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

Random Forests for Big Data

Big Data is one of the major challenges of statistical science and has numerous consequences from algorithmic and theoretical viewpoints. Big Data always involve massive data but they also often include online data and data heterogeneity. Recently some statistical methods have been adapted to process Big Data, like linear regression models, clustering methods and bootstrapping schemes. Based on decision trees combined with aggregation and bootstrap ideas, random forests were introduced by Breiman in 2001. They are a powerful nonparametric statistical method allowing to consider in a single and versatile framework regression problems, as well as two-class and multi-class classification problems. Focusing on classification problems, this paper proposes a selective review of available proposals that deal with scaling random forests to Big Data problems. These proposals rely on parallel environments or on online adaptations of random forests. We also describe how related quantities -- such as out-of-bag error and variable importance -- are addressed in these methods. Then, we formulate various remarks for random forests in the Big Data context. Finally, we experiment five variants on two massive datasets (15 and 120 millions of observations), a simulated one as well as real world data. One variant relies on subsampling while three others are related to parallel implementations of random forests and involve either various adaptations of bootstrap to Big Data or to "divide-and-conquer" approaches. The fifth variant relates on online learning of random forests. These numerical experiments lead to highlight the relative performance of the different variants, as well as some of their limitations

Adversarial Removal of Demographic Attributes from Text Data

Recent advances in Representation Learning and Adversarial Training seem to succeed in removing unwanted features from the learned representation. We show that demographic information of authors is encoded in -- and can be recovered from -- the intermediate representations learned by text-based neural classifiers. The implication is that decisions of classifiers trained on textual data are not agnostic to -- and likely condition on -- demographic attributes. When attempting to remove such demographic information using adversarial training, we find that while the adversarial component achieves chance-level development-set accuracy during training, a post-hoc classifier, trained on the encoded sentences from the first part, still manages to reach substantially higher classification accuracies on the same data. This behavior is consistent across several tasks, demographic properties and datasets. We explore several techniques to improve the effectiveness of the adversarial component. Our main conclusion is a cautionary one: do not rely on the adversarial training to achieve invariant representation to sensitive features

A Multi-Gene Genetic Programming Application for Predicting Students Failure at School

Several efforts to predict student failure rate (SFR) at school accurately still remains a core problem area faced by many in the educational sector. The procedure for forecasting SFR are rigid and most often times require data scaling or conversion into binary form such as is the case of the logistic model which may lead to lose of information and effect size attenuation. Also, the high number of factors, incomplete and unbalanced dataset, and black boxing issues as in Artificial Neural Networks and Fuzzy logic systems exposes the need for more efficient tools. Currently the application of Genetic Programming (GP) holds great promises and has produced tremendous positive results in different sectors. In this regard, this study developed GPSFARPS, a software application to provide a robust solution to the prediction of SFR using an evolutionary algorithm known as multi-gene genetic programming. The approach is validated by feeding a testing data set to the evolved GP models. Result obtained from GPSFARPS simulations show its unique ability to evolve a suitable failure rate expression with a fast convergence at 30 generations from a maximum specified generation of 500. The multi-gene system was also able to minimize the evolved model expression and accurately predict student failure rate using a subset of the original expressionComment: 14 pages, 9 figures, Journal paper. arXiv admin note: text overlap with arXiv:1403.0623 by other author

Learning From Labeled And Unlabeled Data: An Empirical Study Across Techniques And Domains

There has been increased interest in devising learning techniques that combine unlabeled data with labeled data ? i.e. semi-supervised learning. However, to the best of our knowledge, no study has been performed across various techniques and different types and amounts of labeled and unlabeled data. Moreover, most of the published work on semi-supervised learning techniques assumes that the labeled and unlabeled data come from the same distribution. It is possible for the labeling process to be associated with a selection bias such that the distributions of data points in the labeled and unlabeled sets are different. Not correcting for such bias can result in biased function approximation with potentially poor performance. In this paper, we present an empirical study of various semi-supervised learning techniques on a variety of datasets. We attempt to answer various questions such as the effect of independence or relevance amongst features, the effect of the size of the labeled and unlabeled sets and the effect of noise. We also investigate the impact of sample-selection bias on the semi-supervised learning techniques under study and implement a bivariate probit technique particularly designed to correct for such bias