License

Code in the shorkie-paper repository — including this documentation — is released under the Apache License 2.0.

Copyright 2025 Calico Life Sciences LLC

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

    http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.

Full text: LICENSE.

Other terms

  • Model weights on gs://seqnn-share are released alongside the paper.

  • Third-party benchmark datasets (the 1002 Yeast Genomes resources, the DREAM Challenge data, the published eQTL studies) carry their own terms — see the original sources listed in Citation and Datasets.

  • The reference genome is derived from Ensembl Fungi release 59 (assembly GCA_000146045.2), redistributed here for reproducibility.

  • The model framework lives in baskerville-yeast and westminster, which carry their own licenses.