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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 [opencode@microsoft.com](mailto:opencode@microsoft.com) with questions or concerns

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PhyAGI.
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.

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NOTICES AND INFORMATION
Do Not Translate or Localize
This software incorporates material from third parties.
**Component.** https://github.com/Dao-AILab/flash-attention
**Open Source License/Copyright Notice.**
BSD 3-Clause License
Copyright (c) 2022, the respective contributors, as shown by the AUTHORS file.
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of the copyright holder nor the names of its
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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---
inference: false
license: mit
license_link: https://huggingface.co/microsoft/phi-2/resolve/main/LICENSE
language:
- en
pipeline_tag: text-generation
tags:
- nlp
- code
- biology
- medical
---
## Model Summary
MedPhi-2 is a Phi-2, **2.7 billion** parameters, further trained for the biomedical domain.
It was proposed in MedExQA paper.
<h1> 🧑‍⚕️ MedExQA </h1>
<h3> Medical Question Answering Benchmark with Multiple Explanations </h3>
<p>
📄 <a href="https://arxiv.org/abs/2406.06331" target="_blank">Paper</a> • ⏬ <a href="https://huggingface.co/datasets/bluesky333/MedExQA" target="_blank">Dataset</a> • ⚕️ <a href="https://huggingface.co/bluesky333/medphi2" target="_blank">MedPhi2</a><br>
</p>
## Model Details
### Model Description
<!-- Provide a longer summary of what this model is. -->
- **Model type:** Clinical LLM (Large Language Model)
- **Language(s) (NLP):** English
- **License:** [MIT license](https://huggingface.co/microsoft/phi-2/resolve/main/LICENSE)
- **Finetuned from model [optional]:** Phi-2
## Citation
<!-- If there is a paper or blog post introducing the model, the APA and Bibtex information for that should go in this section. -->
**BibTeX:**
```
@article{kim2024medexqa,
title={MedExQA: Medical Question Answering Benchmark with Multiple Explanations},
author={Kim, Yunsoo and Wu, Jinge and Abdulle, Yusuf and Wu, Honghan},
journal={arXiv e-prints},
pages={arXiv--2406},
year={2024}
}
```

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<!-- 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
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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:
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<!-- END MICROSOFT SECURITY.MD BLOCK -->

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"epoch": 3.0,
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"train_steps_per_second": 0.251
}

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{
"_name_or_path": "./model/phi2-knowmed-pretrain",
"architectures": [
"PhiForCausalLM"
],
"attention_dropout": 0.0,
"auto_map": {
"AutoConfig": "configuration_phi.PhiConfig",
"AutoModel": "modeling_phi.PhiForCausalLM",
"AutoModelForCausalLM": "modeling_phi.PhiForCausalLM"
},
"bos_token_id": null,
"embd_pdrop": 0.0,
"eos_token_id": null,
"hidden_act": "gelu_new",
"hidden_size": 2560,
"initializer_range": 0.02,
"intermediate_size": 10240,
"layer_norm_eps": 1e-05,
"max_position_embeddings": 2048,
"model_type": "phi",
"num_attention_heads": 32,
"num_hidden_layers": 32,
"num_key_value_heads": 32,
"partial_rotary_factor": 0.4,
"qk_layernorm": false,
"resid_pdrop": 0.1,
"rope_scaling": null,
"rope_theta": 10000.0,
"tie_word_embeddings": false,
"torch_dtype": "bfloat16",
"transformers_version": "4.37.1",
"use_cache": false,
"vocab_size": 51200
}

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# coding=utf-8
# Copyright 2023 Microsoft and the HuggingFace Inc. team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
""" Phi model configuration"""
from transformers.configuration_utils import PretrainedConfig
from transformers.utils import logging
logger = logging.get_logger(__name__)
PHI_PRETRAINED_CONFIG_ARCHIVE_MAP = {
"microsoft/phi-2": "https://huggingface.co/microsoft/phi-2/resolve/main/config.json",
}
class PhiConfig(PretrainedConfig):
r"""
This is the configuration class to store the configuration of a [`PhiModel`]. It is used to instantiate an Phi
model according to the specified arguments, defining the model architecture. Instantiating a configuration with the
defaults will yield a similar configuration to that of the Phi
[microsoft/phi-1](https://huggingface.co/microsoft/phi-1).
Configuration objects inherit from [`PretrainedConfig`] and can be used to control the model outputs. Read the
documentation from [`PretrainedConfig`] for more information.
Args:
vocab_size (`int`, *optional*, defaults to 51200):
Vocabulary size of the Phi model. Defines the number of different tokens that can be represented by the
`inputs_ids` passed when calling [`PhiModel`].
hidden_size (`int`, *optional*, defaults to 2048):
Dimension of the hidden representations.
intermediate_size (`int`, *optional*, defaults to 8192):
Dimension of the MLP representations.
num_hidden_layers (`int`, *optional*, defaults to 24):
Number of hidden layers in the Transformer decoder.
num_attention_heads (`int`, *optional*, defaults to 32):
Number of attention heads for each attention layer in the Transformer decoder.
num_key_value_heads (`int`, *optional*):
This is the number of key_value heads that should be used to implement Grouped Query Attention. If
`num_key_value_heads=num_attention_heads`, the model will use Multi Head Attention (MHA), if
`num_key_value_heads=1 the model will use Multi Query Attention (MQA) otherwise GQA is used. When
converting a multi-head checkpoint to a GQA checkpoint, each group key and value head should be constructed
by meanpooling all the original heads within that group. For more details checkout [this
paper](https://arxiv.org/pdf/2305.13245.pdf). If it is not specified, will default to
`num_attention_heads`.
resid_pdrop (`float`, *optional*, defaults to 0.0):
Dropout probability for mlp outputs.
embd_pdrop (`int`, *optional*, defaults to 0.0):
The dropout ratio for the embeddings.
attention_dropout (`float`, *optional*, defaults to 0.0):
The dropout ratio after computing the attention scores.
hidden_act (`str` or `function`, *optional*, defaults to `"gelu_new"`):
The non-linear activation function (function or string) in the decoder.
max_position_embeddings (`int`, *optional*, defaults to 2048):
The maximum sequence length that this model might ever be used with. Phi-1 and Phi-1.5 supports up to 2048
tokens.
initializer_range (`float`, *optional*, defaults to 0.02):
The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
layer_norm_eps (`float`, *optional*, defaults to 1e-05):
The epsilon used by the rms normalization layers.
use_cache (`bool`, *optional*, defaults to `True`):
Whether or not the model should return the last key/values attentions (not used by all models). Only
relevant if `config.is_decoder=True`. Whether to tie weight embeddings or not.
tie_word_embeddings (`bool`, *optional*, defaults to `False`):
Whether to tie weight embeddings
rope_theta (`float`, *optional*, defaults to 10000.0):
The base period of the RoPE embeddings.
rope_scaling (`Dict`, *optional*):
Dictionary containing the scaling configuration for the RoPE embeddings. Currently supports two scaling
strategies: linear and dynamic. Their scaling factor must be an float greater than 1. The expected format
is `{"type": strategy name, "factor": scaling factor}`. When using this flag, don't update
`max_position_embeddings` to the expected new maximum. See the following thread for more information on how
these scaling strategies behave:
https://www.reddit.com/r/LocalPersimmon/comments/14mrgpr/dynamically_scaled_rope_further_increases/. This
is an experimental feature, subject to breaking API changes in future versions.
partial_rotary_factor (`float`, *optional*, defaults to 0.5):
Percentage of the query and keys which will have rotary embedding.
qk_layernorm (`bool`, *optional*, defaults to `False`):
Whether or not to normalize the Queries and Keys after projecting the hidden states.
bos_token_id (`int`, *optional*, defaults to 1):
Denotes beginning of sequences token id.
eos_token_id (`int`, *optional*, defaults to 2):
Denotes end of sequences token id.
Example:
```python
>>> from transformers import PhiModel, PhiConfig
>>> # Initializing a Phi-1 style configuration
>>> configuration = PhiConfig.from_pretrained("microsoft/phi-1")
>>> # Initializing a model from the configuration
>>> model = PhiModel(configuration)
>>> # Accessing the model configuration
>>> configuration = model.config
```"""
model_type = "phi"
keys_to_ignore_at_inference = ["past_key_values"]
def __init__(
self,
vocab_size=51200,
hidden_size=2048,
intermediate_size=8192,
num_hidden_layers=24,
num_attention_heads=32,
num_key_value_heads=None,
resid_pdrop=0.0,
embd_pdrop=0.0,
attention_dropout=0.0,
hidden_act="gelu_new",
max_position_embeddings=2048,
initializer_range=0.02,
layer_norm_eps=1e-5,
use_cache=True,
tie_word_embeddings=False,
rope_theta=10000.0,
rope_scaling=None,
partial_rotary_factor=0.5,
qk_layernorm=False,
bos_token_id=1,
eos_token_id=2,
**kwargs,
):
self.vocab_size = vocab_size
self.hidden_size = hidden_size
self.intermediate_size = intermediate_size
self.num_hidden_layers = num_hidden_layers
self.num_attention_heads = num_attention_heads
if num_key_value_heads is None:
num_key_value_heads = num_attention_heads
self.num_key_value_heads = num_key_value_heads
self.resid_pdrop = resid_pdrop
self.embd_pdrop = embd_pdrop
self.attention_dropout = attention_dropout
self.hidden_act = hidden_act
self.max_position_embeddings = max_position_embeddings
self.initializer_range = initializer_range
self.layer_norm_eps = layer_norm_eps
self.use_cache = use_cache
self.rope_theta = rope_theta
self.rope_scaling = rope_scaling
self.partial_rotary_factor = partial_rotary_factor
self.qk_layernorm = qk_layernorm
self._rope_scaling_validation()
super().__init__(
bos_token_id=bos_token_id,
eos_token_id=eos_token_id,
tie_word_embeddings=tie_word_embeddings,
**kwargs,
)
# Copied from transformers.models.llama.configuration_llama.LlamaConfig._rope_scaling_validation
def _rope_scaling_validation(self):
"""
Validate the `rope_scaling` configuration.
"""
if self.rope_scaling is None:
return
if not isinstance(self.rope_scaling, dict) or len(self.rope_scaling) != 2:
raise ValueError(
"`rope_scaling` must be a dictionary with with two fields, `type` and `factor`, "
f"got {self.rope_scaling}"
)
rope_scaling_type = self.rope_scaling.get("type", None)
rope_scaling_factor = self.rope_scaling.get("factor", None)
if rope_scaling_type is None or rope_scaling_type not in ["linear", "dynamic"]:
raise ValueError(
f"`rope_scaling`'s type field must be one of ['linear', 'dynamic'], got {rope_scaling_type}"
)
if rope_scaling_factor is None or not isinstance(rope_scaling_factor, float) or rope_scaling_factor <= 1.0:
raise ValueError(f"`rope_scaling`'s factor field must be a float > 1, got {rope_scaling_factor}")

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{
"_from_model_config": true,
"transformers_version": "4.37.1"
}

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"padding_side": "right",
"split_special_tokens": false,
"tokenizer_class": "CodeGenTokenizer",
"unk_token": "<|endoftext|>"
}

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vocab.json Normal file

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