The automatic extraction of chemical information from text requires the recognition of chemical entity mentions as one of its key steps. When developing supervised named entity recognition (NER) systems, the availability of a large, manually annotated text corpus is desirable. Furthermore, large corpora permit the robust evaluation and comparison of different approaches that detect chemicals in documents. We present the CHEMDNER corpus, a collection of 10,000 PubMed abstracts that contain a total of 84,355 chemical entity mentions labeled manually by expert chemistry literature curators, following annotation guidelines specifically defined for this task. The abstracts of the CHEMDNER corpus were selected to be representative for all major chemical disciplines. Each of the chemical entity mentions was manually labeled according to its structure-associated chemical entity mention (SACEM) class: abbreviation, family, formula, identifier, multiple, systematic and trivial. The difficulty and consistency of tagging chemicals in text was measured using an agreement study between annotators, obtaining a percentage agreement of 91. For a subset of the CHEMDNER corpus (the test set of 3,000 abstracts) we provide not only the Gold Standard manual annotations, but also mentions automatically detected by the 26 teams that participated in the BioCreative IV CHEMDNER chemical mention recognition task. In addition, we release the CHEMDNER silver standard corpus of automatically extracted mentions from 17,000 randomly selected PubMed abstracts. A version of the CHEMDNER corpus in the BioC format has been generated as well. We propose a standard for required minimum information about entity annotations for the construction of domain specific corpora on chemical and drug entities. The CHEMDNER corpus and annotation guidelines are available at: http://www.biocreative.org/resources/biocreative-iv/chemdner-corpus/

Molecular graph representation learning has shown considerable strength in molecular analysis and drug discovery. Due to the difficulty of obtaining molecular property labels, pre-training models based on self-supervised learning has become increasingly popular in molecular representation learning. Notably, Graph Neural Networks (GNN) are employed as the backbones to encode implicit representations of molecules in most existing works. However, vanilla GNN encoders ignore chemical structural information and functions implied in molecular motifs, and obtaining the graph-level representation via the READOUT function hinders the interaction of graph and node representations. In this paper, we propose Hierarchical Molecular Graph Self-supervised Learning (HiMol), which introduces a pre-training framework to learn molecule representation for property prediction. First, we present a Hierarchical Molecular Graph Neural Network (HMGNN), which encodes motif structure and extracts node-motif-graph hierarchical molecular representations. Then, we introduce Multi-level Self-supervised Pre-training (MSP), in which corresponding multi-level generative and predictive tasks are designed as self-supervised signals of HiMol model. Finally, superior molecular property prediction results on both classification and regression tasks demonstrate the effectiveness of HiMol. Moreover, the visualization performance in the downstream dataset shows that the molecule representations learned by HiMol can capture chemical semantic information and properties.

Drug-drug interaction (DDI) extraction as a typical relation extraction task in natural language processing (NLP) has always attracted great attention. Most state-of-the-art DDI extraction systems are based on support vector machines (SVM) with a large number of manually defined features. Recently, convolutional neural networks (CNN), a robust machine learning method which almost does not need manually defined features, has exhibited great potential for many NLP tasks. It is worth employing CNN for DDI extraction, which has never been investigated. We proposed a CNN-based method for DDI extraction. Experiments conducted on the 2013 DDIExtraction challenge corpus demonstrate that CNN is a good choice for DDI extraction. The CNN-based DDI extraction method achieves anF-score of 69.75%, which outperforms the existing best performing method by 2.75%.

Objective Named entity recognition (NER) is one of the fundamental tasks in natural language processing. In the medical domain, there have been a numb

Entity recognition is one of the most primary steps for text analysis and has long attracted considerable attention from researchers. In the clinical domain, various types of entities, such as clinical entities and protected health information (PHI), widely exist in clinical texts. Recognizing these entities has become a hot topic in clinical natural language processing (NLP), and a large number of traditional machine learning methods, such as support vector machine and conditional random field, have been deployed to recognize entities from clinical texts in the past few years. In recent years, recurrent neural network (RNN), one of deep learning methods that has shown great potential on many problems including named entity recognition, also has been gradually used for entity recognition from clinical texts. In this paper, we comprehensively investigate the performance of LSTM (long-short term memory), a representative variant of RNN, on clinical entity recognition and protected health information recognition. The LSTM model consists of three layers: input layer – generates representation of each word of a sentence; LSTM layer – outputs another word representation sequence that captures the context information of each word in this sentence; Inference layer – makes tagging decisions according to the output of LSTM layer, that is, outputting a label sequence. Experiments conducted on corpora of the 2010, 2012 and 2014 i2b2 NLP challenges show that LSTM achieves highest micro-average F1-scores of 85.81% on the 2010 i2b2 medical concept extraction, 92.29% on the 2012 i2b2 clinical event detection, and 94.37% on the 2014 i2b2 de-identification, which is considerably competitive with other state-of-the-art systems. LSTM that requires no hand-crafted feature has great potential on entity recognition from clinical texts. It outperforms traditional machine learning methods that suffer from fussy feature engineering. A possible future direction is how to integrate knowledge bases widely existing in the clinical domain into LSTM, which is a case of our future work. Moreover, how to use LSTM to recognize entities in specific formats is also another possible future direction.