User expectations of web search are changing. They are expecting search engines to answer questions, to be more conversational, and to offer means to complete tasks on their behalf. At the same time, to increase the breadth of tasks that personal digital assistants (PDAs), such as Microsoft»s Cortana or Amazon»s Alexa, are capable of, PDAs need to better utilize information about the world, a significant amount of which is available in the knowledge bases and answers built for search engines. It thus seems likely that the underlying systems that power web search and PDAs will converge. This demonstration presents a system that merges elements of traditional multi-turn dialog systems with web based question answering. This demo focuses on the automatic composition of semantic functional units, Botlets, to generate responses to user»s natural language (NL) queries. We show that such a system can be trained to combine information from search engine answers with PDA tasks to enable new user experiences.

Next Generation Sequencing (NGS) technologies have led to fast and inexpensive production of large amounts of biological sequence data, including nucleotide sequences and derived protein sequences. These fast-increasing volumes of data pose challenges to computational methods for annotation. Machine learning approaches, primarily supervised algorithms, have been widely used to assist with classification tasks in bioinformatics. However, supervised algorithms rely on large amounts of labeled data in order to produce quality predictors. Oftentimes, labeled data is difficult and expensive to acquire in sufficiently large quantities. When only limited amounts of labeled data but considerably larger amounts of unlabeled data are available for a specific annotation problem, semi-supervised learning approaches represent a cost-effective alternative. In this work, we focus on a special case of semi-supervised learning, namely transductive learning, in which the algorithm has access during the training phase to the instances that need to be labeled. Transduction is particularly suitable for biological sequence classification, where the goal is generally to label a given set of unlabeled instances. However, a challenge that needs to be addressed in this context consists of identification of compact sets of informative features. Given the lack of labeled data, standard supervised feature selection methods may result in unreliable features. Therefore, we study recently proposed unsupervised feature construction approaches together with transductive learning. Experimental results on two classification problems, namely cassette exon identification and protein localization, show that the unsupervised features result in better performance than the supervised features.

The reduced cost of the next generation sequencing technologies provides opportunities to study non-model organisms. However, one challenge is the large volume of data generated and, thus, the need to use automated approaches to annotate these data. Machine learning algorithms could provide a cost-effective solution but they need lots of labeled data and informative features to represent these data. Our proposed approach addresses both these problems by using a domain adaptation classifier in conjunction with features generated with unsupervised techniques to annotate biological sequence data.

Alternative splicing is a phenomenon that gives rise to multiple mRNA transcripts from a single gene. It is believed that a large number of genes undergoes alternative splicing. Predicting alternative splicing events is a problem of great interest, as it can help the understanding of transcript diversity. Supervised machine learning approaches can be used to predict alternative splicing events at genome level. However, supervised approaches require large amounts of labeled data to learn accurate classifiers. While large amounts of genomic data are produced by the new sequencing technologies, labeling these data can be costly and time consuming. Therefore, semi- supervised learning approaches that can make use of large amounts of unlabeled data, in addition to small amounts of labeled data are highly desirable. In this work, we study the usefulness of a semi-supervised learning approach, co-training, for classifying exons as alternatively spliced or constitutive. The co-training algorithm makes use of two views of the data to iteratively learn two classifiers that can inform each other, at each step, with their best predictions on the unlabeled data. We consider two sets of features for constructing views for the problem of predicting alternatively spliced exons: exonic splicing enhancers and intronic regulatory sequences. We use the Naive Bayes Multinomial algorithm as a base classifier in our study. Experimental results show that the usage of the unlabeled data can result in better classifiers as compared to those obtained from the small amount of labeled data alone.