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README.md

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+---
+language:
+- multilingual
+pipeline_tag: image-text-to-text
+tags:
+- vision
+widget:
+- messages:
+  - role: user
+    content: <|image_1|>\nDescribe bones on this chest X-ray?
+library_name: transformers
+---
+# ChexFract: Specialized Vision-Language Models for Fracture Detection in Chest X-rays
+
+This repository contains the pre-trained models from our paper "ChexFract: From General to Specialized - Enhancing Fracture Description Generation in Medical AI".
+
+## 📋 Overview
+
+ChexFract models are specialized vision-language models fine-tuned for accurate fracture detection and description in chest X-ray images. These models significantly outperform general-purpose radiology report generation systems on fracture-specific tasks.
+
+## 🏆 Model Performance
+
+### Released Models
+
+We release two best-performing models, each optimized for their respective encoder architecture:
+
+1. **ChexFract-MAIRA-2** (Best F1-Score with MAIRA-2 encoder)
+   - **Configuration:** Templated text + Fine-tuned encoder (unfrozen)
+   - **ROC-AUC:** 0.713
+   - **F1-Score:** 0.629
+   - **Accuracy:** 0.748
+   - **Precision:** 0.682
+   - **Recall:** 0.584
+
+2. **ChexFract-CheXagent** (Best F1-Score with CheXagent encoder)
+   - **Configuration:** Templated text + Fine-tuned encoder (unfrozen)
+   - **ROC-AUC:** 0.697
+   - **F1-Score:** 0.591
+   - **Accuracy:** 0.752
+   - **Precision:** 0.750
+   - **Recall:** 0.487
+
+## 🚀 Quick Start
+
+### Installation
+
+```bash
+pip install torch torchvision transformers pillow
+```
+
+### Basic Usage
+
+**Using CheXagent encoder model:**
+```python
+from transformers import AutoModelForCausalLM, AutoProcessor
+from PIL import Image
+
+# Load model and processor
+model = AutoModelForCausalLM.from_pretrained("AIRI-Institute/chexfract-chexagent", trust_remote_code=True)
+processor = AutoProcessor.from_pretrained("AIRI-Institute/chexfract-chexagent", trust_remote_code=True)
+
+messages = [{"role": "user", "content": "<|image_1|>\nDescribe bones on this chest X-ray"}]
+
+# Load chest X-ray image
+image = Image.open("chest_xray.png")
+prompt = processor.tokenizer.apply_chat_template(messages, tokenize=False, add_generation_prompt=True)
+
+# Generate fracture description
+inputs = processor(prompt, image, return_tensors="pt")
+outputs = model.generate(**inputs, eos_token_id=processor.tokenizer.eos_token_id, max_new_tokens=1024)
+description = processor.decode(outputs[0, inputs['input_ids'].shape[1]:], skip_special_tokens=True)
+
+print(f"Fracture description: {description}")
+```
+
+## 📈 Performance Comparison
+
+| Model | ROC-AUC | F1-Score | Accuracy | Precision | Recall |
+|-------|---------|----------|----------|-----------|--------|
+| General MAIRA-2 (baseline) | 0.518 | 0.085 | 0.645 | 0.777 | 0.045 |
+| **ChexFract-MAIRA-2** | **0.713** | **0.629** | **0.748** | **0.682** | **0.584** |
+| General CheXagent (baseline) | 0.604 | 0.376 | 0.700 | 0.791 | 0.246 |
+| **ChexFract-CheXagent** | **0.697** | **0.591** | **0.752** | **0.750** | **0.487** |
+
+## 🔬 Model Architecture
+
+Both models share the same architecture but use different visual encoders:
+
+- **ChexFract-MAIRA-2:**
+  - **Visual Encoder:** [Rad-DINO (from MAIRA-2)](https://huggingface.co/microsoft/rad-dino-maira-2)
+  - **Language Model:** [Phi-3.5 Vision Instruct](https://huggingface.co/microsoft/Phi-3.5-vision-instruct) (3.8B parameters)
+  - **Training:** Fine-tuned encoder (unfrozen) + templated text on ChexFract dataset
+
+- **ChexFract-CheXagent:**
+  - **Visual Encoder:** [CheXagent-2-3b encoder](https://huggingface.co/StanfordAIMI/CheXagent-2-3b)
+  - **Language Model:** [Phi-3.5 Vision Instruct](https://huggingface.co/microsoft/Phi-3.5-vision-instruct) (3.8B parameters)
+  - **Training:** Fine-tuned encoder (unfrozen) + templated text on ChexFract dataset
+
+## ⚠️ Limitations and Clinical Use
+
+**Important:** These models are designed for **research purposes**. They are **NOT intended for standalone diagnostic use**.
+
+## 📝 Citation
+
+If you use these models in your research, please cite:
+
+```bibtex
+@article{chexfract2025,
+  title={ChexFract: From General to Specialized - Enhancing Fracture Description Generation in Medical AI},
+  author={Nechaev, Nikolay and Przhezdzetskaia, Evgeniia and Umerenkov, Dmitry and Dylov, Dmitry V.},
+  journal={arXiv preprint arXiv:XXXX.XXXXX},
+  year={2025},
+  institution={Artificial Intelligence Research Institute (AIRI)}
+}
+```
+
+## 📄 License
+
+### Model License
+
+**Important:** These models are derivative works based on multiple pre-trained models. The license for these models is subject to the most restrictive terms among the base model licenses.
+
+**Effective License:** These models are provided under terms compatible with the most restrictive license among the base model licenses. Users must comply with ALL applicable base model licenses.
+
+**Base Model Licenses:**
+- **Rad-DINO encoder (from MAIRA-2):** Microsoft Research License Agreement (MSRLA) - see [microsoft/rad-dino-maira-2](https://huggingface.co/microsoft/rad-dino-maira-2) for full terms
+- **CheXagent-2-3b encoder:** Creative Commons Attribution Non Commercial 4.0 (CC-BY-NC-4.0) - see [StanfordAIMI/CheXagent-2-3b](https://huggingface.co/StanfordAIMI/CheXagent-2-3b) for full terms
+- **Phi-3.5 Vision Instruct:** MIT License - see [microsoft/Phi-3.5-vision-instruct](https://huggingface.co/microsoft/Phi-3.5-vision-instruct) for full license terms
+
+**⚠️ IMPORTANT - Commercial Use Restrictions:**
+- **CheXagent-2-3b** uses CC-BY-NC-4.0, which **PROHIBITS commercial use** without explicit permission
+- **Rad-DINO (MAIRA-2)** uses MSRLA, which typically has **restrictions on commercial use** without permission
+- **Phi-3.5** uses MIT License, which allows commercial use
+
+**The most restrictive license applies:** These models are **NOT licensed for commercial use** due to CC-BY-NC-4.0 and MSRLA restrictions. For commercial use, you must obtain appropriate licenses from the original model owners.
+
+**Before using these models, you must:**
+1. Review the license terms of all base models in their original repositories
+2. Ensure your use case complies with all applicable licenses (especially for commercial purposes)
+3. Include appropriate attribution and copyright notices as required by each license
+4. Obtain commercial licenses if needed from model owners (Microsoft for MAIRA-2, Stanford for CheXagent)
+
+### Additional License Information
+
+The fine-tuning code and modifications specific to this work may be subject to additional licensing terms. Please review all applicable licenses before commercial use.
+
+## 👥 Authors
+
+- **Nikolay Nechaev** - Artificial Intelligence Research Institute (AIRI)
+- **Evgeniia Przhezdzetskaia** - Artificial Intelligence Research Institute (AIRI)
+- **Dmitry Umerenkov** - Artificial Intelligence Research Institute (AIRI)
+- **Dmitry V. Dylov** - Artificial Intelligence Research Institute (AIRI)
+
+## 🔗 Related Resources
+
+- **Paper:** [arXiv link]
+
+## 🙏 Acknowledgments
+
+We thank the contributors to the MIMIC-CXR, PadChest, BIMCV-COVID19, CheXpert, and OpenI datasets for making their data publicly available. We also acknowledge the computational resources provided for this research.
+
+## 📧 Contact
+
+For questions or issues, please contact:
+- **Email:** nechaev@airi.net
+- **Institution:** Artificial Intelligence Research Institute (AIRI), Moscow, Russia
+
+---
+
+**Disclaimer:** These models are provided for research purposes only. They are not intended for clinical use without proper validation and regulatory approval.
+

config.json

@@ -0,0 +1,159 @@
+{
+  "_name_or_path": "Data/models/phi-chex-ft",
+  "architectures": [
+    "ChexBonesForCausalLM"
+  ],
+  "attention_dropout": 0.0,
+  "auto_map": {
+    "AutoConfig": "configuration_chexbones.ChexBonesConfig",
+    "AutoModelForCausalLM": "modeling_chexbones.ChexBonesForCausalLM"
+  },
+  "bos_token_id": 1,
+  "embd_layer": {
+    "embedding_cls": "image",
+    "projection_cls": "mlp",
+    "use_hd_transform": true,
+    "with_learnable_separator": true
+  },
+  "embd_pdrop": 0.0,
+  "eos_token_id": 2,
+  "hidden_act": "silu",
+  "hidden_size": 3072,
+  "img_processor": {
+    "image_dim_out": 1408,
+    "image_size": 448,
+    "model_type": "chexagent_vision_model",
+    "num_hidden_layers": 40
+  },
+  "initializer_range": 0.02,
+  "intermediate_size": 8192,
+  "max_position_embeddings": 131072,
+  "model_type": "phi3_chex",
+  "num_attention_heads": 32,
+  "num_hidden_layers": 32,
+  "num_key_value_heads": 32,
+  "original_max_position_embeddings": 4096,
+  "pad_token_id": 32000,
+  "projector_lr": 0.001,
+  "resid_pdrop": 0.0,
+  "rms_norm_eps": 1e-05,
+  "rope_scaling": {
+    "long_factor": [
+      1.0800000429153442,
+      1.1100000143051147,
+      1.1399999856948853,
+      1.340000033378601,
+      1.5899999141693115,
+      1.600000023841858,
+      1.6200000047683716,
+      2.620000123977661,
+      3.2300000190734863,
+      3.2300000190734863,
+      4.789999961853027,
+      7.400000095367432,
+      7.700000286102295,
+      9.09000015258789,
+      12.199999809265137,
+      17.670000076293945,
+      24.46000099182129,
+      28.57000160217285,
+      30.420001983642578,
+      30.840002059936523,
+      32.590003967285156,
+      32.93000411987305,
+      42.320003509521484,
+      44.96000289916992,
+      50.340003967285156,
+      50.45000457763672,
+      57.55000305175781,
+      57.93000411987305,
+      58.21000289916992,
+      60.1400032043457,
+      62.61000442504883,
+      62.62000274658203,
+      62.71000289916992,
+      63.1400032043457,
+      63.1400032043457,
+      63.77000427246094,
+      63.93000411987305,
+      63.96000289916992,
+      63.970001220703125,
+      64.02999877929688,
+      64.06999969482422,
+      64.08000183105469,
+      64.12000274658203,
+      64.41000366210938,
+      64.4800033569336,
+      64.51000213623047,
+      64.52999877929688,
+      64.83999633789062
+    ],
+    "short_factor": [
+      1.08,
+      1.1,
+      1.1300000000000001,
+      1.2800000000000002,
+      1.3100000000000003,
+      1.4500000000000004,
+      1.4500000000000004,
+      1.9500000000000008,
+      2.030000000000001,
+      2.4299999999999926,
+      2.5699999999999896,
+      2.9499999999999815,
+      3.729999999999965,
+      3.869999999999962,
+      4.189999999999955,
+      4.43999999999995,
+      4.6399999999999455,
+      4.979999999999938,
+      5.159999999999934,
+      5.279999999999932,
+      5.759999999999922,
+      5.889999999999919,
+      5.889999999999919,
+      5.969999999999917,
+      6.089999999999915,
+      6.2799999999999105,
+      6.7699999999999,
+      6.8899999999998975,
+      7.109999999999893,
+      7.129999999999892,
+      7.179999999999891,
+      7.289999999999889,
+      7.339999999999888,
+      7.559999999999883,
+      7.619999999999882,
+      7.69999999999988,
+      7.879999999999876,
+      7.879999999999876,
+      7.879999999999876,
+      7.939999999999875,
+      7.949999999999875,
+      7.979999999999874,
+      8.19999999999987,
+      8.439999999999864,
+      8.469999999999864,
+      8.589999999999861,
+      8.809999999999857,
+      8.999999999999853
+    ],
+    "type": "su"
+  },
+  "rope_theta": 10000.0,
+  "sliding_window": 262144,
+  "tie_word_embeddings": false,
+  "tokenizer_model_max_length": 131072,
+  "tokenizer_padding_side": "right",
+  "torch_dtype": "bfloat16",
+  "transformers_version": "4.45.2",
+  "use_cache": true,
+  "vision_config": {
+    "image_dim_out": 1408,
+    "image_size": 448,
+    "model_type": "chexagent_vision_model",
+    "num_hidden_layers": 40
+  },
+  "vision_lr": 2e-06,
+  "vocab_size": 32064
+}

configuration_chexbones.py

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+# coding=utf-8
+# Copyright 2024 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.
+
+
+from transformers.configuration_utils import PretrainedConfig
+from transformers.utils import logging
+from typing import Union
+import os
+
+
+logger = logging.get_logger(__name__)
+
+CHEXBONES_PRETRAINED_CONFIG_ARCHIVE_MAP = {
+    "AIRI/chexfract-chexagent": "./config.json",
+}
+
+#from https://huggingface.co/StanfordAIMI/CheXagent-8b/blob/main/configuration_chexagent.py
+class CheXagentVisionConfig(PretrainedConfig):
+    model_type = "chexagent_vision_model"
+
+    def __init__(
+            self,
+            hidden_size=1408,
+            intermediate_size=6144,
+            num_hidden_layers=39,
+            num_attention_heads=16,
+            image_size=224,
+            patch_size=14,
+            hidden_act="gelu",
+            layer_norm_eps=1e-6,
+            attention_dropout=0.0,
+            initializer_range=1e-10,
+            qkv_bias=True,
+            **kwargs,
+    ):
+        super().__init__(**kwargs)
+
+        self.hidden_size = hidden_size
+        self.intermediate_size = intermediate_size
+        self.num_hidden_layers = num_hidden_layers
+        self.num_attention_heads = num_attention_heads
+        self.patch_size = patch_size
+        self.image_size = image_size
+        self.initializer_range = initializer_range
+        self.attention_dropout = attention_dropout
+        self.layer_norm_eps = layer_norm_eps
+        self.hidden_act = hidden_act
+        self.qkv_bias = qkv_bias
+
+    @classmethod
+    def from_pretrained(cls, pretrained_model_name_or_path: Union[str, os.PathLike], **kwargs) -> "PretrainedConfig":
+        cls._set_token_in_kwargs(kwargs)
+
+        config_dict, kwargs = cls.get_config_dict(pretrained_model_name_or_path, **kwargs)
+
+        if config_dict.get("model_type") == "chexagent":
+            config_dict = config_dict["vision_config"]
+
+        if "model_type" in config_dict and hasattr(cls, "model_type") and config_dict["model_type"] != cls.model_type:
+            logger.warning(
+                f"You are using a model of type {config_dict['model_type']} to instantiate a model of type "
+                f"{cls.model_type}. This is not supported for all configurations of models and can yield errors."
+            )
+
+        return cls.from_dict(config_dict, **kwargs)
+
+
+class ChexBonesConfig(PretrainedConfig):
+    r"""
+    This is the configuration class to store the configuration of a [`ChexBonesModel`]. It is used to instantiate a ChexBones
+    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
+    [microsoft/Phi-3-vision-128k-instruct](https://huggingface.co/microsoft/Phi-3-vision-128k-instruct).
+
+    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 32064):
+            Vocabulary size of the Phi-3-V model. Defines the number of different tokens that can be represented by the
+            `inputs_ids` passed when calling [`ChexBonesModel`].
+        hidden_size (`int`, *optional*, defaults to 3072):
+            Dimension of the hidden representations.
+        intermediate_size (`int`, *optional*, defaults to 8192):
+            Dimension of the MLP representations.
+        num_hidden_layers (`int`, *optional*, defaults to 32):
+            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 `"silu"`):
+            The non-linear activation function (function or string) in the decoder.
+        max_position_embeddings (`int`, *optional*, defaults to 4096):
+            The maximum sequence length that this model might ever be used with.
+        original_max_position_embeddings (`int`, *optional*, defaults to 4096):
+            The maximum sequence length that this model was trained with. This is used to determine the size of the
+            original RoPE embeddings when using long scaling.
+        initializer_range (`float`, *optional*, defaults to 0.02):
+            The standard deviation of the truncated_normal_initializer for initializing all weight matrices.
+        rms_norm_eps (`float`, *optional*, defaults to 1e-05):
+            The epsilon value used for the RMSNorm.
+        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*):
+            The scaling strategy for the RoPE embeddings. If `None`, no scaling is applied. If a dictionary, it must
+            contain the following keys: `type`, `short_factor` and `long_factor`. The `type` must be either `su` or `yarn` and
+            the `short_factor` and `long_factor` must be lists of numbers with the same length as the hidden size
+            divided by the number of attention heads divided by 2.
+        bos_token_id (`int`, *optional*, defaults to 1):
+            The id of the "beginning-of-sequence" token.
+        eos_token_id (`int`, *optional*, defaults to 32000):
+            The id of the "end-of-sequence" token.
+        pad_token_id (`int`, *optional*, defaults to 32000):
+            The id of the padding token.
+        sliding_window (`int`, *optional*):
+            Sliding window attention window size. If `None`, no sliding window is applied.
+        embd_layer (`str`, *optional*, defaults to `"default"`):
+            The embedding layer to use. Can be either `"default"` or `"image"`. "default" uses the standard embedding for text. 
+
+    
+    ```"""
+
+    model_type = "ChexBonesModel"
+    keys_to_ignore_at_inference = ["past_key_values"]
+
+    def __init__(
+        self,
+        vocab_size=32064,
+        hidden_size=3072,
+        intermediate_size=8192,
+        num_hidden_layers=32,
+        num_attention_heads=32,
+        num_key_value_heads=None,
+        resid_pdrop=0.0,
+        embd_pdrop=0.0,
+        attention_dropout=0.0,
+        hidden_act="silu",
+        max_position_embeddings=4096,
+        original_max_position_embeddings=4096,
+        initializer_range=0.02,
+        rms_norm_eps=1e-5,
+        use_cache=True,
+        tie_word_embeddings=False,
+        rope_theta=10000.0,
+        rope_scaling=None,
+        bos_token_id=1,
+        eos_token_id=32000,
+        pad_token_id=32000,
+        sliding_window=None,
+        embd_layer: str = "default",
+        **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.original_max_position_embeddings = original_max_position_embeddings
+        self.initializer_range = initializer_range
+        self.rms_norm_eps = rms_norm_eps
+        self.use_cache = use_cache
+        self.rope_theta = rope_theta
+        self.rope_scaling = rope_scaling
+        self._rope_scaling_validation()
+        self.sliding_window = sliding_window
+        self.embd_layer = embd_layer
+        
+
+
+        super().__init__(
+            bos_token_id=bos_token_id,
+            eos_token_id=eos_token_id,
+            pad_token_id=pad_token_id,
+            tie_word_embeddings=tie_word_embeddings,
+            **kwargs,
+        )
+
+    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) != 3:
+            raise ValueError(
+                "`rope_scaling` must be a dictionary with three fields, `type`, `short_factor` and `long_factor`, "
+                f"got {self.rope_scaling}"
+            )
+        rope_scaling_type = self.rope_scaling.get("type", None)
+        rope_scaling_short_factor = self.rope_scaling.get("short_factor", None)
+        rope_scaling_long_factor = self.rope_scaling.get("long_factor", None)
+        if rope_scaling_type is None or rope_scaling_type not in ["su", "yarn"]:
+            raise ValueError(f"`rope_scaling`'s type field must be one of ['su', 'yarn'], got {rope_scaling_type}")
+        if not (
+            isinstance(rope_scaling_short_factor, list)
+            and all(isinstance(x, (int, float)) for x in rope_scaling_short_factor)
+        ):
+            raise ValueError(
+                f"`rope_scaling`'s short_factor field must be a list of numbers, got {rope_scaling_short_factor}"
+            )
+        if not len(rope_scaling_short_factor) == self.hidden_size // self.num_attention_heads // 2:
+            raise ValueError(
+                f"`rope_scaling`'s short_factor field must have length {self.hidden_size // self.num_attention_heads // 2}, got {len(rope_scaling_short_factor)}"
+            )
+        if not (
+            isinstance(rope_scaling_long_factor, list)
+            and all(isinstance(x, (int, float)) for x in rope_scaling_long_factor)
+        ):
+            raise ValueError(
+                f"`rope_scaling`'s long_factor field must be a list of numbers, got {rope_scaling_long_factor}"
+            )
+        if not len(rope_scaling_long_factor) == self.hidden_size // self.num_attention_heads // 2:
+            raise ValueError(
+                f"`rope_scaling`'s long_factor field must have length {self.hidden_size // self.num_attention_heads // 2}, got {len(rope_scaling_long_factor)}"
+            )
+            
+  

generation_config.json

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+  "bos_token_id": 1,
+  "eos_token_id": 2,
+  "pad_token_id": 32000,
+  "transformers_version": "4.45.2"
+}

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+}

modeling_chexbones.py

@@ -0,0 +1,1825 @@
+# coding=utf-8
+# Copyright 2025 AIRI
+#
+# 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.
+
+
+import inspect
+import math
+import warnings
+from typing import List, Optional, Tuple, Union
+
+import torch
+import torch.nn.functional as F
+from torch import nn
+from torch.nn import BCEWithLogitsLoss, CrossEntropyLoss, MSELoss
+
+from transformers.activations import ACT2FN
+from transformers.cache_utils import Cache, DynamicCache
+from transformers.modeling_attn_mask_utils import _prepare_4d_causal_attention_mask
+from transformers.modeling_outputs import (
+    BaseModelOutputWithPast,
+    CausalLMOutputWithPast,
+    SequenceClassifierOutputWithPast,
+    TokenClassifierOutput,
+)
+from transformers import AutoModel
+from transformers.modeling_utils import PreTrainedModel
+from transformers.utils import (
+    add_code_sample_docstrings,
+    add_start_docstrings,
+    add_start_docstrings_to_model_forward,
+    is_flash_attn_greater_or_equal_2_10,
+    logging,
+    replace_return_docstrings,
+)
+from .configuration_chexbones import ChexBonesConfig, CheXagentVisionConfig
+
+from transformers.modeling_outputs import (
+    BaseModelOutput,
+ 
+    BaseModelOutputWithPooling
+)
+
+try:
+    from flash_attn import flash_attn_func, flash_attn_varlen_func
+    from flash_attn.bert_padding import index_first_axis, pad_input, unpad_input  # noqa
+
+    _flash_supports_window_size = "window_size" in list(inspect.signature(flash_attn_func).parameters)
+except ImportError:
+    pass
+
+import torch
+from torch import nn
+from transformers import  PretrainedConfig
+from transformers.utils import logging
+
+logger = logging.get_logger(__name__)
+
+_CONFIG_FOR_DOC = "ChexBonesConfig"
+
+
+MAX_INPUT_ID = int(1e9)
+
+
+#from ChexAgent https://huggingface.co/StanfordAIMI/CheXagent-8b/blob/main/modeling_chexagent.py
+
+class CheXagentVisionEmbeddings(nn.Module):
+    def __init__(self, config: CheXagentVisionConfig):
+        super().__init__()
+        self.config = config
+        self.embed_dim = config.hidden_size
+        self.image_size = config.image_size
+        self.patch_size = config.patch_size
+
+        self.class_embedding = nn.Parameter(torch.randn(1, 1, self.embed_dim))
+
+        self.patch_embedding = nn.Conv2d(
+            in_channels=3, out_channels=self.embed_dim, kernel_size=self.patch_size, stride=self.patch_size
+        )
+
+        self.num_patches = (self.image_size // self.patch_size) ** 2
+        self.num_positions = self.num_patches + 1
+
+        self.position_embedding = nn.Parameter(torch.randn(1, self.num_positions, self.embed_dim))
+
+    def forward(self, pixel_values: torch.FloatTensor) -> torch.Tensor:
+        batch_size = pixel_values.shape[0]
+        target_dtype = self.patch_embedding.weight.dtype
+        patch_embeds = self.patch_embedding(pixel_values.to(dtype=target_dtype))  # shape = [*, width, grid, grid]
+        patch_embeds = patch_embeds.flatten(2).transpose(1, 2)
+
+        class_embeds = self.class_embedding.expand(batch_size, 1, -1).to(target_dtype)
+        embeddings = torch.cat([class_embeds, patch_embeds], dim=1)
+        embeddings = embeddings + self.position_embedding[:, : embeddings.size(1), :].to(target_dtype)
+        return embeddings
+
+
+class CheXagentAttention(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.embed_dim = config.hidden_size
+        self.num_heads = config.num_attention_heads
+        self.head_dim = self.embed_dim // self.num_heads
+        if self.head_dim * self.num_heads != self.embed_dim:
+            raise ValueError(
+                f"embed_dim must be divisible by num_heads (got `embed_dim`: {self.embed_dim} and `num_heads`:"
+                f" {self.num_heads})."
+            )
+        self.scale = self.head_dim ** -0.5
+        self.dropout = nn.Dropout(config.attention_dropout)
+
+        # small tweak here compared to CLIP, no bias here
+        self.qkv = nn.Linear(self.embed_dim, 3 * self.embed_dim, bias=False)
+
+        if config.qkv_bias:
+            q_bias = nn.Parameter(torch.zeros(self.embed_dim))
+            v_bias = nn.Parameter(torch.zeros(self.embed_dim))
+        else:
+            q_bias = None
+            v_bias = None
+
+        if q_bias is not None:
+            qkv_bias = torch.cat((q_bias, torch.zeros_like(v_bias, requires_grad=False), v_bias))
+            self.qkv.bias = nn.Parameter(qkv_bias)
+
+        self.projection = nn.Linear(self.embed_dim, self.embed_dim)
+
+    def _shape(self, tensor: torch.Tensor, seq_len: int, bsz: int):
+        return tensor.view(bsz, seq_len, self.num_heads, self.head_dim).transpose(1, 2).contiguous()
+
+    def forward(
+            self,
+            hidden_states: torch.Tensor,
+            head_mask: Optional[torch.Tensor] = None,
+            output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        bsz, tgt_len, embed_dim = hidden_states.size()
+
+        mixed_qkv = self.qkv(hidden_states)
+
+        mixed_qkv = mixed_qkv.reshape(bsz, tgt_len, 3, self.num_heads, embed_dim // self.num_heads).permute(
+            2, 0, 3, 1, 4
+        )
+        query_states, key_states, value_states = mixed_qkv[0], mixed_qkv[1], mixed_qkv[2]
+
+        # Take the dot product between "query" and "key" to get the raw attention scores.
+        attention_scores = torch.matmul(query_states, key_states.transpose(-1, -2))
+
+        attention_scores = attention_scores * self.scale
+
+        # Normalize the attention scores to probabilities.
+        attention_probs = nn.functional.softmax(attention_scores, dim=-1)
+
+        # This is actually dropping out entire tokens to attend to, which might
+        # seem a bit unusual, but is taken from the original Transformer paper.
+        attention_probs = self.dropout(attention_probs)
+
+        # Mask heads if we want to
+        if head_mask is not None:
+            attention_probs = attention_probs * head_mask
+
+        context_layer = torch.matmul(attention_probs, value_states).permute(0, 2, 1, 3)
+
+        new_context_layer_shape = context_layer.size()[:-2] + (self.embed_dim,)
+        context_layer = context_layer.reshape(new_context_layer_shape)
+
+        output = self.projection(context_layer)
+
+        outputs = (output, attention_probs) if output_attentions else (output, None)
+
+        return outputs
+
+
+class CheXagentMLP(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+        self.config = config
+        self.activation_fn = ACT2FN[config.hidden_act]
+        self.fc1 = nn.Linear(config.hidden_size, config.intermediate_size)
+        self.fc2 = nn.Linear(config.intermediate_size, config.hidden_size)
+
+    def forward(self, hidden_states: torch.Tensor) -> torch.Tensor:
+        hidden_states = self.fc1(hidden_states)
+        hidden_states = self.activation_fn(hidden_states)
+        hidden_states = self.fc2(hidden_states)
+        return hidden_states
+
+
+class CheXagentEncoderLayer(nn.Module):
+    def __init__(self, config: CheXagentVisionConfig):
+        super().__init__()
+        self.embed_dim = config.hidden_size
+        self.self_attn = CheXagentAttention(config)
+        self.layer_norm1 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
+        self.mlp = CheXagentMLP(config)
+        self.layer_norm2 = nn.LayerNorm(self.embed_dim, eps=config.layer_norm_eps)
+
+    def forward(
+            self,
+            hidden_states: torch.Tensor,
+            attention_mask: torch.Tensor,
+            output_attentions: Optional[bool] = False,
+    ) -> Tuple[torch.FloatTensor]:
+        residual = hidden_states
+        hidden_states = self.layer_norm1(hidden_states)
+        hidden_states, attn_weights = self.self_attn(
+            hidden_states=hidden_states,
+            head_mask=attention_mask,
+            output_attentions=output_attentions,
+        )
+        hidden_states = hidden_states + residual
+        residual = hidden_states
+        hidden_states = self.layer_norm2(hidden_states)
+        hidden_states = self.mlp(hidden_states)
+
+        hidden_states = hidden_states + residual
+
+        outputs = (hidden_states,)
+
+        if output_attentions:
+            outputs += (attn_weights,)
+
+        return outputs
+
+
+class CheXagentPreTrainedModel(PreTrainedModel):
+    config_class = CheXagentVisionConfig
+    base_model_prefix = "chexagent"
+    supports_gradient_checkpointing = True
+    _no_split_modules = [
+        "CheXagentQFormerEmbeddings",
+        "CheXagentAttention",
+        "CheXagentQFormerMultiHeadAttention",
+        "CheXagentQFormerSelfOutput",
+    ]
+    _keep_in_fp32_modules = []
+
+    def _init_weights(self, module):
+        """Initialize the weights"""
+        factor = self.config.initializer_range
+        if isinstance(module, nn.Conv2d) or isinstance(module, nn.Embedding) or isinstance(module, nn.Linear):
+            module.weight.data.normal_(mean=0.0, std=factor)
+            if hasattr(module, "bias") and module.bias is not None:
+                module.bias.data.zero_()
+
+        if isinstance(module, CheXagentVisionEmbeddings):
+            if hasattr(self.config, "vision_config"):
+                factor = self.config.vision_config.initializer_range
+            nn.init.trunc_normal_(module.position_embedding, mean=0.0, std=factor)
+            nn.init.trunc_normal_(module.class_embedding, mean=0.0, std=factor)
+
+        elif isinstance(module, nn.LayerNorm):
+            module.bias.data.zero_()
+            module.weight.data.fill_(1.0)
+        elif isinstance(module, nn.Linear) and module.bias is not None:
+            module.bias.data.zero_()
+
+
+class CheXagentEncoder(nn.Module):
+    def __init__(self, config: CheXagentVisionConfig):
+        super().__init__()
+        self.config = config
+        self.layers = nn.ModuleList([CheXagentEncoderLayer(config) for _ in range(config.num_hidden_layers)])
+        self.gradient_checkpointing = False
+
+    def forward(
+            self,
+            inputs_embeds,
+            attention_mask: Optional[torch.Tensor] = None,
+            output_attentions: Optional[bool] = None,
+            output_hidden_states: Optional[bool] = None,
+            return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, BaseModelOutput]:
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        encoder_states = () if output_hidden_states else None
+        all_attentions = () if output_attentions else None
+        hidden_states = inputs_embeds
+        for idx, encoder_layer in enumerate(self.layers):
+            if output_hidden_states:
+                encoder_states = encoder_states + (hidden_states,)
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    encoder_layer.__call__,
+                    hidden_states,
+                    attention_mask,
+                    output_attentions,
+                )
+            else:
+                layer_outputs = encoder_layer(hidden_states, attention_mask, output_attentions=output_attentions, )
+
+            hidden_states = layer_outputs[0]
+
+            if output_attentions:
+                all_attentions = all_attentions + (layer_outputs[1],)
+
+        if output_hidden_states:
+            encoder_states = encoder_states + (hidden_states,)
+
+        if not return_dict:
+            return tuple(v for v in [hidden_states, encoder_states, all_attentions] if v is not None)
+        return BaseModelOutput(
+            last_hidden_state=hidden_states, hidden_states=encoder_states, attentions=all_attentions
+        )
+
+
+class CheXagentVisionModel(CheXagentPreTrainedModel):
+    main_input_name = "pixel_values"
+    config_class = CheXagentVisionConfig
+
+    def __init__(self, config: CheXagentVisionConfig):
+        super().__init__(config)
+        self.config = config
+        embed_dim = config.hidden_size
+
+        self.embeddings = CheXagentVisionEmbeddings(config)
+        self.encoder = CheXagentEncoder(config)
+        self.post_layernorm = nn.LayerNorm(embed_dim, eps=config.layer_norm_eps)
+
+        self.post_init()
+
+    def forward(
+            self,
+            pixel_values: Optional[torch.FloatTensor] = None,
+            output_attentions: Optional[bool] = None,
+            output_hidden_states: Optional[bool] = None,
+            return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, BaseModelOutputWithPooling]:
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        if pixel_values is None:
+            raise ValueError("You have to specify pixel_values")
+        hidden_states = self.embeddings(pixel_values)
+
+        encoder_outputs = self.encoder(
+            inputs_embeds=hidden_states,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        last_hidden_state = encoder_outputs[0]
+        last_hidden_state = self.post_layernorm(last_hidden_state)
+
+        pooled_output = last_hidden_state[:, 0, :]
+        pooled_output = self.post_layernorm(pooled_output)
+
+        if not return_dict:
+            return (last_hidden_state, pooled_output) + encoder_outputs[1:]
+
+        return BaseModelOutputWithPooling(
+            last_hidden_state=last_hidden_state,
+            pooler_output=pooled_output,
+            hidden_states=encoder_outputs.hidden_states,
+            attentions=encoder_outputs.attentions,
+        )
+
+    def get_input_embeddings(self):
+        return self.embeddings
+
+
+
+#from https://huggingface.co/microsoft/Phi-3.5-vision-instruct/blob/main/modeling_phi3_v.py
+class Phi3ImageEmbedding(nn.Module):
+    """Phi3 Image embedding."""
+
+    def __init__(self, config: PretrainedConfig, wte=None, **kwargs) -> None:
+        super().__init__()
+
+        # n_embed or hidden_size
+        hidden_size = config.n_embd if hasattr(config, 'n_embd') else config.hidden_size
+        if hasattr(config, 'embd_pdrop') or hasattr(config, 'embed_pdrop'):
+            embd_drop = config.embd_pdrop if hasattr(config, 'embd_pdrop') else config.embed_pdrop
+            self.drop = nn.Dropout(embd_drop)
+        else:
+            self.drop = None
+
+        self.wte = wte
+
+        if isinstance(config.img_processor, dict) and config.img_processor.get('model_type', None) == 'chexagent_vision_model':
+            assert 'image_dim_out' in config.img_processor, 'image_dim_out must be provided for CLIPVisionModel'
+
+            
+            self.img_processor = CheXagentVisionModel(config=CheXagentVisionConfig(**config.img_processor))
+            image_dim_out = self.img_processor.config.hidden_size
+        else:
+            raise NotImplementedError(f'img_processor = {config.img_processor}, not implemented')
+
+        if isinstance(config.img_processor, dict):
+            self.layer_idx = config.img_processor.get('layer_idx', -2)
+            self.type_feature = config.img_processor.get('type_feature', 'patch')
+        else:
+            self.layer_idx = -2
+            self.type_feature = 'patch'
+            
+        self.image_dim_out = image_dim_out
+        self.img_sizes = None
+
+        projection_cls = kwargs.get('projection_cls', 'linear')
+        if projection_cls == 'linear':
+            self.img_projection = nn.Linear(image_dim_out, hidden_size)
+        elif projection_cls == 'mlp':
+            dim_projection = hidden_size
+            depth = 2
+            scale = 1
+            activation = nn.GELU()
+            layers = [nn.Linear(image_dim_out, dim_projection)]
+            for _ in range(1, depth):
+                layers.extend([activation,
+                                nn.Linear(int(dim_projection*scale), dim_projection)])
+            self.img_projection = nn.Sequential(*layers)
+        else:
+            raise NotImplementedError(f'projection_cls = {projection_cls}, not implemented')
+
+        self.vocab_size = config.vocab_size
+        self.img_features = None
+
+
+    def set_img_features(self, img_features: torch.FloatTensor) -> None:
+        self.img_features = img_features
+
+    def set_img_sizes(self, img_sizes: torch.LongTensor) -> None:
+        self.img_sizes = img_sizes
+
+    def get_img_features(self, img_embeds: torch.FloatTensor) -> torch.FloatTensor:
+        LAYER_IDX = self.layer_idx
+        TYPE_FEATURE = self.type_feature
+
+        img_processor_output = self.img_processor(img_embeds, output_hidden_states=True)
+        img_feature = img_processor_output.hidden_states[LAYER_IDX]
+
+        if TYPE_FEATURE == "patch":
+            patch_feature = img_feature[:, 1:]
+            return patch_feature
+
+        raise NotImplementedError
+
+    def forward(
+        self, input_ids: torch.LongTensor, pixel_values: torch.FloatTensor, image_sizes=None
+    ) -> torch.FloatTensor:
+        input_shape = input_ids.size()
+        input_ids = input_ids.view(-1, input_shape[-1])
+
+        # positions for image tokens
+        positions = torch.nonzero((input_ids < 0) & (input_ids > -MAX_INPUT_ID), as_tuple=True)
+        has_image = len(positions[0].tolist()) > 0
+        input_ids = input_ids.clamp_min(0).clamp_max(self.vocab_size).detach()
+        hidden_states = self.wte(input_ids)
+
+        if has_image:
+            num_images, num_crops, c, h, w = pixel_values.shape
+            assert c == 3 #and h == w == 336
+            img_features = self.get_img_features(pixel_values.flatten(0, 1))
+            image_features_proj = self.hd_feature_transform(img_features, image_sizes)
+            hidden_states = hidden_states.index_put(
+                positions, image_features_proj, accumulate=False
+            )
+
+        if self.drop is not None:
+            hidden_states = self.drop(hidden_states)
+
+        return hidden_states
+
+    def hd_feature_transform(self, image_features, image_sizes):
+        """
+        Remake
+        """
+        if isinstance(self.img_projection, nn.Sequential):
+            target_device = self.img_projection[0].bias.device
+            target_dtype = self.img_projection[0].bias.dtype
+        else:  # It's a single nn.Linear layer
+            target_device = self.img_projection.bias.device
+            target_dtype = self.img_projection.bias.dtype
+            
+        #all_image_embeddings = image_features.flatten(0,1)
+
+        image_features_proj = self.img_projection(
+            image_features.flatten(0,1).to(target_device).to(target_dtype)
+        )
+
+        return image_features_proj
+
+
+
+logger = logging.get_logger(__name__)
+
+
+# Copied from transformers.models.llama.modeling_llama.LlamaRMSNorm with Llama->Phi3
+class Phi3RMSNorm(nn.Module):
+    def __init__(self, hidden_size, eps=1e-6):
+        """
+        Phi3RMSNorm is equivalent to T5LayerNorm
+        """
+        super().__init__()
+        self.weight = nn.Parameter(torch.ones(hidden_size))
+        self.variance_epsilon = eps
+
+    def forward(self, hidden_states):
+        input_dtype = hidden_states.dtype
+        hidden_states = hidden_states.to(torch.float32)
+        variance = hidden_states.pow(2).mean(-1, keepdim=True)
+        hidden_states = hidden_states * torch.rsqrt(variance + self.variance_epsilon)
+        return self.weight * hidden_states.to(input_dtype)
+
+
+# Copied from transformers.models.llama.modeling_llama._get_unpad_data
+def _get_unpad_data(attention_mask):
+    seqlens_in_batch = attention_mask.sum(dim=-1, dtype=torch.int32)
+    indices = torch.nonzero(attention_mask.flatten(), as_tuple=False).flatten()
+    max_seqlen_in_batch = seqlens_in_batch.max().item()
+    cu_seqlens = F.pad(torch.cumsum(seqlens_in_batch, dim=0, dtype=torch.int32), (1, 0))
+    return (
+        indices,
+        cu_seqlens,
+        max_seqlen_in_batch,
+    )
+
+
+# Copied from transformers.models.gemma.modeling_gemma.GemmaRotaryEmbedding with gemma->phi3, Gemma->Phi3
+class Phi3RotaryEmbedding(nn.Module):
+    def __init__(self, dim, max_position_embeddings=2048, base=10000, device=None):
+        super().__init__()
+
+        self.dim = dim
+        self.max_position_embeddings = max_position_embeddings
+        self.base = base
+        self.register_buffer("inv_freq", None, persistent=False)
+
+    @torch.no_grad()
+    def forward(self, x, position_ids, seq_len=None):
+        # x: [bs, num_attention_heads, seq_len, head_size]
+        if self.inv_freq is None:
+            self.inv_freq = 1.0 / (
+                self.base ** (torch.arange(0, self.dim, 2, dtype=torch.int64, device=x.device).float() / self.dim)
+            )
+        inv_freq_expanded = self.inv_freq[None, :, None].float().expand(position_ids.shape[0], -1, 1)
+        position_ids_expanded = position_ids[:, None, :].float()
+        # Force float32 since bfloat16 loses precision on long contexts
+        # See https://github.com/huggingface/transformers/pull/29285
+        device_type = x.device.type
+        device_type = device_type if isinstance(device_type, str) and device_type != "mps" else "cpu"
+        with torch.autocast(device_type=device_type, enabled=False):
+            freqs = (inv_freq_expanded.float() @ position_ids_expanded.float()).transpose(1, 2)
+            emb = torch.cat((freqs, freqs), dim=-1)
+            cos = emb.cos()
+            sin = emb.sin()
+        return cos.to(dtype=x.dtype), sin.to(dtype=x.dtype)
+
+
+class Phi3SuScaledRotaryEmbedding(Phi3RotaryEmbedding):
+    def __init__(self, dim, config, device=None):
+        super().__init__(dim, config.max_position_embeddings, config.rope_theta, device)
+
+        self.short_factor = config.rope_scaling["short_factor"]
+        self.long_factor = config.rope_scaling["long_factor"]
+        self.original_max_position_embeddings = config.original_max_position_embeddings
+
+    @torch.no_grad()
+    def forward(self, x, position_ids, seq_len=None):
+        seq_len = seq_len or torch.max(position_ids) + 1
+        if seq_len > self.original_max_position_embeddings:
+            ext_factors = torch.tensor(self.long_factor, dtype=torch.float32, device=x.device)
+        else:
+            ext_factors = torch.tensor(self.short_factor, dtype=torch.float32, device=x.device)
+
+        inv_freq_shape = torch.arange(0, self.dim, 2, dtype=torch.int64, device=x.device).float() / self.dim
+        self.inv_freq = 1.0 / (ext_factors * self.base**inv_freq_shape)
+
+        inv_freq_expanded = self.inv_freq[None, :, None].float().expand(position_ids.shape[0], -1, 1)
+        position_ids_expanded = position_ids[:, None, :].float()
+
+        # Force float32 since bfloat16 loses precision on long contexts
+        # See https://github.com/huggingface/transformers/pull/29285
+        device_type = x.device.type
+        device_type = device_type if isinstance(device_type, str) and device_type != "mps" else "cpu"
+        with torch.autocast(device_type=device_type, enabled=False):
+            freqs = (inv_freq_expanded.float() @ position_ids_expanded.float()).transpose(1, 2)
+            emb = torch.cat((freqs, freqs), dim=-1)
+
+            scale = self.max_position_embeddings / self.original_max_position_embeddings
+            if scale <= 1.0:
+                scaling_factor = 1.0
+            else:
+                scaling_factor = math.sqrt(1 + math.log(scale) / math.log(self.original_max_position_embeddings))
+
+            cos = emb.cos() * scaling_factor
+            sin = emb.sin() * scaling_factor
+        return cos.to(dtype=x.dtype), sin.to(dtype=x.dtype)
+
+
+class Phi3YarnScaledRotaryEmbedding(Phi3RotaryEmbedding):
+    def __init__(self, dim, config, device=None):
+        super().__init__(dim, config.max_position_embeddings, config.rope_theta, device)
+
+        self.short_factor = config.rope_scaling["short_factor"]
+        self.long_factor = config.rope_scaling["long_factor"]
+        self.original_max_position_embeddings = config.original_max_position_embeddings
+
+    @torch.no_grad()
+    def forward(self, x, position_ids, seq_len=None):
+        seq_len = torch.max(position_ids) + 1
+        if seq_len > self.original_max_position_embeddings:
+            ext_factors = torch.tensor(self.long_factor, dtype=torch.float32, device=x.device)
+        else:
+            ext_factors = torch.tensor(self.short_factor, dtype=torch.float32, device=x.device)
+
+        inv_freq_shape = torch.arange(0, self.dim, 2, dtype=torch.int64, device=x.device).float() / self.dim
+        self.inv_freq = 1.0 / (ext_factors * self.base**inv_freq_shape)
+
+        inv_freq_expanded = self.inv_freq[None, :, None].float().expand(position_ids.shape[0], -1, 1)
+        position_ids_expanded = position_ids[:, None, :].float()
+
+        # Force float32 since bfloat16 loses precision on long contexts
+        # See https://github.com/huggingface/transformers/pull/29285
+        device_type = x.device.type
+        device_type = device_type if isinstance(device_type, str) and device_type != "mps" else "cpu"
+        with torch.autocast(device_type=device_type, enabled=False):
+            freqs = (inv_freq_expanded.float() @ position_ids_expanded.float()).transpose(1, 2)
+            emb = torch.cat((freqs, freqs), dim=-1)
+
+            scale = self.max_position_embeddings / self.original_max_position_embeddings
+            if scale <= 1.0:
+                scaling_factor = 1.0
+            else:
+                scaling_factor = 0.1 * math.log(scale) + 1.0
+
+            cos = emb.cos() * scaling_factor
+            sin = emb.sin() * scaling_factor
+        return cos.to(dtype=x.dtype), sin.to(dtype=x.dtype)
+
+
+# Copied from transformers.models.llama.modeling_llama.rotate_half
+def rotate_half(x):
+    """Rotates half the hidden dims of the input."""
+    x1 = x[..., : x.shape[-1] // 2]
+    x2 = x[..., x.shape[-1] // 2 :]
+    return torch.cat((-x2, x1), dim=-1)
+
+
+# Copied from transformers.models.llama.modeling_llama.apply_rotary_pos_emb
+def apply_rotary_pos_emb(q, k, cos, sin, position_ids=None, unsqueeze_dim=1):
+    """Applies Rotary Position Embedding to the query and key tensors.
+
+    Args:
+        q (`torch.Tensor`): The query tensor.
+        k (`torch.Tensor`): The key tensor.
+        cos (`torch.Tensor`): The cosine part of the rotary embedding.
+        sin (`torch.Tensor`): The sine part of the rotary embedding.
+        position_ids (`torch.Tensor`, *optional*):
+            Deprecated and unused.
+        unsqueeze_dim (`int`, *optional*, defaults to 1):
+            The 'unsqueeze_dim' argument specifies the dimension along which to unsqueeze cos[position_ids] and
+            sin[position_ids] so that they can be properly broadcasted to the dimensions of q and k. For example, note
+            that cos[position_ids] and sin[position_ids] have the shape [batch_size, seq_len, head_dim]. Then, if q and
+            k have the shape [batch_size, heads, seq_len, head_dim], then setting unsqueeze_dim=1 makes
+            cos[position_ids] and sin[position_ids] broadcastable to the shapes of q and k. Similarly, if q and k have
+            the shape [batch_size, seq_len, heads, head_dim], then set unsqueeze_dim=2.
+    Returns:
+        `tuple(torch.Tensor)` comprising of the query and key tensors rotated using the Rotary Position Embedding.
+    """
+    cos = cos.unsqueeze(unsqueeze_dim)
+    sin = sin.unsqueeze(unsqueeze_dim)
+    q_embed = (q * cos) + (rotate_half(q) * sin)
+    k_embed = (k * cos) + (rotate_half(k) * sin)
+    return q_embed, k_embed
+
+
+class Phi3MLP(nn.Module):
+    def __init__(self, config):
+        super().__init__()
+
+        self.config = config
+        self.gate_up_proj = nn.Linear(config.hidden_size, 2 * config.intermediate_size, bias=False)
+        self.down_proj = nn.Linear(config.intermediate_size, config.hidden_size, bias=False)
+
+        self.activation_fn = ACT2FN[config.hidden_act]
+
+    def forward(self, hidden_states: torch.FloatTensor) -> torch.FloatTensor:
+        up_states = self.gate_up_proj(hidden_states)
+
+        gate, up_states = up_states.chunk(2, dim=-1)
+        up_states = up_states * self.activation_fn(gate)
+
+        return self.down_proj(up_states)
+
+
+# Copied from transformers.models.llama.modeling_llama.repeat_kv with llama->phi
+def repeat_kv(hidden_states: torch.Tensor, n_rep: int) -> torch.Tensor:
+    """
+    This is the equivalent of torch.repeat_interleave(x, dim=1, repeats=n_rep). The hidden states go from (batch,
+    num_key_value_heads, seqlen, head_dim) to (batch, num_attention_heads, seqlen, head_dim)
+    """
+    batch, num_key_value_heads, slen, head_dim = hidden_states.shape
+    if n_rep == 1:
+        return hidden_states
+    hidden_states = hidden_states[:, :, None, :, :].expand(batch, num_key_value_heads, n_rep, slen, head_dim)
+    return hidden_states.reshape(batch, num_key_value_heads * n_rep, slen, head_dim)
+
+
+class Phi3Attention(nn.Module):
+    """Multi-headed attention from 'Attention Is All You Need' paper"""
+
+    def __init__(self, config: ChexBonesConfig, layer_idx: Optional[int] = None):
+        super().__init__()
+        self.config = config
+        self.layer_idx = layer_idx
+        if layer_idx is None:
+            logger.warning_once(
+                f"Instantiating {self.__class__.__name__} without passing a `layer_idx` is not recommended and will "
+                "lead to errors during the forward call if caching is used. Please make sure to provide a `layer_idx` "
+                "when creating this class."
+            )
+
+        self.attention_dropout = config.attention_dropout
+        self.hidden_size = config.hidden_size
+        self.num_heads = config.num_attention_heads
+        self.head_dim = self.hidden_size // self.num_heads
+        self.num_key_value_heads = config.num_key_value_heads
+        self.num_key_value_groups = self.num_heads // self.num_key_value_heads
+        self.max_position_embeddings = config.max_position_embeddings
+        self.original_max_position_embeddings = config.original_max_position_embeddings
+        self.rope_theta = config.rope_theta
+        self.rope_scaling = config.rope_scaling
+        self.is_causal = True
+
+        if (self.head_dim * self.num_heads) != self.hidden_size:
+            raise ValueError(
+                f"hidden_size must be divisible by num_heads (got `hidden_size`: {self.hidden_size}"
+                f" and `num_heads`: {self.num_heads})."
+            )
+
+        op_size = self.num_heads * self.head_dim + 2 * (self.num_key_value_heads * self.head_dim)
+        self.o_proj = nn.Linear(self.num_heads * self.head_dim, self.hidden_size, bias=False)
+        self.qkv_proj = nn.Linear(self.hidden_size, op_size, bias=False)
+        self._init_rope()
+
+    def _init_rope(self):
+        if self.rope_scaling is None:
+            self.rotary_emb = Phi3RotaryEmbedding(
+                self.head_dim,
+                max_position_embeddings=self.max_position_embeddings,
+                base=self.rope_theta,
+            )
+        else:
+            scaling_type = self.config.rope_scaling["type"]
+            if scaling_type == "su":
+                self.rotary_emb = Phi3SuScaledRotaryEmbedding(self.head_dim, self.config)
+            elif scaling_type == "yarn":
+                self.rotary_emb = Phi3YarnScaledRotaryEmbedding(self.head_dim, self.config)
+            else:
+                raise ValueError(f"Unknown RoPE scaling type {scaling_type}")
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_value: Optional[Cache] = None,
+        output_attentions: bool = False,
+        use_cache: bool = False,
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        logger.warning_once("You are not running the flash-attention implementation, expect numerical differences.")
+
+        bsz, q_len, _ = hidden_states.size()
+
+        qkv = self.qkv_proj(hidden_states)
+        query_pos = self.num_heads * self.head_dim
+        query_states = qkv[..., :query_pos]
+        key_states = qkv[..., query_pos : query_pos + self.num_key_value_heads * self.head_dim]
+        value_states = qkv[..., query_pos + self.num_key_value_heads * self.head_dim :]
+
+        query_states = query_states.view(bsz, q_len, self.num_heads, self.head_dim).transpose(1, 2)
+        key_states = key_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+        value_states = value_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+
+        kv_seq_len = key_states.shape[-2]
+        if past_key_value is not None:
+            if self.layer_idx is None:
+                raise ValueError(
+                    f"The cache structure has changed since version v4.36. If you are using {self.__class__.__name__} "
+                    "for auto-regressive decoding with k/v caching, please make sure to initialize the attention class "
+                    "with a layer index."
+                )
+            kv_seq_len += past_key_value.get_usable_length(kv_seq_len, self.layer_idx)
+        cos, sin = self.rotary_emb(value_states, position_ids, seq_len=kv_seq_len)
+
+        query_states, key_states = apply_rotary_pos_emb(query_states, key_states, cos, sin, position_ids)
+
+        if past_key_value is not None:
+            cache_kwargs = {"sin": sin, "cos": cos}  # Specific to RoPE models
+            key_states, value_states = past_key_value.update(key_states, value_states, self.layer_idx, cache_kwargs)
+
+        # repeat k/v heads if n_kv_heads < n_heads
+        key_states = repeat_kv(key_states, self.num_key_value_groups)
+        value_states = repeat_kv(value_states, self.num_key_value_groups)
+
+        attn_weights = torch.matmul(query_states, key_states.transpose(2, 3)) / math.sqrt(self.head_dim)
+
+        if attn_weights.size() != (bsz, self.num_heads, q_len, kv_seq_len):
+            raise ValueError(
+                f"Attention weights should be of size {(bsz, self.num_heads, q_len, kv_seq_len)}, but is"
+                f" {attn_weights.size()}"
+            )
+
+        if attention_mask is not None:
+            if attention_mask.size() != (bsz, 1, q_len, kv_seq_len):
+                raise ValueError(
+                    f"Attention mask should be of size {(bsz, 1, q_len, kv_seq_len)}, but is {attention_mask.size()}"
+                )
+            attn_weights = attn_weights + attention_mask
+
+        # upcast attention to fp32
+        attn_weights = nn.functional.softmax(attn_weights, dim=-1, dtype=torch.float32).to(value_states.dtype)
+        attn_weights = nn.functional.dropout(attn_weights, p=self.attention_dropout, training=self.training)
+
+        attn_output = torch.matmul(attn_weights, value_states)
+
+        if attn_output.size() != (bsz, self.num_heads, q_len, self.head_dim):
+            raise ValueError(
+                f"`attn_output` should be of size {(bsz, self.num_heads, q_len, self.head_dim)}, but is"
+                f" {attn_output.size()}"
+            )
+
+        attn_output = attn_output.transpose(1, 2).contiguous()
+        attn_output = attn_output.reshape(bsz, q_len, self.hidden_size)
+
+        attn_output = self.o_proj(attn_output)
+
+        if not output_attentions:
+            attn_weights = None
+
+        return attn_output, attn_weights, past_key_value
+
+
+class Phi3FlashAttention2(Phi3Attention):
+    """
+    Phi-3 flash attention module. This module inherits from `Phi3Attention` as the weights of the module stays
+    untouched. The only required change would be on the forward pass where it needs to correctly call the public API of
+    flash attention and deal with padding tokens in case the input contains any of them.
+    """
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaFlashAttention2.__init__
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+
+        # TODO: Should be removed once Flash Attention for RoCm is bumped to 2.1.
+        # flash_attn<2.1 generates top-left aligned causal mask, while what is needed here is bottom-right alignement, that was made default for flash_attn>=2.1. This attribute is used to handle this difference. Reference: https://github.com/Dao-AILab/flash-attention/releases/tag/v2.1.0.
+        # Beware that with flash_attn<2.1, using q_seqlen != k_seqlen (except for the case q_seqlen == 1) produces a wrong mask (top-left).
+        self._flash_attn_uses_top_left_mask = not is_flash_attn_greater_or_equal_2_10()
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.LongTensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_value: Optional[Cache] = None,
+        output_attentions: bool = False,
+        use_cache: bool = False,
+        **kwargs,
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        # Phi3FlashAttention2 attention does not support output_attentions
+
+        if not _flash_supports_window_size:
+            logger.warning_once(
+                "The current flash attention version does not support sliding window attention. Please use `attn_implementation='eager'` or upgrade flash-attn library."
+            )
+            raise ValueError("The current flash attention version does not support sliding window attention.")
+
+        output_attentions = False
+
+        if "padding_mask" in kwargs:
+            warnings.warn(
+                "Passing `padding_mask` is deprecated and will be removed in v4.37. Please make sure use `attention_mask` instead.`"
+            )
+
+            # overwrite attention_mask with padding_mask
+            attention_mask = kwargs.pop("padding_mask")
+
+        bsz, q_len, _ = hidden_states.size()
+
+        qkv = self.qkv_proj(hidden_states)
+        query_pos = self.num_heads * self.head_dim
+        query_states = qkv[..., :query_pos]
+        key_states = qkv[..., query_pos : query_pos + self.num_key_value_heads * self.head_dim]
+        value_states = qkv[..., query_pos + self.num_key_value_heads * self.head_dim :]
+
+        # Flash attention requires the input to have the shape
+        # batch_size x seq_length x head_dim x hidden_dim
+        # therefore we just need to keep the original shape
+        query_states = query_states.view(bsz, q_len, self.num_heads, self.head_dim).transpose(1, 2)
+        key_states = key_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+        value_states = value_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+
+        kv_seq_len = key_states.shape[-2]
+        if past_key_value is not None:
+            if self.layer_idx is None:
+                raise ValueError(
+                    f"The cache structure has changed since version v4.36. If you are using {self.__class__.__name__} "
+                    "for auto-regressive decoding with k/v caching, please make sure to initialize the attention class "
+                    "with a layer index."
+                )
+            kv_seq_len += past_key_value.get_usable_length(kv_seq_len, self.layer_idx)
+
+        # Because the input can be padded, the absolute sequence length depends on the max position id.
+        rotary_seq_len = max(kv_seq_len, position_ids[:, -1].max().item()) + 1
+        cos, sin = self.rotary_emb(value_states, position_ids, seq_len=rotary_seq_len)
+
+        query_states, key_states = apply_rotary_pos_emb(query_states, key_states, cos, sin, position_ids)
+
+        use_sliding_windows = (
+            _flash_supports_window_size
+            and getattr(self.config, "sliding_window", None) is not None
+            and kv_seq_len > self.config.sliding_window
+        )
+
+        if past_key_value is not None:
+            # Activate slicing cache only if the config has a value `sliding_windows` attribute
+            cache_has_contents = past_key_value.get_seq_length(self.layer_idx) > 0
+            if (
+                getattr(self.config, "sliding_window", None) is not None
+                and kv_seq_len > self.config.sliding_window
+                and cache_has_contents
+            ):
+                slicing_tokens = 1 - self.config.sliding_window
+
+                past_key = past_key_value[self.layer_idx][0]
+                past_value = past_key_value[self.layer_idx][1]
+
+                past_key = past_key[:, :, slicing_tokens:, :].contiguous()
+                past_value = past_value[:, :, slicing_tokens:, :].contiguous()
+
+                if past_key.shape[-2] != self.config.sliding_window - 1:
+                    raise ValueError(
+                        f"past key must have a shape of (`batch_size, num_heads, self.config.sliding_window-1, head_dim`), got"
+                        f" {past_key.shape}"
+                    )
+
+                if attention_mask is not None:
+                    attention_mask = attention_mask[:, slicing_tokens:]
+                    attention_mask = torch.cat([attention_mask, torch.ones_like(attention_mask[:, -1:])], dim=-1)
+
+            cache_kwargs = {"sin": sin, "cos": cos}  # Specific to RoPE models
+            key_states, value_states = past_key_value.update(key_states, value_states, self.layer_idx, cache_kwargs)
+
+        # repeat k/v heads if n_kv_heads < n_heads
+        key_states = repeat_kv(key_states, self.num_key_value_groups)
+        value_states = repeat_kv(value_states, self.num_key_value_groups)
+
+        attn_dropout = self.attention_dropout if self.training else 0.0
+
+        # In PEFT, usually we cast the layer norms in float32 for training stability reasons
+        # therefore the input hidden states gets silently casted in float32. Hence, we need
+        # cast them back in the correct dtype just to be sure everything works as expected.
+        # This might slowdown training & inference so it is recommended to not cast the LayerNorms
+        # in fp32.
+
+        if query_states.dtype == torch.float32:
+            if torch.is_autocast_enabled():
+                target_dtype = torch.get_autocast_gpu_dtype()
+            # Handle the case where the model is quantized
+            elif hasattr(self.config, "_pre_quantization_dtype"):
+                target_dtype = self.config._pre_quantization_dtype
+            else:
+                target_dtype = self.qkv_proj.weight.dtype
+
+            logger.warning_once(
+                f"The input hidden states seems to be silently casted in float32, this might be related to"
+                f" the fact you have upcasted embedding or layer norm layers in float32. We will cast back the input in"
+                f" {target_dtype}."
+            )
+
+            query_states = query_states.to(target_dtype)
+            key_states = key_states.to(target_dtype)
+            value_states = value_states.to(target_dtype)
+
+        # Reashape to the expected shape for Flash Attention
+        query_states = query_states.transpose(1, 2)
+        key_states = key_states.transpose(1, 2)
+        value_states = value_states.transpose(1, 2)
+
+        attn_output = self._flash_attention_forward(
+            query_states,
+            key_states,
+            value_states,
+            attention_mask,
+            q_len,
+            dropout=attn_dropout,
+            use_sliding_windows=use_sliding_windows,
+        )
+
+        attn_output = attn_output.reshape(bsz, q_len, self.hidden_size).contiguous()
+        attn_output = self.o_proj(attn_output)
+
+        if not output_attentions:
+            attn_weights = None
+
+        return attn_output, attn_weights, past_key_value
+
+    # Copied from transformers.models.mistral.modeling_mistral.MistralFlashAttention2._flash_attention_forward
+    def _flash_attention_forward(
+        self,
+        query_states,
+        key_states,
+        value_states,
+        attention_mask,
+        query_length,
+        dropout=0.0,
+        softmax_scale=None,
+        use_sliding_windows=False,
+    ):
+        """
+        Calls the forward method of Flash Attention - if the input hidden states contain at least one padding token
+        first unpad the input, then computes the attention scores and pad the final attention scores.
+
+        Args:
+            query_states (`torch.Tensor`):
+                Input query states to be passed to Flash Attention API
+            key_states (`torch.Tensor`):
+                Input key states to be passed to Flash Attention API
+            value_states (`torch.Tensor`):
+                Input value states to be passed to Flash Attention API
+            attention_mask (`torch.Tensor`):
+                The padding mask - corresponds to a tensor of size `(batch_size, seq_len)` where 0 stands for the
+                position of padding tokens and 1 for the position of non-padding tokens.
+            dropout (`float`):
+                Attention dropout
+            softmax_scale (`float`, *optional*):
+                The scaling of QK^T before applying softmax. Default to 1 / sqrt(head_dim)
+            use_sliding_windows (`bool`, *optional*):
+                Whether to activate sliding window attention.
+        """
+        if not self._flash_attn_uses_top_left_mask:
+            causal = self.is_causal
+        else:
+            # TODO: Remove the `query_length != 1` check once Flash Attention for RoCm is bumped to 2.1. For details, please see the comment in LlamaFlashAttention2 __init__.
+            causal = self.is_causal and query_length != 1
+
+        # Contains at least one padding token in the sequence
+        if attention_mask is not None:
+            batch_size = query_states.shape[0]
+            query_states, key_states, value_states, indices_q, cu_seq_lens, max_seq_lens = self._upad_input(
+                query_states, key_states, value_states, attention_mask, query_length
+            )
+
+            cu_seqlens_q, cu_seqlens_k = cu_seq_lens
+            max_seqlen_in_batch_q, max_seqlen_in_batch_k = max_seq_lens
+
+            if not use_sliding_windows:
+                attn_output_unpad = flash_attn_varlen_func(
+                    query_states,
+                    key_states,
+                    value_states,
+                    cu_seqlens_q=cu_seqlens_q,
+                    cu_seqlens_k=cu_seqlens_k,
+                    max_seqlen_q=max_seqlen_in_batch_q,
+                    max_seqlen_k=max_seqlen_in_batch_k,
+                    dropout_p=dropout,
+                    softmax_scale=softmax_scale,
+                    causal=causal,
+                )
+            else:
+                attn_output_unpad = flash_attn_varlen_func(
+                    query_states,
+                    key_states,
+                    value_states,
+                    cu_seqlens_q=cu_seqlens_q,
+                    cu_seqlens_k=cu_seqlens_k,
+                    max_seqlen_q=max_seqlen_in_batch_q,
+                    max_seqlen_k=max_seqlen_in_batch_k,
+                    dropout_p=dropout,
+                    softmax_scale=softmax_scale,
+                    causal=causal,
+                    window_size=(self.config.sliding_window, self.config.sliding_window),
+                )
+
+            attn_output = pad_input(attn_output_unpad, indices_q, batch_size, query_length)
+        else:
+            if not use_sliding_windows:
+                attn_output = flash_attn_func(
+                    query_states,
+                    key_states,
+                    value_states,
+                    dropout,
+                    softmax_scale=softmax_scale,
+                    causal=causal,
+                )
+            else:
+                attn_output = flash_attn_func(
+                    query_states,
+                    key_states,
+                    value_states,
+                    dropout,
+                    softmax_scale=softmax_scale,
+                    causal=causal,
+                    window_size=(self.config.sliding_window, self.config.sliding_window),
+                )
+
+        return attn_output
+
+    # Copied from transformers.models.mistral.modeling_mistral.MistralFlashAttention2._upad_input
+    def _upad_input(self, query_layer, key_layer, value_layer, attention_mask, query_length):
+        batch_size, kv_seq_len, num_heads, head_dim = key_layer.shape
+
+        # On the first iteration we need to properly re-create the padding mask
+        # by slicing it on the proper place
+        if kv_seq_len != attention_mask.shape[-1]:
+            attention_mask_num_tokens = attention_mask.shape[-1]
+            attention_mask = attention_mask[:, attention_mask_num_tokens - kv_seq_len :]
+
+        indices_k, cu_seqlens_k, max_seqlen_in_batch_k = _get_unpad_data(attention_mask)
+
+        key_layer = index_first_axis(key_layer.reshape(batch_size * kv_seq_len, num_heads, head_dim), indices_k)
+        value_layer = index_first_axis(value_layer.reshape(batch_size * kv_seq_len, num_heads, head_dim), indices_k)
+
+        if query_length == kv_seq_len:
+            query_layer = index_first_axis(
+                query_layer.reshape(batch_size * kv_seq_len, num_heads, head_dim), indices_k
+            )
+            cu_seqlens_q = cu_seqlens_k
+            max_seqlen_in_batch_q = max_seqlen_in_batch_k
+            indices_q = indices_k
+        elif query_length == 1:
+            max_seqlen_in_batch_q = 1
+            cu_seqlens_q = torch.arange(
+                batch_size + 1, dtype=torch.int32, device=query_layer.device
+            )  # There is a memcpy here, that is very bad.
+            indices_q = cu_seqlens_q[:-1]
+            query_layer = query_layer.squeeze(1)
+        else:
+            # The -q_len: slice assumes left padding.
+            attention_mask = attention_mask[:, -query_length:]
+            query_layer, indices_q, cu_seqlens_q, max_seqlen_in_batch_q = unpad_input(query_layer, attention_mask)
+
+        return (
+            query_layer,
+            key_layer,
+            value_layer,
+            indices_q,
+            (cu_seqlens_q, cu_seqlens_k),
+            (max_seqlen_in_batch_q, max_seqlen_in_batch_k),
+        )
+
+
+# copied from transformers.models.llama.modeling_llama.LlamaSdpaAttention with Llama->Phi3
+# TODO @Arthur no longer copied from LLama after static cache
+class Phi3SdpaAttention(Phi3Attention):
+    """
+    Phi3 attention module using torch.nn.functional.scaled_dot_product_attention. This module inherits from
+    `Phi3Attention` as the weights of the module stays untouched. The only changes are on the forward pass to adapt to
+    SDPA API.
+    """
+
+    # Adapted from Phi3Attention.forward
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_value: Optional[Cache] = None,
+        output_attentions: bool = False,
+        use_cache: bool = False,
+    ) -> Tuple[torch.Tensor, Optional[torch.Tensor], Optional[Tuple[torch.Tensor]]]:
+        if output_attentions:
+            # TODO: Improve this warning with e.g. `model.config.attn_implementation = "manual"` once this is implemented.
+            logger.warning_once(
+                "ChexBonesModel is using Phi3SdpaAttention, but `torch.nn.functional.scaled_dot_product_attention` does not support `output_attentions=True`. Falling back to the manual attention implementation, "
+                'but specifying the manual implementation will be required from Transformers version v5.0.0 onwards. This warning can be removed using the argument `attn_implementation="eager"` when loading the model.'
+            )
+            return super().forward(
+                hidden_states=hidden_states,
+                attention_mask=attention_mask,
+                position_ids=position_ids,
+                past_key_value=past_key_value,
+                output_attentions=output_attentions,
+                use_cache=use_cache,
+            )
+
+        bsz, q_len, _ = hidden_states.size()
+
+        qkv = self.qkv_proj(hidden_states)
+        query_pos = self.num_heads * self.head_dim
+        query_states = qkv[..., :query_pos]
+        key_states = qkv[..., query_pos : query_pos + self.num_key_value_heads * self.head_dim]
+        value_states = qkv[..., query_pos + self.num_key_value_heads * self.head_dim :]
+
+        query_states = query_states.view(bsz, q_len, self.num_heads, self.head_dim).transpose(1, 2)
+        key_states = key_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+        value_states = value_states.view(bsz, q_len, self.num_key_value_heads, self.head_dim).transpose(1, 2)
+
+        kv_seq_len = key_states.shape[-2]
+        if past_key_value is not None:
+            kv_seq_len += past_key_value.get_usable_length(kv_seq_len, self.layer_idx)
+        cos, sin = self.rotary_emb(value_states, position_ids, seq_len=kv_seq_len)
+
+        query_states, key_states = apply_rotary_pos_emb(query_states, key_states, cos, sin, position_ids)
+
+        if past_key_value is not None:
+            cache_kwargs = {"sin": sin, "cos": cos}  # Specific to RoPE models
+            key_states, value_states = past_key_value.update(key_states, value_states, self.layer_idx, cache_kwargs)
+
+        key_states = repeat_kv(key_states, self.num_key_value_groups)
+        value_states = repeat_kv(value_states, self.num_key_value_groups)
+
+        if attention_mask is not None:
+            if attention_mask.size() != (bsz, 1, q_len, kv_seq_len):
+                raise ValueError(
+                    f"Attention mask should be of size {(bsz, 1, q_len, kv_seq_len)}, but is {attention_mask.size()}"
+                )
+
+        # SDPA with memory-efficient backend is currently (torch==2.1.2) bugged with non-contiguous inputs with custom attn_mask,
+        # Reference: https://github.com/pytorch/pytorch/issues/112577.
+        if query_states.device.type == "cuda" and attention_mask is not None:
+            query_states = query_states.contiguous()
+            key_states = key_states.contiguous()
+            value_states = value_states.contiguous()
+
+        attn_output = torch.nn.functional.scaled_dot_product_attention(
+            query_states,
+            key_states,
+            value_states,
+            attn_mask=attention_mask,
+            dropout_p=self.attention_dropout if self.training else 0.0,
+            # The q_len > 1 is necessary to match with AttentionMaskConverter.to_causal_4d that does not create a causal mask in case q_len == 1.
+            is_causal=self.is_causal and attention_mask is None and q_len > 1,
+        )
+
+        attn_output = attn_output.transpose(1, 2).contiguous()
+        attn_output = attn_output.view(bsz, q_len, self.hidden_size)
+
+        attn_output = self.o_proj(attn_output)
+
+        return attn_output, None, past_key_value
+
+
+PHI3_ATTENTION_CLASSES = {
+    "eager": Phi3Attention,
+    "flash_attention_2": Phi3FlashAttention2,
+    "sdpa": Phi3SdpaAttention,
+}
+
+
+class Phi3DecoderLayer(nn.Module):
+    def __init__(self, config: ChexBonesConfig, layer_idx: int):
+        super().__init__()
+
+        self.config = config
+        self.self_attn = PHI3_ATTENTION_CLASSES[config._attn_implementation](config, layer_idx=layer_idx)
+
+        self.mlp = Phi3MLP(config)
+        self.input_layernorm = Phi3RMSNorm(config.hidden_size, eps=config.rms_norm_eps)
+
+        self.resid_attn_dropout = nn.Dropout(config.resid_pdrop)
+        self.resid_mlp_dropout = nn.Dropout(config.resid_pdrop)
+        self.post_attention_layernorm = Phi3RMSNorm(config.hidden_size, eps=config.rms_norm_eps)
+
+    def forward(
+        self,
+        hidden_states: torch.Tensor,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_value: Optional[Tuple[torch.Tensor]] = None,
+        output_attentions: Optional[bool] = False,
+        use_cache: Optional[bool] = False,
+        **kwargs,
+    ) -> Tuple[torch.FloatTensor, Optional[Tuple[torch.FloatTensor, torch.FloatTensor]]]:
+        if "padding_mask" in kwargs:
+            warnings.warn(
+                "Passing `padding_mask` is deprecated and will be removed in v4.37. Please make sure use `attention_mask` instead.`"
+            )
+        """
+        Args:
+            hidden_states (`torch.FloatTensor`):
+                input to the layer of shape `(batch, seq_len, embed_dim)`
+            attention_mask (`torch.FloatTensor`, *optional*): attention mask of size
+                `(batch, 1, tgt_len, src_len)` where padding elements are indicated by very large negative values.
+            position_ids (`torch.LongTensor` of shape `({0})`, *optional*):
+                Indices of positions of each input sequence tokens in the position embeddings. Selected in the range
+                `[0, config.n_positions - 1]`. [What are position IDs?](../glossary#position-ids)
+            output_attentions (`bool`, *optional*):
+                Whether or not to return the attentions tensors of all attention layers. See `attentions` under
+                returned tensors for more detail.
+            use_cache (`bool`, *optional*):
+                If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding
+                (see `past_key_values`).
+            past_key_value (`Tuple(torch.FloatTensor)`, *optional*): cached past key and value projection states
+        """
+
+        residual = hidden_states
+
+        hidden_states = self.input_layernorm(hidden_states)
+
+        # Self Attention
+        attn_outputs, self_attn_weights, present_key_value = self.self_attn(
+            hidden_states=hidden_states,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            past_key_value=past_key_value,
+            output_attentions=output_attentions,
+            use_cache=use_cache,
+        )
+
+        hidden_states = residual + self.resid_attn_dropout(attn_outputs)
+
+        residual = hidden_states
+        hidden_states = self.post_attention_layernorm(hidden_states)
+        hidden_states = self.mlp(hidden_states)
+        hidden_states = residual + self.resid_mlp_dropout(hidden_states)
+
+        outputs = (hidden_states,)
+
+        if output_attentions:
+            outputs += (self_attn_weights,)
+
+        if use_cache:
+            outputs += (present_key_value,)
+
+        return outputs
+
+
+CHEXBONES_START_DOCSTRING = r"""
+    
+"""
+
+
+@add_start_docstrings(
+    "Chex Bones Model.",
+    CHEXBONES_START_DOCSTRING,
+)
+class ChexBonesPreTrainedModel(PreTrainedModel):
+    config_class = ChexBonesConfig
+    base_model_prefix = "model"
+    supports_gradient_checkpointing = True
+    _no_split_modules = ["Phi3DecoderLayer"]
+    _skip_keys_device_placement = "past_key_values"
+    _supports_flash_attn_2 = True
+    _supports_sdpa = False
+    _supports_cache_class = True
+
+    _version = "0.0.5"
+
+    def _init_weights(self, module):
+        std = self.config.initializer_range
+        if isinstance(module, nn.Linear):
+            module.weight.data.normal_(mean=0.0, std=std)
+            if module.bias is not None:
+                module.bias.data.zero_()
+        elif isinstance(module, nn.Embedding):
+            module.weight.data.normal_(mean=0.0, std=std)
+            if module.padding_idx is not None:
+                module.weight.data[module.padding_idx].zero_()
+
+
+CHEXBONES_INPUTS_DOCSTRING = r"""
+    Args:
+        input_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`):
+            Indices of input sequence tokens in the vocabulary. Padding will be ignored by default should you provide
+            it.
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            [What are input IDs?](../glossary#input-ids)
+        attention_mask (`torch.Tensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Mask to avoid performing attention on padding token indices. Mask values selected in `[0, 1]`:
+
+            - 1 for tokens that are **not masked**,
+            - 0 for tokens that are **masked**.
+
+            [What are attention masks?](../glossary#attention-mask)
+
+            Indices can be obtained using [`AutoTokenizer`]. See [`PreTrainedTokenizer.encode`] and
+            [`PreTrainedTokenizer.__call__`] for details.
+
+            If `past_key_values` is used, optionally only the last `input_ids` have to be input (see
+            `past_key_values`).
+
+            If you want to change padding behavior, you should read [`modeling_opt._prepare_decoder_attention_mask`]
+            and modify to your needs. See diagram 1 in [the paper](https://arxiv.org/abs/1910.13461) for more
+            information on the default strategy.
+
+            - 1 indicates the head is **not masked**,
+            - 0 indicates the head is **masked**.
+        position_ids (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+            Indices of positions of each input sequence tokens in the position embeddings. Selected in the range `[0,
+            config.n_positions - 1]`.
+
+            [What are position IDs?](../glossary#position-ids)
+        past_key_values (`Cache` or `tuple(tuple(torch.FloatTensor))`, *optional*):
+            Pre-computed hidden-states (key and values in the self-attention blocks and in the cross-attention
+            blocks) that can be used to speed up sequential decoding. This typically consists in the `past_key_values`
+            returned by the model at a previous stage of decoding, when `use_cache=True` or `config.use_cache=True`.
+
+            Two formats are allowed:
+            - a [`~cache_utils.Cache`] instance;
+            - Tuple of `tuple(torch.FloatTensor)` of length `config.n_layers`, with each tuple having 2 tensors of
+            shape `(batch_size, num_heads, sequence_length, embed_size_per_head)`). This is also known as the legacy
+            cache format.
+
+            The model will output the same cache format that is fed as input. If no `past_key_values` are passed, the
+            legacy cache format will be returned.
+
+            If `past_key_values` are used, the user can optionally input only the last `input_ids` (those that don't
+            have their past key value states given to this model) of shape `(batch_size, 1)` instead of all `input_ids`
+            of shape `(batch_size, sequence_length)`.
+        inputs_embeds (`torch.FloatTensor` of shape `(batch_size, sequence_length, hidden_size)`, *optional*):
+            Optionally, instead of passing `input_ids` you can choose to directly pass an embedded representation. This
+            is useful if you want more control over how to convert `input_ids` indices into associated vectors than the
+            model's internal embedding lookup matrix.
+        pixel_values (`torch.FloatTensor` of shape `(batch_size, num_channels, image_size, image_size)):
+            The tensors corresponding to the input images. Pixel values can be obtained using [`AutoImageProcessor`].
+            See [`ChexBonesImageProcessor.__call__`] for details.
+        image_sizes (`torch.LongTensor` of shape `(batch_size, 2)`, *optional*):
+            The sizes of the images in the batch, being (height, width) for each image.
+        use_cache (`bool`, *optional*):
+            If set to `True`, `past_key_values` key value states are returned and can be used to speed up decoding (see
+            `past_key_values`).
+        output_attentions (`bool`, *optional*):
+            Whether or not to return the attentions tensors of all attention layers. See `attentions` under returned
+            tensors for more detail.
+        output_hidden_states (`bool`, *optional*):
+            Whether or not to return the hidden states of all layers. See `hidden_states` under returned tensors for
+            more detail.
+        return_dict (`bool`, *optional*):
+            Whether or not to return a [`~utils.ModelOutput`] instead of a plain tuple.
+"""
+
+
+#copied from transformers.models.phi-3.5-vision-instruct.modeling_phi3_v.Phi3VModel with Phi3->ChexBones
+@add_start_docstrings(
+    "Chex Bones - CheXAgent",
+    CHEXBONES_START_DOCSTRING,
+)
+class ChexBonesModel(ChexBonesPreTrainedModel):
+    """
+    """
+
+    def __init__(self, config: ChexBonesConfig):
+        super().__init__(config)
+        self.padding_idx = config.pad_token_id
+        self.vocab_size = config.vocab_size
+
+        self.embed_tokens = nn.Embedding(config.vocab_size, config.hidden_size, self.padding_idx)
+        self.embed_dropout = nn.Dropout(config.embd_pdrop)
+
+        self.vision_embed_tokens = None
+        if isinstance(config.embd_layer, dict):
+            # vision embedding layer
+            embedding_config = {
+                'embedding_cls': config.embd_layer['embedding_cls'],
+                **config.embd_layer
+            }
+            self.vision_embed_tokens = Phi3ImageEmbedding(config, wte=self.embed_tokens, **embedding_config)
+            # # set wte the same for vision embedding
+            # self.vision_embed_tokens.wte.weight = self.embed_tokens.weight
+
+        self.layers = nn.ModuleList(
+            [Phi3DecoderLayer(config, layer_idx) for layer_idx in range(config.num_hidden_layers)]
+        )
+        self._attn_implementation = config._attn_implementation
+        self.norm = Phi3RMSNorm(config.hidden_size, eps=config.rms_norm_eps)
+
+        self.gradient_checkpointing = False
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    def get_input_embeddings(self):
+        return self.embed_tokens
+
+    def set_input_embeddings(self, value):
+        self.embed_tokens = value
+
+    @add_start_docstrings_to_model_forward(CHEXBONES_INPUTS_DOCSTRING)
+    def forward(
+        self,
+        input_ids: torch.LongTensor = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[List[torch.FloatTensor]] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        pixel_values: Optional[torch.FloatTensor] = None,
+        image_sizes: Optional[torch.LongTensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, BaseModelOutputWithPast]:
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        use_cache = use_cache if use_cache is not None else self.config.use_cache
+
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        # retrieve input_ids and inputs_embeds
+        if input_ids is not None and inputs_embeds is not None:
+            raise ValueError("You cannot specify both input_ids and inputs_embeds at the same time")
+        elif input_ids is not None:
+            batch_size, seq_length = input_ids.shape[:2]
+        elif inputs_embeds is not None:
+            batch_size, seq_length = inputs_embeds.shape[:2]
+        else:
+            raise ValueError("You have to specify either input_ids or inputs_embeds")
+
+        past_key_values_length = 0
+
+        if self.gradient_checkpointing and self.training:
+            if use_cache:
+                logger.warning_once(
+                    "`use_cache=True` is incompatible with gradient checkpointing. Setting `use_cache=False`..."
+                )
+                use_cache = False
+
+        if use_cache:
+            use_legacy_cache = not isinstance(past_key_values, Cache)
+            if use_legacy_cache:
+                past_key_values = DynamicCache.from_legacy_cache(past_key_values)
+            past_key_values_length = past_key_values.get_usable_length(seq_length)
+
+        if position_ids is None:
+            device = input_ids.device if input_ids is not None else inputs_embeds.device
+            position_ids = torch.arange(
+                past_key_values_length, seq_length + past_key_values_length, dtype=torch.long, device=device
+            )
+            position_ids = position_ids.unsqueeze(0).view(-1, seq_length)
+        else:
+            position_ids = position_ids.view(-1, seq_length).long()
+
+        if inputs_embeds is None:
+            if pixel_values is not None and image_sizes is not None:
+                assert self.vision_embed_tokens is not None, "Vision embedding layer is not defined"
+                inputs_embeds = self.vision_embed_tokens(input_ids, pixel_values=pixel_values, image_sizes=image_sizes)
+            else:
+                inputs_embeds = self.embed_tokens(input_ids)
+
+        if attention_mask is not None and self._attn_implementation == "flash_attention_2" and use_cache:
+            is_padding_right = attention_mask[:, -1].sum().item() != batch_size
+            if is_padding_right:
+                raise ValueError(
+                    "You are attempting to perform batched generation with padding_side='right'"
+                    " this may lead to unexpected behaviour for Flash Attention version of ChexBones. Make sure to "
+                    " call `tokenizer.padding_side  = 'left'` before tokenizing the input. "
+                )
+
+        if self._attn_implementation == "flash_attention_2":
+            # 2d mask is passed through the layers
+            attention_mask = attention_mask if (attention_mask is not None and 0 in attention_mask) else None
+        else:
+            # 4d mask is passed through the layers
+            attention_mask = _prepare_4d_causal_attention_mask(
+                attention_mask,
+                (batch_size, seq_length),
+                inputs_embeds,
+                past_key_values_length,
+                sliding_window=self.config.sliding_window,
+            )
+
+        hidden_states = inputs_embeds
+
+        # decoder layers
+        all_hidden_states = () if output_hidden_states else None
+        all_self_attns = () if output_attentions else None
+        next_decoder_cache = None
+
+        for decoder_layer in self.layers:
+            if output_hidden_states:
+                all_hidden_states += (hidden_states,)
+
+            if self.gradient_checkpointing and self.training:
+                layer_outputs = self._gradient_checkpointing_func(
+                    decoder_layer.__call__,
+                    hidden_states,
+                    attention_mask,
+                    position_ids,
+                    past_key_values,
+                    output_attentions,
+                    use_cache,
+                )
+            else:
+                layer_outputs = decoder_layer(
+                    hidden_states,
+                    attention_mask=attention_mask,
+                    position_ids=position_ids,
+                    past_key_value=past_key_values,
+                    output_attentions=output_attentions,
+                    use_cache=use_cache,
+                )
+
+            hidden_states = layer_outputs[0]
+
+            if use_cache:
+                next_decoder_cache = layer_outputs[2 if output_attentions else 1]
+
+            if output_attentions:
+                all_self_attns += (layer_outputs[1],)
+
+        hidden_states = self.norm(hidden_states)
+
+        # add hidden states from the last decoder layer
+        if output_hidden_states:
+            all_hidden_states += (hidden_states,)
+
+        next_cache = None
+        if use_cache:
+            next_cache = next_decoder_cache.to_legacy_cache() if use_legacy_cache else next_decoder_cache
+        if not return_dict:
+            return tuple(v for v in [hidden_states, next_cache, all_hidden_states, all_self_attns] if v is not None)
+        return BaseModelOutputWithPast(
+            last_hidden_state=hidden_states,
+            past_key_values=next_cache,
+            hidden_states=all_hidden_states,
+            attentions=all_self_attns,
+        )
+
+#copied from transformers.models.phi-3.5-vision-instruct.modeling_phi3_v.Phi3VForCausalLM with Phi3->ChexBones
+class ChexBonesForCausalLM(ChexBonesPreTrainedModel):
+    _tied_weights_keys = ["lm_head.weight", 'model.embed_tokens.weight', 'model.vision_embed_tokens.wte.weight']
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.__init__ with Llama->Phi3
+    def __init__(self, config):
+        super().__init__(config)
+        self.model = ChexBonesModel(config)
+        self.vocab_size = config.vocab_size
+        self.lm_head = nn.Linear(config.hidden_size, config.vocab_size, bias=False)
+
+        # Initialize weights and apply final processing
+        self.post_init()
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.get_input_embeddings
+    def get_input_embeddings(self):
+        return self.model.embed_tokens
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.set_input_embeddings
+    def set_input_embeddings(self, value):
+        self.model.embed_tokens = value
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.get_output_embeddings
+    def get_output_embeddings(self):
+        return self.lm_head
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.set_output_embeddings
+    def set_output_embeddings(self, new_embeddings):
+        self.lm_head = new_embeddings
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.set_decoder
+    def set_decoder(self, decoder):
+        self.model = decoder
+
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM.get_decoder
+    def get_decoder(self):
+        return self.model
+
+    # Ignore copy
+    @add_start_docstrings_to_model_forward(CHEXBONES_INPUTS_DOCSTRING)
+    @replace_return_docstrings(output_type=CausalLMOutputWithPast, config_class=_CONFIG_FOR_DOC)
+    def forward(
+        self,
+        input_ids: torch.LongTensor = None,
+        attention_mask: Optional[torch.Tensor] = None,
+        position_ids: Optional[torch.LongTensor] = None,
+        past_key_values: Optional[List[torch.FloatTensor]] = None,
+        inputs_embeds: Optional[torch.FloatTensor] = None,
+        pixel_values: Optional[torch.FloatTensor] = None,
+        image_sizes: Optional[torch.LongTensor] = None,
+        labels: Optional[torch.LongTensor] = None,
+        use_cache: Optional[bool] = None,
+        output_attentions: Optional[bool] = None,
+        output_hidden_states: Optional[bool] = None,
+        return_dict: Optional[bool] = None,
+    ) -> Union[Tuple, CausalLMOutputWithPast]:
+        r"""
+        Args:
+            labels (`torch.LongTensor` of shape `(batch_size, sequence_length)`, *optional*):
+                Labels for computing the masked language modeling loss. Indices should either be in `[0, ...,
+                config.vocab_size]` or -100 (see `input_ids` docstring). Tokens with indices set to `-100` are ignored
+                (masked), the loss is only computed for the tokens with labels in `[0, ..., config.vocab_size]`.
+
+        Returns:
+        ```"""
+
+        output_attentions = output_attentions if output_attentions is not None else self.config.output_attentions
+        output_hidden_states = (
+            output_hidden_states if output_hidden_states is not None else self.config.output_hidden_states
+        )
+        return_dict = return_dict if return_dict is not None else self.config.use_return_dict
+
+        # decoder outputs consists of (dec_features, layer_state, dec_hidden, dec_attn)
+        outputs = self.model(
+            input_ids=input_ids,
+            attention_mask=attention_mask,
+            position_ids=position_ids,
+            past_key_values=past_key_values,
+            inputs_embeds=inputs_embeds,
+            pixel_values=pixel_values,
+            image_sizes=image_sizes,
+            use_cache=use_cache,
+            output_attentions=output_attentions,
+            output_hidden_states=output_hidden_states,
+            return_dict=return_dict,
+        )
+
+        hidden_states = outputs[0]
+        logits = self.lm_head(hidden_states)
+        logits = logits.float()
+
+        loss = None
+        if labels is not None:
+            # Shift so that tokens < n predict n
+            shift_logits = logits[..., :-1, :].contiguous()
+            shift_labels = labels[..., 1:].contiguous()
+            # Flatten the tokens
+            loss_fct = CrossEntropyLoss()
+            shift_logits = shift_logits.view(-1, self.config.vocab_size)
+            shift_labels = shift_labels.view(-1)
+            # Enable model parallelism
+            shift_labels = shift_labels.to(shift_logits.device)
+            loss = loss_fct(shift_logits, shift_labels)
+
+        if not return_dict:
+            output = (logits,) + outputs[1:]
+            return (loss,) + output if loss is not None else output
+
+        return CausalLMOutputWithPast(
+            loss=loss,
+            logits=logits,
+            past_key_values=outputs.past_key_values,
+            hidden_states=outputs.hidden_states,
+            attentions=outputs.attentions,
+        )
+
+    # Copied from transformers.models.persimmon.modeling_persimmon.PersimmonForCausalLM.prepare_inputs_for_generation
+    def prepare_inputs_for_generation(
+        self, input_ids, past_key_values=None, attention_mask=None, inputs_embeds=None, pixel_values=None, image_sizes=None, **kwargs
+    ):
+        # When the first time input length reached long and short factor switching point, enforce re-compute cache
+        # It will cause downside of slower at this single token position, however, better than current failure.
+        if past_key_values and self.config.rope_scaling and input_ids.shape[1] >= self.config.original_max_position_embeddings + 1:
+            past_length = past_key_values.seen_tokens if isinstance(past_key_values, Cache) else past_key_values[0][0].shape[2]
+            if past_length <= self.config.original_max_position_embeddings:
+                past_key_values = None
+
+        if past_key_values is not None:
+            if isinstance(past_key_values, Cache):
+                cache_length = past_key_values.get_seq_length()
+                past_length = past_key_values.seen_tokens
+                max_cache_length = past_key_values.get_max_length()
+            else:
+                cache_length = past_length = past_key_values[0][0].shape[2]
+                max_cache_length = None
+
+            # Keep only the unprocessed tokens:
+            # 1 - If the length of the attention_mask exceeds the length of input_ids, then we are in a setting where
+            # some of the inputs are exclusively passed as part of the cache (e.g. when passing input_embeds as
+            # input)
+            if attention_mask is not None and attention_mask.shape[1] > input_ids.shape[1]:
+                input_ids = input_ids[:, -(attention_mask.shape[1] - past_length) :]
+            # 2 - If the past_length is smaller than input_ids', then input_ids holds all input tokens. We can discard
+            # input_ids based on the past_length.
+            elif past_length < input_ids.shape[1]:
+                input_ids = input_ids[:, past_length:]
+            # 3 - Otherwise (past_length >= input_ids.shape[1]), let's assume input_ids only has unprocessed tokens.
+
+            # If we are about to go beyond the maximum cache length, we need to crop the input attention mask.
+            if (
+                max_cache_length is not None
+                and attention_mask is not None
+                and cache_length + input_ids.shape[1] > max_cache_length
+            ):
+                attention_mask = attention_mask[:, -max_cache_length:]
+
+        position_ids = kwargs.get("position_ids", None)
+        if attention_mask is not None and position_ids is None:
+            # create position_ids on the fly for batch generation
+            position_ids = attention_mask.long().cumsum(-1) - 1
+            position_ids.masked_fill_(attention_mask == 0, 1)
+            if past_key_values:
+                position_ids = position_ids[:, -input_ids.shape[1] :]
+
+        # if `inputs_embeds` are passed, we only want to use them in the 1st generation step
+        if inputs_embeds is not None and past_key_values is None:
+            model_inputs = {"inputs_embeds": inputs_embeds}
+        else:
+            model_inputs = {"input_ids": input_ids}
+
+        model_inputs.update(
+            {
+                "position_ids": position_ids,
+                "past_key_values": past_key_values,
+                "use_cache": kwargs.get("use_cache"),
+                "attention_mask": attention_mask,
+                "pixel_values": pixel_values,
+                "image_sizes": image_sizes,
+            }
+        )
+        return model_inputs
+
+    @staticmethod
+    # Copied from transformers.models.llama.modeling_llama.LlamaForCausalLM._reorder_cache
+    def _reorder_cache(past_key_values, beam_idx):
+        reordered_past = ()
+        for layer_past in past_key_values:
+            reordered_past += (
+                tuple(past_state.index_select(0, beam_idx.to(past_state.device)) for past_state in layer_past),
+            )
+        return reordered_past
+

preprocessor_config.json

@@ -0,0 +1,31 @@
+{
+  "auto_map": {
+    "AutoProcessor": "processing_chexbones.ChexBonesProcessor"
+  },
+  "crop_size": {
+    "height": 448,
+    "width": 448
+  },
+  "do_convert_rgb": true,
+  "do_normalize": true,
+  "do_rescale": true,
+  "do_resize": true,
+  "image_mean": [
+    0.48145466,
+    0.4578275,
+    0.40821073
+  ],
+  "image_processor_type": "BlipImageProcessor",
+  "image_std": [
+    0.26862954,
+    0.26130258,
+    0.27577711
+  ],
+  "processor_class": "ChexBonesProcessor",
+  "resample": 3,
+  "rescale_factor": 0.00392156862745098,
+  "size": {
+    "height": 448,
+    "width": 448
+  }
+}

processing_chexbones.py

@@ -0,0 +1,249 @@
+# coding=utf-8
+# Copyright 2024 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.
+
+import re
+from typing import List, Optional, Union
+
+import torch
+
+from transformers.feature_extraction_utils import BatchFeature
+from transformers.image_utils import ImageInput
+from transformers.processing_utils import ProcessorMixin
+from transformers.tokenization_utils_base import PaddingStrategy, TextInput, TruncationStrategy
+from transformers.utils import TensorType
+
+
+from typing import List, Optional, Union
+
+import numpy as np
+
+from transformers.image_processing_utils import BatchFeature
+from transformers.image_utils import (
+    ImageInput,
+)
+from transformers.utils import TensorType, is_vision_available, logging
+
+
+logger = logging.get_logger(__name__)
+
+
+if is_vision_available():
+    from PIL import Image
+
+import torch
+
+
+
+def pad_to_max_num_crops_tensor(images, max_crops=5):
+    """
+    images: B x 3 x H x W, B<=max_crops
+    """
+    B, _, H, W = images.shape
+    if B < max_crops:
+        pad = torch.zeros(max_crops - B, 3, H, W, dtype=images.dtype, device=images.device)
+        images = torch.cat([images, pad], dim=0)
+    return images
+
+DINO_NUM_TOKENS = 1024
+
+
+#copied from transformers.models.phi-3.5-vision-instruct.processing_phi3.Phi3Processor with Phi3->ChexBones
+class ChexBonesProcessor(ProcessorMixin):
+    r"""
+
+    """
+
+    attributes = [ "tokenizer", "image_processor"]
+    image_processor_class = "BlipImageProcessor"
+    tokenizer_class = ("LlamaTokenizer", "LlamaTokenizerFast")
+    special_image_token = "<|image|>"
+    # valid_kwargs = ['dino_config']    #stay it here
+
+
+    def __init__(self, tokenizer, image_processor):
+        #self.image_processor = AutoImageProcessor.from_pretrained(dino_checkpoint)
+        self.image_processor = image_processor # BitImageProcessor(**dino_config)
+        self.tokenizer = tokenizer
+        self.num_img_tokens = DINO_NUM_TOKENS
+        self.img_tokens = [f"<|image_{i+1}|>" for i in range(1000000)]
+        self.chat_template = None
+
+    def __call__(
+        self,
+        text: Union[TextInput, List[TextInput]],
+        images: ImageInput = None,
+        padding: Union[bool, str, PaddingStrategy] = False,
+        truncation: Union[bool, str, TruncationStrategy] = None,
+        max_length=None,
+        return_tensors: Optional[Union[str, TensorType]] = TensorType.PYTORCH,
+    ) -> BatchFeature:
+        """
+        Main method to prepare for the model one or several sequences(s) and image(s). This method forwards the `text`
+        and `kwargs` arguments to LlamaTokenizerFast's [`~LlamaTokenizerFast.__call__`] if `text` is not `None` to encode
+        the text. To prepare the image(s), this method forwards the `images` and `kwrags` arguments to
+        ChexBonesImageProcessor's if `images` is not `None`. Please refer to the doctsring
+        of the above two methods for more information.
+
+        Args:
+            text (`str`, `List[str]`, `List[List[str]]`):
+                The sequence or batch of sequences to be encoded. Each sequence can be a string or a list of strings
+                (pretokenized string). If the sequences are provided as list of strings (pretokenized), you must set
+                `is_split_into_words=True` (to lift the ambiguity with a batch of sequences).
+            images (`PIL.Image.Image`, `np.ndarray`, `torch.Tensor`, `List[PIL.Image.Image]`, `List[np.ndarray]`, `List[torch.Tensor]`):
+                The image or batch of images to be prepared. Each image can be a PIL image, NumPy array or PyTorch
+                tensor. Both channels-first and channels-last formats are supported.
+            padding (`bool`, `str` or [`~utils.PaddingStrategy`], *optional*, defaults to `False`):
+                Select a strategy to pad the returned sequences (according to the model's padding side and padding
+                index) among:
+                - `True` or `'longest'`: Pad to the longest sequence in the batch (or no padding if only a single
+                  sequence if provided).
+                - `'max_length'`: Pad to a maximum length specified with the argument `max_length` or to the maximum
+                  acceptable input length for the model if that argument is not provided.
+                - `False` or `'do_not_pad'` (default): No padding (i.e., can output a batch with sequences of different
+                  lengths).
+            max_length (`int`, *optional*):
+                Maximum length of the returned list and optionally padding length (see above).
+            truncation (`bool`, *optional*):
+                Activates truncation to cut input sequences longer than `max_length` to `max_length`.
+            return_tensors (`str` or [`~utils.TensorType`], *optional*):
+                If set, will return tensors of a particular framework. Acceptable values are:
+
+                - `'tf'`: Return TensorFlow `tf.constant` objects.
+                - `'pt'`: Return PyTorch `torch.Tensor` objects.
+                - `'np'`: Return NumPy `np.ndarray` objects.
+                - `'jax'`: Return JAX `jnp.ndarray` objects.
+
+        Returns:
+            [`BatchFeature`]: A [`BatchFeature`] with the following fields:
+
+            - **input_ids** -- List of token ids to be fed to a model. Returned when `text` is not `None`.
+            - **attention_mask** -- List of indices specifying which tokens should be attended to by the model (when
+              `return_attention_mask=True` or if *"attention_mask"* is in `self.model_input_names` and if `text` is not
+              `None`).
+            - **pixel_values** -- Pixel values to be fed to a model. Returned when `images` is not `None`.
+        """
+        if images is not None:
+            image_inputs = self.image_processor(images, return_tensors=return_tensors)
+            batch_size = image_inputs['pixel_values'].shape[0]
+            image_inputs = {"pixel_values": image_inputs['pixel_values'][:,None,...], 
+                "image_sizes": torch.Tensor([448,448])[None,...].repeat(batch_size,1),
+                "num_img_tokens": torch.Tensor([DINO_NUM_TOKENS]).to( dtype=torch.uint16)[None,...].repeat(batch_size,1)
+                }
+        else:
+            image_inputs = {}
+        inputs = self._convert_images_texts_to_inputs(image_inputs, text, padding=padding, truncation=truncation, max_length=max_length, return_tensors=return_tensors)
+        return inputs
+
+    def calc_num_image_tokens(self, images: ImageInput):
+        """ Calculate the number of image tokens for each image.
+        Args:
+            images (`ImageInput`):
+                Image to preprocess. Expects a single or batch of images with pixel values ranging from 0 to 255. If
+                passing in images with pixel values between 0 and 1, set `do_rescale=False`.
+        """
+        return DINO_NUM_TOKENS
+        #return self.image_processor.calc_num_image_tokens(images)
+        
+    def calc_num_image_tokens_from_image_size(self, width, height):
+        """ Calculate the number of image token for an image with given width and height.
+        Args:
+            width (`int`):
+                Width of the image.
+            height (`int`):
+                Height of the image.
+        """
+        return DINO_NUM_TOKENS
+        #return self.image_processor.calc_num_image_tokens_from_image_size(width, height)
+    
+    
+    @property 
+    def special_image_token_id(self):
+        return self.tokenizer.convert_tokens_to_ids(self.special_image_token)
+
+    def get_special_image_token_id(self):
+        return self.tokenizer.convert_tokens_to_ids(self.special_image_token)
+    
+    def _convert_images_texts_to_inputs(self, images, texts, padding=False, truncation=None, max_length=None, return_tensors=None):
+
+        if not len(images):
+            model_inputs = self.tokenizer(texts, return_tensors=return_tensors, padding=padding, truncation=truncation, max_length=max_length)
+            return BatchFeature(data={**model_inputs})
+
+        pattern = r"<\|image_\d+\|>"
+        prompt_chunks = [self.tokenizer(chunk).input_ids for chunk in re.split(pattern, texts)] 
+
+        if 'num_img_tokens' in images:
+            num_img_tokens = images['num_img_tokens']
+        else:
+            assert 'num_crops' in images, 'num_crops must be provided in images if num_img_tokens is not provided'
+            num_crops = images['num_crops']
+            num_img_tokens = [_num_crops * self.num_img_tokens for _num_crops in num_crops] 
+
+        images, image_sizes = images['pixel_values'], images['image_sizes']
+
+        # image_tags needs to start from 1 to n
+        image_tags = re.findall(pattern, texts) 
+        # image_ids = [int(s.split("|")[1].split("_")[-1]) * -1 for s in image_tags]
+        # image_ids_pad = [[iid]*num_img_tokens[i] for i, iid in enumerate(image_ids)]
+        image_ids = [int(s.split("|")[1].split("_")[-1]) for s in image_tags]
+        unique_image_ids = sorted(list(set(image_ids)))
+        # image_ids must start from 1, and must be continuous int, e.g. [1, 2, 3], cannot be [1, 4, 5]
+        # check the condition
+        assert unique_image_ids == list(range(1, len(unique_image_ids)+1)), f"image_ids must start from 1, and must be continuous int, e.g. [1, 2, 3], cannot be {unique_image_ids}"
+        # total images must be the same as the number of image tags
+        assert len(unique_image_ids) == len(images), f"total images must be the same as the number of image tags, got {len(unique_image_ids)} image tags and {len(images)} images"
+
+        image_ids_pad = [[-iid]*num_img_tokens[iid-1] for iid in image_ids]
+
+        def insert_separator(X, sep_list):
+            if len(X) > len(sep_list):
+                sep_list.append([])
+            return [ele for sublist in zip(X, sep_list) for ele in sublist]
+        input_ids = []
+        offset = 0                
+        for x in insert_separator(prompt_chunks, image_ids_pad):
+            input_ids.extend(x[offset:])
+
+        input_ids = torch.tensor(input_ids, dtype=torch.long).unsqueeze(0)
+        attention_mask = (input_ids > -1000000).to(torch.long)
+
+        return BatchFeature(data={"input_ids": input_ids,
+                                  "attention_mask": attention_mask,
+                                  "pixel_values": images, 
+                                  "image_sizes": image_sizes})
+
+
+    # Copied from transformers.models.clip.processing_clip.CLIPProcessor.batch_decode with CLIP->Llama
+    def batch_decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to LlamaTokenizerFast's [`~PreTrainedTokenizer.batch_decode`]. Please
+        refer to the docstring of this method for more information.
+        """
+        return self.tokenizer.batch_decode(*args, **kwargs)
+
+    # Copied from transformers.models.clip.processing_clip.CLIPProcessor.decode with CLIP->Llama
+    def decode(self, *args, **kwargs):
+        """
+        This method forwards all its arguments to LlamaTokenizerFast's [`~PreTrainedTokenizer.decode`]. Please refer to
+        the docstring of this method for more information.
+        """
+        return self.tokenizer.decode(*args, **kwargs)
+
+    @property
+    # Copied from transformers.models.clip.processing_clip.CLIPProcessor.model_input_names
+    def model_input_names(self):
+        tokenizer_input_names = self.tokenizer.model_input_names
+        image_processor_input_names = self.image_processor.model_input_names
+        return list(dict.fromkeys(tokenizer_input_names + image_processor_input_names))

processor_config.json

@@ -0,0 +1,6 @@
+{
+  "auto_map": {
+    "AutoProcessor": "processing_chexbones.ChexBonesProcessor"
+  },
+  "processor_class": "ChexBonesProcessor"
+}

special_tokens_map.json

@@ -0,0 +1,30 @@
+{
+  "additional_special_tokens": [
+    "<|system|>",
+    "<|end|>",
+    "<|user|>",
+    "<|end|>"
+  ],
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "content": "<|endoftext|>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": "<unk>",
+  "unk_token": {
+    "content": "<unk>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

@@ -0,0 +1,414 @@
+{
+  "add_bos_token": true,
+  "add_eos_token": false,
+  "add_prefix_space": null,
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "<s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": false
+    },
+    "32000": {
+      "content": "<|endoftext|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "32001": {
+      "content": "<|assistant|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32002": {
+      "content": "<|placeholder1|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32003": {
+      "content": "<|placeholder2|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "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": false,
+      "single_word": false,
+      "special": true
+    },
+    "32007": {
+      "content": "<|end|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "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": false,
+      "single_word": false,
+      "special": true
+    },
+    "32011": {
+      "content": "<|placeholder7|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32012": {
+      "content": "<|placeholder8|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32013": {
+      "content": "<|placeholder9|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32014": {
+      "content": "<|placeholder10|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32015": {
+      "content": "<|placeholder11|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32016": {
+      "content": "<|placeholder12|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32017": {
+      "content": "<|placeholder13|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32018": {
+      "content": "<|placeholder14|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32019": {
+      "content": "<|placeholder15|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32020": {
+      "content": "<|placeholder16|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32021": {
+      "content": "<|placeholder17|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
+      "single_word": false,
+      "special": true
+    },
+    "32022": {
+      "content": "<|placeholder18|>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": true,
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+  },
+  "additional_special_tokens": [
+    "<|system|>",
+    "<|end|>",
+    "<|user|>",
+    "<|end|>"
+  ],
+  "auto_map": {
+    "AutoProcessor": "processing_phi3_dino.Phi3DinoProcessor"
+  },
+  "bos_token": "<s>",
+  "chat_template": "{% for message in messages %}{{'<|' + message['role'] + '|>' + '\n' + message['content'] + '<|end|>\n' }}{% endfor %}{% if add_generation_prompt and messages[-1]['role'] != 'assistant' %}{{- '<|assistant|>\n' -}}{% endif %}",
+  "clean_up_tokenization_spaces": false,
+  "eos_token": "<|endoftext|>",
+  "legacy": false,
+  "model_max_length": 131072,
+  "num_crops": 16,
+  "pad_token": "<unk>",
+  "padding_side": "right",
+  "processor_class": "Phi3DinoProcessor",
+  "sp_model_kwargs": {},
+  "tokenizer_class": "LlamaTokenizer",
+  "unk_token": "<unk>",
+  "use_default_system_prompt": false
+}