Simple and efficient classification scheme based on specific vocabulary

Assuming a binomial distribution for word occurrence, we propose computing a standardized Z score to define the specific vocabulary of a subset compared to that of the entire corpus. This approach is applied to weight terms (character n-gram, word, stem, lemma or sequence of them) which characterize a document. We then show how these Z score values can be used to derive a simple and efficient categorization scheme. To evaluate this proposition and demonstrate its effectiveness, we develop two experiments. First, the system must categorize speeches given by B. Obama as being either electoral or presidential speech. In a second experiment, sentences are extracted from these speeches and then categorized under the headings electoral or presidential. Based on these evaluations, the proposed classification scheme tends to perform better than a support vector machine model for both experiments, on the one hand, and on the other, shows a better performance level than a Naïve Bayes classifier on the first test and a slightly lower performance on the second (10-fold cross validation

Adversarial Reprogramming of Text Classification Neural Networks

Adversarial Reprogramming has demonstrated success in utilizing pre-trained neural network classifiers for alternative classification tasks without modification to the original network. An adversary in such an attack scenario trains an additive contribution to the inputs to repurpose the neural network for the new classification task. While this reprogramming approach works for neural networks with a continuous input space such as that of images, it is not directly applicable to neural networks trained for tasks such as text classification, where the input space is discrete. Repurposing such classification networks would require the attacker to learn an adversarial program that maps inputs from one discrete space to the other. In this work, we introduce a context-based vocabulary remapping model to reprogram neural networks trained on a specific sequence classification task, for a new sequence classification task desired by the adversary. We propose training procedures for this adversarial program in both white-box and black-box settings. We demonstrate the application of our model by adversarially repurposing various text-classification models including LSTM, bi-directional LSTM and CNN for alternate classification tasks

Towards automatic classification within the ChEBI ontology

*Background*
Appearing in a wide variety of contexts, biochemical 'small molecules' are a core element of biomedical data. Chemical ontologies, which provide stable identifiers and a shared vocabulary for use in referring to such biochemical small molecules, are crucial to enable the interoperation of such data. One such chemical ontology is ChEBI (Chemical Entities of Biological Interest), a candidate member ontology of the OBO Foundry. ChEBI is a publicly available, manually annotated database of chemical entities and contains around 18000 annotated entities as of the last release (May 2009). ChEBI provides stable unique identifiers for chemical entities; a controlled vocabulary in the form of recommended names (which are unique and unambiguous), common synonyms, and systematic chemical names; cross-references to other databases; and a structural and role-based classification within the ontology. ChEBI is widely used for annotation of chemicals within biological databases, text-mining, and data integration. ChEBI can be accessed online at "http://www.ebi.ac.uk/chebi/":http://www.ebi.ac.uk/chebi/ and the full dataset is available for download in various formats including SDF and OBO.

*Automated Classification*
The selection of chemical entities for inclusion in the ChEBI database is user-driven. As the use of ChEBI has grown, so too has the backlog of user-requested entries. Inevitably, the annotation backlog creates a bottleneck, and to speed up the annotation process, ChEBI has recently released a submission tool which allows community submissions of chemical entities, groups, and classes. However, classification of chemical entities within the ontology is a difficult and niche activity, and it is unlikely that the community as a whole will be able or willing to correctly and consistently classify each submitted entity, creating required classes where they are missing. As a result, it is likely that while the size of the database grows, the ontological classification will become less sophisticated, unless the classification of new entities is assisted computationally. In addition, the ChEBI database is expecting substantial size growth in the next year, so automatic classification, which has up till now not been possible, is urgently required. Automatic classification would also enable the ChEBI ontology classes to be applied to other compound databases such as PubChem. 

*Description Logic Reasoning*
Description logic based reasoning technology is a prime candidate for development of such an automatic classification system as it allows the rules of the classification system to be encoded within the knowledgebase. Already at 18000 entities, ChEBI is a fair size for a real-world application of description logic reasoning technology, and as the ontology is enhanced with a richer density of asserted relationships, the classification will become more complex and challenging. We have successfully tested a description logic-based classification of chemical entities based on specified structural properties using the hypertableaux-based HermiT reasoner, and found it to be sufficiently efficient to be feasible for use in a production environment on a database of the size that ChEBI is now. However, much work still remains to enrich the ChEBI knowledgebase itself with the properties needed to provide the formal class definitions for use in the automated classification, and to assess the efficiency of the available description logic reasoning technology on a database the size of ChEBI's forecast future growth.

*Acknowledgements*
ChEBI is funded by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific Programme, and by the BBSRC, grant agreement number BB/G022747/1 within the “Bioinformatics and biological resources” fund

A Bilingual Thesaurus of Everyday Life in Medieval England: Some Issues at the Interface of Semantics and Lexicography

This paper reports on issues at the interface between semantics and lexicography that arose out of the data collection and classification of vocabulary in Anglo-Norman and Middle English in order to create a bilingual thesaurus of everyday life in medieval England. The Bilingual Thesaurus project is based at Birmingham City University and the University of Westminster. Issues to be resolved included the definition of an occupational domain; the creation of a methodology of data collection; the delimitation of domain-specific vocabulary; making distinctions between sense and usage; and the categorisation of the lexical items. Some of these issues are general to thesaurus-making, some are specific to the making of historical thesauruses, while some are unique to the production of a thesaurus of two languages whose use overlapped for several centuries in the late medieval period in England

Retrieval Models for Genre Classification

Genre provides a characterization of a document with respect to its form or functional trait. Genre is orthogonal to topic, rendering genre information a powerful filter technology for information seekers in digital libraries. However, an efficient means for genre classification is an open and controversially discussed issue. This paper gives an overview and presents new results related to automatic genre classification of text documents. We present a comprehensive survey which contrasts the genre retrieval models that have been developed for Web and non-Web corpora. With the concept of genre-specific core vocabularies the paper provides an original contribution related to computational aspects and classification performance of genre retrieval models: we show how such vocabularies are acquired automatically and introduce new concentration measures that quantify the vocabulary distribution in a sensible way. Based on these findings we construct lightweight genre retrieval models and evaluate their discriminative power and computational efficiency. The presented concepts go beyond the existing utilization of vocabulary-centered, genre-revealing features and open new possibilities for the construction of genre classifiers that operate in real-time

Infectious Disease Ontology

Technological developments have resulted in tremendous increases in the volume and diversity of the data and information that must be processed in the course of biomedical and clinical research and practice. Researchers are at the same time under ever greater pressure to share data and to take steps to ensure that data resources are interoperable. The use of ontologies to annotate data has proven successful in supporting these goals and in providing new possibilities for the automated processing of data and information. In this chapter, we describe different types of vocabulary resources and emphasize those features of formal ontologies that make them most useful for computational applications. We describe current uses of ontologies and discuss future goals for ontology-based computing, focusing on its use in the field of infectious diseases. We review the largest and most widely used vocabulary resources relevant to the study of infectious diseases and conclude with a description of the Infectious Disease Ontology (IDO) suite of interoperable ontology modules that together cover the entire infectious disease domain

Analysis of equivalence mapping for terminology services

This paper assesses the range of equivalence or mapping types required to facilitate interoperability in the context of a distributed terminology server. A detailed set of mapping types were examined, with a view to determining their validity for characterizing relationships between mappings from selected terminologies (AAT, LCSH, MeSH, and UNESCO) to the Dewey Decimal Classification (DDC) scheme. It was hypothesized that the detailed set of 19 match types proposed by Chaplan in 1995 is unnecessary in this context and that they could be reduced to a less detailed conceptually-based set. Results from an extensive mapping exercise support the main hypothesis and a generic suite of match types are proposed, although doubt remains over the current adequacy of the developing Simple Knowledge Organization System (SKOS) Core Mapping Vocabulary Specification (MVS) for inter-terminology mapping