scholarly journals Machine Learning Undercounts Reproductive Organs on Herbarium Specimens but Accurately Derives Their Quantitative Phenological Status: A Case Study of Streptanthus tortuosus

Plants ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 2471
Author(s):  
Natalie L. R. Love ◽  
Pierre Bonnet ◽  
Hervé Goëau ◽  
Alexis Joly ◽  
Susan J. Mazer

Machine learning (ML) can accelerate the extraction of phenological data from herbarium specimens; however, no studies have assessed whether ML-derived phenological data can be used reliably to evaluate ecological patterns. In this study, 709 herbarium specimens representing a widespread annual herb, Streptanthus tortuosus, were scored both manually by human observers and by a mask R-CNN object detection model to (1) evaluate the concordance between ML and manually-derived phenological data and (2) determine whether ML-derived data can be used to reliably assess phenological patterns. The ML model generally underestimated the number of reproductive structures present on each specimen; however, when these counts were used to provide a quantitative estimate of the phenological stage of plants on a given sheet (i.e., the phenological index or PI), the ML and manually-derived PI’s were highly concordant. Moreover, herbarium specimen age had no effect on the estimated PI of a given sheet. Finally, including ML-derived PIs as predictor variables in phenological models produced estimates of the phenological sensitivity of this species to climate, temporal shifts in flowering time, and the rate of phenological progression that are indistinguishable from those produced by models based on data provided by human observers. This study demonstrates that phenological data extracted using machine learning can be used reliably to estimate the phenological stage of herbarium specimens and to detect phenological patterns.

BioScience ◽  
2020 ◽  
Vol 70 (7) ◽  
pp. 610-620 ◽  
Author(s):  
Katelin D Pearson ◽  
Gil Nelson ◽  
Myla F J Aronson ◽  
Pierre Bonnet ◽  
Laura Brenskelle ◽  
...  

Abstract Machine learning (ML) has great potential to drive scientific discovery by harvesting data from images of herbarium specimens—preserved plant material curated in natural history collections—but ML techniques have only recently been applied to this rich resource. ML has particularly strong prospects for the study of plant phenological events such as growth and reproduction. As a major indicator of climate change, driver of ecological processes, and critical determinant of plant fitness, plant phenology is an important frontier for the application of ML techniques for science and society. In the present article, we describe a generalized, modular ML workflow for extracting phenological data from images of herbarium specimens, and we discuss the advantages, limitations, and potential future improvements of this workflow. Strategic research and investment in specimen-based ML methods, along with the aggregation of herbarium specimen data, may give rise to a better understanding of life on Earth.


2020 ◽  
Vol 8 (6) ◽  
Author(s):  
Hervé Goëau ◽  
Adán Mora‐Fallas ◽  
Julien Champ ◽  
Natalie L. Rossington Love ◽  
Susan J. Mazer ◽  
...  

i-com ◽  
2021 ◽  
Vol 20 (1) ◽  
pp. 19-32
Author(s):  
Daniel Buschek ◽  
Charlotte Anlauff ◽  
Florian Lachner

Abstract This paper reflects on a case study of a user-centred concept development process for a Machine Learning (ML) based design tool, conducted at an industry partner. The resulting concept uses ML to match graphical user interface elements in sketches on paper to their digital counterparts to create consistent wireframes. A user study (N=20) with a working prototype shows that this concept is preferred by designers, compared to the previous manual procedure. Reflecting on our process and findings we discuss lessons learned for developing ML tools that respect practitioners’ needs and practices.


2021 ◽  
Vol 11 (13) ◽  
pp. 5826
Author(s):  
Evangelos Axiotis ◽  
Andreas Kontogiannis ◽  
Eleftherios Kalpoutzakis ◽  
George Giannakopoulos

Ethnopharmacology experts face several challenges when identifying and retrieving documents and resources related to their scientific focus. The volume of sources that need to be monitored, the variety of formats utilized, and the different quality of language use across sources present some of what we call “big data” challenges in the analysis of this data. This study aims to understand if and how experts can be supported effectively through intelligent tools in the task of ethnopharmacological literature research. To this end, we utilize a real case study of ethnopharmacology research aimed at the southern Balkans and the coastal zone of Asia Minor. Thus, we propose a methodology for more efficient research in ethnopharmacology. Our work follows an “expert–apprentice” paradigm in an automatic URL extraction process, through crawling, where the apprentice is a machine learning (ML) algorithm, utilizing a combination of active learning (AL) and reinforcement learning (RL), and the expert is the human researcher. ML-powered research improved the effectiveness and efficiency of the domain expert by 3.1 and 5.14 times, respectively, fetching a total number of 420 relevant ethnopharmacological documents in only 7 h versus an estimated 36 h of human-expert effort. Therefore, utilizing artificial intelligence (AI) tools to support the researcher can boost the efficiency and effectiveness of the identification and retrieval of appropriate documents.


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