| # 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. |
|
|
