LICENSE

# PROPRIETARY SOURCE CODE LICENSE (NON-COMMERCIAL + NEGOTIATED COMMERCIAL)

Copyright (c) 2026 Benjamin Isaac Wilson. All rights reserved.

1. PERMITTED USE
This software and its source code are provided for the following purposes:
   a. Evaluation: For prospective employers and collaborators to assess the Author's technical expertise.
   b. Academic Research: For students, researchers, and faculty at academic institutions for the purpose of scientific investigation.
   c. Non-Profit: For use by registered non-profit organizations in pursuit of their non-commercial missions.

2. COMMERCIAL USE (NEGOTIATED AGREEMENT REQUIRED)
Use of this software, its source code, or derivative works by for-profit entities, or for any commercial or revenue-generating purposes, is strictly prohibited without a separate, written license agreement negotiated with and signed by the Author.

Foundation Model Disclaimer: This software is designed to be backbone-agnostic and relies on third-party foundation models for feature extraction. A commercial agreement with the Author covers ONLY the SpatialTranscriptFormer source code, architecture, and intellectual property. It DOES NOT grant commercial use rights for restricted third-party models (e.g., CTransPath or Phikon). To use this software commercially, you must pair it with a backbone model that has a compatible commercial-friendly license (e.g., Apache 2.0 models like Hibou, Virchow, or H-Optimus-0).

Dataset Disclaimer: This project utilizes third-party datasets, primarily HEST-1k. These datasets are subject to their own respective licenses (e.g., CC BY-NC-SA 4.0 for HEST-1k). A commercial agreement with the Author DOES NOT grant any rights to use, redistribute, or commercially exploit restricted third-party data. Commercial users must ensure they have independent legal rights to any training or evaluation data used within this framework.

MSigDB Disclaimer: The Pathway Bottleneck and Reconstruction components utilize MSigDB Hallmark gene sets (Broad Institute). Content from MSigDB (v6.0-v7.5.1, v2022.1+) is protected by copyright (c) 2004-2025 Broad Institute, Inc., MIT, and Regents of the University of California, and is provided under CC BY 4.0. Users are responsible for complying with attribution requirements and any third-party restrictions (e.g., KEGG, BioCarta) that may apply to specific subsets of the data.

Interested parties should contact the Author directly to discuss commercial licensing terms.

1. ATTRIBUTION
Any publication, presentation, or public report that uses this software or its results must provide clear attribution to the Author (Benjamin Isaac Wilson) and reference this repository.

2. RESTRICTIONS
Unless explicitly authorized in writing by the Author, the following actions are strictly prohibited:
   a. Redistribution: You may not redistribute, sell, or publish the source code or any derivative works to third parties.
   b. Sublicensing: You may not grant sublicenses to others.

3. OWNERSHIP
All intellectual property rights, including but not limited to copyright, patents, and trade secrets, remain solely with the Author. Core architectural components, original methodologies, and academic attributions are documented in the [IP Statement](docs/IP_STATEMENT.md).

4. NO WARRANTY
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

For inquiries regarding commercial licensing or further collaboration, please contact the Author directly.