A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience

Matthew Shardlow, Meizhi Ju, Maolin Li, Christian O’Reilly, Elisabetta Iavarone, John McNaught, Sophia Ananiadou

Research output: Contribution to journalArticlepeer-review


The curation of neuroscience entities is crucial to ongoing efforts in neuroinformatics and computational neuroscience, such as those being deployed in the context of continuing large-scale brain modelling projects. However, manually sifting through thousands of articles for new information about modelled entities is a painstaking and low-reward task. Text mining can be used to help a curator extract relevant information from this literature in a systematic way. We propose the application of text mining methods for the neuroscience literature. Specifically, two computational neuroscientists annotated a corpus of entities pertinent to neuroscience using active learning techniques to enable
swift, targeted annotation. We then trained machine learning models to recognise the entities that have been identified. The entities covered are Neuron Types, Brain Regions, Experimental Values, Units, Ion Currents, Channels, and Conductances and Model organisms. We tested a traditional rule-based
approach, a conditional random field and a model using deep learning named entity recognition, finding that the deep learning model was superior. Our final results show that we can detect a range of named entities of interest to the neuroscientist with a macro average precision, recall and F1 score of 0.866, 0.817 and 0.837 respectively. The contributions of this work are as follows: 1) We provide a set of Named Entity Recognition (NER) tools that are capable of detecting neuroscience entities with performance above or similar to prior work. 2) We propose a methodology for training NER tools for neuroscience that requires very little training data to get strong performance. This can be adapted for any sub-domain within neuroscience. 3) We provide a small corpus with annotations for multiple entity types, as well as annotation guidelines to help others reproduce our experiments.
Original languageEnglish
Pages (from-to)391-406
Number of pages16
Issue number3
Early online date15 Nov 2018
Publication statusPublished - 15 Jul 2019


  • Annotation
  • Conditional random field
  • Corpus
  • Data curation
  • Data mining
  • Deep learning
  • Named entity recognition
  • Text mining


Dive into the research topics of 'A Text Mining Pipeline Using Active and Deep Learning Aimed at Curating Information in Computational Neuroscience'. Together they form a unique fingerprint.

Cite this