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CODE_OF_CONDUCT.md

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+# Microsoft Open Source Code of Conduct
+
+This project has adopted the [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/).
+
+Resources:
+
+- [Microsoft Open Source Code of Conduct](https://opensource.microsoft.com/codeofconduct/)
+- [Microsoft Code of Conduct FAQ](https://opensource.microsoft.com/codeofconduct/faq/)
+- Contact [[email protected]](mailto:[email protected]) with questions or concerns

LICENSE

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+Microsoft.
+Copyright (c) Microsoft Corporation.
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+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
+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.

README.md

@@ -1,3 +1,226 @@
----
-license: mit
----
+---
+license: mit
+datasets:
+- microsoft/mediflow
+- ncbi/pubmed
+- starmpcc/Asclepius-Synthetic-Clinical-Notes
+- akemiH/NoteChat
+- zhengyun21/PMC-Patients
+- jpcorb20/medical_wikipedia
+language:
+- en
+base_model:
+- microsoft/Phi-3.5-mini-instruct
+library_name: transformers
+tags:
+- merge
+- mergekit
+- medical
+- clinical
+---
+# Model Card for MediPhi-Instruct
+
+## Model Summary
+
+The MediPhi Model Collection comprises 7 small language models of 3.8B parameters from the base model `Phi-3.5-mini-instruct` specialized in the medical and clinical domains. The collection is designed in a modular fashion. Five MediPhi experts are fine-tuned on various medical corpora (i.e. PubMed commercial, Medical Wikipedia, Medical Guidelines, Medical Coding, and open-source clinical documents) and merged back with the SLERP method in their base model to conserve general abilities. One model combined all five experts into one general expert with the multi-model merging method BreadCrumbs. Finally, we clinically aligned this general expert using our large-scale MediFlow corpora (see dataset `microsoft/mediflow`) to obtain the final expert model `MediPhi-Instruct`.
+
+## Model Details
+### Model Description
+
+This model is the `MediPhi-Instruct` aligned to accomplish clinical NLP tasks.
+
+- **Developed by:** Microsoft Healthcare \& Life Sciences
+- **Model type:** Phi3
+- **Language(s) (NLP):** English
+- **License:** MIT
+- **Finetuned from model:** `microsoft/MediPhi`, and originally from `microsoft/Phi-3.5-mini-instruct`
+
+### Model Sources
+
+- **Repository:** Current HF repo
+- **Paper:** [A Modular Approach for Clinical SLMs Driven by Synthetic Data with Pre-Instruction Tuning, Model Merging, and Clinical-Tasks Alignment](https://arxiv.org/abs/2505.10717)
+
+## Intended Uses
+### Primary Use Cases
+The model is intended for research use in English, especially clinical natural language processing. The model provides uses for research which require:
+
+- **Medically adapted language models**
+- Memory/compute constrained environments
+- Latency bound scenarios
+
+Our model is designed to accelerate research on language models in medical and clinical scenarios. It should be used for research purposes, i.e., in benchmarking context or with expert user verification of the outputs.
+
+### Use Case Considerations
+Our models are not specifically designed or evaluated for all downstream purposes. Researchers (or developers) should consider common limitations of language models as they select use cases, and evaluate and mitigate for accuracy, safety, and fariness before using within a specific downstream use case, particularly for high risk scenarios. Researchers (or developers) should be aware of and adhere to applicable laws or regulations (including privacy, trade compliance laws, etc.) that are relevant to their use case.
+
+**Nothing contained in this Model Card should be interpreted as or deemed a restriction or modification to the license the model is released under.**
+
+### Responsible AI Considerations
+Like other language models, the Phi family of models and the MediPhi collection can potentially behave in ways that are unfair, unreliable, or offensive. Some of the limiting behaviors to be aware of include:
+
+- Quality of Service: The Phi and MediPhi models are trained primarily on English text and some additional multilingual text. Languages other than English will experience worse performance as well as performance disparities across non-English. English language varieties with less representation in the training data might experience worse performance than standard American English.
+- Multilingual performance and safety gaps: We believe it is important to make language models more widely available across different languages, but the Phi 3 models still exhibit challenges common across multilingual releases. As with any deployment of LLMs, developers will be better positioned to test for performance or safety gaps for their linguistic and cultural context and customize the model with additional fine-tuning and appropriate safeguards.
+- Representation of Harms & Perpetuation of Stereotypes: These models can over- or under-represent groups of people, erase representation of some groups, or reinforce demeaning or negative stereotypes. Despite safety post-training, these limitations may still be present due to differing levels of representation of different groups, cultural contexts, or prevalence of examples of negative stereotypes in training data that reflect real-world patterns and societal biases.
+- Inappropriate or Offensive Content: These models may produce other types of inappropriate or offensive content, which may make it inappropriate to deploy for sensitive contexts without additional mitigations that are specific to the case.
+Information Reliability: Language models can generate nonsensical content or fabricate content that might sound reasonable but is inaccurate or outdated.
+- Limited Scope for Code: Majority of Phi-3 training data is based in Python and use common packages such as "typing, math, random, collections, datetime, itertools". If the model generates Python scripts that utilize other packages or scripts in other languages, we strongly recommend users manually verify all API uses.
+- Long Conversation: Phi-3 models, like other models, can in some cases generate responses that are repetitive, unhelpful, or inconsistent in very long chat sessions in both English and non-English languages. Developers are encouraged to place appropriate mitigations, like limiting conversation turns to account for the possible conversational drift
+
+Researchers should apply responsible AI best practices, including mapping, measuring, and mitigating risks associated with their specific use case and cultural, linguistic context. They are encouraged to rigorously evaluate the model for their use case, fine-tune the models when possible and leverage the models as part of broader AI systems with language-specific safeguards in place. Important areas for consideration include:
+
+- Allocation: Models may not be suitable for scenarios that could have consequential impact on legal status or the allocation of resources or life opportunities (ex: housing, employment, credit, etc.) without further assessments and additional debiasing techniques.
+- High-Risk Scenarios: Researchers should assess the suitability of using models in high-risk scenarios where unfair, unreliable or offensive outputs might be extremely costly or lead to harm. This includes providing advice in sensitive or expert domains where accuracy and reliability are critical (ex: legal or health advice). Additional safeguards should be implemented at the application level according to the deployment context.
+- Misinformation: Models may produce inaccurate information. Researchers should follow transparency best practices and inform end-users they are interacting with an AI system. At the application level, developers can build feedback mechanisms and pipelines to ground responses in use-case specific, contextual information, a technique known as Retrieval Augmented Generation (RAG).
+- Generation of Harmful Content: Researchers should assess outputs for their context and use available safety classifiers or custom solutions appropriate for their use case.
+- Misuse: Other forms of misuse such as fraud, spam, or malware production may be possible, and developers should ensure that their applications do not violate applicable laws and regulations.
+
+## How to Get Started with the Model
+
+### Input Format
+
+    <|system|>
+    GIVE A ROLE AND INSTRUCTIONS FOR CLINICAL NLPTASKS<|end|>
+    <|user|>
+    INPUT DOCUMENT<|end|>
+    <|assistant|>
+
+### Loading the model locally
+
+    import torch
+    from transformers import AutoModelForCausalLM, AutoTokenizer, pipeline
+
+    torch.random.manual_seed(0)
+
+    model_name = "microsoft/MediPhi-Instruct"
+    model = AutoModelForCausalLM.from_pretrained(
+        model_name,
+        device_map="cuda",
+        torch_dtype="auto",
+        trust_remote_code=True,
+    )
+    tokenizer = AutoTokenizer.from_pretrained(model_name)
+
+    prompt = "Operative Report:\nPerformed: Cholecystectomy\nOperative Findings: The gallbladder contained multiple stones and had thickening of its wall. Mild peritoneal fluid was noted."
+
+    messages = [
+        {"role": "system", "content": "Extract medical keywords from this operative notes focus on anatomical, pathological, or procedural vocabulary."},
+        {"role": "user", "content": prompt},
+    ]
+
+    pipe = pipeline(
+        "text-generation",
+        model=model,
+        tokenizer=tokenizer,
+    )
+
+    generation_args = {
+        "max_new_tokens": 500,
+        "return_full_text": False,
+        "temperature": 0.0,
+        "do_sample": False,
+    }
+
+    output = pipe(messages, **generation_args)
+    print(output[0]['generated_text'])
+    # gallbladder stones, wall thickening, peritoneal fluid
+
+Notes: If you want to use flash attention, call `AutoModelForCausalLM.from_pretrained()` with `attn_implementation="flash_attention_2"`.
+
+### More Information
+
+Check `microsoft/Phi-3.5-mini-instruct` for details about the tokenizer, requirements and basic capabilities.
+
+## Training Details
+
+### Training Data
+
+Continual Pre-training:
+- PubMed (commercial subset) and abstracts from `ncbi/pubmed`.
+- Medical Guideline `epfl-llm/guidelines`.
+- Medical Wikipedia `jpcorb20/medical_wikipedia`.
+- Medical Coding: ICD10CM, ICD10PROC, ICD9CM, ICD9PROC, and ATC.
+- Clinical documents:
+    - `zhengyun21/PMC-Patients`, `akemiH/NoteChat`, and `starmpcc/Asclepius-Synthetic-Clinical-Notes` (only commercial-friendly licenses across all three datasets)
+    - mtsamples
+
+Clinical alignment:
+- `microsoft/mediflow`
+
+See paper for details.
+
+### Training Procedure
+
+Modular training making five experts from the base model with pre-instruction tuning, merging them into one model and finally clinically aligning it. See paper for details.
+
+## Evaluation
+
+#### CLUE+ Benchmark
+
+|              | Phi-3.5-mini-instruct | PubMed | Clinical | MedWiki | Guideline | MedCode | MediPhi | MediPhi-Instruct |
+|:-------------|----------------------:|-------:|---------:|--------:|----------:|--------:|--------:|-----------------:|
+| **MedNLI**       | 66.6 | 68.3 | 69.2 | 72.8 | 70.3 | 68.5 | 66.9 | 71.0 |
+| **PLS**          | 28.4 | 29.2 | 29.4 | 29.2 | 29.8 | 22.3 | 28.8 | 26.0 |
+| **MeQSum**       | 36.7 | 37.6 | 38.1 | 37.6 | 37.6 | 33.5 | 37.9 | 42.8 |
+| **LH**           | 45.9 | 45.7 | 43.5 | 43.6 | 41.1 | 45.7 | 45.7 | 45.0 |
+| **MeDiSumQA**    | 25.9 | 26.3 | 26.7 | 25.1 | 25.1 | 23.6 | 26.1 | 29.1 |
+| **MeDiSumCode**  | 41.1 | 41.0 | 40.5 | 41.7 | 41.9 | 39.0 | 41.7 | 37.2 |
+| **RRS QA**       | 41.2 | 44.1 | 52.1 | 46.7 | 48.9 | 45.6 | 44.5 | 61.6 |
+| **MedicationQA** | 11.2 | 10.3 | 12.0 | 12.2 | 11.9 | 12.0 | 11.3 | 19.3 |
+| **MEDEC**        | 14.8 | 22.2 | 34.5 | 28.8 | 28.3 | 18.1 | 29.1 | 34.4 |
+| **ACI**          | 42.3 | 42.7 | 43.9 | 44.7 | 44.7 | 39.0 | 44.3 | 43.5 |
+| **SDoH**         | 35.1 | 35.8 | 35.8 | 43.6 | 41.0 | 24.8 | 39.7 | 56.7 |
+| **ICD10CM**      | 49.3 | 49.5 | 49.6 | 50.2 | 49.8 | 68.7 | 55.5 | 54.9 |
+| **Average**      | **36.5** | **37.7** | **39.6** | **39.7** | **39.2** | **36.7** | **39.3** | **43.4** |
+
+New real-world benchmarking also demonstrated good performances on clinical information extraction task: [2507.05517](https://arxiv.org/abs/2507.05517).
+
+#### Red Teaming
+
+We carried out a [Medical Red Teaming Protocol of Language Models](https://arxiv.org/abs/2507.07248) in which we demonstrate broad conversation of original Phi3.5 safety abilities (see [Phi-3 Safety Post-Training](https://arxiv.org/abs/2407.13833)). All six merged MediPhi models fully conserve their base model's safety capabilities. For `MediPhi-Instruct`, it conserved safe behaviors towards jailbreaking and harmfulness, as well as it is improving considerably on groundedness. We further demonstrate safe behaviours at refusing or giving warnings with limited responses for nearly all harmful queries from clinican and patient user perspectives, based on MedSafetyBench and our PatientSafetyBench.
+
+## Technical Specifications
+
+### Model Architecture
+
+Phi-3.5-mini has 3.8B parameters and is a dense decoder-only Transformer model using the same tokenizer as Phi-3 Mini. It is best suited for prompts using chat format but plain text is also possible. The default context length is of 128K tokens.
+
+#### Hardware
+
+Note that by default, the Phi-3.5-mini-instruct model uses flash attention, which requires certain types of GPU hardware to run. We have tested on the following GPU types:
+- NVIDIA A100
+- NVIDIA A6000
+- NVIDIA H100
+
+If you want to run the model on:
+- NVIDIA V100 or earlier generation GPUs: call AutoModelForCausalLM.from_pretrained() with attn_implementation="eager"
+
+#### Software
+
+- [PyTorch](https://github.com/pytorch/pytorch)
+- [Transformers](https://github.com/huggingface/transformers)
+- [Flash-Attention](https://github.com/HazyResearch/flash-attention)
+
+## License
+
+The model is licensed under the [MIT license](https://huggingface.co/microsoft/Phi-3.5-mini-instruct/blob/main/LICENSE).
+
+## Trademarks
+This project may contain trademarks or logos for projects, products, or services. Authorized use of Microsoft trademarks or logos is subject to and must follow [Microsoft’s Trademark & Brand Guidelines](https://www.microsoft.com/en-us/legal/intellectualproperty/trademarks). Use of Microsoft trademarks or logos in modified versions of this project must not cause confusion or imply Microsoft sponsorship. Any use of third-party trademarks or logos are subject to those third-party’s policies.
+
+## Citation
+
+    @article{corbeil2025modular,
+        title={A Modular Approach for Clinical SLMs Driven by Synthetic Data with Pre-Instruction Tuning, Model Merging, and Clinical-Tasks Alignment},
+        author={Corbeil, Jean-Philippe and Dada, Amin and Attendu, Jean-Michel and Abacha, Asma Ben and Sordoni, Alessandro and Caccia, Lucas and Beaulieu, Fran{\c{c}}ois and Lin, Thomas and Kleesiek, Jens and Vozila, Paul},
+        journal={arXiv preprint arXiv:2505.10717},
+        year={2025}
+    }
+
+
+## Model Card Authors
+
+Jean-Philippe Corbeil
+
+## Model Card Contact
+
+[email protected]

SECURITY.md

@@ -0,0 +1,41 @@
+<!-- BEGIN MICROSOFT SECURITY.MD V0.0.9 BLOCK -->
+
+## Security
+
+Microsoft takes the security of our software products and services seriously, which includes all source code repositories managed through our GitHub organizations, which include [Microsoft](https://github.com/Microsoft), [Azure](https://github.com/Azure), [DotNet](https://github.com/dotnet), [AspNet](https://github.com/aspnet) and [Xamarin](https://github.com/xamarin).
+
+If you believe you have found a security vulnerability in any Microsoft-owned repository that meets [Microsoft's definition of a security vulnerability](https://aka.ms/security.md/definition), please report it to us as described below.
+
+## Reporting Security Issues
+
+**Please do not report security vulnerabilities through public GitHub issues.**
+
+Instead, please report them to the Microsoft Security Response Center (MSRC) at [https://msrc.microsoft.com/create-report](https://aka.ms/security.md/msrc/create-report).
+
+If you prefer to submit without logging in, send email to [[email protected]](mailto:[email protected]).  If possible, encrypt your message with our PGP key; please download it from the [Microsoft Security Response Center PGP Key page](https://aka.ms/security.md/msrc/pgp).
+
+You should receive a response within 24 hours. If for some reason you do not, please follow up via email to ensure we received your original message. Additional information can be found at [microsoft.com/msrc](https://www.microsoft.com/msrc). 
+
+Please include the requested information listed below (as much as you can provide) to help us better understand the nature and scope of the possible issue:
+
+  * Type of issue (e.g. buffer overflow, SQL injection, cross-site scripting, etc.)
+  * Full paths of source file(s) related to the manifestation of the issue
+  * The location of the affected source code (tag/branch/commit or direct URL)
+  * Any special configuration required to reproduce the issue
+  * Step-by-step instructions to reproduce the issue
+  * Proof-of-concept or exploit code (if possible)
+  * Impact of the issue, including how an attacker might exploit the issue
+
+This information will help us triage your report more quickly.
+
+If you are reporting for a bug bounty, more complete reports can contribute to a higher bounty award. Please visit our [Microsoft Bug Bounty Program](https://aka.ms/security.md/msrc/bounty) page for more details about our active programs.
+
+## Preferred Languages
+
+We prefer all communications to be in English.
+
+## Policy
+
+Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://aka.ms/security.md/cvd).
+
+<!-- END MICROSOFT SECURITY.MD BLOCK -->

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+            "special": true
+        },
+        "32004": {
+            "content": "<|placeholder3|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32005": {
+            "content": "<|placeholder4|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32006": {
+            "content": "<|system|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32007": {
+            "content": "<|end|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32008": {
+            "content": "<|placeholder5|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32009": {
+            "content": "<|placeholder6|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        },
+        "32010": {
+            "content": "<|user|>",
+            "lstrip": false,
+            "normalized": false,
+            "rstrip": true,
+            "single_word": false,
+            "special": true
+        }
+    },
+    "bos_token": "<s>",
+    "chat_template": "{% for message in messages %}{% if message['role'] == 'system' and message['content'] %}{{'<|system|>\n' + message['content'] + '<|end|>\n'}}{% elif message['role'] == 'user' %}{{'<|user|>\n' + message['content'] + '<|end|>\n'}}{% elif message['role'] == 'assistant' %}{{'<|assistant|>\n' + message['content'] + '<|end|>\n'}}{% endif %}{% endfor %}{% if add_generation_prompt %}{{ '<|assistant|>\n' }}{% else %}{{ eos_token }}{% endif %}",
+    "clean_up_tokenization_spaces": false,
+    "eos_token": "<|endoftext|>",
+    "legacy": false,
+    "model_max_length": 131072,
+    "pad_token": "<|endoftext|>",
+    "padding_side": "left",
+    "sp_model_kwargs": {},
+    "tokenizer_class": "LlamaTokenizer",
+    "unk_token": "<unk>",
+    "use_default_system_prompt": false
+}