KvGR: A Graph-Based Interface for Explorative Sequential Question Answering on Heterogeneous Information Sources
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ABSTRACT:
SUBMITTER: Jose J
PROVIDER: S-EPMC7148211 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
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Project description:Question answering (QA) is a hot field of research in Natural Language Processing. A big challenge in this field is to answer questions from knowledge-dependable domain. Since traditional QA hardly satisfies some knowledge-dependable situations, such as disease diagnosis, drug recommendation, etc. In recent years, researches focus on knowledge-based question answering (KBQA). However, there still exist some problems in KBQA, traditional KBQA is limited by a range of historical cases and takes too much human labor. To address the problems, in this paper, we propose an approach of knowledge graph based question answering (KGQA) method for medical domain, which firstly constructs a medical knowledge graph by extracting named entities and relations between the entities from medical documents. Then, in order to understand a question, it extracts the key information in the question according to the named entities, and meanwhile, it recognizes the questions' intentions by adopting information gain. The next an inference method based on weighted path ranking on the knowledge graph is proposed to score the related entities according to the key information and intention of a given question. Finally, it extracts the inferred candidate entities to construct answers. Our approach can understand questions, connect the questions to the knowledge graph and inference the answers on the knowledge graph. Theoretical analysis and real-life experimental results show the efficiency of our approach.
| S-EPMC8444078 | biostudies-literature
Project description:BackgroundIn recent years, large language models (LLMs) have shown promise in various domains, notably in biomedical sciences. However, their real-world application is often limited by issues like erroneous outputs and hallucinatory responses.ResultsWe developed the knowledge graph-based thought (KGT) framework, an innovative solution that integrates LLMs with knowledge graphs (KGs) to improve their initial responses by utilizing verifiable information from KGs, thus significantly reducing factual errors in reasoning. The KGT framework demonstrates strong adaptability and performs well across various open-source LLMs. Notably, KGT can facilitate the discovery of new uses for existing drugs through potential drug-cancer associations and can assist in predicting resistance by analyzing relevant biomarkers and genetic mechanisms. To evaluate the knowledge graph question answering task within biomedicine, we utilize a pan-cancer knowledge graph to develop a pan-cancer question answering benchmark, named pan-cancer question answering.ConclusionsThe KGT framework substantially improves the accuracy and utility of LLMs in the biomedical field. This study serves as a proof of concept, demonstrating its exceptional performance in biomedical question answering.
| S-EPMC11702363 | biostudies-literature
Project description:Many different methods for prompting large language models have been developed since the emergence of OpenAI's ChatGPT in November 2022. In this work, we evaluate six different few-shot prompting methods. The first set of experiments evaluates three frameworks that focus on the quantity or type of shots in a prompt: a baseline method with a simple prompt and a small number of shots, random few-shot prompting with 10, 20, and 30 shots, and similarity-based few-shot prompting. The second set of experiments target optimizing the prompt or enhancing shots through Large Language Model (LLM)-generated explanations, using three prompting frameworks: Explain then Translate, Question Decomposition Meaning Representation, and Optimization by Prompting. We evaluate these six prompting methods on the newly created Spider4SPARQL benchmark, as it is the most complex SPARQL-based Knowledge Graph Question Answering (KGQA) benchmark to date. Across the various prompting frameworks used, the commercial model is unable to achieve a score over 51%, indicating that KGQA, especially for complex queries, with multiple hops, set operations and filters remains a challenging task for LLMs. Our experiments find that the most successful prompting framework for KGQA is a simple prompt combined with an ontology and five random shots.
| S-EPMC11770024 | biostudies-literature
Project description:Knowledge graphs have become a common approach for knowledge representation. Yet, the application of graph methodology is elusive due to the sheer number and complexity of knowledge sources. In addition, semantic incompatibilities hinder efforts to harmonize and integrate across these diverse sources. As part of The Biomedical Translator Consortium, we have developed a knowledge graph-based question-answering system designed to augment human reasoning and accelerate translational scientific discovery: the Translator system. We have applied the Translator system to answer biomedical questions in the context of a broad array of diseases and syndromes, including Fanconi anemia, primary ciliary dyskinesia, multiple sclerosis, and others. A variety of collaborative approaches have been used to research and develop the Translator system. One recent approach involved the establishment of a monthly "Question-of-the-Month (QotM) Challenge" series. Herein, we describe the structure of the QotM Challenge; the six challenges that have been conducted to date on drug-induced liver injury, cannabidiol toxicity, coronavirus infection, diabetes, psoriatic arthritis, and ATP1A3-related phenotypes; the scientific insights that have been gleaned during the challenges; and the technical issues that were identified over the course of the challenges and that can now be addressed to foster further development of the prototype Translator system. We close with a discussion on Large Language Models such as ChatGPT and highlight differences between those models and the Translator system.
| S-EPMC10603356 | biostudies-literature
Project description:The COVID-19 global pandemic has resulted in international efforts to understand, track, and mitigate the disease, yielding a significant corpus of COVID-19 and SARS-CoV-2-related publications across scientific disciplines. Throughout 2020, over 400,000 coronavirus-related publications have been collected through the COVID-19 Open Research Dataset. Here, we present CO-Search, a semantic, multi-stage, search engine designed to handle complex queries over the COVID-19 literature, potentially aiding overburdened health workers in finding scientific answers and avoiding misinformation during a time of crisis. CO-Search is built from two sequential parts: a hybrid semantic-keyword retriever, which takes an input query and returns a sorted list of the 1000 most relevant documents, and a re-ranker, which further orders them by relevance. The retriever is composed of a deep learning model (Siamese-BERT) that encodes query-level meaning, along with two keyword-based models (BM25, TF-IDF) that emphasize the most important words of a query. The re-ranker assigns a relevance score to each document, computed from the outputs of (1) a question-answering module which gauges how much each document answers the query, and (2) an abstractive summarization module which determines how well a query matches a generated summary of the document. To account for the relatively limited dataset, we develop a text augmentation technique which splits the documents into pairs of paragraphs and the citations contained in them, creating millions of (citation title, paragraph) tuples for training the retriever. We evaluate our system ( http://einstein.ai/covid ) on the data of the TREC-COVID information retrieval challenge, obtaining strong performance across multiple key information retrieval metrics.
| S-EPMC8041998 | biostudies-literature
Project description:BackgroundInjection drug use (IDU) can increase mortality and morbidity. Therefore, identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients' electronic health records (EHR) is difficult because there is no other structured data available, such as International Classification of Disease (ICD) codes, and IDU is most often documented in unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools.MethodsTo address this gap in clinical information, we design a question-answering (QA) framework to extract information on IDU from clinical notes for use in clinical operations. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We use 2323 clinical notes of 1145 patients curated from the US Department of Veterans Affairs (VA) Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model's ability to extract IDU-related information from temporally out-of-distribution data.ResultsHere, we show that for a strict match between gold-standard and predicted answers, the QA model achieves a 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains a 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data.ConclusionsOur study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.
| S-EPMC10991373 | biostudies-literature
Project description:ObjectivesRadiology reports contain important clinical information that can be used to automatically construct fine-grained labels for applications requiring deep phenotyping. We propose a two-turn question answering (QA) method based on a transformer language model, BERT, for extracting detailed spatial information from radiology reports. We aim to demonstrate the advantage that a multi-turn QA framework provides over sequence-based methods for extracting fine-grained information.MethodsOur proposed method identifies spatial and descriptor information by answering queries given a radiology report text. We frame the extraction problem such that all the main radiology entities (e.g., finding, device, anatomy) and the spatial trigger terms (denoting the presence of a spatial relation between finding/device and anatomical location) are identified in the first turn. In the subsequent turn, various other contextual information that acts as important spatial roles with respect to a spatial trigger term are extracted along with identifying the spatial and other descriptor terms qualifying a radiological entity. The queries are constructed using separate templates for the two turns and we employ two query variations in the second turn.ResultsWhen compared to the best-reported work on this task using a traditional sequence tagging method, the two-turn QA model exceeds its performance on every component. This includes promising improvements of 12, 13, and 12 points in the average F1 scores for identifying the spatial triggers, Figure, and Ground frame elements, respectively.DiscussionOur experiments suggest that incorporating domain knowledge in the query (a general description about a frame element) helps in obtaining better results for some of the spatial and descriptive frame elements, especially in the case of the clinical pre-trained BERT model. We further highlight that the two-turn QA approach fits well for extracting information for complex schema where the objective is to identify all the frame elements linked to each spatial trigger and finding/device/anatomy entity, thereby enabling the extraction of more comprehensive information in the radiology domain.ConclusionExtracting fine-grained spatial information from text in the form of answering natural language queries holds potential in achieving better results when compared to more standard sequence labeling-based approaches.
| S-EPMC9072592 | biostudies-literature
Project description:SummaryKnowledge graphs (KGs) are quickly becoming a common-place tool for storing relationships between entities from which higher-level reasoning can be conducted. KGs are typically stored in a graph-database format, and graph-database queries can be used to answer questions of interest that have been posed by users such as biomedical researchers. For simple queries, the inclusion of direct connections in the KG and the storage and analysis of query results are straightforward; however, for complex queries, these capabilities become exponentially more challenging with each increase in complexity of the query. For instance, one relatively complex query can yield a KG with hundreds of thousands of query results. Thus, the ability to efficiently query, store, rank and explore sub-graphs of a complex KG represents a major challenge to any effort designed to exploit the use of KGs for applications in biomedical research and other domains. We present Reasoning Over Biomedical Objects linked in Knowledge Oriented Pathways as an abstraction layer and user interface to more easily query KGs and store, rank and explore query results.Availability and implementationAn instance of the ROBOKOP UI for exploration of the ROBOKOP Knowledge Graph can be found at http://robokop.renci.org. The ROBOKOP Knowledge Graph can be accessed at http://robokopkg.renci.org. Code and instructions for building and deploying ROBOKOP are available under the MIT open software license from https://github.com/NCATS-Gamma/robokop.Supplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC6954664 | biostudies-literature
Project description:Open-domain question answering (OpenQA) is one of the most challenging yet widely investigated problems in natural language processing. It aims at building a system that can answer any given question from large-scale unstructured text or structured knowledge-base. To solve this problem, researchers traditionally use information retrieval methods to retrieve the most relevant documents and then use answer extractions techniques to extract the answer or passage from the candidate documents. In recent years, deep learning techniques have shown great success in OpenQA by using dense representation for document retrieval and reading comprehension for answer extraction. However, despite the advancement in the English language OpenQA, other languages such as Arabic have received less attention and are often addressed using traditional methods. In this paper, we use deep learning methods for Arabic OpenQA. The model consists of document retrieval to retrieve passages relevant to a question from large-scale free text resources such as Wikipedia and an answer reader to extract the precise answer to the given question. The model implements dense passage retriever for the passage retrieval task and the AraELECTRA for the reading comprehension task. The result was compared to traditional Arabic OpenQA approaches and deep learning methods in the English OpenQA. The results show that the dense passage retriever outperforms the traditional Term Frequency-Inverse Document Frequency (TF-IDF) information retriever in terms of the top-20 passage retrieval accuracy and improves our end-to-end question answering system in two Arabic question-answering benchmark datasets.
| S-EPMC9138168 | biostudies-literature
Project description:Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/.
| S-EPMC4572360 | biostudies-literature