cafaeval-protea/CITATION.cff at main · frapercan/cafaeval-protea · GitHub

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cff-version: 1.2.0
message: >-
  If you use this software, please cite the original upstream publication
  (Piovesan et al., 2024) as the primary reference. This fork is a modified
  derivative work and is not a replacement for the upstream citation.
type: software
title: "cafaeval-protea"
authors:
  - family-names: "Pérez Canales"
    given-names: "Francisco Miguel"
    email: "frapercan1@alum.us.es"
abstract: >-
  Modified fork of CAFA-evaluator-PK providing performance optimizations
  for local iteration. Scoring semantics (Fmax, Smin, weighted variants,
  Partial-Knowledge evaluation) are preserved and validated against the
  unmodified upstream via a bit-exact parity harness.
license: GPL-3.0-or-later
repository-code: "https://github.com/frapercan/cafaeval-protea"
url: "https://github.com/BioComputingUP/CAFA-evaluator"

preferred-citation:
  type: article
  title: >-
    CAFA-evaluator: A Python Tool for Benchmarking Ontological
    Classification Methods
  authors:
    - family-names: Piovesan
      given-names: Damiano
    - family-names: Zago
      given-names: Davide
    - family-names: Joshi
      given-names: Parnal
    - family-names: "De Paolis Kaluza"
      given-names: "M. Clara"
    - family-names: Mehdiabadi
      given-names: Mahta
    - family-names: Ramola
      given-names: Rashika
    - family-names: Monzon
      given-names: "Alexander Miguel"
    - family-names: Reade
      given-names: Walter
    - family-names: Friedberg
      given-names: Iddo
    - family-names: Radivojac
      given-names: Predrag
    - family-names: Tosatto
      given-names: "Silvio C. E."
  journal: "Bioinformatics Advances"
  year: 2024
  doi: "10.1093/bioadv/vbae043"

references:
  - type: software
    title: "CAFA-evaluator-PK"
    authors:
      - family-names: "De Paolis"
        given-names: Clara
    repository-code: "https://github.com/claradepaolis/CAFA-evaluator-PK"
    license: GPL-3.0-or-later
    notes: >-
      Direct parent of this fork. Adds Partial-Knowledge evaluation and
      terms-of-interest filtering to the upstream CAFA-evaluator.
  - type: software
    title: "CAFA-evaluator-PK-speedup"
    authors:
      - family-names: Dolgorukova
        given-names: Antonina
        alias: T0chka
    repository-code: "https://github.com/T0chka/CAFA-evaluator-PK-speedup"
    license: GPL-3.0-or-later
    notes: >-
      Source of the Phase A algorithmic speedups cherry-picked into this
      fork (weighted-only fast path, cached children lists, fill-mode
      restricted to zero rows, incremental parser counters, shared-memory
      parallel propagation, fork-pool initializer pattern for the
      threshold sweep). Shared in the CAFA 6 Kaggle discussion post #664359
      "Speeding up cafaeval".