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

Popular Ensemble Methods: An Empirical Study

An ensemble consists of a set of individually trained classifiers (such as neural networks or decision trees) whose predictions are combined when classifying novel instances. Previous research has shown that an ensemble is often more accurate than any of the single classifiers in the ensemble. Bagging (Breiman, 1996c) and Boosting (Freund and Shapire, 1996; Shapire, 1990) are two relatively new but popular methods for producing ensembles. In this paper we evaluate these methods on 23 data sets using both neural networks and decision trees as our classification algorithm. Our results clearly indicate a number of conclusions. First, while Bagging is almost always more accurate than a single classifier, it is sometimes much less accurate than Boosting. On the other hand, Boosting can create ensembles that are less accurate than a single classifier -- especially when using neural networks. Analysis indicates that the performance of the Boosting methods is dependent on the characteristics of the data set being examined. In fact, further results show that Boosting ensembles may overfit noisy data sets, thus decreasing its performance. Finally, consistent with previous studies, our work suggests that most of the gain in an ensemble's performance comes in the first few classifiers combined; however, relatively large gains can be seen up to 25 classifiers when Boosting decision trees

Content-Based Book Recommending Using Learning for Text Categorization

Recommender systems improve access to relevant products and information by making personalized suggestions based on previous examples of a user's likes and dislikes. Most existing recommender systems use social filtering methods that base recommendations on other users' preferences. By contrast, content-based methods use information about an item itself to make suggestions. This approach has the advantage of being able to recommended previously unrated items to users with unique interests and to provide explanations for its recommendations. We describe a content-based book recommending system that utilizes information extraction and a machine-learning algorithm for text categorization. Initial experimental results demonstrate that this approach can produce accurate recommendations.Comment: 8 pages, 3 figures, Submission to Fourth ACM Conference on Digital Librarie

Prospects of a mathematical theory of human behavior in complex man-machine systems tasks

A hierarchy of human activities is derived by analyzing automobile driving in general terms. A structural description leads to a block diagram and a time-sharing computer analogy. The range of applicability of existing mathematical models is considered with respect to the hierarchy of human activities in actual complex tasks. Other mathematical tools so far not often applied to man machine systems are also discussed. The mathematical descriptions at least briefly considered here include utility, estimation, control, queueing, and fuzzy set theory as well as artificial intelligence techniques. Some thoughts are given as to how these methods might be integrated and how further work might be pursued

Machine Learning Techniques for Stellar Light Curve Classification

We apply machine learning techniques in an attempt to predict and classify stellar properties from noisy and sparse time series data. We preprocessed over 94 GB of Kepler light curves from MAST to classify according to ten distinct physical properties using both representation learning and feature engineering approaches. Studies using machine learning in the field have been primarily done on simulated data, making our study one of the first to use real light curve data for machine learning approaches. We tuned our data using previous work with simulated data as a template and achieved mixed results between the two approaches. Representation learning using a Long Short-Term Memory (LSTM) Recurrent Neural Network (RNN) produced no successful predictions, but our work with feature engineering was successful for both classification and regression. In particular, we were able to achieve values for stellar density, stellar radius, and effective temperature with low error (~ 2 - 4%) and good accuracy (~ 75%) for classifying the number of transits for a given star. The results show promise for improvement for both approaches upon using larger datasets with a larger minority class. This work has the potential to provide a foundation for future tools and techniques to aid in the analysis of astrophysical data.Comment: Accepted to The Astronomical Journa

The management of context-sensitive features: A review of strategies

In this paper, we review five heuristic strategies for handling context- sensitive features in supervised machine learning from examples. We discuss two methods for recovering lost (implicit) contextual information. We mention some evidence that hybrid strategies can have a synergetic effect. We then show how the work of several machine learning researchers fits into this framework. While we do not claim that these strategies exhaust the possibilities, it appears that the framework includes all of the techniques that can be found in the published literature on context-sensitive learning