Sequence labeling serves as the most commonly used scheme for Chinese named entity recognition(NER). However, traditional sequence labeling methods classify tokens within an entity into different classes according to their positions. As a result, different tokens in the same entity may be learned with representations that are isolated and unrelated in target representation space, which could finally negatively affect the subsequent performance of token classification. In this paper, we point out and define this problem as Entity Representation Segmentation in Label-semantics. And then we present NerCo: Named entity recognition with Contrastive learning, a novel NER framework which can better exploit labeled data and avoid the above problem. Following the pretrain-finetune paradigm, NerCo firstly guides the encoder to learn powerful label-semantics based representations by gathering the encoded token representations of the same Semantic Class while pushing apart that of different. Subsequently, NerCo finetunes the learned encoder for final entity prediction. Extensive experiments on several datasets demonstrate that our framework can consistently improve the baseline and achieve state-of-the-art performance.

Nested named entities (nested NEs) refer to the situation where one named entity is included or nested within another named entity, which cannot be recognized by the traditional sequence labeling methods. Recently, span-based methods have become the mainstream methods for nested Named Entity Recognition (nested NER). The fundamental concept behind this method is to enumerate nearly all potential spans as entity mentions and subsequently classify them. However, span-based methods independently classify spans without considering the semantic relations among them, which negatively impacts the span representation. To address the issue, we propose a novel deep learning architecture for nested NER that explores interactive and contrastive relations among spans. Specifically, we design a scale transformation mechanism that embeds geometric information into span representations, which enhances the model's ability to encode interactive relations between spans. Additionally, we introduce a supervised contrastive learning loss that pulls apart highly overlapping spans in the embedding space to encode the contrastive relations. Experiments show that our method achieves state-of-the-art or competitive performance on three publicly nested NER datasets, thus validating its effectiveness.

MOTIVATION: A biochemical reaction, bio-event, depicts the relationships between participating entities. Current text mining research has been focusing on identifying bio-events from scientific literature. However, rare efforts have been dedicated to normalize bio-events extracted from scientific literature with the entries in the curated reaction databases, which could disambiguate the events and further support interconnecting events into biologically meaningful and complete networks. RESULTS: In this paper, we propose BioNorm, a novel method of normalizing bio-events extracted from scientific literature to entries in the bio-molecular reaction database, e.g. IntAct. BioNorm considers event normalization as a paraphrase identification problem. It represents an entry as a natural language statement by combining multiple types of information contained in it. Then, it predicts the semantic similarity between the natural language statement and the statements mentioning events in scientific literature using a long short-term memory recurrent neural network (LSTM). An event will be normalized to the entry if the two statements are paraphrase. To the best of our knowledge, this is the first attempt of event normalization in the biomedical text mining. The experiments have been conducted using the molecular interaction data from IntAct. The results demonstrate that the method could achieve F-score of 0.87 in normalizing event-containing statements. AVAILABILITY AND IMPLEMENTATION: The source code is available at the gitlab repository https://gitlab.com/BioAI/leen and BioASQvec Plus is available on figshare https://figshare.com/s/45896c31d10c3f6d857a.