skip to main content


Title: Identifying Chemical Reactions and Their Associated Attributes in Patents
Chemical patents are an essential source of information about novel chemicals and chemical reactions. However, with the increasing volume of such patents, mining information about these chemicals and chemical reactions has become a time-intensive and laborious endeavor. In this study, we present a system to extract chemical reaction events from patents automatically. Our approach consists of two steps: 1) named entity recognition (NER)—the automatic identification of chemical reaction parameters from the corresponding text, and 2) event extraction (EE)—the automatic classifying and linking of entities based on their relationships to each other. For our NER system, we evaluate bidirectional long short-term memory (BiLSTM)-based and bidirectional encoder representations from transformer (BERT)-based methods. For our EE system, we evaluate BERT-based, convolutional neural network (CNN)-based, and rule-based methods. We evaluate our NER and EE components independently and as an end-to-end system, reporting the precision, recall, and F 1 score. Our results show that the BiLSTM-based method performed best at identifying the entities, and the CNN-based method performed best at extracting events.  more » « less
Award ID(s):
1651957
PAR ID:
10312160
Author(s) / Creator(s):
; ; ; ;
Date Published:
Journal Name:
Frontiers in Research Metrics and Analytics
Volume:
6
ISSN:
2504-0537
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Abstract Motivation

    Best performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models.

    Results

    We propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems.

    Availability and implementation

    The GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN.

    Supplementary information

    Supplementary data are available at Bioinformatics online.

     
    more » « less
  2. Social media platforms are playing increasingly critical roles in disaster response and rescue operations. During emergencies, users can post rescue requests along with their addresses on social media, while volunteers can search for those messages and send help. However, efficiently leveraging social media in rescue operations remains challenging because of the lack of tools to identify rescue request messages on social media automatically and rapidly. Analyzing social media data, such as Twitter data, relies heavily on Natural Language Processing (NLP) algorithms to extract information from texts. The introduction of bidirectional transformers models, such as the Bidirectional Encoder Representations from Transformers (BERT) model, has significantly outperformed previous NLP models in numerous text analysis tasks, providing new opportunities to precisely understand and classify social media data for diverse applications. This study developed and compared ten VictimFinder models for identifying rescue request tweets, three based on milestone NLP algorithms and seven BERT-based. A total of 3191 manually labeled disaster-related tweets posted during 2017 Hurricane Harvey were used as the training and testing datasets. We evaluated the performance of each model by classification accuracy, computation cost, and model stability. Experiment results show that all BERT-based models have significantly increased the accuracy of categorizing rescue-related tweets. The best model for identifying rescue request tweets is a customized BERT-based model with a Convolutional Neural Network (CNN) classifier. Its F1-score is 0.919, which outperforms the baseline model by 10.6%. The developed models can promote social media use for rescue operations in future disaster events. 
    more » « less
  3. null (Ed.)

    Named entity recognition (NER) is a fundamental task in the natural language processing (NLP) area. Recently, representation learning methods (e.g., character embedding and word embedding) have achieved promising recognition results. However, existing models only consider partial features derived from words or characters while failing to integrate semantic and syntactic information (e.g., capitalization, inter-word relations, keywords, lexical phrases, etc.) from multi-level perspectives. Intuitively, multi-level features can be helpful when recognizing named entities from complex sentences. In this study, we propose a novel framework called attention-based multi-level feature fusion (AMFF), which is used to capture the multi-level features from different perspectives to improve NER. Our model consists of four components to respectively capture the local character-level, global character-level, local word-level, and global word-level features, which are then fed into a BiLSTM-CRF network for the final sequence labeling. Extensive experimental results on four benchmark datasets show that our proposed model outperforms a set of state-of-the-art baselines.

     
    more » « less
  4. Modern machine learning algorithms are capable of providing remarkably accurate point-predictions; however, questions remain about their statistical reliability. Unlike conventional machine learning methods, conformal prediction algorithms return confidence sets (i.e., set-valued predictions) that correspond to a given significance level. Moreover, these confidence sets are valid in the sense that they guarantee finite sample control over type 1 error probabilities, allowing the practitioner to choose an acceptable error rate. In our paper, we propose inductive conformal prediction (ICP) algorithms for the tasks of text infilling and part-of-speech (POS) prediction for natural language data. We construct new ICP-enhanced algorithms for POS tagging based on BERT (bidirectional encoder representations from transformers) and BiLSTM (bidirectional long short-term memory) models. For text infilling, we design a new ICP-enhanced BERT algorithm. We analyze the performance of the algorithms in simulations using the Brown Corpus, which contains over 57,000 sentences. Our results demonstrate that the ICP algorithms are able to produce valid set-valued predictions that are small enough to be applicable in real-world applications. We also provide a real data example for how our proposed set-valued predictions can improve machine generated audio transcriptions. 
    more » « less
  5. We present CyBERT, a domain-specific Bidirectional Encoder Representations from Transformers (BERT) model, fine-tuned with a large corpus of textual cybersecurity data. State-of-the-art natural language models that can process dense, fine-grained textual threat, attack, and vulnerability information can provide numerous benefits to the cybersecurity community. The primary contribution of this paper is providing the security community with an initial fine-tuned BERT model that can perform a variety of cybersecurity-specific downstream tasks with high accuracy and efficient use of resources. We create a cybersecurity corpus from open-source unstructured and semi-unstructured Cyber Threat Intelligence (CTI) data and use it to fine-tune a base BERT model with Masked Language Modeling (MLM) to recognize specialized cybersecurity entities. We evaluate the model using various downstream tasks that can benefit modern Security Operations Centers (SOCs). The finetuned CyBERT model outperforms the base BERT model in the domain-specific MLM evaluation. We also provide use-cases of CyBERT application in cybersecurity based downstream tasks. 
    more » « less