New Resources and Perspectives for Biomedical Event Extraction

Event extraction is a major focus of recent work in biomedical information extraction. Despite substantial advances, many challenges still remain for reliable automatic extraction of events from text. We introduce a new biomedical event extraction resource consisting of analyses automatically created by systems participating in the recent BioNLP Shared Task (ST) 2011. In providing for the first time the outputs of a broad set of state-ofthe-art event extraction systems, this resource opens many new opportunities for studying aspects of event extraction, from the identification of common errors to the study of effective approaches to combining the strengths of systems. We demonstrate these opportunities through a multi-system analysis on three BioNLP ST 2011 main tasks, focusing on events that none of the systems can successfully extract. We further argue for new perspectives to the performance evaluation of domain event extraction systems, considering a document-level, “off-the-page ” representation and evaluation to complement the mentionlevel evaluations pursued in most recent work.

Interactive exploration and model analysis for coreference annotation

I present the design and implementation of an interactive visualization- and exploration-framework for coreference annotations. It is designed to meet the needs of multiple different users on a modern and multifaceted graphical exploration tool. To demonstrate its suitability for these various needs I outline several use cases and how the framework can help users in their individual tasks. It offers the user different views on the data with additional functionality to compare several annotations. Complex analysis of annotated corpora is supported by means of a search engine which lets the user construct queries both in a graphical and textual form. Both qualitative and quantitative result breakdowns are available and the implementation features specialized visualizations to aggregate complex search results. The framework is extensible in many ways and can be customized to handle additional data formats

Using the web to resolve coreferent bridging in German newspaper text

We adopt Markert and Nissim (2005)’s approach of using the World Wide Web to resolve cases of coreferent bridging for German and discuss the strength and weaknesses of this approach. As the general approach of using surface patterns to get information on ontological relations between lexical items has only been tried on English, it is also interesting to see whether the approach works for German as well as it does for English and what differences between these languages need to be accounted for. We also present a novel approach for combining several patterns that yields an ensemble that outperforms the best-performing single patterns in terms of both precision and recall

Leveraging syntactic parsing to improve event annotation matching

Detecting event mentions is the first step in event extraction from text and annotating them is a notoriously difficult task. Evaluating annotator consistency is crucial when building datasets for mention detection. When event mentions are allowed to cover many tokens, annotators may disagree on their span, which means that overlapping annotations may then refer to the same event or to different events. This paper explores different fuzzy matching functions which aim to resolve this ambiguity. The functions extract the sets of syntactic heads present in the annotations, use the Dice coefficient to measure the similarity between sets and return a judgment based on a given threshold. The functions are tested against the judgments of a human evaluator and a comparison is made between sets of tokens and sets of syntactic heads. The best-performing function is a head-based function that is found to agree with the human evaluator in 89% of cases

Joint Video and Text Parsing for Understanding Events and Answering Queries

We propose a framework for parsing video and text jointly for understanding events and answering user queries. Our framework produces a parse graph that represents the compositional structures of spatial information (objects and scenes), temporal information (actions and events) and causal information (causalities between events and fluents) in the video and text. The knowledge representation of our framework is based on a spatial-temporal-causal And-Or graph (S/T/C-AOG), which jointly models possible hierarchical compositions of objects, scenes and events as well as their interactions and mutual contexts, and specifies the prior probabilistic distribution of the parse graphs. We present a probabilistic generative model for joint parsing that captures the relations between the input video/text, their corresponding parse graphs and the joint parse graph. Based on the probabilistic model, we propose a joint parsing system consisting of three modules: video parsing, text parsing and joint inference. Video parsing and text parsing produce two parse graphs from the input video and text respectively. The joint inference module produces a joint parse graph by performing matching, deduction and revision on the video and text parse graphs. The proposed framework has the following objectives: Firstly, we aim at deep semantic parsing of video and text that goes beyond the traditional bag-of-words approaches; Secondly, we perform parsing and reasoning across the spatial, temporal and causal dimensions based on the joint S/T/C-AOG representation; Thirdly, we show that deep joint parsing facilitates subsequent applications such as generating narrative text descriptions and answering queries in the forms of who, what, when, where and why. We empirically evaluated our system based on comparison against ground-truth as well as accuracy of query answering and obtained satisfactory results

Comparing Humans and Models on a Similar Scale: Towards Cognitive Gender Bias Evaluation in Coreference Resolution

Spurious correlations were found to be an important factor explaining model performance in various NLP tasks (e.g., gender or racial artifacts), often considered to be ''shortcuts'' to the actual task. However, humans tend to similarly make quick (and sometimes wrong) predictions based on societal and cognitive presuppositions. In this work we address the question: can we quantify the extent to which model biases reflect human behaviour? Answering this question will help shed light on model performance and provide meaningful comparisons against humans. We approach this question through the lens of the dual-process theory for human decision-making. This theory differentiates between an automatic unconscious (and sometimes biased) ''fast system'' and a ''slow system'', which when triggered may revisit earlier automatic reactions. We make several observations from two crowdsourcing experiments of gender bias in coreference resolution, using self-paced reading to study the ''fast'' system, and question answering to study the ''slow'' system under a constrained time setting. On real-world data humans make $\sim$3\% more gender-biased decisions compared to models, while on synthetic data models are $\sim$12\% more biased