A Medical Information Extraction Workbench to Process German Clinical Text

Background: In the information extraction and natural language processing domain, accessible datasets are crucial to reproduce and compare results. Publicly available implementations and tools can serve as benchmark and facilitate the development of more complex applications. However, in the context of clinical text processing the number of accessible datasets is scarce -- and so is the number of existing tools. One of the main reasons is the sensitivity of the data. This problem is even more evident for non-English languages. Approach: In order to address this situation, we introduce a workbench: a collection of German clinical text processing models. The models are trained on a de-identified corpus of German nephrology reports. Result: The presented models provide promising results on in-domain data. Moreover, we show that our models can be also successfully applied to other biomedical text in German. Our workbench is made publicly available so it can be used out of the box, as a benchmark or transferred to related problems.

Why only Micro-F1? Class Weighting of Measures for Relation Classification

Relation classification models are conventionally evaluated using only a single measure, e.g., micro-F1, macro-F1 or AUC. In this work, we analyze weighting schemes, such as micro and macro, for imbalanced datasets. We introduce a framework for weighting schemes, where existing schemes are extremes, and two new intermediate schemes. We show that reporting results of different weighting schemes better highlights strengths and weaknesses of a model.

A Comparative Study of Pre-trained Encoders for Low-Resource Named Entity Recognition

Pre-trained language models (PLM) are effective components of few-shot named entity recognition (NER) approaches when augmented with continued pre-training on task-specific out-of-domain data or fine-tuning on in-domain data. However, their performance in low-resource scenarios, where such data is not available, remains an open question. We introduce an encoder evaluation framework, and use it to systematically compare the performance of state-of-the-art pre-trained representations on the task of low-resource NER. We analyze a wide range of encoders pre-trained with different strategies, model architectures, intermediate-task fine-tuning, and contrastive learning. Our experimental results across ten benchmark NER datasets in English and German show that encoder performance varies significantly, suggesting that the choice of encoder for a specific low-resource scenario needs to be carefully evaluated.

Defx at SemEval-2020 Task 6: Joint Extraction of Concepts and Relations for Definition Extraction

Definition Extraction systems are a valuable knowledge source for both humans and algorithms. In this paper we describe our submissions to the DeftEval shared task (SemEval-2020 Task 6), which is evaluated on an English textbook corpus. We provide a detailed explanation of our system for the joint extraction of definition concepts and the relations among them. Furthermore we provide an ablation study of our model variations and describe the results of an error analysis.

Bootstrapping Named Entity Recognition in E-Commerce with Positive Unlabeled Learning

Named Entity Recognition (NER) in domains like e-commerce is an understudied problem due to the lack of annotated datasets. Recognizing novel entity types in this domain, such as products, components, and attributes, is challenging because of their linguistic complexity and the low coverage of existing knowledge resources. To address this problem, we present a bootstrapped positive-unlabeled learning algorithm that integrates domain-specific linguistic features to quickly and efficiently expand the seed dictionary. The model achieves an average F1 score of 72.02% on a novel dataset of product descriptions, an improvement of 3.63% over a baseline BiLSTM classifier, and in particular exhibits better recall (4.96% on average).

TACRED Revisited: A Thorough Evaluation of the TACRED Relation Extraction Task

TACRED (Zhang et al., 2017) is one of the largest, most widely used crowdsourced datasets in Relation Extraction (RE). But, even with recent advances in unsupervised pre-training and knowledge enhanced neural RE, models still show a high error rate. In this paper, we investigate the questions: Have we reached a performance ceiling or is there still room for improvement? And how do crowd annotations, dataset, and models contribute to this error rate? To answer these questions, we first validate the most challenging 5K examples in the development and test sets using trained annotators. We find that label errors account for 8% absolute F1 test error, and that more than 50% of the examples need to be relabeled. On the relabeled test set the average F1 score of a large baseline model set improves from 62.1 to 70.1. After validation, we analyze misclassifications on the challenging instances, categorize them into linguistically motivated error groups, and verify the resulting error hypotheses on three state-of-the-art RE models. We show that two groups of ambiguous relations are responsible for most of the remaining errors and that models may adopt shallow heuristics on the dataset when entities are not masked.

Considering Likelihood in NLP Classification Explanations with Occlusion and Language Modeling

Recently, state-of-the-art NLP models gained an increasing syntactic and semantic understanding of language, and explanation methods are crucial to understand their decisions. Occlusion is a well established method that provides explanations on discrete language data, e.g. by removing a language unit from an input and measuring the impact on a model's decision. We argue that current occlusion-based methods often produce invalid or syntactically incorrect language data, neglecting the improved abilities of recent NLP models. Furthermore, gradient-based explanation methods disregard the discrete distribution of data in NLP. Thus, we propose OLM: a novel explanation method that combines occlusion and language models to sample valid and syntactically correct replacements with high likelihood, given the context of the original input. We lay out a theoretical foundation that alleviates these weaknesses of other explanation methods in NLP and provide results that underline the importance of considering data likelihood in occlusion-based explanation.

Probing Linguistic Features of Sentence-Level Representations in Neural Relation Extraction

Despite the recent progress, little is known about the features captured by state-of-the-art neural relation extraction (RE) models. Common methods encode the source sentence, conditioned on the entity mentions, before classifying the relation. However, the complexity of the task makes it difficult to understand how encoder architecture and supporting linguistic knowledge affect the features learned by the encoder. We introduce 14 probing tasks targeting linguistic properties relevant to RE, and we use them to study representations learned by more than 40 different encoder architecture and linguistic feature combinations trained on two datasets, TACRED and SemEval 2010 Task 8. We find that the bias induced by the architecture and the inclusion of linguistic features are clearly expressed in the probing task performance. For example, adding contextualized word representations greatly increases performance on probing tasks with a focus on named entity and part-of-speech information, and yields better results in RE. In contrast, entity masking improves RE, but considerably lowers performance on entity type related probing tasks.

Layerwise Relevance Visualization in Convolutional Text Graph Classifiers

Representations in the hidden layers of Deep Neural Networks (DNN) are often hard to interpret since it is difficult to project them into an interpretable domain. Graph Convolutional Networks (GCN) allow this projection, but existing explainability methods do not exploit this fact, i.e. do not focus their explanations on intermediate states. In this work, we present a novel method that traces and visualizes features that contribute to a classification decision in the visible and hidden layers of a GCN. Our method exposes hidden cross-layer dynamics in the input graph structure. We experimentally demonstrate that it yields meaningful layerwise explanations for a GCN sentence classifier.

Fine-tuning Pre-Trained Transformer Language Models to Distantly Supervised Relation Extraction

Distantly supervised relation extraction is widely used to extract relational facts from text, but suffers from noisy labels. Current relation extraction methods try to alleviate the noise by multi-instance learning and by providing supporting linguistic and contextual information to more efficiently guide the relation classification. While achieving state-of-the-art results, we observed these models to be biased towards recognizing a limited set of relations with high precision, while ignoring those in the long tail. To address this gap, we utilize a pre-trained language model, the OpenAI Generative Pre-trained Transformer (GPT) [Radford et al., 2018]. The GPT and similar models have been shown to capture semantic and syntactic features, and also a notable amount of "common-sense" knowledge, which we hypothesize are important features for recognizing a more diverse set of relations. By extending the GPT to the distantly supervised setting, and fine-tuning it on the NYT10 dataset, we show that it predicts a larger set of distinct relation types with high confidence. Manual and automated evaluation of our model shows that it achieves a state-of-the-art AUC score of 0.422 on the NYT10 dataset, and performs especially well at higher recall levels.