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BenjaminIsaac0111 merged 1 commit into from
Jun 29, 2026
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docs: audit comments/docs, fix stf-predict, relicense to Apache-2.0 #14

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24 changes: 24 additions & 0 deletions CITATION.cff
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cff-version: 1.2.0
message: "If you use this software in academic work, please cite it as below."
title: SpatialTranscriptFormer
abstract: >-
A transformer framework that predicts spatially-resolved biological pathway
activity directly from H&E histology. Learnable pathway tokens cross-attend to
histology patch features (a configurable quad-flow interaction), and a
dot-product + Softplus head produces per-spot pathway-activity scores supervised
against offline-computed targets.
type: software
authors:
- family-names: Wilson
given-names: "Benjamin Isaac"
version: "0.1.0"
license: Apache-2.0
repository-code: "https://github.com/BenjaminIsaac0111/SpatialTranscriptFormer"
url: "https://github.com/BenjaminIsaac0111/SpatialTranscriptFormer"
keywords:
- spatial transcriptomics
- computational pathology
- deep learning
- pathway activity
- histology
- transformer
8 changes: 3 additions & 5 deletions CONTRIBUTING.md
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> [!IMPORTANT]
> This project is a **Work in Progress**. We are actively refining the core interaction logic and scaling behaviors. Expect breaking changes in the CLI and data schemas.

## Intellectual Property & Licensing
## Licensing of Contributions

SpatialTranscriptFormer is protected under a **Proprietary Source Code License**.
SpatialTranscriptFormer is released under the **[Apache License 2.0](LICENSE)**.

- **Academic/Non-Profit**: We encourage contributions from the research community. Contributions made under an academic affiliation are generally welcome.
- **Commercial/For-Profit**: Contributions from commercial entities or individuals intended for profit-seeking use require a separate agreement.
- **Assignment**: By submitting a Pull Request, you agree that your contributions will be licensed under the project's existing license, granting the author the right to include them in both the open-access and proprietary versions of the software.
By submitting a contribution (e.g. a Pull Request), you agree that your contribution is licensed to the project and its users under the same Apache-2.0 license ("inbound = outbound"), and you confirm you have the right to submit it under that license. Please don't include third-party code or data whose license is incompatible with Apache-2.0.

## Development Workflow

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214 changes: 190 additions & 24 deletions LICENSE
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# PROPRIETARY SOURCE CODE LICENSE (NON-COMMERCIAL + NEGOTIATED COMMERCIAL)

Copyright (c) 2026 Benjamin Isaac Wilson. All rights reserved.
Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/

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.
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION

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.
1. Definitions.

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).
"License" shall mean the terms and conditions for use, reproduction,
and distribution as defined by Sections 1 through 9 of this document.

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.
"Licensor" shall mean the copyright owner or entity authorized by
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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.
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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).
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38 changes: 38 additions & 0 deletions NOTICE
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SpatialTranscriptFormer
Copyright 2026 Benjamin Isaac Wilson

Licensed under the Apache License, Version 2.0 (the "License"); you may not use
this file except in compliance with the License. A copy of the License is
provided in the LICENSE file and at http://www.apache.org/licenses/LICENSE-2.0

================================================================================
Third-party components and data
================================================================================

This framework integrates with, and/or interoperates with, third-party
software, model weights, and datasets that are governed by their own licenses.
These are NOT redistributed in this repository: they are downloaded or supplied
by the user at runtime and remain subject to their original terms. The Apache
2.0 license over this source code does not grant any rights to them.

- HEST-1k dataset (Mahmood Lab) — CC BY-NC-SA 4.0 (non-commercial, share-alike).
Used here for research/benchmarking only. Users must obtain independent rights
for any commercial or non-research use.

- MSigDB Hallmark gene sets (Broad Institute) — copyright (c) 2004-2025 Broad
Institute, Inc., MIT, and the Regents of the University of California; provided
under CC BY 4.0 (attribution required). Individual gene sets may carry
additional third-party terms (e.g. KEGG, BioCarta).

- Pathology foundation-model backbones (e.g. CTransPath, Phikon, GigaPath,
Hibou) — each subject to its own license. Some are gated or restricted and may
prohibit commercial use. Select a backbone whose license fits your use case.

================================================================================
Conceptual attribution
================================================================================

The multimodal pathway-histology interaction framing was conceptually inspired
by SURVPATH (Jaume et al., 2024; https://arxiv.org/abs/2303.15545). No SURVPATH
source code is used, copied, or adapted in this project; the implementation here
is original.
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