Dynamic β-VAEs for quantifying biodiversity by clustering optically recorded insect signals

• Published in: Ecological informatics Vol. 66; p. 101456
• Main Authors: Rydhmer, Klas, Selvan, Raghavendra
• Format: Journal Article
• Language: English
• Published: Elsevier B.V 01.12.2021
• Subjects: Biodiversity; Insect classification; Unsupervised clustering; VAE; VAE; Biodiversity; Unsupervised clustering; Insect classification
• ISSN: 1574-9541
• DOI: 10.1016/j.ecoinf.2021.101456

[Display omitted] •First application of a Variational Auto Encoder (VAE) for biodiversity assessment of insect signals.•The proposed dynamic β-VAE is capable of clustering optically recorded insect signals using a compact 2-d space.•The β-coefficient is dynamically adjusted to balance the trade-off between reconstruction and regularization terms.•The proposed unsupervised model is outperforming conventional methods, such as PCA and HCA.•Adding semi-supervision improves upon the unsupervised model results even further. While insects are the largest and most diverse group of terrestrial animals, constituting ca. 80% of all known species, they are difficult to study due to their small size and similarity between species. Conventional monitoring techniques depend on time consuming trapping methods and tedious microscope-based work by skilled experts in order to identify the caught insect specimen at species, or even family level. Researchers and policy makers are in urgent need of a scalable monitoring tool in order to conserve biodiversity and secure human food production due to the rapid decline in insect numbers. Novel automated optical monitoring equipment can record tens of thousands of insect observations in a single day and the ability to identify key targets at species level can be a vital tool for entomologists, biologists and agronomists. Recent work has aimed for a broader analysis using unsupervised clustering as a proxy for conventional biodiversity measures, such as species richness and species evenness, without actually identifying the species of the detected target. In order to improve upon existing insect clustering methods, we propose an adaptive variant of the variational autoencoder (VAE) which is capable of clustering data by phylogenetic groups. The proposed dynamic β-VAE dynamically adapts the scaling of the reconstruction and regularization loss terms (β value) yielding useful latent representations of the input data. We demonstrate the usefulness of the dynamic β-VAE on optically recorded insect signals from regions of southern Scandinavia to cluster unlabelled targets into possible species. We also demonstrate improved clustering performance in a semi-supervised setting using a small subset of labelled data. These experimental results, in both unsupervised- and semi-supervised settings, with the dynamic β-VAE are promising and, in the near future, can be deployed to monitor insects and conserve the rapidly declining insect biodiversity.