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LICENSE

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+# PolyForm Noncommercial License 1.0.0
+
+<https://polyformproject.org/licenses/noncommercial/1.0.0>
+
+## Acceptance
+
+In order to get any license under these terms, you must agree
+to them as both strict obligations and conditions to all
+your licenses.
+
+## Copyright License
+
+The licensor grants you a copyright license for the
+software to do everything you might do with the software
+that would otherwise infringe the licensor's copyright
+in it for any permitted purpose.  However, you may
+only distribute the software according to [Distribution
+License](#distribution-license) and make changes or new works
+based on the software according to [Changes and New Works
+License](#changes-and-new-works-license).
+
+## Distribution License
+
+The licensor grants you an additional copyright license
+to distribute copies of the software.  Your license
+to distribute covers distributing the software with
+changes and new works permitted by [Changes and New Works
+License](#changes-and-new-works-license).
+
+## Notices
+
+You must ensure that anyone who gets a copy of any part of
+the software from you also gets a copy of these terms or the
+URL for them above, as well as copies of any plain-text lines
+beginning with `Required Notice:` that the licensor provided
+with the software.  For example:
+
+> Required Notice: Copyright AI Whisperers (https://github.com/Ai-Whisperers)
+
+## Changes and New Works License
+
+The licensor grants you an additional copyright license to
+make changes and new works based on the software for any
+permitted purpose.
+
+## Patent License
+
+The licensor grants you a patent license for the software that
+covers patent claims the licensor can license, or becomes able
+to license, that you would infringe by using the software.
+
+## Noncommercial Purposes
+
+Any noncommercial purpose is a permitted purpose.
+
+## Personal Uses
+
+Personal use for research, experiment, and testing for
+the benefit of public knowledge, personal study, private
+entertainment, hobby projects, amateur pursuits, or religious
+observance, without any anticipated commercial application,
+is use for a permitted purpose.
+
+## Noncommercial Organizations
+
+Use by any charitable organization, educational institution,
+public research organization, public safety or health
+organization, environmental protection organization, or
+government institution is use for a permitted purpose
+regardless of the source of funding or obligations resulting
+from the funding.
+
+## Fair Use
+
+You may have "fair use" rights for the software under the
+law. These terms do not limit them.
+
+## No Other Rights
+
+These terms do not allow you to sublicense or transfer any of
+your licenses to anyone else, or prevent the licensor from
+granting licenses to anyone else.  These terms do not imply
+any other licenses.
+
+## Patent Defense
+
+If you make any written claim that the software infringes or
+contributes to infringement of any patent, your patent license
+for the software granted under these terms ends immediately. If
+your company makes such a claim, your patent license ends
+immediately for work on behalf of your company.
+
+## Violations
+
+The first time you are notified in writing that you have
+violated any of these terms, or done anything with the software
+not covered by your licenses, your licenses can nonetheless
+continue if you come into full compliance with these terms,
+and take practical steps to correct past violations, within
+32 days of receiving notice.  Otherwise, all your licenses
+end immediately.
+
+## No Liability
+
+***As far as the law allows, the software comes as is, without
+any warranty or condition, and the licensor will not be liable
+to you for any damages arising out of these terms or the use
+or nature of the software, under any kind of legal claim.***
+
+## Definitions
+
+The **licensor** is the entity offering these terms, and the
+**software** is the software the licensor makes available
+under these terms.
+
+**You** refers to the individual or entity agreeing to these
+terms.
+
+**Your company** is any legal entity, sole proprietorship,
+or other kind of organization that you work for, plus all
+organizations that have control over, are under the control of,
+or are under common control with that organization.  **Control**
+means ownership of substantially all the assets of an entity,
+or the power to direct its management and policies by vote,
+contract, or otherwise.  Control can be direct or indirect.
+
+**Your licenses** are all the licenses granted to you for the
+software under these terms.
+
+**Use** means anything you do with the software requiring one
+of your licenses.
+
+---
+
+Required Notice: Copyright 2024-2025 AI Whisperers (https://github.com/Ai-Whisperers)
+
+## Additional Terms for Ternary VAEs Bioinformatics
+
+### Permitted Uses (Noncommercial)
+
+The following uses are explicitly permitted under this license:
+
+1. **Academic Research**: Use in university research, thesis work, and academic publications
+2. **Educational Use**: Teaching, coursework, and educational demonstrations
+3. **Student Projects**: Individual or group student assignments and projects
+4. **Open Source Contributions**: Contributing improvements back to this project
+5. **Personal Learning**: Self-study and skill development
+6. **Public Health Research**: Research benefiting public health outcomes
+7. **Non-profit Research**: Use by registered non-profit organizations
+
+### Commercial Use Requires Separate License
+
+Commercial use includes, but is not limited to:
+
+1. Use in products or services sold for profit
+2. Use in internal tools at for-profit companies
+3. Use by consulting firms for client work
+4. Training commercial AI/ML models
+5. Integration into proprietary software
+6. Use in clinical trials sponsored by for-profit entities
+
+**For commercial licensing inquiries, contact: support@aiwhisperers.com**
+
+### Attribution Requirements
+
+When using this software in academic publications, please cite:
+
+```bibtex
+@software{ternary_vaes_bioinformatics,
+  author = {{AI Whisperers}},
+  title = {Ternary VAEs Bioinformatics: Hyperbolic Geometry for Discrete Algebraic Structures},
+  year = {2024-2025},
+  url = {https://github.com/Ai-Whisperers/ternary-vaes-bioinformatics},
+  license = {PolyForm Noncommercial 1.0.0}
+}
+```
+
+### Trained Model Weights and Checkpoints
+
+All trained model weights and checkpoint files (including but not limited to *.pt, *.pth files) are covered by this license.
+
+**Covered Assets**:
+- Variational autoencoder (VAE) model weights
+- Encoder and decoder neural network parameters
+- Hyperbolic projection layer weights
+- All checkpoint files in `results/checkpoints/`
+- Pre-trained embeddings and representations
+
+**Restrictions**:
+Model weights may NOT be:
+1. Used for commercial purposes without a separate commercial license
+2. Redistributed without this LICENSE file and proper attribution
+3. Used to train derivative commercial models or products
+4. Incorporated into proprietary or commercial software
+
+**Permitted Uses**:
+Model weights MAY be used for:
+1. Academic research and publications
+2. Educational purposes and coursework
+3. Non-commercial experimentation
+4. Reproduction of results in academic papers
+
+For commercial use of trained model weights, contact: support@aiwhisperers.com
+
+### Research Data and Predictions
+
+Research data, analysis results, and third-party predictions (e.g., AlphaFold3 outputs) are subject to additional restrictions. See `research/LICENSE.md` and the NOTICE file for details.

requirements.txt

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+torch>=2.0.0
+numpy
+scipy

test_inference.py

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+import torch
+from trainable_codon_encoder import TrainableCodonEncoder
+
+def test():
+    print("Testing Ternary Codon Encoder inference...")
+    model = TrainableCodonEncoder(latent_dim=16, hidden_dim=64)
+    checkpoint = torch.load("pytorch_model.bin", map_location="cpu", weights_only=False)
+    model.load_state_dict(checkpoint["model_state_dict"])
+    model.eval()
+
+    # ATG index is 14
+    codon_idx = torch.tensor([14])
+    with torch.no_grad():
+        z_hyp = model(codon_idx)
+
+    print(f"Codon index: {codon_idx.item()}")
+    print(f"Hyperbolic Embedding shape: {z_hyp.shape}")
+    print(f"Embedding: {z_hyp[0, :5]}...")
+    print("Test passed!")
+
+if __name__ == "__main__":
+    test()