Roser Morante

Learning the Scope of Hedge Cues in Biomedical Texts

Identifying hedged information in biomedical literature is an important subtask in information extraction because it would be misleading to extract speculative information as factual information. In this paper we present a machine learning system that finds the scope of hedge cues in biomedical texts. The system is based on a similar system that finds the scope of negation cues. We show that the same scope finding approach can be applied to both negation and hedging. To investigate the robustness of the approach, the system is tested on the three subcorpora of the BioScope corpus that represent different text types.

A Metalearning Approach to Processing the Scope of Negation

Finding negation signals and their scope in text is an important subtask in information extraction. In this paper we present a machine learning system that finds the scope of negation in biomedical texts. The system combines several classifiers and works in two phases. To investigate the robustness of the approach, the system is tested on the three subcorpora of the BioScope corpus representing different text types. It achieves the best results to date for this task, with an error reduction of 32.07% compared to current state of the art results.

Modality and negation: An introduction to the special issue

Traditionally, most research in NLP has focused on propositional aspects of meaning. To truly understand language, however, extra-propositional aspects are equally important. Modality and negation typically contribute significantly to these extra-propositional meaning aspects. Although modality and negation have often been neglected by mainstream computational linguistics, interest has grown in recent years, as evidenced by several annotation projects dedicated to these phenomena. Researchers have started to work on modeling factuality, belief and certainty, detecting speculative sentences and hedging, identifying contradictions, and determining the scope of expressions of modality and negation. In this article, we will provide an overview of how modality and negation have been modeled in computational linguistics.

Assessment of NER solutions against the first and second CALBC Silver Standard Corpus

BackgroundCompetitions in text mining have been used to measure the performance of automatic text processing solutions against a manually annotated gold standard corpus (GSC). The preparation of the GSC is time-consuming and costly and the final corpus consists at the most of a few thousand documents annotated with a limited set of semantic groups. To overcome these shortcomings, the CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions, the first version of the Silver Standard Corpus (SSC-I). The four semantic groups are chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). This corpus has been used for the First CALBC Challenge asking the participants to annotate the corpus with their text processing solutions.ResultsAll four PPs from the CALBC project and in addition, 12 challenge participants (CPs) contributed annotated data sets for an evaluation against the SSC-I. CPs could ignore the training data and deliver the annotations from their genuine annotation system, or could train a machine-learning approach on the provided pre-annotated data. In general, the performances of the annotation solutions were lower for entities from the categories CHED and PRGE in comparison to the identification of entities categorized as DISO and SPE. The best performance over all semantic groups were achieved from two annotation solutions that have been trained on the SSC-I.The data sets from participants were used to generate the harmonised Silver Standard Corpus II (SSC-II), if the participant did not make use of the annotated data set from the SSC-I for training purposes. The performances of the participants’ solutions were again measured against the SSC-II. The performances of the annotation solutions showed again better results for DISO and SPE in comparison to CHED and PRGE.ConclusionsThe SSC-I delivers a large set of annotations (1,121,705) for a large number of documents (100,000 Medline abstracts). The annotations cover four different semantic groups and are sufficiently homogeneous to be reproduced with a trained classifier leading to an average F-measure of 85%. Benchmarking the annotation solutions against the SSC-II leads to better performance for the CPs’ annotation solutions in comparison to the SSC-I.

QA4MRE 2011-2013: Overview of Question Answering for Machine Reading Evaluation

This paper describes the methodology for testing the performance of Machine Reading systems through Question Answering and Reading Comprehension Tests. This was the attempt of the QA4MRE challenge which was run as a Lab at CLEF 2011---2013. The traditional QA task was replaced by a new Machine Reading task, whose intention was to ask questions that required a deep knowledge of individual short texts and in which systems were required to choose one answer, by analysing the corresponding test document in conjunction with background text collections provided by the organization. Four different tasks have been organized during these years: Main Task, Processing Modality and Negation for Machine Reading, Machine Reading of Biomedical Texts about Alzheimers disease, and Entrance Exams. This paper describes their motivation, their goals, their methodology for preparing the data sets, their background collections, their metrics used for the evaluation, and the lessons learned along these three years.

Kernel-Based logical and relational learning with klog for hedge cue detection

Hedge cue detection is a Natural Language Processing (NLP) task that consists of determining whether sentences contain hedges. These linguistic devices indicate that authors do not or cannot back up their opinions or statements with facts. This binary classification problem, i.e. distinguishing factual versus uncertain sentences, only recently received attention in the NLP community. We use kLog, a new logical and relational language for kernel-based learning, to tackle this problem. We present results on the CoNLL 2010 benchmark dataset that consists of a set of paragraphs from Wikipedia, one of the domains in which uncertainty detection has become important. Our approach shows competitive results compared to state-of-the-art systems.

Joint Memory-Based Learning of Syntactic and Semantic Dependencies in Multiple Languages

In this paper we present a system submitted to the CoNLL Shared Task 2009 performing the identification and labeling of syntactic and semantic dependencies in multiple languages. Dependencies are truly jointly learned, i.e. as if they were a single task. The system works in two phases: a classification phase in which three classifiers predict different types of information, and a ranking phase in which the output of the classifiers is combined.

A Combined Memory-Based Semantic Role Labeler of English

A PWM solenoid operated valve control (42) arrangement which substantially eliminates supply voltage (70) dependent variability of the valve (30-40) without the expense or inefficiency of a conventional voltage regulator. The coil of the solenoid valve is pulse-width-modulated in relation to the commanded output result and the energization periods are submodulated in relation to the magnitude of the supply voltage. The effective voltage applied to the coil, and hence the operating characteristics of the solenoid valve, are thereby made substantially independent of supply voltage variations.

Highlights of the BioTM 2010 workshop on advances in bio text mining

This meeting report gives an overview of the keynote lectures, the panel discussion and a selection of the contributed presentations. The workshop was held in Gent, Belgium on May 10-11. It featured a tutorial aimed towards a broad audience of (computational) biologists, (computational) linguists and researchers working purely on text mining.

Beyond sentence-level semantic role labeling: linking argument structures in discourse

Semantic role labeling is traditionally viewed as a sentence-level task concerned with identifying semantic arguments that are overtly realized in a fairly local context (i.e., a clause or sentence). However, this local view potentially misses important information that can only be recovered if local argument structures are linked across sentence boundaries. One important link concerns semantic arguments that remain locally unrealized (null instantiations) but can be inferred from the context. In this paper, we report on the SemEval 2010 Task-10 on “Linking Events and Their Participants in Discourse”, that addressed this problem. We discuss the corpus that was created for this task, which contains annotations on multiple levels: predicate argument structure (FrameNet and PropBank), null instantiations, and coreference. We also provide an analysis of the task and its difficulties.