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Research Use Disclaimer

Important Notice

THE PATHWAY SUBTYPING FRAMEWORK IS PROVIDED FOR RESEARCH PURPOSES ONLY.

This software and its outputs are intended solely for:

  • Scientific research and exploration
  • Hypothesis generation
  • Educational purposes
  • Method development and benchmarking

Not for Clinical Use

This framework is NOT intended for and should NOT be used for:

  • Clinical diagnosis of any disease or condition
  • Treatment selection or modification
  • Genetic counseling without professional oversight
  • Medical decision-making of any kind
  • Insurance, employment, or legal decisions
  • Prenatal screening or selection
  • Any application affecting patient care

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.

Limitations

Users must understand that:

  1. Subtypes are hypotheses: Clustering results represent statistical patterns, not validated biological entities
  2. No causality: Pathway associations do not establish causal relationships
  3. No individual prediction: Results describe group patterns, not individual outcomes
  4. Validation required: All findings require independent experimental validation
  5. Context-dependent: Results may not generalize across populations or datasets

Appropriate Use

Before using this framework, users should:

  • Read and understand the Limitations document
  • Understand the statistical methods employed
  • Have appropriate expertise in genomics and bioinformatics
  • Plan for independent validation of any findings
  • Consider ethical implications of their research

Citation

If you use this framework in published research, please cite appropriately and include a statement acknowledging the research-only nature of the tool.

Liability

IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS 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.

The authors and contributors bear no responsibility for any misuse of this software or misinterpretation of its outputs.

Data Provenance and Integrity

This project contains zero proprietary, commercial, or third-party customer data. The authors affirm the following:

What IS in this repository

Data Type Location Origin Contains Real Patient Data?
Synthetic VCF data/sample/synthetic_cohort.vcf Computationally generated by SyntheticDataGenerator using random number generators with fixed seeds No — all variants, genotypes, and sample IDs are fabricated
Synthetic phenotypes data/sample/synthetic_phenotypes.csv Computationally generated alongside the synthetic VCF No — all sample IDs, ages, and subtype labels are fabricated
Pathway gene lists data/pathways/*.gmt Curated from publicly available, peer-reviewed scientific literature and open-access databases (SFARI Gene, KEGG, Reactome, MSigDB, Gene Ontology) No — gene symbols are standard public scientific identifiers
Source code src/pathway_subtyping/ Original implementations by the author, using standard open-source libraries No — contains algorithms, not data
Test data tests/ Generated in-memory by test fixtures using numpy.random.RandomState No — ephemeral synthetic data for unit testing

What is NOT in this repository

  • No real patient data, clinical records, or protected health information (PHI)
  • No data from any employer, client, customer, or commercial entity
  • No data obtained under any Data Use Agreement (DUA) or Non-Disclosure Agreement (NDA)
  • No proprietary databases, licensed datasets, or subscription-access content
  • No data from any Life Sciences company, pharmaceutical company, or healthcare organization
  • No data copied, derived from, or inspired by any commercial or institutional database

Independence Statement

This project was developed entirely as an independent, personal research initiative. It was not created as part of any employment, consulting engagement, or commercial project. All code was written from scratch by the author using publicly documented statistical methods and standard open-source libraries (scikit-learn, scipy, numpy, pandas). The author had no access to, and did not use, any proprietary data or proprietary software in the creation of this framework.

Verification

The provenance of all data in this repository can be independently verified:

  1. Synthetic data: Run python -m pathway_subtyping.cli run --config configs/test_synthetic.yaml to regenerate the synthetic dataset from scratch using the deterministic seed. The output is identical each time because the data is purely algorithmic.
  2. Pathway gene lists: Every gene symbol in the GMT files can be verified against the publicly accessible databases cited in data/pathways/README.md (SFARI Gene, KEGG, Reactome, Gene Ontology).
  3. Source code: The entire git history is public, showing all code was developed through original commits. No external data files were ever imported from private sources.

Questions

If you are uncertain whether your intended use is appropriate, please:

  1. Consult with a biostatistician
  2. Consult with a genetic counselor (for any clinical context)
  3. Open a discussion on the GitHub repository

By using this software, you acknowledge that you have read, understood, and agree to abide by this disclaimer.