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

KACST Arabic Text Classification Project: Overview and Preliminary Results

Electronically formatted Arabic free-texts can be found in abundance these days on the World Wide Web, often linked to commercial enterprises and/or government organizations. Vast tracts of knowledge and relations lie hidden within these texts, knowledge that can be exploited once the correct intelligent tools have been identified and applied. For example, text mining may help with text classification and categorization. Text classification aims to automatically assign text to a predefined category based on identifiable linguistic features. Such a process has different useful applications including, but not restricted to, E-Mail spam detection, web pages content filtering, and automatic message routing. In this paper an overview of King Abdulaziz City for Science and Technology (KACST) Arabic Text Classification Project will be illustrated along with some preliminary results. This project will contribute to the better understanding and elaboration of Arabic text classification techniques

Mental distress detection and triage in forum posts: the LT3 CLPsych 2016 shared task system

This paper describes the contribution of LT3 for the CLPsych 2016 Shared Task on automatic triage of mental health forum posts. Our systems use multiclass Support Vector Machines (SVM), cascaded binary SVMs and ensembles with a rich feature set. The best systems obtain macro-averaged F-scores of 40% on the full task and 80% on the green versus alarming distinction. Multiclass SVMs with all features score best in terms of F-score, whereas feature filtering with bi-normal separation and classifier ensembling are found to improve recall of alarming posts

Evaluation of linear classifiers on articles containing pharmacokinetic evidence of drug-drug interactions

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, the inclusion of literature mining methodologies in DDI workflows is still very preliminary. One area that can benefit from literature mining is the automatic identification of a large number of potential DDIs, whose pharmacological mechanisms and clinical significance can then be studied via in vitro pharmacology and in populo pharmaco-epidemiology. Experiments. We implemented a set of classifiers for identifying published articles relevant to experimental pharmacokinetic DDI evidence. These documents are important for identifying causal mechanisms behind putative drug-drug interactions, an important step in the extraction of large numbers of potential DDIs. We evaluate performance of several linear classifiers on PubMed abstracts, under different feature transformation and dimensionality reduction methods. In addition, we investigate the performance benefits of including various publicly-available named entity recognition features, as well as a set of internally-developed pharmacokinetic dictionaries. Results. We found that several classifiers performed well in distinguishing relevant and irrelevant abstracts. We found that the combination of unigram and bigram textual features gave better performance than unigram features alone, and also that normalization transforms that adjusted for feature frequency and document length improved classification. For some classifiers, such as linear discriminant analysis (LDA), proper dimensionality reduction had a large impact on performance. Finally, the inclusion of NER features and dictionaries was found not to help classification.Comment: Pacific Symposium on Biocomputing, 201

Follow-up question handling in the IMIX and Ritel systems: A comparative study

One of the basic topics of question answering (QA) dialogue systems is how follow-up questions should be interpreted by a QA system. In this paper, we shall discuss our experience with the IMIX and Ritel systems, for both of which a follow-up question handling scheme has been developed, and corpora have been collected. These two systems are each other's opposites in many respects: IMIX is multimodal, non-factoid, black-box QA, while Ritel is speech, factoid, keyword-based QA. Nevertheless, we will show that they are quite comparable, and that it is fruitful to examine the similarities and differences. We shall look at how the systems are composed, and how real, non-expert, users interact with the systems. We shall also provide comparisons with systems from the literature where possible, and indicate where open issues lie and in what areas existing systems may be improved. We conclude that most systems have a common architecture with a set of common subtasks, in particular detecting follow-up questions and finding referents for them. We characterise these tasks using the typical techniques used for performing them, and data from our corpora. We also identify a special type of follow-up question, the discourse question, which is asked when the user is trying to understand an answer, and propose some basic methods for handling it

Highly comparative feature-based time-series classification

A highly comparative, feature-based approach to time series classification is introduced that uses an extensive database of algorithms to extract thousands of interpretable features from time series. These features are derived from across the scientific time-series analysis literature, and include summaries of time series in terms of their correlation structure, distribution, entropy, stationarity, scaling properties, and fits to a range of time-series models. After computing thousands of features for each time series in a training set, those that are most informative of the class structure are selected using greedy forward feature selection with a linear classifier. The resulting feature-based classifiers automatically learn the differences between classes using a reduced number of time-series properties, and circumvent the need to calculate distances between time series. Representing time series in this way results in orders of magnitude of dimensionality reduction, allowing the method to perform well on very large datasets containing long time series or time series of different lengths. For many of the datasets studied, classification performance exceeded that of conventional instance-based classifiers, including one nearest neighbor classifiers using Euclidean distances and dynamic time warping and, most importantly, the features selected provide an understanding of the properties of the dataset, insight that can guide further scientific investigation

All mixed up? Finding the optimal feature set for general readability prediction and its application to English and Dutch

Readability research has a long and rich tradition, but there has been too little focus on general readability prediction without targeting a specific audience or text genre. Moreover, though NLP-inspired research has focused on adding more complex readability features there is still no consensus on which features contribute most to the prediction. In this article, we investigate in close detail the feasibility of constructing a readability prediction system for English and Dutch generic text using supervised machine learning. Based on readability assessments by both experts and a crowd, we implement different types of text characteristics ranging from easy-to-compute superficial text characteristics to features requiring a deep linguistic processing, resulting in ten different feature groups. Both a regression and classification setup are investigated reflecting the two possible readability prediction tasks: scoring individual texts or comparing two texts. We show that going beyond correlation calculations for readability optimization using a wrapper-based genetic algorithm optimization approach is a promising task which provides considerable insights in which feature combinations contribute to the overall readability prediction. Since we also have gold standard information available for those features requiring deep processing we are able to investigate the true upper bound of our Dutch system. Interestingly, we will observe that the performance of our fully-automatic readability prediction pipeline is on par with the pipeline using golden deep syntactic and semantic information