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In the last decade, institutions from around the world have implemented initiatives for digitizing biological collections (biocollections) and sharing their information online. The transcription of the metadata from photographs of specimens' labels is performed through human-centered approaches (e.g., crowdsourcing) because fully automated Information Extraction (IE) methods still generate a significant number of errors. The integration of human and machine tasks has been proposed to accelerate the IE from the billions of specimens waiting to be digitized. Nevertheless, in order to conduct research and trying new techniques, IE practitioners need to prepare sets of images, crowdsourcing experiments, recruit volunteers, process the transcriptions, generate ground truth values, program automated methods, etc. These research resources and processes require time and effort to be developed and architected into a functional system. In this paper, we present a simulator intended to accelerate the ability to experiment with workflows for extracting Darwin Core (DC) terms from images of specimens. The so-called HuMaIN Simulator includes the engine, the human-machine IE workflows for three DC terms, the code of the automated IE methods, crowdsourced and ground truth transcriptions of the DC terms of three biocollections, and several experiments that exemplify its potential use. The simulator adds Human-in-the-loop capabilities, for iterative IE and research on optimal methods. Its practical design permits the quick definition, customization, and implementation of experimental IE scenarios.
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SELFIE: Self-Aware Information Extraction from Digitized Biocollections
Biological collections store information with broad societal and environmental impact. In the last 15 years, after worldwide investments and crowdsourcing efforts, 25% of the collected specimens have been digitized; a process that includes the imaging of text attached to specimens and subsequent extraction of information from the resulting image. This information extraction (IE) process is complex, thus slow and typically involving human tasks. We propose a hybrid (Human-Machine) information extraction model that efficiently uses resources of different cost (machines, volunteers and/or experts) and speeds up the biocollections' digitization process, while striving to maintain the same quality as human-only IE processes. In the proposed model, called SELFIE, self-aware IE processes determine whether their output quality is satisfactory. If the quality is unsatisfactory, additional or alternative processes that yield higher quality output at higher cost are triggered. The effectiveness of this model is demonstrated by three SELFIE workflows for the extraction of Darwin-core terms from specimens' images. Compared to the traditional human-driven IE approach, SELFIE workflows showed, on average, a reduction of 27% in the information-capture time and a decrease of 32% in the required number of humans and their associated cost, while the quality of the results was negligibly reduced by 0.27%.
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- Award ID(s):
- 1535086
- PAR ID:
- 10159730
- Date Published:
- Journal Name:
- 2017 IEEE 13th International Conference on e-Science (eScience), Auckland, New Zealand
- Page Range / eLocation ID:
- 69 to 78
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.1109/eScience.2017.19
