Temporal Relation Extraction in Clinical Texts

Unstructured data in electronic health records, represented by clinical texts, are a vast source of healthcare information because they describe a patient's journey, including clinical findings, procedures, and information about the continuity of care. The publication of several studies on temporal relation extraction from clinical texts during the last decade and the realization of multiple shared tasks highlight the importance of this research theme. Therefore, we propose a review of temporal relation extraction in clinical texts. We analyzed 105 articles and verified that relations between events and document creation time, a coarse temporality type, were addressed with traditional machine learning–based models with few recent initiatives to push the state-of-the-art with deep learning–based models. For temporal relations between entities (event and temporal expressions) in the document, factors such as dataset imbalance because of candidate pair generation and task complexity directly affect the system's performance. The state-of-the-art resides on attention-based models, with contextualized word representations being fine-tuned for temporal relation extraction. However, further experiments and advances in the research topic are required until real-time clinical domain applications are released. Furthermore, most of the publications mainly reside on the same dataset, hindering the need for new annotation projects that provide datasets for different medical specialties, clinical text types, and even languages.

MiDTD: A Simple and Effective Distillation Framework for Distantly Supervised Relation Extraction

Relation extraction (RE), an important information extraction task, faced the great challenge brought by limited annotation data. To this end, distant supervision was proposed to automatically label RE data, and thus largely increased the number of annotated instances. Unfortunately, lots of noise relation annotations brought by automatic labeling become a new obstacle. Some recent studies have shown that the teacher-student framework of knowledge distillation can alleviate the interference of noise relation annotations via label softening. Nevertheless, we find that they still suffer from two problems: propagation of inaccurate dark knowledge and constraint of a unified distillation temperature . In this article, we propose a simple and effective Multi-instance Dynamic Temperature Distillation (MiDTD) framework, which is model-agnostic and mainly involves two modules: multi-instance target fusion (MiTF) and dynamic temperature regulation (DTR). MiTF combines the teacher’s predictions for multiple sentences with the same entity pair to amend the inaccurate dark knowledge in each student’s target. DTR allocates alterable distillation temperatures to different training instances to enable the softness of most student’s targets to be regulated to a moderate range. In experiments, we construct three concrete MiDTD instantiations with BERT, PCNN, and BiLSTM-based RE models, and the distilled students significantly outperform their teachers and the state-of-the-art (SOTA) methods.

A Co-Embedding Model with Variational Auto-Encoder for Knowledge Graphs

Knowledge graph (KG) embedding has been widely studied to obtain low-dimensional representations for entities and relations. It serves as the basis for downstream tasks, such as KG completion and relation extraction. Traditional KG embedding techniques usually represent entities/relations as vectors or tensors, mapping them in different semantic spaces and ignoring the uncertainties. The affinities between entities and relations are ambiguous when they are not embedded in the same latent spaces. In this paper, we incorporate a co-embedding model for KG embedding, which learns low-dimensional representations of both entities and relations in the same semantic space. To address the issue of neglecting uncertainty for KG components, we propose a variational auto-encoder that represents KG components as Gaussian distributions. In addition, compared with previous methods, our method has the advantages of high quality and interpretability. Our experimental results on several benchmark datasets demonstrate our model’s superiority over the state-of-the-art baselines.

Predicting the impact of online news articles – is information necessary?

We exploit the Twitter platform to create a dataset of news articles derived from tweets concerning COVID-19, and use the associated tweets to define a number of popularity measures. The focus on (potentially) biomedical news articles allows the quantity of biomedically valid information (as extracted by biomedical relation extraction) to be included in the list of explored features. Aside from forming part of a systematic correlation exploration, the features – ranging from the semantic relations through readability measures to the article’s digital content – are used within a number of machine learning classifier and regression algorithms. Unsurprisingly, the results support that for more complex articles (as determined by a readability measure) more sophisticated syntactic structure may be expected. A weak correlation is found with information within an article suggesting that other factors, such as numbers of videos, have a notable impact on the popularity of a news article. The best popularity prediction performance is obtained using a random forest machine learning algorithm, and the feature describing the quantity of biomedical information is in the top 3 most important features in almost a third of the experiments performed. Additionally, this feature is found to be more valuable than the widely used named entity recognition.

Biomedical relation extraction via knowledge-enhanced reading comprehension

Background In biomedical research, chemical and disease relation extraction from unstructured biomedical literature is an essential task. Effective context understanding and knowledge integration are two main research problems in this task. Most work of relation extraction focuses on classification for entity mention pairs. Inspired by the effectiveness of machine reading comprehension (RC) in the respect of context understanding, solving biomedical relation extraction with the RC framework at both intra-sentential and inter-sentential levels is a new topic worthy to be explored. Except for the unstructured biomedical text, many structured knowledge bases (KBs) provide valuable guidance for biomedical relation extraction. Utilizing knowledge in the RC framework is also worthy to be investigated. We propose a knowledge-enhanced reading comprehension (KRC) framework to leverage reading comprehension and prior knowledge for biomedical relation extraction. First, we generate questions for each relation, which reformulates the relation extraction task to a question answering task. Second, based on the RC framework, we integrate knowledge representation through an efficient knowledge-enhanced attention interaction mechanism to guide the biomedical relation extraction. Results The proposed model was evaluated on the BioCreative V CDR dataset and CHR dataset. Experiments show that our model achieved a competitive document-level F1 of 71.18% and 93.3%, respectively, compared with other methods. Conclusion Result analysis reveals that open-domain reading comprehension data and knowledge representation can help improve biomedical relation extraction in our proposed KRC framework. Our work can encourage more research on bridging reading comprehension and biomedical relation extraction and promote the biomedical relation extraction.

Analysis of the Full-Size Russian Corpus of Internet Drug Reviews with Complex NER Labeling Using Deep Learning Neural Networks and Language Models

The paper presents the full-size Russian corpus of Internet users’ reviews on medicines with complex named entity recognition (NER) labeling of pharmaceutically relevant entities. We evaluate the accuracy levels reached on this corpus by a set of advanced deep learning neural networks for extracting mentions of these entities. The corpus markup includes mentions of the following entities: medication (33,005 mentions), adverse drug reaction (1778), disease (17,403), and note (4490). Two of them—medication and disease—include a set of attributes. A part of the corpus has a coreference annotation with 1560 coreference chains in 300 documents. A multi-label model based on a language model and a set of features has been developed for recognizing entities of the presented corpus. We analyze how the choice of different model components affects the entity recognition accuracy. Those components include methods for vector representation of words, types of language models pre-trained for the Russian language, ways of text normalization, and other pre-processing methods. The sufficient size of our corpus allows us to study the effects of particularities of annotation and entity balancing. We compare our corpus to existing ones by the occurrences of entities of different types and show that balancing the corpus by the number of texts with and without adverse drug event (ADR) mentions improves the ADR recognition accuracy with no notable decline in the accuracy of detecting entities of other types. As a result, the state of the art for the pharmacological entity extraction task for the Russian language is established on a full-size labeled corpus. For the ADR entity type, the accuracy achieved is 61.1% by the F1-exact metric, which is on par with the accuracy level for other language corpora with similar characteristics and ADR representativeness. The accuracy of the coreference relation extraction evaluated on our corpus is 71%, which is higher than the results achieved on the other Russian-language corpora.