Improving the accuracy of automated labeling of specimen images datasets via a confidence-based process - Datasets

This dataset contains supporting data for a research project aimed at analysing herbarium samples from the New England area at a large scale with deep learning techniques. Details on the methodology are shared in the acompanying paper (to be published).

Content:

• dataset600k_withAI.csv : A dataset of over 600.000 herbarium samples with its record metadata and a corresponding AI phenological annotations with matching confidence scores. The entirety of the record headers are provided, extracted directly from the NEVP portal. In addition, the AI labels are defined by the following headers. These 8 columns represent 4 binary classifiers with the Presence/Absence of each 4 traits and corresponding confidence (as a percentage - presence/absence percentages sum to 1).
  

  • Flowering

    Not Flowering

    Budding

    Not Budding

    Fruiting

    Not Fruiting

    Reproductive

    Not Reproductive

• data_species_with_statuses.csv: A processed dataset summarizing flowering period shift at a species level. Two types of headers are provided.
  • First metadata concerning the flowering shift and the data used to compute that value: 

    • genus	genus_species	slope	nb_specimens	p_value_significance	trend_category
      Genus of the species	Binomial name of the species	Regression slope defining the flowering shift as a slope	Number of herbarium specimens used to compute the shift	P-value significance of the slope being non-zero. ('Non Significant'/'Significant')	Summary of the shift as a binary characteristic ('Earlier'/'Later')

  • Second, metadata summarizing various traits associated to each species:

    • lifeform_status	native_introduced_status	wetland_status	seasonality_average	seasonality_spread
      Growth form from the USDA PLANTS Database. 'Forb_Herb', 'Shrub_Tree' or 'Vine'	'Native'/'Introduced' status from the USDA PLANTS Database.	National Wetland Plant List (NWPL) Wetland Indicator Status within the Northcentral and Northeast Region 'OBL'/'FACW'/'FAC'/'FACU'/'UPL'	A characteristic of the flowering season of the species based on the mean Day of Year of the analysed specimens: if <=180: 'Early', else 'Late'	A characteristic of the flowering season of the species based on the spread of the flowering season. Less than 28 days: 'Narrow', larger: 'Large'.

       

• phylogenetic_tree.tre: The raw data used to generate the visualization of the flowering seasonality character and the detected flowering shift foreach species on a phylogenetic tree.
• phylogenetic_processed_dataset.csv: The processed dataset resuting from the phylogenetic signal analysis. For each trait, an associated significance binary value is provided.