# Third-party notices

The study weights, PCA components and loading adapters use the MIT license
in `LICENSE`, with the Microsoft copyright notice. Third-party files retain
the licenses and copyright notices listed below.

## Paper code and gene order

- Project: https://github.com/microsoft/scFM-dataselection
- Included gene-order file: `public-resources/sctab/adata_var.csv`.
- License: MIT, Copyright (c) Microsoft Corporation.
- Full notice: `licenses/scFM-dataselection-MIT.txt`.

## SSL implementation

- Project: https://github.com/v-mahughes/ssl_in_scg
- Included source files: `public-resources/ssl-source/base.py` and
  `public-resources/ssl-source/cellnet_autoencoder.py`.
- Authors credited by the project: Till Richter, Mojtaba Bahrami, Yufan Xia
  and Felix Fischer.
- License: MIT, Copyright (c) 2024 Till Richter.
- Full notice: `licenses/ssl_in_scg-MIT.txt`.

The loading adapters in `tools/` use these source files to construct the models.

## Geneformer tokenizer files

- Source: https://github.com/lcrawlab/Geneformer
- Original project: https://huggingface.co/ctheodoris/Geneformer
- Original work: Christine V. Theodoris and collaborators.
- Included dictionaries: `token_dictionary.pkl`, `gene_median_dictionary.pkl`
  and `gene_name_id_dict.pkl` in `public-resources/geneformer/`.
- License: Apache-2.0.
- Full terms: `licenses/Geneformer-Apache-2.0.txt`.

The Geneformer weights are models trained for this study, not upstream
Geneformer pretrained weights.

## SCimilarity network implementation

- Project: https://github.com/Genentech/scimilarity
- Included source: `tools/_scimilarity_networks.py`, the unmodified
  `scimilarity/nn_models.py` from version 0.4.1.
- License: Apache-2.0, Copyright 2023 Genentech, Inc.
- Full notice and terms: `licenses/SCimilarity-Apache-2.0.txt`.

The SCimilarity encoder and decoder weights were trained for this study;
they are distributed under MIT, separately from the upstream implementation.

## Dependencies and data

Runtime packages are installed separately and retain their own licenses.
The scTab corpus is not included. See https://github.com/theislab/scTab for
dataset access and terms, and the paper code for preprocessing.