Automatic document classification of biological literature

Background: Document classification is a wide-spread problem with many applications, from organizing search engine snippets to spam filtering. We previously described Textpresso, a text-mining system for biological literature, which marks up full text according to a shallow ontology that includes terms of biological interest. This project investigates document classification in the context of biological literature, making use of the Textpresso markup of a corpus of Caenorhabditis elegans literature. Results: We present a two-step text categorization algorithm to classify a corpus of C. elegans papers. Our classification method first uses a support vector machine-trained classifier, followed by a novel, phrase-based clustering algorithm. This clustering step autonomously creates cluster labels that are descriptive and understandable by humans. This clustering engine performed better on a standard test-set (Reuters 21578) compared to previously published results (F-value of 0.55 vs. 0.49), while producing cluster descriptions that appear more useful. A web interface allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept. Conclusions: We have demonstrated a simple method to classify biological documents that embodies an improvement over current methods. While the classification results are currently optimized for Caenorhabditis elegans papers by human-created rules, the classification engine can be adapted to different types of documents. We have demonstrated this by presenting a web interface that allows researchers to quickly navigate through the hierarchy and look for documents that belong to a specific concept

CoaCor: Code Annotation for Code Retrieval with Reinforcement Learning

To accelerate software development, much research has been performed to help people understand and reuse the huge amount of available code resources. Two important tasks have been widely studied: code retrieval, which aims to retrieve code snippets relevant to a given natural language query from a code base, and code annotation, where the goal is to annotate a code snippet with a natural language description. Despite their advancement in recent years, the two tasks are mostly explored separately. In this work, we investigate a novel perspective of Code annotation for Code retrieval (hence called `CoaCor'), where a code annotation model is trained to generate a natural language annotation that can represent the semantic meaning of a given code snippet and can be leveraged by a code retrieval model to better distinguish relevant code snippets from others. To this end, we propose an effective framework based on reinforcement learning, which explicitly encourages the code annotation model to generate annotations that can be used for the retrieval task. Through extensive experiments, we show that code annotations generated by our framework are much more detailed and more useful for code retrieval, and they can further improve the performance of existing code retrieval models significantly.Comment: 10 pages, 2 figures. Accepted by The Web Conference (WWW) 201

Empirical Study of Training-Set Creation for Software Architecture Traceability Methods

Machine-learning algorithms have the potential to support trace retrieval methods making significant reductions in costs and human-involvement required for the creation and maintenance of traceability links between system requirements, system architecture, and the source code. These algorithms can be trained how to detect the relevant architecture and can then be sent to find it on its own. However, the long-term reductions in cost and effort face a significant upfront cost in the initial training of the algorithm. This cost comes in the form of needing to create training sets of code, which train the algorithm how to identify traceability links. These supervised or semi-supervised training methods require the involvement of highly trained, and thus expensive, experts to collect, and format, these data-sets. In this thesis, three baseline methods training datasets creation are presented. These methods are (i) Manual Expert-based, which involves a human-compiled dataset, (ii) Automated Web-Mining, which creates training datasets by collecting and data-mining APIs (specifically from technical-programming websites), and (iii) Automated Big-Data Analysis, which data-mines ultra-large code repositories to generate the training datasets. The trace-link creation accuracy achieved using each of these three methods is compared, and the cost/benefit comparisons between them is discussed. Furthermore, in a related area, potential correlations between training set size and the accuracy of recovering trace links is investigated. The results of this area of study indicate that the automated techniques, capable of creating very large training sets, allow for sufficient reliability in the problem of tracing architectural tactics. This indicates that these automated methods have potential applications in other areas of software traceability