scholarly journals Self-Attention-Based Models for the Extraction of Molecular Interactions from Biological Texts

Biomolecules ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1591
Author(s):  
Prashant Srivastava ◽  
Saptarshi Bej ◽  
Kristina Yordanova ◽  
Olaf Wolkenhauer
Keyword(s):  
Language Processing ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Literature Mining ◽  
Interaction Extraction ◽  
Database Curation ◽  
Biological Literature

For any molecule, network, or process of interest, keeping up with new publications on these is becoming increasingly difficult. For many cellular processes, the amount molecules and their interactions that need to be considered can be very large. Automated mining of publications can support large-scale molecular interaction maps and database curation. Text mining and Natural-Language-Processing (NLP)-based techniques are finding their applications in mining the biological literature, handling problems such as Named Entity Recognition (NER) and Relationship Extraction (RE). Both rule-based and Machine-Learning (ML)-based NLP approaches have been popular in this context, with multiple research and review articles examining the scope of such models in Biological Literature Mining (BLM). In this review article, we explore self-attention-based models, a special type of Neural-Network (NN)-based architecture that has recently revitalized the field of NLP, applied to biological texts. We cover self-attention models operating either at the sentence level or an abstract level, in the context of molecular interaction extraction, published from 2019 onwards. We conducted a comparative study of the models in terms of their architecture. Moreover, we also discuss some limitations in the field of BLM that identifies opportunities for the extraction of molecular interactions from biological text.

scholarly journals Self-Attention Based Models for the Extraction of Molecular Interactions from Biological Texts

2021 ◽  
Author(s):  
Prashant Srivastava ◽  
Saptarshi Bej ◽  
Kristina Yordanova ◽  
Olaf Wolkenhauer
Keyword(s):  
Language Processing ◽  
Molecular Interactions ◽  
Molecular Interaction ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Literature Mining ◽  
Interaction Extraction ◽  
Database Curation ◽  
Biological Literature

For any molecule, network, or process of interest, to keep up with new publications on these, is becoming increasingly difficult. For many cellular processes, molecules and their interactions that need to be considered can be very large. Automated mining of publications can support large scale molecular interaction maps and database curation. Text mining and Natural Language Processing (NLP)-based techniques are finding their applications in mining the biological literature, handling problems such as Named Entity Recognition (NER) and Relationship Extraction (RE). Both rule-based and machine learning (ML)-based NLP approaches have been popular in this context, with multiple research and review articles examining the scope of such models in Biological Literature Mining (BLM). In this review article, we explore self-attention based models, a special type of neural network (NN)-based architectures that have recently revitalized the field of NLP, applied to biological texts. We cover self-attention models operating either at a sentence level or an abstract level, in the context of molecular interaction extraction, published from 2019 onwards. We conduct a comparative study of the models in terms of their architecture. Moreover, we also discuss some limitations in the field of BLM that identifies opportunities for the extraction of molecular interactions from biological text.

scholarly journals An Attention-Based Model Using Character Composition of Entities in Chinese Relation Extraction

Information ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 79 ◽  
Author(s):  
Xiaoyu Han ◽  
Yue Zhang ◽  
Wenkai Zhang ◽  
Tinglei Huang
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Additional Information ◽  
Named Entity ◽  
Proposed Model ◽  
The Relationship ◽  
Crucial Part

Relation extraction is a vital task in natural language processing. It aims to identify the relationship between two specified entities in a sentence. Besides information contained in the sentence, additional information about the entities is verified to be helpful in relation extraction. Additional information such as entity type getting by NER (Named Entity Recognition) and description provided by knowledge base both have their limitations. Nevertheless, there exists another way to provide additional information which can overcome these limitations in Chinese relation extraction. As Chinese characters usually have explicit meanings and can carry more information than English letters. We suggest that characters that constitute the entities can provide additional information which is helpful for the relation extraction task, especially in large scale datasets. This assumption has never been verified before. The main obstacle is the lack of large-scale Chinese relation datasets. In this paper, first, we generate a large scale Chinese relation extraction dataset based on a Chinese encyclopedia. Second, we propose an attention-based model using the characters that compose the entities. The result on the generated dataset shows that these characters can provide useful information for the Chinese relation extraction task. By using this information, the attention mechanism we used can recognize the crucial part of the sentence that can express the relation. The proposed model outperforms other baseline models on our Chinese relation extraction dataset.

scholarly journals The sale of heritage on eBay: Market trends and cultural value

2020 ◽  
Vol 7 (2) ◽  
pp. 205395172096886
Author(s):  
Mark Altaweel ◽  
Tasoula Georgiou Hadjitofi
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Conditional Random Fields ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Cultural Value ◽  
Named Entity ◽  
Online Marketplace ◽  
Large Scale Analysis ◽  
Market Trends

The marketisation of heritage has been a major topic of interest among heritage specialists studying how the online marketplace shapes sales. Missing from that debate is a large-scale analysis seeking to understand market trends on popular selling platforms such as eBay. Sites such as eBay can inform what heritage items are of interest to the wider public, and thus what is potentially of greater cultural value, while also demonstrating monetary value trends. To better understand the sale of heritage on eBay’s international site, this work applies named entity recognition using conditional random fields, a method within natural language processing, and word dictionaries that inform on market trends. The methods demonstrate how Western markets, particularly the US and UK, have dominated sales for different cultures. Roman, Egyptian, Viking (Norse/Dane) and Near East objects are sold the most. Surprisingly, Cyprus and Egypt, two countries with relatively strict prohibition against the sale of heritage items, make the top 10 selling countries on eBay. Objects such as jewellery, statues and figurines, and religious items sell in relatively greater numbers, while masks and vessels (e.g. vases) sell at generally higher prices. Metal, stone and terracotta are commonly sold materials. More rare materials, such as those made of ivory, papyrus or wood, have relatively higher prices. Few sellers dominate the market, where in some months 40% of sales are controlled by the top 10 sellers. The tool used for the study is freely provided, demonstrating benefits in an automated approach to understanding sale trends.

scholarly journals Mining microbe–disease interactions from literature via a transfer learning model

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Chengkun Wu ◽  
Xinyi Xiao ◽  
Canqun Yang ◽  
JinXiang Chen ◽  
Jiacai Yi ◽  
...  
Keyword(s):  
Text Mining ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Learning Model ◽  
Biomedical Literature ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Interaction Extraction ◽  
Biomedical Texts ◽  
Data Browsing

Abstract Background Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe–disease interactions are hidden in the biomedical literature. The structured databases for microbe–disease interactions are in limited amounts. In this paper, we aim to construct a large-scale database for microbe–disease interactions automatically. We attained this goal via applying text mining methods based on a deep learning model with a moderate curation cost. We also built a user-friendly web interface that allows researchers to navigate and query required information. Results Firstly, we manually constructed a golden-standard corpus and a sliver-standard corpus (SSC) for microbe–disease interactions for curation. Moreover, we proposed a text mining framework for microbe–disease interaction extraction based on a pretrained model BERE. We applied named entity recognition tools to detect microbe and disease mentions from the free biomedical texts. After that, we fine-tuned the pretrained model BERE to recognize relations between targeted entities, which was originally built for drug–target interactions or drug–drug interactions. The introduction of SSC for model fine-tuning greatly improved detection performance for microbe–disease interactions, with an average reduction in error of approximately 10%. The MDIDB website offers data browsing, custom searching for specific diseases or microbes, and batch downloading. Conclusions Evaluation results demonstrate that our method outperform the baseline model (rule-based PKDE4J) with an average $$F_1$$ F 1 -score of 73.81%. For further validation, we randomly sampled nearly 1000 predicted interactions by our model, and manually checked the correctness of each interaction, which gives a 73% accuracy. The MDIDB webiste is freely avaliable throuth http://dbmdi.com/index/

scholarly journals External features enriched model for biomedical question answering

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gezheng Xu ◽  
Wenge Rong ◽  
Yanmeng Wang ◽  
Yuanxin Ouyang ◽  
Zhang Xiong
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Question Answering ◽  
Language Model ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Small Scale ◽  
Original Text ◽  
Specific Domain ◽  
Part Of Speech

Abstract Background Biomedical question answering (QA) is a sub-task of natural language processing in a specific domain, which aims to answer a question in the biomedical field based on one or more related passages and can provide people with accurate healthcare-related information. Recently, a lot of approaches based on the neural network and large scale pre-trained language model have largely improved its performance. However, considering the lexical characteristics of biomedical corpus and its small scale dataset, there is still much improvement room for biomedical QA tasks. Results Inspired by the importance of syntactic and lexical features in the biomedical corpus, we proposed a new framework to extract external features, such as part-of-speech and named-entity recognition, and fused them with the original text representation encoded by pre-trained language model, to enhance the biomedical question answering performance. Our model achieves an overall improvement of all three metrics on BioASQ 6b, 7b, and 8b factoid question answering tasks. Conclusions The experiments on BioASQ question answering dataset demonstrated the effectiveness of our external feature-enriched framework. It is proven by the experiments conducted that external lexical and syntactic features can improve Pre-trained Language Model’s performance in biomedical domain question answering task.

scholarly journals Mining Microbe-disease Interactions From Literature via a Transfer Learning Model

2021 ◽  
Author(s):  
Chengkun Wu ◽  
Xinyi Xiao ◽  
Canqun Yang ◽  
JinXiang Chen ◽  
Jiacai Yi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Text Mining ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Learning Model ◽  
Entity Recognition ◽  
Interaction Extraction ◽  
Golden Standard ◽  
Data Browsing ◽  
Deep Learning Model

Abstract Background: Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale curated databases for microbe-disease interactions are missing, as the amount of related literature is enormous and the curation process is costly and time-consuming. In this paper, we aim to construct a large-scale database for microbe-disease interactions automatically. We attained this goal via applying text mining methods based on a deep learning model with a moderate curation cost. We also built a user-friendly web interface to allow researchers navigate and query desired information. Results: For curation, we manually constructed a golden-standard corpora (GSC) and a sliver-standard corpora (SSC) for microbe-disease interactions. Then we proposed a text mining framework for microbe-disease interaction extraction without having to build a model from scratch. Firstly, we applied named entity recognition (NER) tools to detect microbe and disease mentions from texts. Then we transferred a deep learning model BERE to recognize relations between entities, which was originally built for drug-target interactions or drug-drug interactions. The introduction of SSC for model ne-tuning greatly improves the performance of detection for microbe-disease interactions, with an average reduction in error of approximately 10%. The resulting MDIDB website offers data browsing, custom search for specific diseases or microbes as well as batch download. Conclusions: Evaluation results demonstrate that our method outperform the baseline model (rule-based PKDE4J) with an average F1-score of 73.81%. For further validation, we randomly sampled nearly 1,000 predicted interactions by our model, and manually checked the correctness of each interaction, which gives a 73% accuracy. The MDIDB webiste is freely avaliable throuth http://dbmdi.com/index/

scholarly journals A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Meijing Li ◽  
Tsendsuren Munkhdalai ◽  
Xiuming Yu ◽  
Keun Ho Ryu
Keyword(s):  
Language Processing ◽  
Protein Interaction ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Support Vector ◽  
Protein Protein Interaction ◽  
Named Entity ◽  
Novel Approach ◽  
Interaction Extraction ◽  
Parsing Tree

Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

scholarly journals Feature-Frequency–Adaptive On-line Training for Fast and Accurate Natural Language Processing

2014 ◽  
Vol 40 (3) ◽  
pp. 563-586 ◽  
Author(s):  
Xu Sun ◽  
Wenjie Li ◽  
Houfeng Wang ◽  
Qin Lu
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
On Line ◽  
Core Idea ◽  
Speed And Accuracy ◽  
Feature Frequency

Training speed and accuracy are two major concerns of large-scale natural language processing systems. Typically, we need to make a tradeoff between speed and accuracy. It is trivial to improve the training speed via sacrificing accuracy or to improve the accuracy via sacrificing speed. Nevertheless, it is nontrivial to improve the training speed and the accuracy at the same time, which is the target of this work. To reach this target, we present a new training method, feature-frequency–adaptive on-line training, for fast and accurate training of natural language processing systems. It is based on the core idea that higher frequency features should have a learning rate that decays faster. Theoretical analysis shows that the proposed method is convergent with a fast convergence rate. Experiments are conducted based on well-known benchmark tasks, including named entity recognition, word segmentation, phrase chunking, and sentiment analysis. These tasks consist of three structured classification tasks and one non-structured classification task, with binary features and real-valued features, respectively. Experimental results demonstrate that the proposed method is faster and at the same time more accurate than existing methods, achieving state-of-the-art scores on the tasks with different characteristics.

scholarly journals Open Domain Chinese Triples Hierarchical Extraction Method

2020 ◽  
Vol 10 (14) ◽  
pp. 4819 ◽  
Author(s):  
Chunhui He ◽  
Zhen Tan ◽  
Haoran Wang ◽  
Chong Zhang ◽  
Yanli Hu ◽  
...  
Keyword(s):  
Language Processing ◽  
Extraction Method ◽  
High Performance ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Extraction Methods ◽  
Entity Recognition ◽  
Open Domain ◽  
Stable Performance ◽  
Relation Prediction

Open domain relation prediction is an important task in triples extraction. When faced with the task of constructing large-scale knowledge graph systems, with the exception of structured data, it is necessary to automatically extract triples from a large amount of unstructured text to expand entities and relations. Although a large number of English open relation prediction methods have achieved good performance, the high-performance system for open domain Chinese triples extraction remains undeveloped due to the lack of large-scale Chinese annotation corpora and the difficulty of Chinese language processing. In this paper, we propose an integrated open domain Chinese triples hierarchical extraction method (CTHE) to solve this problem, considering the advantages of Bi-LSTM-CRF and Att-Bi-GRU models based on the pre-trained BERT encoding model. This method can recognize the named entities from Chinese sentences to establish entity pairs, and implement hierarchical extraction of specific and open relations based on the user-defined schema library and attention mechanism. The experimental results demonstrate the effectiveness of this method, which achieved stable performance on the test dataset, and better precision and F1-score in comparison with state-of-the-art Chinese open domain triples extraction methods. Furthermore, a large-scale annotated dataset for a Chinese named entity recognition (NER) task is established, which provides support for research on Chinese NER tasks.

scholarly journals Unsupervised cross-lingual model transfer for named entity recognition with contextualized word representations

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257230
Author(s):  
Huijiong Yan ◽  
Tao Qian ◽  
Liang Xie ◽  
Shanguang Chen
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Competitive Performance ◽  
Named Entity ◽  
Model Transfer ◽  
The Cross ◽  
Cross Lingual

Named entity recognition (NER) is one fundamental task in the natural language processing (NLP) community. Supervised neural network models based on contextualized word representations can achieve highly-competitive performance, which requires a large-scale manually-annotated corpus for training. While for the resource-scarce languages, the construction of such as corpus is always expensive and time-consuming. Thus, unsupervised cross-lingual transfer is one good solution to address the problem. In this work, we investigate the unsupervised cross-lingual NER with model transfer based on contextualized word representations, which greatly advances the cross-lingual NER performance. We study several model transfer settings of the unsupervised cross-lingual NER, including (1) different types of the pretrained transformer-based language models as input, (2) the exploration strategies of the multilingual contextualized word representations, and (3) multi-source adaption. In particular, we propose an adapter-based word representation method combining with parameter generation network (PGN) better to capture the relationship between the source and target languages. We conduct experiments on a benchmark ConLL dataset involving four languages to simulate the cross-lingual setting. Results show that we can obtain highly-competitive performance by cross-lingual model transfer. In particular, our proposed adapter-based PGN model can lead to significant improvements for cross-lingual NER.

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