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In the field of Information Retrieval, biomedical question answering is a specialized task that focuses on answering questions related to medical and healthcare domains. The goal is to provide accurate and relevant answers to the posed queries related to medical conditions, treatments, procedures, medications, and other healthcare-related topics. Well-designed models should efficiently retrieve relevant passages. Early retrieval models can quickly retrieve passages but often with low precision. In contrast, recently developed Large Language Models can retrieve documents with high precision but at a slower pace. To tackle this issue, we propose a two-stage retrieval approach that initially utilizes BM25 for a preliminary search to identify potential candidate documents; subsequently, a Large Language Model is fine-tuned to evaluate the relevance of query–document pairs. Experimental results indicate that our approach achieves comparative performances on the BioASQ and the TREC-COVID datasets. [ABSTRACT FROM AUTHOR]

Featured Application: In the biomedical field, accessing data by classical methods is getting more difficult day by day, as it is in any other field, due to the data growth rate. Different methods are needed to access the desired data more quickly. In particular, more specific methods need to be developed for question answering systems. In this study, a model is proposed for the document retrieval and answer extraction modules which are a part of biomedical question answering systems. In this paper, we describe our biomedical document retrieval system and answers extraction module, which is part of the biomedical question answering system. Approximately 26.5 million PubMed articles are indexed as a corpus with the Apache Lucene text search engine. Our proposed system consists of three parts. The first part is the question analysis module, which analyzes the question and enriches it with biomedical concepts related to its wording. The second part of the system is the document retrieval module. In this step, the proposed system is tested using different information retrieval models, like the Vector Space Model, Okapi BM25, and Query Likelihood. The third part is the document re-ranking module, which is responsible for re-arranging the documents retrieved in the previous step. For this study, we tested our proposed system with 6B training questions from the BioASQ challenge task. We obtained the best MAP score on the document retrieval phase when we used Query Likelihood with the Dirichlet Smoothing model. We used the sequential dependence model at the re-rank phase, but this model produced a worse MAP score than the previous phase. In similarity calculation, we included the Named Entity Recognition (NER), UMLS Concept Unique Identifiers (CUI), and UMLS Semantic Types of the words in the question to find the sentences containing the answer. Using this approach, we observed a performance enhancement of roughly 25% for the top 20 outcomes, surpassing another method employed in this study, which relies solely on textual similarity. [ABSTRACT FROM AUTHOR]

In the field of Information Retrieval, biomedical question answering is a specialized task that focuses on answering questions related to medical and healthcare domains. The goal is to provide accurate and relevant answers to the posed queries related to medical conditions, treatments, procedures, medications, and other healthcare-related topics. Well-designed models should efficiently retrieve relevant passages. Early retrieval models can quickly retrieve passages but often with low precision. In contrast, recently developed Large Language Models can retrieve documents with high precision but at a slower pace. To tackle this issue, we propose a two-stage retrieval approach that initially utilizes BM25 for a preliminary search to identify potential candidate documents; subsequently, a Large Language Model is fine-tuned to evaluate the relevance of query–document pairs. Experimental results indicate that our approach achieves comparative performances on the BioASQ and the TREC-COVID datasets.

In this paper, we describe our biomedical document retrieval system and answers extraction module, which is part of the biomedical question answering system. Approximately 26.5 million PubMed articles are indexed as a corpus with the Apache Lucene text search engine. Our proposed system consists of three parts. The first part is the question analysis module, which analyzes the question and enriches it with biomedical concepts related to its wording. The second part of the system is the document retrieval module. In this step, the proposed system is tested using different information retrieval models, like the Vector Space Model, Okapi BM25, and Query Likelihood. The third part is the document re-ranking module, which is responsible for re-arranging the documents retrieved in the previous step. For this study, we tested our proposed system with 6B training questions from the BioASQ challenge task. We obtained the best MAP score on the document retrieval phase when we used Query Likelihood with the Dirichlet Smoothing model. We used the sequential dependence model at the re-rank phase, but this model produced a worse MAP score than the previous phase. In similarity calculation, we included the Named Entity Recognition (NER), UMLS Concept Unique Identifiers (CUI), and UMLS Semantic Types of the words in the question to find the sentences containing the answer. Using this approach, we observed a performance enhancement of roughly 25% for the top 20 outcomes, surpassing another method employed in this study, which relies solely on textual similarity.

Biomedical text summarization (BTS) is proving to be an emerging area of work and research with the need for sustainable healthcare applications such as evidence-based medicine practice (EBM) and telemedicine which help effectively support healthcare needs of the society. However, with the rapid growth in the biomedical literature and the diversities in its structure and resources, it is becoming challenging to carry out effective text summarization for better insights. The goal of this work is to conduct a comprehensive systematic literature review of significant and high-impact literary work in BTS with a deep understanding of its major artifacts such as databases, semantic similarity measures, and semantic enrichment approaches. In the systematic literature review conducted, we applied search filters to find high-impact literature in the biomedical text summarization domain from IEEE, SCOPUS, Elsevier, EBSCO, and PubMed databases. The systematic literature review (SLR) yielded 81 works; those were analyzed for qualitative study. The in-depth study of the literature shows the relevance and efficacy of the deep learning (DL) approach, context-aware feature extraction techniques, and their relevance in BTS. Biomedical question answering (BQA) system is one of the most popular applications of text summarizations for building self-sufficient healthcare systems and are pointing to future research directions. The review culminates in realization of a proposed framework for the BQA system MEDIQA with design of better heuristics for content screening, document screening, and relevance ranking. The presented framework provides an evidence-based biomedical question answering model and text summarizer that can lead to real-time evidence-based clinical support system to healthcare practitioners. [ABSTRACT FROM AUTHOR]

Abstract Background Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provide people with accurate healthcare-related information. Recently, a lot of approaches based on the neural network and large scale pre-trained language model have largely improved its performance. However, considering the lexical characteristics of biomedical corpus and its small scale dataset, there is still much improvement room for biomedical QA tasks. Results Inspired by the importance of syntactic and lexical features in the biomedical corpus, we proposed a new framework to extract external features, such as part-of-speech and named-entity recognition, and fused them with the original text representation encoded by pre-trained language model, to enhance the biomedical question answering performance. Our model achieves an overall improvement of all three metrics on BioASQ 6b, 7b, and 8b factoid question answering tasks. Conclusions The experiments on BioASQ question answering dataset demonstrated the effectiveness of our external feature-enriched framework. It is proven by the experiments conducted that external lexical and syntactic features can improve Pre-trained Language Model’s performance in biomedical domain question answering task.

Recent advances have witnessed a trending application of transfer learning in a broad spectrum of natural language processing (NLP) tasks, including question answering (QA). Transfer learning allows a model to inherit domain knowledge obtained from an existing model that has been sufficiently pre-trained. In the biomedical field, most QA datasets are limited by insufficient training examples and the presence of factoid questions. This study proposes a transfer learning-based sentiment-aware model, named SentiMedQAer, for biomedical QA. The proposed method consists of a learning pipeline that utilizes BioBERT to encode text tokens with contextual and domain-specific embeddings, fine-tunes Text-to-Text Transfer Transformer (T5), and RoBERTa models to integrate sentiment information into the model, and trains an XGBoost classifier to output a confidence score to determine the final answer to the question. We validate SentiMedQAer on PubMedQA, a biomedical QA dataset with reasoning-required yes/no questions. Results show that our method outperforms the SOTA by 15.83% and a single human annotator by 5.91%. [ABSTRACT FROM AUTHOR]

Recent advances have witnessed a trending application of transfer learning in a broad spectrum of natural language processing (NLP) tasks, including question answering (QA). Transfer learning allows a model to inherit domain knowledge obtained from an existing model that has been sufficiently pre-trained. In the biomedical field, most QA datasets are limited by insufficient training examples and the presence of factoid questions. This study proposes a transfer learning-based sentiment-aware model, named SentiMedQAer, for biomedical QA. The proposed method consists of a learning pipeline that utilizes BioBERT to encode text tokens with contextual and domain-specific embeddings, fine-tunes Text-to-Text Transfer Transformer (T5), and RoBERTa models to integrate sentiment information into the model, and trains an XGBoost classifier to output a confidence score to determine the final answer to the question. We validate SentiMedQAer on PubMedQA, a biomedical QA dataset with reasoning-required yes/no questions. Results show that our method outperforms the SOTA by 15.83% and a single human annotator by 5.91%.

Background: Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provide people with accurate healthcare-related information. Recently, a lot of approaches based on the neural network and large scale pre-trained language model have largely improved its performance. However, considering the lexical characteristics of biomedical corpus and its small scale dataset, there is still much improvement room for biomedical QA tasks. Results: Inspired by the importance of syntactic and lexical features in the biomedical corpus, we proposed a new framework to extract external features, such as part-of-speech and named-entity recognition, and fused them with the original text representation encoded by pre-trained language model, to enhance the biomedical question answering performance. Our model achieves an overall improvement of all three metrics on BioASQ 6b, 7b, and 8b factoid question answering tasks. Conclusions: The experiments on BioASQ question answering dataset demonstrated the effectiveness of our external feature-enriched framework. It is proven by the experiments conducted that external lexical and syntactic features can improve Pre-trained Language Model's performance in biomedical domain question answering task. [ABSTRACT FROM AUTHOR]

• A hierarchical attention based transfer learning model is proposed for biomedical QA. • BERT is applied to enrich the semantic representation in our model. • Scaled dot-product attention captures the question interaction for passage encoding. • Fine-tuning is used to penalize the deviations from source model's parameters. • The results show that our model outperforms the best solution on BioASQ Task B. Biomedical text mining is becoming increasingly important as the number of biomedical documents grow rapidly. Deep learning has boosted the development of biomedical text mining models. However, as deep learning models require a large amount of training data, a hierarchical attention based transfer learning model is proposed in this paper for the question answering task in biomedical field which lacks of sufficient training data. We adopt BERT (Bidirectional Encoder Representation Transformers), which has the ability to learn from large-scale unsupervised data, to enrich the semantic representation in our model. Especially, the scaled dot-product attention mechanism captures the question interaction clues for passage encoding. The domain adaptation technique of fine-tuning is used to reinforce the performance, which penalizes the deviations from the source model's parameters and remembers the knowledge of source domain. We evaluate the system performance on the open data set of BioASQ-Task B. The results show that our system achieves the state-of-the-art performance without any handcrafted features and outperforms the best solution for factoid questions in 2016 and 2017 BioASQ-Task B. [ABSTRACT FROM AUTHOR]

Domain adaptation is a good way to boost BERT's performance on domain-specific natural language processing (NLP) tasks. Common domain adaptation methods, however, can be deficient in capturing domain knowledge. Meanwhile, the context fragmentation inherent in Transformer-based models also hinders the acquisition of domain knowledge. Considering the semi-structural characteristics of documents and its potential for alleviating these problems, we leverage the semi-structured information of documents to supplement domain knowledge to BERT. To this end, we propose a topic-based domain adaptation method, which enhances the capture of domain knowledge at various levels of text granularity. Specifically, topic masked language modeling is designed at the paragraph level for pre-training; topic subsection matching degree dataset is automatically constructed at the subsection level for intermediate fine-tuning. Experiments are conducted over four biomedical NLP tasks across six datasets. The results show that our method benefits BERT, RoBERTa, SpanBERT, BioBERT, and PubMedBERT in nearly all cases. And we see significant gains in two question answering (QA) tasks, especially customer health QA, the topic-related one, with an average accuracy improvement of 4.8%. Thus, the semi-structured information of documents can be exploited to make BERT capture domain knowledge more effectively. • Topic-based domain adaptation (TDA) is proposed for BERT. • Topic masked language model (TMLM) is designed for pretraining. • Topic subsection matching degree (TSMD) is created for intermediate fine-tuning. • The semi-structured information is critical for domain adaptation of BERT. • TDA helps BERT yield significant gains on customer health QA task. [ABSTRACT FROM AUTHOR]

Large neural-based Pre-trained Language Models (PLM) have recently gained much attention due to their noteworthy performance in many downstream Information Retrieval (IR) and Natural Language Processing (NLP) tasks. PLMs can be categorized as either general-purpose , which are trained on resources such as large-scale Web corpora, and domain-specific which are trained on in-domain or mixed-domain corpora. While domain-specific PLMs have shown promising performance on domain-specific tasks, they are significantly more computationally expensive compared to general-purpose PLMs as they have to be either retrained or trained from scratch. The objective of our work in this paper is to explore whether it would be possible to leverage general-purpose PLMs to show competitive performance to domain-specific PLMs without the need for expensive retraining of the PLMs for domain-specific tasks. By focusing specifically on the recent BioASQ Biomedical Question Answering task, we show how different general-purpose PLMs show synergistic behaviour in terms of performance, which can lead to overall notable performance improvement when used in tandem with each other. More concretely, given a set of general-purpose PLMs, we propose a self-supervised method for training a classifier that systematically selects the PLM that is most likely to answer the question correctly on a per-input basis. We show that through such a selection strategy, the performance of general-purpose PLMs can become competitive with domain-specific PLMs while remaining computationally light since there is no need to retrain the large language model itself. We run experiments on the BioASQ dataset, which is a large-scale biomedical question-answering benchmark. We show that utilizing our proposed selection strategy can show statistically significant performance improvements on general-purpose language models with an average of 16.7% when using only lighter models such as DistilBERT and DistilRoBERTa, as well as 14.2% improvement when using relatively larger models such as BERT and RoBERTa and so, their performance become competitive with domain-specific large language models such as PubMedBERT. [Display omitted] • Exploring General vs. domain-specific languge models in Biomed QA. • Studying the synergy between general PLMs in Biomed QA. • proposing the problem of Language Model Selection for Biomed QA. • proposing novel ML strategy to select accurate PLMs for Biomed QA. [ABSTRACT FROM AUTHOR]

Biomedical question answering is a hot and challenging topic in artificial intelligence and natural language processing as it helps to analyze multiple, large, and fast-growing biomedical knowledge sources. Most researchers manage to address the problem through constructing a knowledge base but these approaches require much expertise as well as workload. In this paper, we propose a two-stage semantic sequential dependence model (SSDM2 ) framework based on a cognitive-inspired model and sequential dependence model (SDM) to answer biomedical questions with relevant snippets in academic papers. Concretely, we firstly search relevant articles and generate candidate snippets with a SSDM, which is proposed to integrate the semantic and sequential information within questions together. Afterwards, another SSDM is utilized to measure the relevances between the questions and corresponding candidate snippets and rank these snippets. A biomedical question answering system is constructed based on the proposed framework and evaluated on 3-year BioASQ 2013-15 benchmarks. Statistics indicate the proposed framework SSDM2 outperforms several state-of-the-art baselines and BioASQ participants. The proposed SSDM2 is an effective and robust framework for biomedical question answering. [ABSTRACT FROM AUTHOR]

Background: Radiology reports are commonly written on free-text using voice recognition devices. Structured reports (SR) have a high potential but they are usually considered more difficult to fill-in so their adoption in clinical practice leads to a lower efficiency. However, some studies have demonstrated that in some cases, producing SRs may require shorter time than plain-text ones. This work focuses on the definition and demonstration of a methodology to evaluate the productivity of software tools for producing radiology reports. A set of SRs for breast cancer diagnosis based on BI-RADS have been developed using this method. An analysis of their efficiency with respect to free-text reports has been performed.Material and Methods: The methodology proposed compares the Elapsed Time (ET) on a set of radiological reports. Free-text reports are produced with the speech recognition devices used in the clinical practice. Structured reports are generated using a web application generated with TRENCADIS framework. A team of six radiologists with three different levels of experience in the breast cancer diagnosis was recruited. These radiologists performed the evaluation, each one introducing 50 reports for mammography, 50 for ultrasound scan and 50 for MRI using both approaches. Also, the Relative Efficiency (REF) was computed for each report, dividing the ET of both methods. We applied the T-Student (T-S) test to compare the ETs and the ANOVA test to compare the REFs. Both tests were computed using the SPSS software.Results: The study produced three DICOM-SR templates for Breast Cancer Diagnosis on mammography, ultrasound and MRI, using RADLEX terms based on BIRADs 5th edition. The T-S test on radiologists with high or intermediate profile, showed that the difference between the ET was only statistically significant for mammography and ultrasound. The ANOVA test performed grouping the REF by modalities, indicated that there were no significant differences between mammograms and ultrasound scans, but both have significant statistical differences with MRI. The ANOVA test of the REF for each modality, indicated that there were only significant differences in Mammography (ANOVA p = 0.024) and Ultrasound (ANOVA p = 0.008). The ANOVA test for each radiologist profile, indicated that there were significant differences on the high profile (ANOVA p = 0.028) and medium (ANOVA p = 0.045).Conclusions: In this work, we have defined and demonstrated a methodology to evaluate the productivity of software tools for producing radiology reports in Breast Cancer. We have evaluated that adopting Structured Reporting in mammography and ultrasound studies in breast cancer diagnosis improves the performance in producing reports. [ABSTRACT FROM AUTHOR]

Background and Objective: Biomedical question type classification is one of the important components of an automatic biomedical question answering system. The performance of the latter depends directly on the performance of its biomedical question type classification system, which consists of assigning a category to each question in order to determine the appropriate answer extraction algorithm. This study aims to automatically classify biomedical questions into one of the four categories: (1) yes/no, (2) factoid, (3) list, and (4) summary.Methods: In this paper, we propose a biomedical question type classification method based on machine learning approaches to automatically assign a category to a biomedical question. First, we extract features from biomedical questions using the proposed handcrafted lexico-syntactic patterns. Then, we feed these features for machine-learning algorithms. Finally, the class label is predicted using the trained classifiers.Results: Experimental evaluations performed on large standard annotated datasets of biomedical questions, provided by the BioASQ challenge, demonstrated that our method exhibits significant improved performance when compared to four baseline systems. The proposed method achieves a roughly 10-point increase over the best baseline in terms of accuracy. Moreover, the obtained results show that using handcrafted lexico-syntactic patterns as features' provider of support vector machine (SVM) lead to the highest accuracy of 89.40 %.Conclusion: The proposed method can automatically classify BioASQ questions into one of the four categories: yes/no, factoid, list, and summary. Furthermore, the results demonstrated that our method produced the best classification performance compared to four baseline systems. [ABSTRACT FROM AUTHOR]

Introduction: Genomic profiling information is frequently available to oncologists, enabling targeted cancer therapy. Because clinically relevant information is rapidly emerging in the literature and elsewhere, there is a need for informatics technologies to support targeted therapies. To this end, we have developed a system for Automated Identification of Molecular Effects of Drugs, to help biomedical scientists curate this literature to facilitate decision support.Objectives: To create an automated system to identify assertions in the literature concerning drugs targeting genes with therapeutic implications and characterize the challenges inherent in automating this process in rapidly evolving domains.Methods: We used subject-predicate-object triples (semantic predications) and co-occurrence relations generated by applying the SemRep Natural Language Processing system to MEDLINE abstracts and ClinicalTrials.gov descriptions. We applied customized semantic queries to find drugs targeting genes of interest. The results were manually reviewed by a team of experts.Results: Compared to a manually curated set of relationships, recall, precision, and F2 were 0.39, 0.21, and 0.33, respectively, which represents a 3- to 4-fold improvement over a publically available set of predications (SemMedDB) alone. Upon review of ostensibly false positive results, 26% were considered relevant additions to the reference set, and an additional 61% were considered to be relevant for review. Adding co-occurrence data improved results for drugs in early development, but not their better-established counterparts.Conclusions: Precision medicine poses unique challenges for biomedical informatics systems that help domain experts find answers to their research questions. Further research is required to improve the performance of such systems, particularly for drugs in development. [ABSTRACT FROM AUTHOR]

Searching for health information online is becoming customary for more and more consumers every day, which makes the need for efficient and reliable question answering systems more pressing. An important contributor to the success rates of these systems is their ability to fully understand the consumers' questions. However, these questions are frequently longer than needed and mention peripheral information that is not useful in finding relevant answers. Question summarization is one of the potential solutions to simplifying long and complex consumer questions before attempting to find an answer. In this paper, we study the task of abstractive summarization for real-world consumer health questions. We develop an abstractive question summarization model that leverages the semantic interpretation of a question via recognition of medical entities, which enables generation of informative summaries. Towards this, we propose multiple Cloze tasks (i.e. the task of filing missing words in a given context) to identify the key medical entities that enforce the model to have better coverage in question-focus recognition. Additionally, we infuse the decoder inputs with question-type information to generate question-type driven summaries. When evaluated on the MeQSum benchmark corpus, our framework outperformed the state-of-the-art method by 10.2 ROUGE-L points. We also conducted a manual evaluation to assess the correctness of the generated summaries. [ABSTRACT FROM AUTHOR]

Abstract: Objectives: In this survey, we reviewed the current state of the art in biomedical QA (Question Answering), within a broader framework of semantic knowledge-based QA approaches, and projected directions for the future research development in this critical area of intersection between Artificial Intelligence, Information Retrieval, and Biomedical Informatics. Materials and methods: We devised a conceptual framework within which to categorize current QA approaches. In particular, we used “semantic knowledge-based QA” as a category under which to subsume QA techniques and approaches, both corpus-based and knowledge base (KB)-based, that utilize semantic knowledge-informed techniques in the QA process, and we further classified those approaches into three subcategories: (1) semantics-based, (2) inference-based, and (3) logic-based. Based on the framework, we first conducted a survey of open-domain or non-biomedical-domain QA approaches that belong to each of the three subcategories. We then conducted an in-depth review of biomedical QA, by first noting the characteristics of, and resources available for, biomedical QA and then reviewing medical QA approaches and biological QA approaches, in turn. The research articles reviewed in this paper were found and selected through online searches. Results: Our review suggested the following tasks ahead for the future research development in this area: (1) Construction of domain-specific typology and taxonomy of questions (biological QA), (2) Development of more sophisticated techniques for natural language (NL) question analysis and classification, (3) Development of effective methods for answer generation from potentially conflicting evidences, (4) More extensive and integrated utilization of semantic knowledge throughout the QA process, and (5) Incorporation of logic and reasoning mechanisms for answer inference. Conclusion: Corresponding to the growth of biomedical information, there is a growing need for QA systems that can help users better utilize the ever-accumulating information. Continued research toward development of more sophisticated techniques for processing NL text, for utilizing semantic knowledge, and for incorporating logic and reasoning mechanisms, will lead to more useful QA systems. [Copyright &y& Elsevier]

Background and Objective: Question answering (QA), the identification of short accurate answers to users questions written in natural language expressions, is a longstanding issue widely studied over the last decades in the open-domain. However, it still remains a real challenge in the biomedical domain as the most of the existing systems support a limited amount of question and answer types as well as still require further efforts in order to improve their performance in terms of precision for the supported questions. Here, we present a semantic biomedical QA system named SemBioNLQA which has the ability to handle the kinds of yes/no, factoid, list, and summary natural language questions.Methods: This paper describes the system architecture and an evaluation of the developed end-to-end biomedical QA system named SemBioNLQA, which consists of question classification, document retrieval, passage retrieval and answer extraction modules. It takes natural language questions as input, and outputs both short precise answers and summaries as results. The SemBioNLQA system, dealing with four types of questions, is based on (1) handcrafted lexico-syntactic patterns and a machine learning algorithm for question classification, (2) PubMed search engine and UMLS similarity for document retrieval, (3) the BM25 model, stemmed words and UMLS concepts for passage retrieval, and (4) UMLS metathesaurus, BioPortal synonyms, sentiment analysis and term frequency metric for answer extraction.Results and Conclusion: Compared with the current state-of-the-art biomedical QA systems, SemBioNLQA, a fully automated system, has the potential to deal with a large amount of question and answer types. SemBioNLQA retrieves quickly users' information needs by returning exact answers (e.g., "yes", "no", a biomedical entity name, etc.) and ideal answers (i.e., paragraph-sized summaries of relevant information) for yes/no, factoid and list questions, whereas it provides only the ideal answers for summary questions. Moreover, experimental evaluations performed on biomedical questions and answers provided by the BioASQ challenge especially in 2015, 2016 and 2017 (as part of our participation), show that SemBioNLQA achieves good performances compared with the most current state-of-the-art systems and allows a practical and competitive alternative to help information seekers find exact and ideal answers to their biomedical questions. The SemBioNLQA source code is publicly available at https://github.com/sarrouti/sembionlqa. [ABSTRACT FROM AUTHOR]

Biomedical question answering (QA) is a challenging task that has not been yet successfully solved, according to results on international benchmarks, such as BioASQ. Recent progress on deep neural networks has led to promising results in domain independent QA, but the lack of large datasets with biomedical question-answer pairs hinders their successful application to the domain of biomedicine. We propose a novel machine-learning based answer processing approach that exploits neural networks in an unsupervised way through word embeddings. Our approach first combines biomedical and general purpose tools to identify the candidate answers from a set of passages. Candidates are then represented using a combination of features based on both biomedical external resources and input textual sources, including features based on word embeddings. Candidates are then ranked based on the score given at the output of a binary classification model, trained from candidates extracted from a small number of questions, related passages and correct answer triplets from the BioASQ challenge. Our experimental results show that the use of word embeddings, combined with other features, improves the performance of answer processing in biomedical question answering. In addition, our results show that the use of several annotators improves the identification of answers in passages. Finally, our approach has participated in the last two versions (2017, 2018) of the BioASQ challenge achieving competitive results. [ABSTRACT FROM AUTHOR]

Background and Objective: Biomedical question type classification is one of the important components of an automatic biomedical question answering system. The performance of the latter depends directly on the performance of its biomedical question type classification system, which consists of assigning a category to each question in order to determine the appropriate answer extraction algorithm. This study aims to automatically classify biomedical questions into one of the four categories: (1) yes/no, (2) factoid, (3) list, and (4) summary., Methods: In this paper, we propose a biomedical question type classification method based on machine learning approaches to automatically assign a category to a biomedical question. First, we extract features from biomedical questions using the proposed handcrafted lexico-syntactic patterns. Then, we feed these features for machine-learning algorithms. Finally, the class label is predicted using the trained classifiers., Results: Experimental evaluations performed on large standard annotated datasets of biomedical questions, provided by the BioASQ challenge, demonstrated that our method exhibits significant improved performance when compared to four baseline systems. The proposed method achieves a roughly 10-point increase over the best baseline in terms of accuracy. Moreover, the obtained results show that using handcrafted lexico-syntactic patterns as features' provider of support vector machine (SVM) lead to the highest accuracy of 89.40 %., Conclusion: The proposed method can automatically classify BioASQ questions into one of the four categories: yes/no, factoid, list, and summary. Furthermore, the results demonstrated that our method produced the best classification performance compared to four baseline systems.