Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

Toward a Flexible Metadata Pipeline for Fish Specimen Images

Flexible metadata pipelines are crucial for supporting the FAIR data principles. Despite this need, researchers seldom report their approaches for identifying metadata standards and protocols that support optimal flexibility. This paper reports on an initiative targeting the development of a flexible metadata pipeline for a collection containing over 300,000 digital fish specimen images, harvested from multiple data repositories and fish collections. The images and their associated metadata are being used for AI-related scientific research involving automated species identification, segmentation and trait extraction. The paper provides contextual background, followed by the presentation of a four-phased approach involving: 1. Assessment of the Problem, 2. Investigation of Solutions, 3. Implementation, and 4. Refinement. The work is part of the NSF Harnessing the Data Revolution, Biology Guided Neural Networks (NSF/HDR-BGNN) project and the HDR Imageomics Institute. An RDF graph prototype pipeline is presented, followed by a discussion of research implications and conclusion summarizing the results.