CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain

The field of natural language processing (NLP) has recently seen a large change towards using pre-trained language models for solving almost any task. Despite showing great improvements in benchmark datasets for various tasks, these models often perform sub-optimal in non-standard domains like the clinical domain where a large gap between pre-training documents and target documents is observed. In this paper, we aim at closing this gap with domain-specific training of the language model and we investigate its effect on a diverse set of downstream tasks and settings. We introduce the pre-trained CLIN-X (Clinical XLM-R) language models and show how CLIN-X outperforms other pre-trained transformer models by a large margin for ten clinical concept extraction tasks from two languages. In addition, we demonstrate how the transformer model can be further improved with our proposed task- and language-agnostic model architecture based on ensembles over random splits and cross-sentence context. Our studies in low-resource and transfer settings reveal stable model performance despite a lack of annotated data with improvements of up to 47 F1 points when only 250 labeled sentences are available. Our results highlight the importance of specialized language models as CLIN-X for concept extraction in non-standard domains, but also show that our task-agnostic model architecture is robust across the tested tasks and languages so that domain- or task-specific adaptations are not required.

Boosting Transformers for Job Expression Extraction and Classification in a Low-Resource Setting

In this paper, we explore possible improvements of transformer models in a low-resource setting. In particular, we present our approaches to tackle the first two of three subtasks of the MEDDOPROF competition, i.e., the extraction and classification of job expressions in Spanish clinical texts. As neither language nor domain experts, we experiment with the multilingual XLM-R transformer model and tackle these low-resource information extraction tasks as sequence-labeling problems. We explore domain- and language-adaptive pretraining, transfer learning and strategic datasplits to boost the transformer model. Our results show strong improvements using these methods by up to 5.3 F1 points compared to a fine-tuned XLM-R model. Our best models achieve 83.2 and 79.3 F1 for the first two tasks, respectively.

To Share or not to Share: Predicting Sets of Sources for Model Transfer Learning

In low-resource settings, model transfer can help to overcome a lack of labeled data for many tasks and domains. However, predicting useful transfer sources is a challenging problem, as even the most similar sources might lead to unexpected negative transfer results. Thus, ranking methods based on task and text similarity may not be sufficient to identify promising sources. To tackle this problem, we propose a method to automatically determine which and how many sources should be exploited. For this, we study the effects of model transfer on sequence labeling across various domains and tasks and show that our methods based on model similarity and support vector machines are able to predict promising sources, resulting in performance increases of up to 24 F1 points.

ANEA: Distant Supervision for Low-Resource Named Entity Recognition

Distant supervision allows obtaining labeled training corpora for low-resource settings where only limited hand-annotated data exists. However, to be used effectively, the distant supervision must be easy to obtain. In this work, we present ANEA, a tool to automatically annotate named entities in text based on entity lists. It spans the whole pipeline from obtaining the lists to analyzing the errors of the distant supervision. A tuning step allows the user to improve the automatic annotation with their linguistic insights without having to manually label or check all tokens. In six low-resource scenarios, we show that the F1-score can be increased by on average 18 points through distantly supervised data obtained by ANEA.

NLNDE at CANTEMIST: Neural Sequence Labeling and Parsing Approaches for Clinical Concept Extraction

The recognition and normalization of clinical information, such as tumor morphology mentions, is an important, but complex process consisting of multiple subtasks. In this paper, we describe our system for the CANTEMIST shared task, which is able to extract, normalize and rank ICD codes from Spanish electronic health records using neural sequence labeling and parsing approaches with context-aware embeddings. Our best system achieves 85.3 F1, 76.7 F1, and 77.0 MAP for the three tasks, respectively.

A Survey on Recent Approaches for Natural Language Processing in Low-Resource Scenarios

Current developments in natural language processing offer challenges and opportunities for low-resource languages and domains. Deep neural networks are known for requiring large amounts of training data which might not be available in resource-lean scenarios. However, there is also a growing body of works to improve the performance in low-resource settings. Motivated by fundamental changes towards neural models and the currently popular pre-train and fine-tune paradigm, we give an overview of promising approaches for low-resource natural language processing. After a discussion about the definition of low-resource scenarios and the different dimensions of data availability, we then examine methods that enable learning when training data is sparse. This includes mechanisms to create additional labeled data like data augmentation and distant supervision as well as transfer learning settings that reduce the need for target supervision. The survey closes with a brief look into methods suggested in non-NLP machine learning communities, which might be beneficial for NLP in low-resource scenarios

Adversarial Learning of Feature-based Meta-Embeddings

Certain embedding types outperform others in different scenarios, e.g., subword-based embeddings can model rare words well and domain-specific embeddings can better represent in-domain terms. Therefore, recent works consider attention-based meta-embeddings to combine different embedding types. We demonstrate that these methods have two shortcomings: First, the attention weights are calculated without knowledge of word properties. Second, the different embedding types can form clusters in the common embedding space, preventing the computation of a meaningful average of different embeddings and thus, reducing performance. We propose to solve these problems by using feature-based meta-embeddings learned with adversarial training. Our experiments and analysis on sentence classification and sequence tagging tasks show that our approach is effective. We set the new state of the art on various datasets across languages and domains.

NLNDE: The Neither-Language-Nor-Domain-Experts' Way of Spanish Medical Document De-Identification

Natural language processing has huge potential in the medical domain which recently led to a lot of research in this field. However, a prerequisite of secure processing of medical documents, e.g., patient notes and clinical trials, is the proper de-identification of privacy-sensitive information. In this paper, we describe our NLNDE system, with which we participated in the MEDDOCAN competition, the medical document anonymization task of IberLEF 2019. We address the task of detecting and classifying protected health information from Spanish data as a sequence-labeling problem and investigate different embedding methods for our neural network. Despite dealing in a non-standard language and domain setting, the NLNDE system achieves promising results in the competition.

NLNDE: Enhancing Neural Sequence Taggers with Attention and Noisy Channel for Robust Pharmacological Entity Detection

Named entity recognition has been extensively studied on English news texts. However, the transfer to other domains and languages is still a challenging problem. In this paper, we describe the system with which we participated in the first subtrack of the PharmaCoNER competition of the BioNLP Open Shared Tasks 2019. Aiming at pharmacological entity detection in Spanish texts, the task provides a non-standard domain and language setting. However, we propose an architecture that requires neither language nor domain expertise. We treat the task as a sequence labeling task and experiment with attention-based embedding selection and the training on automatically annotated data to further improve our system's performance. Our system achieves promising results, especially by combining the different techniques, and reaches up to 88.6% F1 in the competition.

The SOFC-Exp Corpus and Neural Approaches to Information Extraction in the Materials Science Domain

This paper presents a new challenging information extraction task in the domain of materials science. We develop an annotation scheme for marking information on experiments related to solid oxide fuel cells in scientific publications, such as involved materials and measurement conditions. With this paper, we publish our annotation guidelines, as well as our SOFC-Exp corpus consisting of 45 open-access scholarly articles annotated by domain experts. A corpus and an inter-annotator agreement study demonstrate the complexity of the suggested named entity recognition and slot filling tasks as well as high annotation quality. We also present strong neural-network based models for a variety of tasks that can be addressed on the basis of our new data set. On all tasks, using BERT embeddings leads to large performance gains, but with increasing task complexity, adding a recurrent neural network on top seems beneficial. Our models will serve as competitive baselines in future work, and analysis of their performance highlights difficult cases when modeling the data and suggests promising research directions.