Upload folder using huggingface_hub

.gitattributes

@@ -1,35 +1,3 @@
-*.7z filter=lfs diff=lfs merge=lfs -text
-*.arrow filter=lfs diff=lfs merge=lfs -text
 *.bin filter=lfs diff=lfs merge=lfs -text
-*.bz2 filter=lfs diff=lfs merge=lfs -text
-*.ckpt filter=lfs diff=lfs merge=lfs -text
-*.ftz filter=lfs diff=lfs merge=lfs -text
-*.gz filter=lfs diff=lfs merge=lfs -text
-*.h5 filter=lfs diff=lfs merge=lfs -text
-*.joblib filter=lfs diff=lfs merge=lfs -text
-*.lfs.* filter=lfs diff=lfs merge=lfs -text
-*.mlmodel filter=lfs diff=lfs merge=lfs -text
-*.model filter=lfs diff=lfs merge=lfs -text
-*.msgpack filter=lfs diff=lfs merge=lfs -text
-*.npy filter=lfs diff=lfs merge=lfs -text
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-*.pickle filter=lfs diff=lfs merge=lfs -text
-*.pkl filter=lfs diff=lfs merge=lfs -text
-*.pt filter=lfs diff=lfs merge=lfs -text
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-*.rar filter=lfs diff=lfs merge=lfs -text
 *.safetensors filter=lfs diff=lfs merge=lfs -text
-saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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-*.tar filter=lfs diff=lfs merge=lfs -text
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-*tfevents* filter=lfs diff=lfs merge=lfs -text
+tokenizer.json filter=lfs diff=lfs merge=lfs -text

.gitignore

@@ -0,0 +1,25 @@
+# Publish only model artifacts and release documentation at the repository root.
+# Training state, conversion utilities, caches, and subdirectories stay local.
+*
+!/.gitignore
+!/.gitattributes
+!/README.md
+!/LICENSE
+!/NOTICE
+!/pytorch_model.bin
+!/pytorch_model-*.bin
+!/pytorch_model.bin.index.json
+!/model*.safetensors
+!/model.safetensors.index.json
+!/config.json
+!/generation_config.json
+!/preprocessor_config.json
+!/video_preprocessor_config.json
+!/added_tokens.json
+!/special_tokens_map.json
+!/tokenizer.json
+!/tokenizer_config.json
+!/chat_template.jinja
+!/chat_template.json
+!/merges.txt
+!/vocab.json

LICENSE

@@ -0,0 +1,201 @@
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+   limitations under the License.

NOTICE

@@ -0,0 +1,22 @@
+ARIVE model checkpoint
+
+This checkpoint is derived from Qwen3-VL-4B-Instruct, developed by the Qwen team
+and released under the Apache License, Version 2.0.
+
+Upstream model:
+  https://huggingface.co/Qwen/Qwen3-VL-4B-Instruct
+Upstream project:
+  https://github.com/QwenLM/Qwen3-VL
+
+ARIVE modifies the base model by adding a local vision branch and applying
+supervised fine-tuning and GRPO for grounded chest X-ray report generation.
+The modified checkpoint in pytorch_model.bin includes the trained decoder
+and both global and local vision branches. The accompanying configuration,
+tokenizer/processor files, and chat template support the ARIVE inference flow,
+including image observations in assistant messages.
+
+This model distribution is licensed under the Apache License, Version 2.0;
+see LICENSE. Original upstream rights and attribution are retained.
+
+MIMIC-CXR and other restricted source datasets are not distributed with this
+checkpoint. Those datasets retain their own licenses and data use agreements.

README.md

@@ -0,0 +1,72 @@
+---
+license: apache-2.0
+base_model: Qwen/Qwen3-VL-4B-Instruct
+pipeline_tag: image-text-to-text
+tags:
+  - arive
+  - medical
+  - chest-x-ray
+  - report-generation
+---
+
+# ARIVE
+
+ARIVE adapts [Qwen3-VL-4B-Instruct](https://huggingface.co/Qwen/Qwen3-VL-4B-Instruct)
+for grounded chest X-ray report generation. The model identifies anatomical
+regions, produces bounding boxes, and uses a local vision branch to inspect
+image crops before continuing generation.
+
+This repository contains the final trained checkpoint in BF16: the decoder,
+global vision branch, and local vision branch. It was fine-tuned using SFT and
+GRPO on MIMIC-CXR-derived data. Training and inference prompts use `Indication`;
+additional clinical fields are used during data construction.
+
+## Inference
+
+Inference requires the accompanying ARIVE code repository and its dependencies.
+The local vision branch and iterative crop observations require the project's
+custom inference entry point.
+
+Download this model repository to a local directory named `ARIVE` and obtain
+the Qwen3-VL-4B-Instruct base model separately. From the ARIVE code repository
+root, configure the model paths and export the decoder weights for vLLM:
+
+```bash
+export QWENVL_INFER_BASE_MODEL=/path/to/Qwen3-VL-4B-Instruct
+export QWENVL_INFER_VISION_CHECKPOINT=/path/to/ARIVE
+export QWENVL_INFER_VLLM_CHECKPOINT=/path/to/ARIVE-vllm
+
+python tools/export_vllm_checkpoint.py \
+  --src "$QWENVL_INFER_VISION_CHECKPOINT" \
+  --dst "$QWENVL_INFER_VLLM_CHECKPOINT"
+```
+
+The exporter first creates an `ARIVE-safe` intermediate directory that retains
+both vision branches, then creates `ARIVE-vllm` for decoding. Both output
+directories must be absent or empty. Keep the tokenizer, processor, and
+`chat_template.jinja` files with the checkpoint; the exporter copies them.
+
+Configure the evaluation reports, reference reports, clinical context, and
+image paths as described in the code repository's README, then run:
+
+```bash
+CUDA_VISIBLE_DEVICES=0 python inference/infer_mcot.py
+```
+
+## Intended use and limitations
+
+ARIVE is intended for research on chest X-ray report generation and visual
+grounding. It is not intended for clinical diagnosis or patient care. Generated
+findings and bounding boxes may be inaccurate and require independent review.
+
+## License and data
+
+The model checkpoint is released under [Apache-2.0](LICENSE). See [NOTICE](NOTICE)
+for the base model attribution and a description of the modifications.
+
+MIMIC-CXR images, reports, and patient-level training annotations are not
+included. Access to and use of the source data remain subject to the applicable
+[PhysioNet license and data use agreement](https://physionet.org/content/mimic-cxr/).
+The model license does not grant access to or permission to redistribute those
+datasets. The intended-use statement above describes the model's intended
+application and does not add restrictions to Apache-2.0.

added_tokens.json

@@ -0,0 +1,28 @@
+{
+  "</think>": 151668,
+  "</tool_call>": 151658,
+  "</tool_response>": 151666,
+  "<think>": 151667,
+  "<tool_call>": 151657,
+  "<tool_response>": 151665,
+  "<|box_end|>": 151649,
+  "<|box_start|>": 151648,
+  "<|endoftext|>": 151643,
+  "<|file_sep|>": 151664,
+  "<|fim_middle|>": 151660,
+  "<|fim_pad|>": 151662,
+  "<|fim_prefix|>": 151659,
+  "<|fim_suffix|>": 151661,
+  "<|im_end|>": 151645,
+  "<|im_start|>": 151644,
+  "<|image_pad|>": 151655,
+  "<|object_ref_end|>": 151647,
+  "<|object_ref_start|>": 151646,
+  "<|quad_end|>": 151651,
+  "<|quad_start|>": 151650,
+  "<|repo_name|>": 151663,
+  "<|video_pad|>": 151656,
+  "<|vision_end|>": 151653,
+  "<|vision_pad|>": 151654,
+  "<|vision_start|>": 151652
+}

chat_template.jinja

@@ -0,0 +1,135 @@
+{%- if tools %}
+    {{- '<|im_start|>system\n' }}
+    {%- if messages[0].role == 'system' %}
+        {%- if messages[0].content is string %}
+            {{- messages[0].content }}
+        {%- else %}
+            {%- for content in messages[0].content %}
+                {%- if 'text' in content %}
+                    {{- content.text }}
+                {%- endif %}
+            {%- endfor %}
+        {%- endif %}
+        {{- '\n\n' }}
+    {%- endif %}
+    {{- "# Tools\n\nYou may call one or more functions to assist with the user query.\n\nYou are provided with function signatures within <tools></tools> XML tags:\n<tools>" }}
+    {%- for tool in tools %}
+        {{- "\n" }}
+        {{- tool | tojson }}
+    {%- endfor %}
+    {{- "\n</tools>\n\nFor each function call, return a json object with function name and arguments within <tool_call></tool_call> XML tags:\n<tool_call>\n{\"name\": <function-name>, \"arguments\": <args-json-object>}\n</tool_call><|im_end|>\n" }}
+{%- else %}
+    {%- if messages[0].role == 'system' %}
+        {{- '<|im_start|>system\n' }}
+        {%- if messages[0].content is string %}
+            {{- messages[0].content }}
+        {%- else %}
+            {%- for content in messages[0].content %}
+                {%- if 'text' in content %}
+                    {{- content.text }}
+                {%- endif %}
+            {%- endfor %}
+        {%- endif %}
+        {{- '<|im_end|>\n' }}
+    {%- endif %}
+{%- endif %}
+
+{%- set image_count = namespace(value=0) %}
+{%- set video_count = namespace(value=0) %}
+
+{%- for message in messages %}
+    {%- if message.role == "user" %}
+        {{- '<|im_start|>' + message.role + '\n' }}
+        {%- if message.content is string %}
+            {{- message.content }}
+        {%- else %}
+            {%- for content in message.content %}
+                {%- if content.type == 'image' or 'image' in content or 'image_url' in content %}
+                    {%- set image_count.value = image_count.value + 1 %}
+                    {%- if add_vision_id %}Picture {{ image_count.value }}: {% endif -%}
+                    <|vision_start|><|image_pad|><|vision_end|>
+                {%- elif content.type == 'video' or 'video' in content %}
+                    {%- set video_count.value = video_count.value + 1 %}
+                    {%- if add_vision_id %}Video {{ video_count.value }}: {% endif -%}
+                    <|vision_start|><|video_pad|><|vision_end|>
+                {%- elif 'text' in content %}
+                    {{- content.text }}
+                {%- endif %}
+            {%- endfor %}
+        {%- endif %}
+        {{- '<|im_end|>\n' }}
+
+    {%- elif message.role == "assistant" %}
+        {{- '<|im_start|>' + message.role + '\n' }}
+        {%- if message.content is string %}
+            {{- message.content }}
+        {%- else %}
+            {%- for content_item in message.content %}
+                {%- if content_item.type == 'image' or 'image' in content_item or 'image_url' in content_item %}
+                    {%- set image_count.value = image_count.value + 1 %}
+                    {%- if add_vision_id %}Picture {{ image_count.value }}: {% endif -%}
+                    <|vision_start|><|image_pad|><|vision_end|>
+                {%- elif content_item.type == 'video' or 'video' in content_item %}
+                    {%- set video_count.value = video_count.value + 1 %}
+                    {%- if add_vision_id %}Video {{ video_count.value }}: {% endif -%}
+                    <|vision_start|><|video_pad|><|vision_end|>
+                {%- elif 'text' in content_item %}
+                    {{- content_item.text }}
+                {%- endif %}
+            {%- endfor %}
+        {%- endif %}
+
+        {%- if message.tool_calls %}
+            {%- for tool_call in message.tool_calls %}
+                {%- if (loop.first and message.content) or (not loop.first) %}
+                    {{- '\n' }}
+                {%- endif %}
+                {%- if tool_call.function %}
+                    {%- set tool_call = tool_call.function %}
+                {%- endif %}
+                {{- '<tool_call>\n{"name": "' }}
+                {{- tool_call.name }}
+                {{- '", "arguments": ' }}
+                {%- if tool_call.arguments is string %}
+                    {{- tool_call.arguments }}
+                {%- else %}
+                    {{- tool_call.arguments | tojson }}
+                {%- endif %}
+                {{- '}\n</tool_call>' }}
+            {%- endfor %}
+        {%- endif %}
+
+        {{- '<|im_end|>\n' }}
+
+    {%- elif message.role == "tool" %}
+        {%- if loop.first or (messages[loop.index0 - 1].role != "tool") %}
+            {{- '<|im_start|>user' }}
+        {%- endif %}
+        {{- '\n<tool_response>\n' }}
+        {%- if message.content is string %}
+            {{- message.content }}
+        {%- else %}
+            {%- for content in message.content %}
+                {%- if content.type == 'image' or 'image' in content or 'image_url' in content %}
+                    {%- set image_count.value = image_count.value + 1 %}
+                    {%- if add_vision_id %}Picture {{ image_count.value }}: {% endif -%}
+                    <|vision_start|><|image_pad|><|vision_end|>
+                {%- elif content.type == 'video' or 'video' in content %}
+                    {%- set video_count.value = video_count.value + 1 %}
+                    {%- if add_vision_id %}Video {{ video_count.value }}: {% endif -%}
+                    <|vision_start|><|video_pad|><|vision_end|>
+                {%- elif 'text' in content %}
+                    {{- content.text }}
+                {%- endif %}
+            {%- endfor %}
+        {%- endif %}
+        {{- '\n</tool_response>' }}
+        {%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
+            {{- '<|im_end|>\n' }}
+        {%- endif %}
+    {%- endif %}
+{%- endfor %}
+
+{%- if add_generation_prompt %}
+    {{- '<|im_start|>assistant\n' }}
+{%- endif %}

config.json

@@ -0,0 +1,67 @@
+{
+  "architectures": [
+    "Qwen3VLForConditionalGeneration"
+  ],
+  "dtype": "bfloat16",
+  "image_token_id": 151655,
+  "model_type": "qwen3_vl",
+  "text_config": {
+    "attention_bias": false,
+    "attention_dropout": 0.0,
+    "bos_token_id": 151643,
+    "dtype": "bfloat16",
+    "eos_token_id": 151645,
+    "head_dim": 128,
+    "hidden_act": "silu",
+    "hidden_size": 2560,
+    "initializer_range": 0.02,
+    "intermediate_size": 9728,
+    "max_position_embeddings": 262144,
+    "model_type": "qwen3_vl_text",
+    "num_attention_heads": 32,
+    "num_hidden_layers": 36,
+    "num_key_value_heads": 8,
+    "rms_norm_eps": 1e-06,
+    "rope_scaling": {
+      "mrope_interleaved": true,
+      "mrope_section": [
+        24,
+        20,
+        20
+      ],
+      "rope_type": "default"
+    },
+    "rope_theta": 5000000,
+    "tie_word_embeddings": true,
+    "use_cache": true,
+    "vocab_size": 151936
+  },
+  "tie_word_embeddings": true,
+  "transformers_version": "4.57.3",
+  "use_cache": true,
+  "use_local_vision_branch": true,
+  "video_token_id": 151656,
+  "vision_config": {
+    "deepstack_visual_indexes": [
+      5,
+      11,
+      17
+    ],
+    "depth": 24,
+    "dtype": "bfloat16",
+    "hidden_act": "gelu_pytorch_tanh",
+    "hidden_size": 1024,
+    "in_channels": 3,
+    "initializer_range": 0.02,
+    "intermediate_size": 4096,
+    "model_type": "qwen3_vl",
+    "num_heads": 16,
+    "num_position_embeddings": 2304,
+    "out_hidden_size": 2560,
+    "patch_size": 16,
+    "spatial_merge_size": 2,
+    "temporal_patch_size": 2
+  },
+  "vision_end_token_id": 151653,
+  "vision_start_token_id": 151652
+}

generation_config.json

@@ -0,0 +1,13 @@
+{
+  "bos_token_id": 151643,
+  "do_sample": true,
+  "eos_token_id": [
+    151645,
+    151643
+  ],
+  "pad_token_id": 151643,
+  "temperature": 0.7,
+  "top_k": 20,
+  "top_p": 0.8,
+  "transformers_version": "4.57.3"
+}

preprocessor_config.json

@@ -0,0 +1,39 @@
+{
+  "crop_size": null,
+  "data_format": "channels_first",
+  "default_to_square": true,
+  "device": null,
+  "disable_grouping": null,
+  "do_center_crop": null,
+  "do_convert_rgb": true,
+  "do_normalize": true,
+  "do_pad": null,
+  "do_rescale": true,
+  "do_resize": true,
+  "image_mean": [
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+    0.5,
+    0.5
+  ],
+  "image_processor_type": "Qwen2VLImageProcessorFast",
+  "image_std": [
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+    0.5,
+    0.5
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+  "input_data_format": null,
+  "max_pixels": 50176,
+  "merge_size": 2,
+  "min_pixels": 784,
+  "pad_size": null,
+  "patch_size": 16,
+  "processor_class": "Qwen3VLProcessor",
+  "resample": 3,
+  "rescale_factor": 0.00392156862745098,
+  "return_tensors": null,
+  "size": {
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+    "shortest_edge": 784
+  },
+  "temporal_patch_size": 2
+}

special_tokens_map.json

@@ -0,0 +1,31 @@
+{
+  "additional_special_tokens": [
+    "<|im_start|>",
+    "<|im_end|>",
+    "<|object_ref_start|>",
+    "<|object_ref_end|>",
+    "<|box_start|>",
+    "<|box_end|>",
+    "<|quad_start|>",
+    "<|quad_end|>",
+    "<|vision_start|>",
+    "<|vision_end|>",
+    "<|vision_pad|>",
+    "<|image_pad|>",
+    "<|video_pad|>"
+  ],
+  "eos_token": {
+    "content": "<|im_end|>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "<|endoftext|>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer.json

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:aeb13307a71acd8fe81861d94ad54ab689df773318809eed3cbe794b4492dae4
+size 11422654

tokenizer_config.json

@@ -0,0 +1,241 @@
+{
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+  "add_prefix_space": false,
+  "added_tokens_decoder": {
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+      "single_word": false,
+      "special": true
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+      "content": "<|im_start|>",
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+      "special": true
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+      "content": "<|im_end|>",
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+      "special": true
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+    "151646": {
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+      "single_word": false,
+      "special": true
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+    "151647": {
+      "content": "<|object_ref_end|>",
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+      "single_word": false,
+      "special": true
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+      "special": true
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+      "special": true
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+      "special": true
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+    "<|im_end|>",
+    "<|object_ref_start|>",
+    "<|object_ref_end|>",
+    "<|box_start|>",
+    "<|box_end|>",
+    "<|quad_start|>",
+    "<|quad_end|>",
+    "<|vision_start|>",
+    "<|vision_end|>",
+    "<|vision_pad|>",
+    "<|image_pad|>",
+    "<|video_pad|>"
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+  "clean_up_tokenization_spaces": false,
+  "eos_token": "<|im_end|>",
+  "errors": "replace",
+  "extra_special_tokens": {},
+  "fix_mistral_regex": true,
+  "model_max_length": 262144,
+  "pad_token": "<|endoftext|>",
+  "processor_class": "Qwen3VLProcessor",
+  "split_special_tokens": false,
+  "tokenizer_class": "Qwen2Tokenizer",
+  "unk_token": null
+}

video_preprocessor_config.json

@@ -0,0 +1,41 @@
+{
+  "crop_size": null,
+  "data_format": "channels_first",
+  "default_to_square": true,
+  "device": null,
+  "do_center_crop": null,
+  "do_convert_rgb": true,
+  "do_normalize": true,
+  "do_rescale": true,
+  "do_resize": true,
+  "do_sample_frames": true,
+  "fps": 2,
+  "image_mean": [
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+    0.5,
+    0.5
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+  "image_std": [
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+    0.5,
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+  "max_frames": 8,
+  "merge_size": 2,
+  "min_frames": 4,
+  "num_frames": null,
+  "pad_size": null,
+  "patch_size": 16,
+  "processor_class": "Qwen3VLProcessor",
+  "resample": 3,
+  "rescale_factor": 0.00392156862745098,
+  "return_metadata": false,
+  "size": {
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+    "shortest_edge": 200704
+  },
+  "temporal_patch_size": 2,
+  "video_metadata": null,
+  "video_processor_type": "Qwen3VLVideoProcessor"
+}