Using Neural Networks for Relation Extraction from Biomedical Literature

Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely, using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.Comment: Artificial Neural Networks book (Springer) - Chapter 1

The Parallel Meaning Bank: Towards a Multilingual Corpus of Translations Annotated with Compositional Meaning Representations

The Parallel Meaning Bank is a corpus of translations annotated with shared, formal meaning representations comprising over 11 million words divided over four languages (English, German, Italian, and Dutch). Our approach is based on cross-lingual projection: automatically produced (and manually corrected) semantic annotations for English sentences are mapped onto their word-aligned translations, assuming that the translations are meaning-preserving. The semantic annotation consists of five main steps: (i) segmentation of the text in sentences and lexical items; (ii) syntactic parsing with Combinatory Categorial Grammar; (iii) universal semantic tagging; (iv) symbolization; and (v) compositional semantic analysis based on Discourse Representation Theory. These steps are performed using statistical models trained in a semi-supervised manner. The employed annotation models are all language-neutral. Our first results are promising.Comment: To appear at EACL 201

ORTHOGRAPHIC ENRICHMENT FOR ARABIC GRAMMATICAL ANALYSIS

Thesis (Ph.D.) - Indiana University, Linguistics, 2010The Arabic orthography is problematic in two ways: (1) it lacks the short vowels, and this leads to ambiguity as the same orthographic form can be pronounced in many different ways each of which can have its own grammatical category, and (2) the Arabic word may contain several units like pronouns, conjunctions, articles and prepositions without an intervening white space. These two problems lead to difficulties in the automatic processing of Arabic. The thesis proposes a pre-processing scheme that applies word segmentation and word vocalization for the purpose of grammatical analysis: part of speech tagging and parsing. The thesis examines the impact of human-produced vocalization and segmentation on the grammatical analysis of Arabic, then applies a pipeline of automatic vocalization and segmentation for the purpose of Arabic part of speech tagging. The pipeline is then used, along with the POS tags produced, for the purpose of dependency parsing, which produces grammatical relations between the words in a sentence. The study uses the memory-based algorithm for vocalization, segmentation, and part of speech tagging, and the natural language parser MaltParser for dependency parsing. The thesis represents the first approach to the processing of real-world Arabic, and has found that through the correct choice of features and algorithms, the need for pre-processing for grammatical analysis can be minimized

Comparing the Performance of Different NLP Toolkits in Formal and Social Media Text

Nowadays, there are many toolkits available for performing common natural language processing tasks, which enable the development of more powerful applications without having to start from scratch. In fact, for English, there is no need to develop tools such as tokenizers, part-of-speech (POS) taggers, chunkers or named entity recognizers (NER). The current challenge is to select which one to use, out of the range of available tools. This choice may depend on several aspects, including the kind and source of text, where the level, formal or informal, may influence the performance of such tools. In this paper, we assess a range of natural language processing toolkits with their default configuration, while performing a set of standard tasks (e.g. tokenization, POS tagging, chunking and NER), in popular datasets that cover newspaper and social network text. The obtained results are analyzed and, while we could not decide on a single toolkit, this exercise was very helpful to narrow our choice

Statistical Augmentation of a Chinese Machine-Readable Dictionary

We describe a method of using statistically-collected Chinese character groups from a corpus to augment a Chinese dictionary. The method is particularly useful for extracting domain-specific and regional words not readily available in machine-readable dictionaries. Output was evaluated both using human evaluators and against a previously available dictionary. We also evaluated performance improvement in automatic Chinese tokenization. Results show that our method outputs legitimate words, acronymic constructions, idioms, names and titles, as well as technical compounds, many of which were lacking from the original dictionary.Comment: 17 pages, uuencoded compressed PostScrip

Bayesian Information Extraction Network

Dynamic Bayesian networks (DBNs) offer an elegant way to integrate various aspects of language in one model. Many existing algorithms developed for learning and inference in DBNs are applicable to probabilistic language modeling. To demonstrate the potential of DBNs for natural language processing, we employ a DBN in an information extraction task. We show how to assemble wealth of emerging linguistic instruments for shallow parsing, syntactic and semantic tagging, morphological decomposition, named entity recognition etc. in order to incrementally build a robust information extraction system. Our method outperforms previously published results on an established benchmark domain.Comment: 6 page

Sharing Cultural Heritage: the Clavius on the Web Project

In the last few years the amount of manuscripts digitized and made available on the Web has been constantly increasing. However, there is still a considarable lack of results concerning both the explicitation of their content and the tools developed to make it available. The objective of the Clavius on the Web project is to develop a Web platform exposing a selection of Christophorus Clavius letters along with three different levels of analysis: linguistic, lexical and semantic. The multilayered annotation of the corpus involves a XML-TEI encoding followed by a tokenization step where each token is univocally identified through a CTS urn notation and then associated to a part-of-speech and a lemma. The text is lexically and semantically annotated on the basis of a lexicon and a domain ontology, the former structuring the most relevant terms occurring in the text and the latter representing the domain entities of interest (e.g. people, places, etc.). Moreover, each entity is connected to linked and non linked resources, including DBpedia and VIAF. Finally, the results of the three layers of analysis are gathered and shown through interactive visualization and storytelling techniques. A demo version of the integrated architecture was developed

Automatic case acquisition from texts for process-oriented case-based reasoning

This paper introduces a method for the automatic acquisition of a rich case representation from free text for process-oriented case-based reasoning. Case engineering is among the most complicated and costly tasks in implementing a case-based reasoning system. This is especially so for process-oriented case-based reasoning, where more expressive case representations are generally used and, in our opinion, actually required for satisfactory case adaptation. In this context, the ability to acquire cases automatically from procedural texts is a major step forward in order to reason on processes. We therefore detail a methodology that makes case acquisition from processes described as free text possible, with special attention given to assembly instruction texts. This methodology extends the techniques we used to extract actions from cooking recipes. We argue that techniques taken from natural language processing are required for this task, and that they give satisfactory results. An evaluation based on our implemented prototype extracting workflows from recipe texts is provided.Comment: Sous presse, publication pr\'evue en 201