CITATION.cff

abstract: "A grand challenge in biology is to discover evolutionary traits - features of organisms common to a group of species with a shared ancestor in the tree of life (also referred to as phylogenetic tree). With the growing availability of  image repositories in biology, there is a tremendous opportunity to discover evolutionary traits directly from images in the form of a hierarchy of prototypes. However, current prototype-based methods are mostly designed to operate over a flat structure of classes and face several challenges in discovering hierarchical prototypes, including the issue of learning over-specific features at internal nodes. To overcome these challenges, we introduce the framework of Hierarchy aligned Commonality through Prototypical Networks (HComP-Net). We empirically show that HComP-Net learns prototypes that are accurate, semantically consistent, and generalizable to unseen species in comparison to baselines on birds, butterflies, and fishes datasets."
authors:
- family-names: Manogaran
  given-names: Harish Babu
cff-version: 1.0.0
date-released: "2024-09-04"
keywords:
  - "Prototypical networks"
  - "Phylogeny"
  - evolution
  - imageomics
  - "knowledge-guided"
  - CV
  - biology
  - images
  
license: MIT
message: "If you find this software helpful in your research, please cite both the software and our paper."
repository-code: "https://github.com/Imageomics/HComPNet"
title: "HComP-Net"
version: 1.0.0
type: software
preferred-citation:
  type: article
  authors:
    - family-names: Manogaran
      given-names: Harish Babu
    - family-names: Maruf
      given-names: "M."
    - family-names: Daw
      given-names: Arka 
    - family-names: Mehrab
      given-names: Kazi Sajeed
    - family-names: Charpentier
      given-names: Caleb
    - family-names: Uyeda
      given-names: "Josef C."
    - family-names: Dahdul
      given-names: Wasila
    - family-names: Thompson
      given-names: "Matthew J"
    - family-names: Campolongo
      given-names: "Elizabeth G"
    - family-names: Provost
      given-names: "Kaiya L"
    - family-names: Mabee
      given-names: "Paula M."
    - family-names: Lapp
      given-names: Hilmar
    - family-names: Karpatne
      given-names: Anuj

  title: "What Do You See in Common? Learning Hierarchical Prototypes over Tree-of-Life to Discover Evolutionary Traits"
  year: 2024
  journal: 
  doi: