novel approach for finding relevant documents for feedback in query expansion for biomedical document retrieval.  ...  The fusion of automatic and manual feedback for query expansion in biomedical information retrieval experiments shows that manual feedback helps to improve the performance of biomedical IR systems [16  ... 
doi:10.1007/s42979-020-0069-x fatcat:gqczonzbcvc5fofu3dp7mc7dce

Biomedical Document Retrieval for Clinical Decision Support System

Jainisha Sankhavara
2018 Proceedings of ACL 2018, Student Research Workshop  
The availability of huge amount of biomedical literature have opened up new possibilities to apply Information Retrieval and NLP for mining documents from them.  ...  We compare statistical and NLP based approaches of query reformulation for biomedical document retrieval. Also, we have modeled the biomedical document retrieval as a learning to rank problem.  ...  Biomedical Information Retrieval (BIR) seeks special attention due to the characteristics of biomedical terminologies.  ... 
doi:10.18653/v1/p18-3012 dblp:conf/acl/Sankhavara18 fatcat:ggpycr4cfvckrl7j4ddy733hum

A New Retrieval Algorithm Based on Pulse Coupled Neural Network for Biomedical Images

2019 VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE  
In this paper, Pulse Coupled Neural Network (PCNN) based feature descriptor is proposed for retrieval of biomedical images.  ...  Time series is used as an image feature which contains the entire information of the feature, based on which the similar biomedical images are retrieved in our work.  ...  A New Retrieval Algorithm Based on Pulse Coupled Neural Network for Biomedical Images G. Kalaiarasi, K. K.  ... 
doi:10.35940/ijitee.a1003.1191s19 fatcat:dfywj3zoevfytap7dywgwwxjlu

Biomedical Question Answering via Weighted Neural Network Passage Retrieval [chapter]

Ferenc Galkó, Carsten Eickhoff
2018 Lecture Notes in Computer Science  
This paper proposes a weighted cosine distance retrieval scheme based on neural network word embeddings.  ...  In a preliminary processing step, many question answering systems rely on retrieval models for identifying relevant documents and passages.  ...  This paper describes a piece of work in progress, focusing on passage-level retrieval for biomedical question answering on the basis of weighted combinations of neural network word embeddings.  ... 
doi:10.1007/978-3-319-76941-7_39 fatcat:saguy6prrvbldgokn2d52ietyi

Recent Advances in Automated Question Answering In Biomedical Domain [article]

Krishanu Das Baksi
2021 arXiv   pre-print
With the improvements in commercial search engines, users can type in their queries and get a small set of documents most relevant for answering their query, as well as relevant snippets from the documents  ...  Therefore, it has become difficult to keep track of all the information in the domain, even for domain experts.  ...  It was shown that using a hybrid method incorporating a dual encoder BERT model along with BM25 model can improve document retrieval.  ... 
arXiv:2111.05937v1 fatcat:5474jk6ozbalvmfjrgatu4tsna

Introduction to Data Analysis and Visualization in Biomedical Informatics Minitrack

Hesham H. Ali, Kathryn M. Dempsey
2013 2013 46th Hawaii International Conference on System Sciences  
The paper explores ways to improve information retrieval from clinical notes and presents various experimental methods that use medical literature in information retrieval.  ...  With the assumption that previously known methods have strengths and weaknesses, the authors hypothesize that integrating information retrieval techniques will improve performance.  ... 
doi:10.1109/hicss.2013.8 dblp:conf/hicss/AliD13 fatcat:blauunu23vhmnfyvps2nlki7iq

Introduction to Data Analysis and Visualization in Biomedical Informatics Minitrack

Hesham H. Ali, Kathryn M. Dempsey
2014 2014 47th Hawaii International Conference on System Sciences  
The paper explores ways to improve information retrieval from clinical notes and presents various experimental methods that use medical literature in information retrieval.  ...  With the assumption that previously known methods have strengths and weaknesses, the authors hypothesize that integrating information retrieval techniques will improve performance.  ... 
doi:10.1109/hicss.2014.320 dblp:conf/hicss/AliD14 fatcat:urel3za6cvg6tcx6wqpdn6knpm

GRAPHENE

Sendong Zhao, Chang Su, Andrea Sboner, Fei Wang
2019 Proceedings of the 28th ACM International Conference on Information and Knowledge Management - CIKM '19  
Learning to rank minimizes a ranking loss between biomedical articles with the query to learn the retrieval function.  ...  Effective biomedical literature retrieval (BLR) plays a central role in precision medicine informatics. In this paper, we propose GRAPHENE, which is a deep learning based framework for precise BLR.  ...  The results also demonstrated that our GRAPHENE improves previous deep neural retrieval models which represent the document with textual information only, suggesting the necessity of encoding graph-based  ... 
doi:10.1145/3357384.3358038 dblp:conf/cikm/ZhaoSSW19 fatcat:hpll7xork5em7jkoz4kz3m3gry

Minimize the Percentage of Noise in Biomedical Images Using Neural Networks

Abdul Khader Jilani Saudagar
2014 The Scientific World Journal  
The overall goal of the research is to improve the quality of biomedical image for telemedicine with minimum percentages of noise in the retrieved image and to take less computation time.  ...  The novelty of this technique lies in the implementation of spectral coding for biomedical images using neural networks in order to accomplish the above objectives.  ...  This research is financially supported by Scientific Research Deanship, Al Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia, with Fund no. 330909.  ... 
doi:10.1155/2014/757146 pmid:25136685 pmcid:PMC4127272 fatcat:byrxldpmvnbevkphdtb73z4x6u

Calling Attention to Passages for Biomedical Question Answering [chapter]

Tiago Almeida, Sérgio Matos
2020 Lecture Notes in Computer Science  
Question answering can be described as retrieving relevant information for questions expressed in natural language, possibly also generating a natural language answer.  ...  a self-attention layer combined with a weighting mechanism.  ...  Introduction Question Answering (QA) is a subfield of Information Retrieval (IR) that specializes in producing or retrieving a single answer for a natural language question.  ... 
doi:10.1007/978-3-030-45442-5_9 fatcat:jzij73sqr5dq7o56syzni66yte

Slot Filling for Biomedical Information Extraction [article]

Yannis Papanikolaou, Marlene Staib, Justin Grace, Francine Bennett
2022 arXiv   pre-print
We follow the recently proposed paradigm of coupling a Tranformer-based bi-encoder, Dense Passage Retrieval, with a Transformer-based reading comprehension model to extract relations from biomedical text  ...  Information Extraction (IE) from text refers to the task of extracting structured knowledge from unstructured text.  ...  With respect to training, one of the major successes of neural-based retrieval methods has been attributed to being able to present the model with hard negatives, i.e., examples were a previous version  ... 
arXiv:2109.08564v2 fatcat:wyqvbm2pjnfi7enb2hs27ymuja

Towards Robust Neural Retrieval Models with Synthetic Pre-Training [article]

Revanth Gangi Reddy, Vikas Yadav, Md Arafat Sultan, Martin Franz, Vittorio Castelli, Heng Ji, Avirup Sil
2021 arXiv   pre-print
Recent work has shown that commonly available machine reading comprehension (MRC) datasets can be used to train high-performance neural information retrieval (IR) systems.  ...  We show that synthetic training examples generated using a sequence-to-sequence generator can be effective towards this goal: in our experiments, pre-training with synthetic examples improves retrieval  ...  On the far domain, however, Zero-shot neural retrieval accuracy improves with synthetic pre-training (AugDPR) in all out-of-domain test settings.  ... 
arXiv:2104.07800v1 fatcat:hqnrawueuvdhjkqccu2obiviva

Document Retrieval for Precision Medicine Using a Deep Learning Ensemble Method

Zhiqiang Liu, Jingkun Feng, Zhihao Yang, Lei Wang
2021 JMIR Medical Informatics  
With the development of biomedicine, the number of biomedical documents has increased rapidly bringing a great challenge for researchers trying to retrieve the information they need.  ...  Results The proposed ensemble method contributed to the improvement of biomedical retrieval performance.  ...  Biomedical information retrieval (IR) is thus a hot research topic in the biomedical domain.  ... 
doi:10.2196/28272 pmid:34185006 fatcat:36l77khdnncn7pngfnolqletnq
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