TY - JOUR

T1 - Dynamic β-VAEs for quantifying biodiversity by clustering optically recorded insect signals

AU - Rydhmer, Klas

AU - Selvan, Raghavendra

N1 - 25 pages, 6 figures

PY - 2021

Y1 - 2021

N2 - While insects are the largest and most diverse group of 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. 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 $\beta$-VAE dynamically adapts the scaling of the reconstruction and regularization loss terms ($\beta$ value) yielding useful latent representations of the input data. We demonstrate the usefulness of the dynamic $\beta$-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 $\beta$-VAE are promising and, in the near future, can be deployed to monitor insects and conserve the rapidly declining insect biodiversity.

AB - While insects are the largest and most diverse group of 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. 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 $\beta$-VAE dynamically adapts the scaling of the reconstruction and regularization loss terms ($\beta$ value) yielding useful latent representations of the input data. We demonstrate the usefulness of the dynamic $\beta$-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 $\beta$-VAE are promising and, in the near future, can be deployed to monitor insects and conserve the rapidly declining insect biodiversity.

KW - cs.LG

U2 - 10.1016/j.ecoinf.2021.101456

DO - 10.1016/j.ecoinf.2021.101456

M3 - Journal article

VL - 66

JO - Ecological Informatics

JF - Ecological Informatics

SN - 1574-9541

M1 - 101456

ER -