Add SAM License + SAM3 config; composite-license model card

LICENSE

@@ -0,0 +1,201 @@
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README.md

@@ -1,5 +1,7 @@
 ---
-license: apache-2.0
+license: other
+license_name: apache-2.0-and-sam-license
+license_link: LICENSE
 library_name: transformers
 pipeline_tag: image-text-to-text
 tags:
@@ -13,11 +15,17 @@ tags:
   - medical-imaging
 base_model:
   - Qwen/Qwen3-VL-8B-Instruct
+extra_gated_heading: You need to agree to Meta's SAM License to use the medical-image segmentation weights
+extra_gated_description: >-
+  The bulk of this model is Apache-2.0. The medical-image segmentation branch
+  embeds SAM 3 weights, which are governed by Meta's SAM License (see
+  SAM_LICENSE.txt). By accessing these weights you agree to that license,
+  including its acceptable-use restrictions.
 ---
 
 <div align="center">
 
-[🤗 Model](https://huggingface.co/sais-org/Polaris_Pro>) &nbsp;•&nbsp; [💻 GitHub](https://github.com/Shanghai-Academy-of-AI-For-Science/Polaris-Pro) &nbsp;•&nbsp; [📜 Technical Report (coming soon)](#) &nbsp;•&nbsp; [⚖️ License: Apache-2.0](./LICENSE)
+[🤗 Model](https://huggingface.co/sais-org/Polaris_Pro) &nbsp;•&nbsp; [💻 GitHub](https://github.com/Shanghai-Academy-of-AI-For-Science/Polaris-Pro) &nbsp;•&nbsp; [📜 Technical Report (coming soon)](#) &nbsp;•&nbsp; [⚖️ License: Apache-2.0 + SAM License](https://github.com/Shanghai-Academy-of-AI-For-Science/Polaris-Pro/blob/main/LICENSE)
 
 </div>
 
@@ -55,7 +63,7 @@ space — natural language in and out, no per-task fine-tuning.
 | Medical image | —             | ✅         |
 | Text          | ✅            | ✅         |
 
-<sub>**Understanding** = classification / regression / scientific QA. **Generation**: RNA sequence design · Molecule text → SMILES · Weather 10-day global ERA5 0.25° forecast · Medical-image text-prompted segmentation (needs SAM 3).</sub>
+<sub>**Understanding** = classification / regression / scientific QA. **Generation**: RNA sequence design · Molecule text → SMILES · Weather 10-day global ERA5 0.25° forecast · Medical-image text-prompted segmentation (SAM 3-based; Meta SAM License).</sub>
 
 ## Benchmarks
 
@@ -124,16 +132,16 @@ nine imaging modalities, versus six modality-native segmentation specialists.
 | Pathology  |     977 | **87.29** | <u>81.57</u> | 43.44 | 42.06 | 26.08 | 25.38 | 24.69 |
 | Ultrasound |  10,184 | <u>90.54</u> | **91.03** | 89.76 | 57.47 |  5.23 | 17.12 | 22.91 |
 
-<sub>Best overall Dice (All), and best on CT, MRI, pathology, dermoscopy, and endoscopy; on the four modalities where BiomedParse leads, the gap is ≤ 0.5 Dice.</sub>
+<sub>Best overall Dice (All), and best on CT, MRI, pathology, dermoscopy, and endoscopy; on X-ray, Fundus, and Ultrasound the gap to BiomedParse is ≤ 0.5 Dice, and on the smallest split (OCT) it is 1.3.</sub>
 
 ## Usage
 
 Runs via the accompanying code repository (custom multimodal architecture).
 
 ```bash
-git clone https://github.com/Shanghai-Academy-of-AI-For-Science/Polaris-Pro.git && cd Polaris_Pro
+git clone https://github.com/Shanghai-Academy-of-AI-For-Science/Polaris-Pro && cd Polaris-Pro
 pip install -r requirements.txt          # Python 3.10; transformers==5.0.0
-hf download <THIS_REPO> --local-dir ./model
+hf download sais-org/Polaris_Pro --local-dir ./model
 
 export PYTHONPATH=$PWD/code
 python code/inference.py --model_path model --greedy --max_new_tokens 64 \
@@ -142,20 +150,25 @@ python code/inference.py --model_path model --greedy --max_new_tokens 64 \
   --prompt $'<rna>\nWhich family does this non-coding RNA sequence belong to?'
 ```
 
-All scientific encoder/decoder weights (ESM-2, the Suiren molecular graph
-encoder, the RNA/DNA ConvFormers, and the Swin-ViT weather tower) are embedded
-in `model.safetensors`. The only separate download is **SAM 3** for
-medical-image segmentation, under Meta's gated license.
+All weights are contained in `model.safetensors`: the scientific
+encoders/decoders (ESM-2, the Suiren molecular graph encoder, the RNA/DNA
+ConvFormers, the Swin-ViT weather tower) and the fine-tuned SAM 3 branch used
+for medical-image segmentation.
 
 Each task has a specific `--system` prompt that fixes the output format; see
 `run_examples.sh` in the repository for per-task examples, weather, and segmentation.
 
 ## License
 
-Apache-2.0. Built on Qwen3-VL (Apache-2.0); includes merged ESM-2 (MIT) and
-Polaris/Suiren-derived encoders. **Medical-image segmentation needs SAM 3,
-under Meta's separate gated license — not distributed here.** See
-`THIRD_PARTY_LICENSES.md` / `NOTICE` in the code repository.
+**Composite license.** Polaris-Pro's own components — the code, and all weights
+except the SAM 3 branch — are **Apache-2.0**, built on Qwen3-VL (Apache-2.0) and
+including merged ESM-2 (MIT) and Polaris/Suiren-derived encoders.
+
+The **medical-image segmentation branch embeds SAM 3 weights**, which are
+governed by **Meta's SAM License** (`SAM_LICENSE.txt`, shipped alongside these
+weights). SAM 3 use is subject to that license, including its acceptable-use
+restrictions (no military / weapons / illegal uses; Trade-Control compliance).
+See `THIRD_PARTY_LICENSES.md` / `NOTICE` for the full third-party breakdown.
 
 ## Citation
 

SAM_LICENSE.txt

@@ -0,0 +1,61 @@
+SAM License
+Last Updated: November 19, 2025
+
+“Agreement” means the terms and conditions for use, reproduction, distribution and modification of the SAM Materials set forth herein.
+
+
+“SAM Materials” means, collectively, Documentation and the models, software and algorithms, including machine-learning model code, trained model weights, inference-enabling code, training-enabling code, fine-tuning enabling code, and other elements of the foregoing distributed by Meta and made available under this Agreement.
+
+“Documentation” means the specifications, manuals and documentation accompanying
+SAM Materials distributed by Meta.
+
+
+“Licensee” or “you” means you, or your employer or any other person or entity (if you are entering into this Agreement on such person or entity’s behalf), of the age required under applicable laws, rules or regulations to provide legal consent and that has legal authority to bind your employer or such other person or entity if you are entering in this Agreement on their behalf.
+
+
+“Meta” or “we” means Meta Platforms Ireland Limited (if you are located in or, if you are an entity, your principal place of business is in the EEA or Switzerland) or Meta Platforms, Inc. (if you are located outside of the EEA or Switzerland).
+
+
+“Sanctions” means any economic or trade sanctions or restrictions administered or enforced by the United States (including the Office of Foreign Assets Control of the U.S. Department of the Treasury (“OFAC”), the U.S. Department of State and the U.S. Department of Commerce), the United Nations, the European Union, or the United Kingdom.
+
+
+“Trade Controls” means any of the following: Sanctions and applicable export and import controls.
+
+By using or distributing any portion or element of the SAM Materials, you agree to be bound by this Agreement.
+
+
+1. License Rights and Redistribution.
+
+
+a. Grant of Rights. You are granted a non-exclusive, worldwide, non-transferable and royalty-free limited license under Meta’s intellectual property or other rights owned by Meta embodied in the SAM Materials to use, reproduce, distribute, copy, create derivative works of, and make modifications to the SAM Materials.
+
+b. Redistribution and Use.
+i. Distribution of SAM Materials, and any derivative works thereof, are subject to the terms of this Agreement. If you distribute or make the SAM Materials, or any derivative works thereof, available to a third party, you may only do so under the terms of this Agreement and you shall provide a copy of this Agreement with any such SAM Materials.
+
+
+ii.  If you submit for publication the results of research you perform on, using, or otherwise in connection with SAM Materials, you must acknowledge the use of SAM Materials in your publication.
+
+
+iii. Your use of the SAM Materials must comply with applicable laws and regulations, including Trade Control Laws and applicable privacy and data protection laws.
+iv. Your use of the SAM Materials will not involve or encourage others to reverse engineer, decompile or discover the underlying components of the SAM Materials.
+v. You are not the target of Trade Controls and your use of SAM Materials must comply with Trade Controls. You agree not to use, or permit others to use, SAM Materials for any activities subject to the International Traffic in Arms Regulations (ITAR) or end uses prohibited by Trade Controls, including those related to military or warfare purposes, nuclear industries or applications, espionage, or the development or use of guns or illegal weapons.
+2. User Support. Your use of the SAM Materials is done at your own discretion; Meta does not process any information nor provide any service in relation to such use.  Meta is under no obligation to provide any support services for the SAM Materials. Any support provided is “as is”, “with all faults”, and without warranty of any kind.
+
+
+3. Disclaimer of Warranty. UNLESS REQUIRED BY APPLICABLE LAW, THE SAM MATERIALS AND ANY OUTPUT AND RESULTS THEREFROM ARE PROVIDED ON AN “AS IS” BASIS, WITHOUT WARRANTIES OF ANY KIND, AND META DISCLAIMS ALL WARRANTIES OF ANY KIND, BOTH EXPRESS AND IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. YOU ARE SOLELY RESPONSIBLE FOR DETERMINING THE APPROPRIATENESS OF USING OR REDISTRIBUTING THE SAM MATERIALS AND ASSUME ANY RISKS ASSOCIATED WITH YOUR USE OF THE SAM MATERIALS AND ANY OUTPUT AND RESULTS.
+
+4. Limitation of Liability. IN NO EVENT WILL META OR ITS AFFILIATES BE LIABLE UNDER ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, TORT, NEGLIGENCE, PRODUCTS LIABILITY, OR OTHERWISE, ARISING OUT OF THIS AGREEMENT, FOR ANY LOST PROFITS OR ANY DIRECT OR INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR PUNITIVE DAMAGES, EVEN IF META OR ITS AFFILIATES HAVE BEEN ADVISED OF THE POSSIBILITY OF ANY OF THE FOREGOING.
+
+5. Intellectual Property.
+
+
+a. Subject to Meta’s ownership of SAM Materials and derivatives made by or for Meta, with respect to any derivative works and modifications of the SAM Materials that are made by you, as between you and Meta, you are and will be the owner of such derivative works and modifications.
+
+b. If you institute litigation or other proceedings against Meta or any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the SAM Materials, outputs or results, or any portion of any of the foregoing, constitutes infringement of intellectual property or other rights owned or licensable by you, then any licenses granted to you under this Agreement shall terminate as of the date such litigation or claim is filed or instituted. You will indemnify and hold harmless Meta from and against any claim by any third party arising out of or related to your use or distribution of the SAM Materials.
+
+6. Term and Termination. The term of this Agreement will commence upon your acceptance of this Agreement or access to the SAM Materials and will continue in full force and effect until terminated in accordance with the terms and conditions herein. Meta may terminate this Agreement if you are in breach of any term or condition of this Agreement. Upon termination of this Agreement, you shall delete and cease use of the SAM Materials. Sections 3, 4 and 7 shall survive the termination of this Agreement.
+
+7. Governing Law and Jurisdiction. This Agreement will be governed and construed under the laws of the State of California without regard to choice of law principles, and the UN Convention on Contracts for the International Sale of Goods does not apply to this Agreement. The courts of California shall have exclusive jurisdiction of any dispute arising out of this Agreement.
+
+
+8. Modifications and Amendments. Meta may modify this Agreement from time to time; provided that they are similar in spirit to the current version of the Agreement, but may differ in detail to address new problems or concerns. All such changes will be effective immediately. Your continued use of the SAM Materials after any modification to this Agreement constitutes your agreement to such modification. Except as provided in this Agreement, no modification or addition to any provision of this Agreement will be binding unless it is in writing and signed by an authorized representative of both you and Meta.

sam3/LICENSE

@@ -0,0 +1,61 @@
+SAM License
+Last Updated: November 19, 2025
+
+“Agreement” means the terms and conditions for use, reproduction, distribution and modification of the SAM Materials set forth herein.
+
+
+“SAM Materials” means, collectively, Documentation and the models, software and algorithms, including machine-learning model code, trained model weights, inference-enabling code, training-enabling code, fine-tuning enabling code, and other elements of the foregoing distributed by Meta and made available under this Agreement.
+
+“Documentation” means the specifications, manuals and documentation accompanying
+SAM Materials distributed by Meta.
+
+
+“Licensee” or “you” means you, or your employer or any other person or entity (if you are entering into this Agreement on such person or entity’s behalf), of the age required under applicable laws, rules or regulations to provide legal consent and that has legal authority to bind your employer or such other person or entity if you are entering in this Agreement on their behalf.
+
+
+“Meta” or “we” means Meta Platforms Ireland Limited (if you are located in or, if you are an entity, your principal place of business is in the EEA or Switzerland) or Meta Platforms, Inc. (if you are located outside of the EEA or Switzerland).
+
+
+“Sanctions” means any economic or trade sanctions or restrictions administered or enforced by the United States (including the Office of Foreign Assets Control of the U.S. Department of the Treasury (“OFAC”), the U.S. Department of State and the U.S. Department of Commerce), the United Nations, the European Union, or the United Kingdom.
+
+
+“Trade Controls” means any of the following: Sanctions and applicable export and import controls.
+
+By using or distributing any portion or element of the SAM Materials, you agree to be bound by this Agreement.
+
+
+1. License Rights and Redistribution.
+
+
+a. Grant of Rights. You are granted a non-exclusive, worldwide, non-transferable and royalty-free limited license under Meta’s intellectual property or other rights owned by Meta embodied in the SAM Materials to use, reproduce, distribute, copy, create derivative works of, and make modifications to the SAM Materials.
+
+b. Redistribution and Use.
+i. Distribution of SAM Materials, and any derivative works thereof, are subject to the terms of this Agreement. If you distribute or make the SAM Materials, or any derivative works thereof, available to a third party, you may only do so under the terms of this Agreement and you shall provide a copy of this Agreement with any such SAM Materials.
+
+
+ii.  If you submit for publication the results of research you perform on, using, or otherwise in connection with SAM Materials, you must acknowledge the use of SAM Materials in your publication.
+
+
+iii. Your use of the SAM Materials must comply with applicable laws and regulations, including Trade Control Laws and applicable privacy and data protection laws.
+iv. Your use of the SAM Materials will not involve or encourage others to reverse engineer, decompile or discover the underlying components of the SAM Materials.
+v. You are not the target of Trade Controls and your use of SAM Materials must comply with Trade Controls. You agree not to use, or permit others to use, SAM Materials for any activities subject to the International Traffic in Arms Regulations (ITAR) or end uses prohibited by Trade Controls, including those related to military or warfare purposes, nuclear industries or applications, espionage, or the development or use of guns or illegal weapons.
+2. User Support. Your use of the SAM Materials is done at your own discretion; Meta does not process any information nor provide any service in relation to such use.  Meta is under no obligation to provide any support services for the SAM Materials. Any support provided is “as is”, “with all faults”, and without warranty of any kind.
+
+
+3. Disclaimer of Warranty. UNLESS REQUIRED BY APPLICABLE LAW, THE SAM MATERIALS AND ANY OUTPUT AND RESULTS THEREFROM ARE PROVIDED ON AN “AS IS” BASIS, WITHOUT WARRANTIES OF ANY KIND, AND META DISCLAIMS ALL WARRANTIES OF ANY KIND, BOTH EXPRESS AND IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY WARRANTIES OF TITLE, NON-INFRINGEMENT, MERCHANTABILITY, OR FITNESS FOR A PARTICULAR PURPOSE. YOU ARE SOLELY RESPONSIBLE FOR DETERMINING THE APPROPRIATENESS OF USING OR REDISTRIBUTING THE SAM MATERIALS AND ASSUME ANY RISKS ASSOCIATED WITH YOUR USE OF THE SAM MATERIALS AND ANY OUTPUT AND RESULTS.
+
+4. Limitation of Liability. IN NO EVENT WILL META OR ITS AFFILIATES BE LIABLE UNDER ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, TORT, NEGLIGENCE, PRODUCTS LIABILITY, OR OTHERWISE, ARISING OUT OF THIS AGREEMENT, FOR ANY LOST PROFITS OR ANY DIRECT OR INDIRECT, SPECIAL, CONSEQUENTIAL, INCIDENTAL, EXEMPLARY OR PUNITIVE DAMAGES, EVEN IF META OR ITS AFFILIATES HAVE BEEN ADVISED OF THE POSSIBILITY OF ANY OF THE FOREGOING.
+
+5. Intellectual Property.
+
+
+a. Subject to Meta’s ownership of SAM Materials and derivatives made by or for Meta, with respect to any derivative works and modifications of the SAM Materials that are made by you, as between you and Meta, you are and will be the owner of such derivative works and modifications.
+
+b. If you institute litigation or other proceedings against Meta or any entity (including a cross-claim or counterclaim in a lawsuit) alleging that the SAM Materials, outputs or results, or any portion of any of the foregoing, constitutes infringement of intellectual property or other rights owned or licensable by you, then any licenses granted to you under this Agreement shall terminate as of the date such litigation or claim is filed or instituted. You will indemnify and hold harmless Meta from and against any claim by any third party arising out of or related to your use or distribution of the SAM Materials.
+
+6. Term and Termination. The term of this Agreement will commence upon your acceptance of this Agreement or access to the SAM Materials and will continue in full force and effect until terminated in accordance with the terms and conditions herein. Meta may terminate this Agreement if you are in breach of any term or condition of this Agreement. Upon termination of this Agreement, you shall delete and cease use of the SAM Materials. Sections 3, 4 and 7 shall survive the termination of this Agreement.
+
+7. Governing Law and Jurisdiction. This Agreement will be governed and construed under the laws of the State of California without regard to choice of law principles, and the UN Convention on Contracts for the International Sale of Goods does not apply to this Agreement. The courts of California shall have exclusive jurisdiction of any dispute arising out of this Agreement.
+
+
+8. Modifications and Amendments. Meta may modify this Agreement from time to time; provided that they are similar in spirit to the current version of the Agreement, but may differ in detail to address new problems or concerns. All such changes will be effective immediately. Your continued use of the SAM Materials after any modification to this Agreement constitutes your agreement to such modification. Except as provided in this Agreement, no modification or addition to any provision of this Agreement will be binding unless it is in writing and signed by an authorized representative of both you and Meta.

sam3/config.json

@@ -0,0 +1,896 @@
+{
+  "architectures": [
+    "Sam3VideoModel"
+  ],
+  "assoc_iou_thresh": 0.1,
+  "decrease_trk_keep_alive_for_empty_masklets": false,
+  "det_nms_thresh": 0.1,
+  "detector_config": {
+    "detr_decoder_config": {
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sam3/tokenizer_config.json

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