Clinical Assistant Diagnosis for Electronic Medical Record Based on Convolutional Neural Network

Automatically extracting useful information from electronic medical records along with conducting disease diagnoses is a promising task for both clinical decision support(CDS) and neural language processing(NLP). Most of the existing systems are based on artificially constructed knowledge bases, and then auxiliary diagnosis is done by rule matching. In this study, we present a clinical intelligent decision approach based on Convolutional Neural Networks(CNN), which can automatically extract high-level semantic information of electronic medical records and then perform automatic diagnosis without artificial construction of rules or knowledge bases. We use collected 18,590 copies of the real-world clinical electronic medical records to train and test the proposed model. Experimental results show that the proposed model can achieve 98.67\% accuracy and 96.02\% recall, which strongly supports that using convolutional neural network to automatically learn high-level semantic features of electronic medical records and then conduct assist diagnosis is feasible and effective.Comment: 9 pages, 4 figures, Accepted by Scientific Report

Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

User experiments with the Eurovision cross-language image retrieval system

In this paper we present Eurovision, a text-based system for cross-language (CL) image retrieval. The system is evaluated by multilingual users for two search tasks with the system configured in English and five other languages. To our knowledge this is the first published set of user experiments for CL image retrieval. We show that: (1) it is possible to create a usable multilingual search engine using little knowledge of any language other than English, (2) categorizing images assists the user's search, and (3) there are differences in the way users search between the proposed search tasks. Based on the two search tasks and user feedback, we describe important aspects of any CL image retrieval system

From Keyword Search to Exploration: How Result Visualization Aids Discovery on the Web

A key to the Web's success is the power of search. The elegant way in which search results are returned is usually remarkably effective. However, for exploratory search in which users need to learn, discover, and understand novel or complex topics, there is substantial room for improvement. Human computer interaction researchers and web browser designers have developed novel strategies to improve Web search by enabling users to conveniently visualize, manipulate, and organize their Web search results. This monograph offers fresh ways to think about search-related cognitive processes and describes innovative design approaches to browsers and related tools. For instance, while key word search presents users with results for specific information (e.g., what is the capitol of Peru), other methods may let users see and explore the contexts of their requests for information (related or previous work, conflicting information), or the properties that associate groups of information assets (group legal decisions by lead attorney). We also consider the both traditional and novel ways in which these strategies have been evaluated. From our review of cognitive processes, browser design, and evaluations, we reflect on the future opportunities and new paradigms for exploring and interacting with Web search results

Arabic Text Mining

The rapid growth of the internet has increased the number of online texts. This led to the rapid growth of the number of online texts in the Arabic language. The enormous amount of text must be organized into classes to make the analysis process and text retrieval easier. Text classification is, therefore, a key component of text mining. There are numerous systems and approaches for categorizing literature in English, European (French, German, Spanish), and Asian (Chinese, Japanese). In contrast, there are relatively few studies on categorizing Arabic literature due to the difficulty of the Arabic language. In this work, a brief explanation of key ideas relevant to Arabic text mining are introduced then a new classification system for the Arabic language is presented using light stemming and Classifier Na\"ive Bayesian (CNB). Texts from two classes: politics and sports, are included in our corpus. Some texts are added to the system, and the system correctly classified them, demonstrating the effectiveness of the system

Performance Analysis of Machine Learning Approaches in Automatic Classification of Arabic Language

Text classification (TC) is a crucial subject. The number of digital files available on the internet is enormous. The goal of TC is to categorize texts into a series of predetermined groups. The number of studies conducted on the English database is significantly higher than the number of studies conducted on the Arabic database. Therefore, this research analyzes the performance of automatic TC of the Arabic language using Machine Learning (ML) approaches. Further, Single-label Arabic News Articles Datasets (SANAD) are introduced, which contain three different datasets, namely Akhbarona, Khaleej, and Arabiya. Initially, the collected texts are pre-processed in which tokenization and stemming occur. In this research, three kinds of stemming are employed, namely light stemming, Khoja stemming, and no- stemming, to evaluate the effect of the pre-processing technique on Arabic TC performance. Moreover, feature extraction and feature weighting are performed; in feature weighting, the term weighting process is completed by the term frequency- inverse document frequency (tf-idf) method. In addition, this research selects C4.5, Support Vector Machine (SVM), and Naïve Bayes (NB) as a classification algorithm. The results indicated that the SVM and NB methods had attained higher accuracy than the C4.5 method. NB achieved the maximum accuracy with a performance of 99.9%

Utilizing image and caption information for biomedical document classification.

MOTIVATION: Biomedical research findings are typically disseminated through publications. To simplify access to domain-specific knowledge while supporting the research community, several biomedical databases devote significant effort to manual curation of the literature-a labor intensive process. The first step toward biocuration requires identifying articles relevant to the specific area on which the database focuses. Thus, automatically identifying publications relevant to a specific topic within a large volume of publications is an important task toward expediting the biocuration process and, in turn, biomedical research. Current methods focus on textual contents, typically extracted from the title-and-abstract. Notably, images and captions are often used in publications to convey pivotal evidence about processes, experiments and results. RESULTS: We present a new document classification scheme, using both image and caption information, in addition to titles-and-abstracts. To use the image information, we introduce a new image representation, namely Figure-word, based on class labels of subfigures. We use word embeddings for representing captions and titles-and-abstracts. To utilize all three types of information, we introduce two information integration methods. The first combines Figure-words and textual features obtained from captions and titles-and-abstracts into a single larger vector for document representation; the second employs a meta-classification scheme. Our experiments and results demonstrate the usefulness of the newly proposed Figure-words for representing images. Moreover, the results showcase the value of Figure-words, captions and titles-and-abstracts in providing complementary information for document classification; these three sources of information when combined, lead to an overall improved classification performance. AVAILABILITY AND IMPLEMENTATION: Source code and the list of PMIDs of the publications in our datasets are available upon request