scholarly journals LSTMVoter: chemical named entity recognition using a conglomerate of sequence labeling tools

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Wahed Hemati ◽  
Alexander Mehler
2015 ◽  
Vol 12 (2) ◽  
pp. 465-486
Author(s):  
Dejan Mancev ◽  
Branimir Todorovic

Structured learning algorithms usually require inference during the training procedure. Due to their exponential size of output space, the parameter update is performed only on a relatively small collection built from the ?best? structures. The k-best MIRA is an example of an online algorithm which seeks optimal parameters by making updates on k structures with the highest score at a time. Following the idea of using k-best structures during the learning process, in this paper we introduce four new k-best extensions of max-margin structured algorithms. We discuss their properties and connection, and evaluate all algorithms on two sequence labeling problems, the shallow parsing and named entity recognition. The experiments show how the proposed algorithms are affected by the changes of k in terms of the F-measure and computational time, and that the proposed algorithms can improve results in comparison to the single best case. Moreover, the restriction to the single best case produces a comparison of the existing algorithms.


Author(s):  
Minlong Peng ◽  
Qi Zhang ◽  
Xiaoyu Xing ◽  
Tao Gui ◽  
Jinlan Fu ◽  
...  

Word representation is a key component in neural-network-based sequence labeling systems. However, representations of unseen or rare words trained on the end task are usually poor for appreciable performance. This is commonly referred to as the out-of-vocabulary (OOV) problem. In this work, we address the OOV problem in sequence labeling using only training data of the task. To this end, we propose a novel method to predict representations for OOV words from their surface-forms (e.g., character sequence) and contexts. The method is specifically designed to avoid the error propagation problem suffered by existing approaches in the same paradigm. To evaluate its effectiveness, we performed extensive empirical studies on four part-of-speech tagging (POS) tasks and four named entity recognition (NER) tasks. Experimental results show that the proposed method can achieve better or competitive performance on the OOV problem compared with existing state-of-the-art methods.


Author(s):  
Hema R. ◽  
Ajantha Devi

Chemical entities can be represented in different forms like chemical names, chemical formulae, and chemical structures. Because of the different classification frameworks for chemical names, the task of distinguishing proof or extraction of chemical elements with less ambiguous is considered a major test. Compound named entity recognition (NER) is the initial phase in any chemical-related data extraction strategy. The majority of the chemical NER is done utilizing dictionary-based, rule-based, and machine learning procedures. Recently, deep learning methods have evolved, and, in this chapter, the authors sketch out the various deep learning techniques applied for chemical NER. First, the authors introduced the fundamental concepts of chemical named entity recognition, the textual contents of chemical documents, and how these chemicals are represented in chemical literature. The chapter concludes with the strengths and weaknesses of the above methods and also the types of the chemical entities extracted.


2014 ◽  
Vol 11 (3) ◽  
pp. 1-16 ◽  
Author(s):  
Andre Lamurias ◽  
João D. Ferreira ◽  
Francisco M. Couto

Summary Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, “Identifying Interactions between Chemical Entities” (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to stateof- the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.


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