Model Dan Metoda Arsitektur Pada Sistem Tanya Jawab Medis

Pada makalah ini, akan dilakukan survey beberapa penelitian yang membahas mengenai sistem tanya jawab dengan domain pada bidang medis (medical question answering = MedQuAn). Sistem MedQuAn mengolah pertanyaan yang diajukan dalam bentuk teks bahasa alami dan kemudian sistem akan memberikan jawaban yang relevan. Makalah ini mencoba menelaah modul konseptual MedQuAn, bahwa sistem tanya jawab terdiri dari tiga komponen inti yang berbeda beserta metoda/ pendekatan yang digunakan. Ketiga komponen inti tersebut adalah klasifikasi pertanyaan, pencarian dokumen, dan ekstraksi jawaban. Hasil akhir dari survey ini adalah sebuah kontribusi untuk pengembangan penelitian di masa mendatang di domain MedQuAn khususnya untuk sistem tanya jawab medis dengan menggunakan bahasa Indonesia

Model dan Metoda Arsitektur pada Sistem Tanya Jawab Medis

Pada makalah ini, akan dilakukan survey beberapa penelitian yang membahas mengenai sistem tanya jawab dengan domain pada bidang medis (medical question answering = MedQuAn). Sistem MedQuAn mengolah pertanyaan yang diajukan dalam bentuk teks bahasa alami dan kemudian sistem akan memberikan jawaban yang relevan. Makalah ini mencoba menelaah modul konseptual MedQuAn, bahwa sistem tanya jawab terdiri dari tiga komponen inti yang berbeda beserta metoda/ pendekatan yang digunakan. Ketiga komponen inti tersebut adalah klasifikasi pertanyaan, pencarian dokumen, dan ekstraksi jawaban. Hasil akhir dari survey ini adalah sebuah kontribusi untuk pengembangan penelitian di masa mendatang di domain MedQuAn khususnya untuk sistem tanya jawab medis dengan menggunakan bahasa Indonesia

An ontology for clinical questions about the contents of patient notes

AbstractObjectiveMany studies have been completed on question classification in the open domain, however only limited work focuses on the medical domain. As well, to the best of our knowledge, most of these medical question classifications were designed for literature based question and answering systems. This paper focuses on a new direction, which is to design a novel question processing and classification model for answering clinical questions applied to electronic patient notes.MethodsThere are four main steps in the work. Firstly, a relatively large set of clinical questions was collected from staff in an Intensive Care Unit. Then, a clinical question taxonomy was designed for question and answering purposes. Subsequently an annotation guideline was created and used to annotate the question set. Finally, a multilayer classification model was built to classify the clinical questions.ResultsThrough the initial classification experiments, we realized that the general features cannot contribute to high performance of a minimum classifier (a small data set with multiple classes). Thus, an automatic knowledge discovery and knowledge reuse process was designed to boost the performance by extracting and expanding the specific features of the questions. In the evaluation, the results show around 90% accuracy can be achieved in the answerable subclass classification and generic question templates classification. On the other hand, the machine learning method does not perform well at identifying the category of unanswerable questions, due to the asymmetric distribution.ConclusionsIn this paper, a comprehensive study on clinical questions has been completed. A major outcome of this work is the multilayer classification model. It serves as a major component of a patient records based clinical question and answering system as our studies continue. As well, the question collections can be reused by the research community to improve the efficiency of their own question and answering systems

A comparative approach to Question Answering Systems

In this paper I will analyze three different algorithms and approaches to implement Question Answering Systems (QA-Systems). I will analyze the efficiency, strengths, and weaknesses of multiple algorithms by explaining them in detail and comparing them with each other. The overarching aim of this thesis is to explore ideas that can be used to create a truly open context QA-System. Open context QA-Systems remain an open problem. The various algorithms and approaches presented in this work will be focused on complex questions. Complex questions are usually verbose and the context of the question is equally important to answer the query as is the question itself. Such questions represent an interesting problem in the field because they can be answered and written in a number of distinct ways. Also, the answer structure is not always the same and the QA-System needs to compensate for this. The analysis of complex questions differ between contexts. Contexts are the topic to which a complex question belongs, e.g. Biology, literature, etc… The analysis of the answer also differs according to the corpus used. Corpus is a set of documents, belonging to a specific context, where we can find the answer to a specified question. I will start by explaining various algorithms and approaches. I will then analyze its different parts. Finally, I will present some ideas on how to implement QA-Systems

Question answering systems for health professionals at the point of care -- a systematic review

Objective: Question answering (QA) systems have the potential to improve the quality of clinical care by providing health professionals with the latest and most relevant evidence. However, QA systems have not been widely adopted. This systematic review aims to characterize current medical QA systems, assess their suitability for healthcare, and identify areas of improvement. Materials and methods: We searched PubMed, IEEE Xplore, ACM Digital Library, ACL Anthology and forward and backward citations on 7th February 2023. We included peer-reviewed journal and conference papers describing the design and evaluation of biomedical QA systems. Two reviewers screened titles, abstracts, and full-text articles. We conducted a narrative synthesis and risk of bias assessment for each study. We assessed the utility of biomedical QA systems. Results: We included 79 studies and identified themes, including question realism, answer reliability, answer utility, clinical specialism, systems, usability, and evaluation methods. Clinicians' questions used to train and evaluate QA systems were restricted to certain sources, types and complexity levels. No system communicated confidence levels in the answers or sources. Many studies suffered from high risks of bias and applicability concerns. Only 8 studies completely satisfied any criterion for clinical utility, and only 7 reported user evaluations. Most systems were built with limited input from clinicians. Discussion: While machine learning methods have led to increased accuracy, most studies imperfectly reflected real-world healthcare information needs. Key research priorities include developing more realistic healthcare QA datasets and considering the reliability of answer sources, rather than merely focusing on accuracy.Comment: Accepted to the Journal of the American Medical Informatics Association (JAMIA

Named Entity Recognition in Chinese Clinical Text

Objective: Named entity recognition (NER) is one of the fundamental tasks in natural language processing (NLP). In the medical domain, there have been a number of studies on NER in English clinical notes; however, very limited NER research has been done on clinical notes written in Chinese. The goal of this study is to develop corpora, methods, and systems for NER in Chinese clinical text. Materials and methods: To study entities in Chinese clinical text, we started with building annotated clinical corpora in Chinese. We developed an NER annotation guideline in Chinese by extending the one used in the 2010 i2b2 NLP challenge. We randomly selected 400 admission notes and 400 discharge summaries from Peking Union Medical College Hospital (PUMCH) in China. For each note, four types of entities including clinical problems, procedures, labs, and medications were annotated according to the developed guideline. In addition, an annotation tool was developed to assist two MD students to annotate Chinese clinical documents. A comparison of entity distribution between Chinese and English clinical notes (646 English and 400 Chinese discharge summaries) was performed using the annotated corpora, to identify the important features for NER. In the NER study, two-thirds of the 400 notes were used for training the NER systems and one-third were used for testing. We investigated the effects of different types of features including bag-of-characters, word segmentation, part-of-speech, and section information, with different machine learning (ML) algorithms including Conditional Random Fields (CRF), Support Vector Machines (SVM), Maximum Entropy (ME), and Structural Support Vector Machines (SSVM) on the Chinese clinical NER task. All classifiers were trained on the training dataset, evaluated on the test set, and microaveraged precision, recall, and F-measure were reported. Results: Our evaluation on the independent test set showed that most types of features were beneficial to Chinese NER systems, although the improvements were limited. By combining word segmentation and section information, the system achieved the highest performance, indicating that these two types of features are complementary to each other. When the same types of optimized features were used, CRF and SSVM outperformed SVM and ME. More specifically, SSVM reached the highest performance among the four algorithms, with F-measures of 93.51% and 90.01% for admission notes and discharge summaries respectively. Conclusions: In this study, we created large annotated datasets of Chinese admission notes and discharge summaries and then systematically evaluated different types of features (e.g., syntactic, semantic, and segmentation information) and four ML algorithms including CRF, SVM, SSVM, and ME for clinical NER in Chinese. To the best of our knowledge, this is one of the earliest comprehensive effort in Chinese clinical NER research and we believe it will provide valuable insights to NLP research in Chinese clinical text. Our results suggest that both word segmentation and section information improves NER in Chinese clinical text, and SSVM, a recent sequential labelling algorithm, outperformed CRF and other classification algorithms. Our best system achieved F-measures of 90.01% and 93.52% on Chinese discharge summaries and admission notes, respectively, indicating a promising start on Chinese NLP research

A knowledge based method for the medical question answering problem

In this paper, a restricted domain question answering (QA) system is described. The design architecture of this QA system and the features that allow the adaptation of the QA system to the medical domain are also presented. The advantages of this QA system include the simple process of defining the question taxonomy answered by the system as well as the possibility of locally or remotely managed document collections. The main computing methods of the QA system are based on the application of natural language processing (NLP) techniques to infer the logic forms and on the treatment of the logic forms. The knowledge of the system is acquired through the use of two different resources: Unified Medical Language System (UMLS) to handle the medical terminology and WordNet to manage the open-domain terminology.This work has been partially funded by the Spanish Government funder project CICyT number TIN2006-15265-C06-0 and PROFIT number PI051438, by the European Union under project number FP6-IST-2005-33860 and by the Valencia Government under project number GV06/028