Relating Developers’ Concepts and Artefact Vocabulary in a Financial Software Module

Developers working on unfamiliar systems are challenged to accurately identify where and how high-level concepts are implemented in the source code. Without additional help, concept location can become a tedious, time-consuming and error-prone task. In this paper we study an industrial financial application for which we had access to the user guide, the source code, and some change requests. We compared the relative importance of the domain concepts, as understood by developers, in the user manual and in the source code. We also searched the code for the concepts occurring in change requests, to see if they could point developers to code to be modified. We varied the searches (using exact and stem matching, discarding stop-words, etc.) and present the precision and recall. We discuss the implication of our results for maintenance

A lightweight web video model with content and context descriptions for integration with linked data

The rapid increase of video data on the Web has warranted an urgent need for effective representation, management and retrieval of web videos. Recently, many studies have been carried out for ontological representation of videos, either using domain dependent or generic schemas such as MPEG-7, MPEG-4, and COMM. In spite of their extensive coverage and sound theoretical grounding, they are yet to be widely used by users. Two main possible reasons are the complexities involved and a lack of tool support. We propose a lightweight video content model for content-context description and integration. The uniqueness of the model is that it tries to model the emerging social context to describe and interpret the video. Our approach is grounded on exploiting easily extractable evolving contextual metadata and on the availability of existing data on the Web. This enables representational homogeneity and a firm basis for information integration among semantically-enabled data sources. The model uses many existing schemas to describe various ontology classes and shows the scope of interlinking with the Linked Data cloud

Towards Building a Knowledge Base of Monetary Transactions from a News Collection

We address the problem of extracting structured representations of economic events from a large corpus of news articles, using a combination of natural language processing and machine learning techniques. The developed techniques allow for semi-automatic population of a financial knowledge base, which, in turn, may be used to support a range of data mining and exploration tasks. The key challenge we face in this domain is that the same event is often reported multiple times, with varying correctness of details. We address this challenge by first collecting all information pertinent to a given event from the entire corpus, then considering all possible representations of the event, and finally, using a supervised learning method, to rank these representations by the associated confidence scores. A main innovative element of our approach is that it jointly extracts and stores all attributes of the event as a single representation (quintuple). Using a purpose-built test set we demonstrate that our supervised learning approach can achieve 25% improvement in F1-score over baseline methods that consider the earliest, the latest or the most frequent reporting of the event.Comment: Proceedings of the 17th ACM/IEEE-CS Joint Conference on Digital Libraries (JCDL '17), 201

On the Effect of Semantically Enriched Context Models on Software Modularization

Many of the existing approaches for program comprehension rely on the linguistic information found in source code, such as identifier names and comments. Semantic clustering is one such technique for modularization of the system that relies on the informal semantics of the program, encoded in the vocabulary used in the source code. Treating the source code as a collection of tokens loses the semantic information embedded within the identifiers. We try to overcome this problem by introducing context models for source code identifiers to obtain a semantic kernel, which can be used for both deriving the topics that run through the system as well as their clustering. In the first model, we abstract an identifier to its type representation and build on this notion of context to construct contextual vector representation of the source code. The second notion of context is defined based on the flow of data between identifiers to represent a module as a dependency graph where the nodes correspond to identifiers and the edges represent the data dependencies between pairs of identifiers. We have applied our approach to 10 medium-sized open source Java projects, and show that by introducing contexts for identifiers, the quality of the modularization of the software systems is improved. Both of the context models give results that are superior to the plain vector representation of documents. In some cases, the authoritativeness of decompositions is improved by 67%. Furthermore, a more detailed evaluation of our approach on JEdit, an open source editor, demonstrates that inferred topics through performing topic analysis on the contextual representations are more meaningful compared to the plain representation of the documents. The proposed approach in introducing a context model for source code identifiers paves the way for building tools that support developers in program comprehension tasks such as application and domain concept location, software modularization and topic analysis

Large-scale event extraction from literature with multi-level gene normalization

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons -Attribution - Share Alike (CC BY-SA) license

Community next steps for making globally unique identifiers work for biocollections data

Biodiversity data is being digitized and made available online at a rapidly increasing rate but current practices typically do not preserve linkages between these data, which impedes interoperation, provenance tracking, and assembly of larger datasets. For data associated with biocollections, the biodiversity community has long recognized that an essential part of establishing and preserving linkages is to apply globally unique identifiers at the point when data are generated in the field and to persist these identifiers downstream, but this is seldom implemented in practice. There has neither been coalescence towards one single identifier solution (as in some other domains), nor even a set of recommended best practices and standards to support multiple identifier schemes sharing consistent responses. In order to further progress towards a broader community consensus, a group of biocollections and informatics experts assembled in Stockholm in October 2014 to discuss community next steps to overcome current roadblocks. The workshop participants divided into four groups focusing on: identifier practice in current field biocollections; identifier application for legacy biocollections; identifiers as applied to biodiversity data records as they are published and made available in semantically marked-up publications; and cross-cutting identifier solutions that bridge across these domains. The main outcome was consensus on key issues, including recognition of differences between legacy and new biocollections processes, the need for identifier metadata profiles that can report information on identifier persistence missions, and the unambiguous indication of the type of object associated with the identifier. Current identifier characteristics are also summarized, and an overview of available schemes and practices is provided