Browsing by Author "Balhoff, James P."

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    Discovering Novel Biological Traits From Images Using Phylogeny-Guided Neural Networks
    Elhamod, Mohannad; Khurana, Mridul; Manogaran, Harish Babu; Uyeda, Josef C.; Balk, Meghan A.; Dahdul, Wasila; Bakış, Yasin; Bart, Henry L. Jr.; Mabee, Paula M.; Lapp, Hilmar; Balhoff, James P.; Charpentier, Caleb; Carlyn, David; Chao, Wei-Lun; Stewart, Charles V.; Rubenstein, Daniel I.; Berger-Wolf, Tanya; Karpatne, Anuj (ACM, 2023-08-06)
    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.
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    Phenoscape: Semantic analysis of organismal traits and genes yields insights in evolutionary biology
    Mabee, Paula M.; Dahdul, Wasila M.; Balhoff, James P.; Lapp, Hilmar; Manda, Prashanti; Uyeda, Josef C.; Vision, Todd; Westerfield, Monte (PeerJ, 2018-06-13)
    The study of how the observable features of organisms, i.e., their phenotypes, result from the complex interplay between genetics, development, and the environment, is central to much research in biology. The varied language used in the description of phenotypes, however, impedes the large scale and interdisciplinary analysis of phenotypes by computational methods. The Phenoscape project (www.phenoscape.org) has developed semantic annotation tools and a gene–phenotype knowledgebase, the Phenoscape KB, that uses machine reasoning to connect evolutionary phenotypes from the comparative literature to mutant phenotypes from model organisms. The semantically annotated data enables the linking of novel species phenotypes with candidate genes that may underlie them. Semantic annotation of evolutionary phenotypes further enables previously difficult or novel analyses of comparative anatomy and evolution. These include generating large, synthetic character matrices of presence/absence phenotypes based on inference, and searching for taxa and genes with similar variation profiles using semantic similarity. Phenoscape is further extending these tools to enable users to automatically generate synthetic supermatrices for diverse character types, and use the domain knowledge encoded in ontologies for evolutionary trait analysis. Curating the annotated phenotypes necessary for this research requires significant human curator effort, although semi-automated natural language processing tools promise to expedite the curation of free text. As semantic tools and methods are developed for the biodiversity sciences, new insights from the increasingly connected stores of interoperable phenotypic and genetic data are anticipated.