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.gitattributes CHANGED
@@ -33,3 +33,4 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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+ {
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+ "</think>": 151668,
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+ "</tool_call>": 151658,
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+ "</tool_response>": 151666,
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+ "<think>": 151667,
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+ "<tool_call>": 151657,
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+ "<tool_response>": 151665,
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+ "<image_gen>": 151669,
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+ "<image_edit>": 151670,
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+ "<linear_cla>": 151671,
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+ "<linear_pre>": 151672,
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+ "<|file_sep|>": 151664,
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+ "<|fim_suffix|>": 151661,
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+ "<|video_pad|>": 151656,
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+ }
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+ {%- set image_count = namespace(value=0) %}
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+ {%- set video_count = namespace(value=0) %}
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+ {%- macro render_content(content, do_vision_count) %}
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+ {%- if content is string %}
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+ {{- content }}
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+ {%- else %}
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+ {%- for item in content %}
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+ {%- if 'image' in item or 'image_url' in item or item.type == 'image' %}
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+ {%- if do_vision_count %}
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+ {%- set image_count.value = image_count.value + 1 %}
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+ {%- endif %}
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+ {%- if add_vision_id %}Picture {{ image_count.value }}: {% endif -%}
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+ <|vision_start|><|image_pad|><|vision_end|>
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+ {%- elif 'video' in item or item.type == 'video' %}
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+ {%- if do_vision_count %}
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+ {%- set video_count.value = video_count.value + 1 %}
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+ {%- endif %}
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+ {%- if add_vision_id %}Video {{ video_count.value }}: {% endif -%}
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+ <|vision_start|><|video_pad|><|vision_end|>
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+ {%- elif 'text' in item %}
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+ {{- item.text }}
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+ {%- endif %}
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+ {%- endfor %}
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+ {%- endif %}
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+ {%- endmacro %}
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+ {%- if tools %}
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+ {{- '<|im_start|>system\n' }}
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+ {%- if messages[0].role == 'system' %}
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+ {{- render_content(messages[0].content, false) + '\n\n' }}
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+ {%- endif %}
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+ {{- "# 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>" }}
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+ {%- for tool in tools %}
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+ {{- "\n" }}
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+ {{- tool | tojson }}
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+ {%- endfor %}
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+ {{- "\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" }}
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+ {%- else %}
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+ {%- if messages[0].role == 'system' %}
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+ {{- '<|im_start|>system\n' + render_content(messages[0].content, false) + '<|im_end|>\n' }}
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+ {%- endif %}
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+ {%- endif %}
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+ {%- set ns = namespace(multi_step_tool=true, last_query_index=messages|length - 1) %}
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+ {%- for message in messages[::-1] %}
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+ {%- set index = (messages|length - 1) - loop.index0 %}
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+ {%- if ns.multi_step_tool and message.role == "user" %}
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+ {%- set content = render_content(message.content, false) %}
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+ {%- if not(content.startswith('<tool_response>') and content.endswith('</tool_response>')) %}
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+ {%- set ns.multi_step_tool = false %}
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+ {%- set ns.last_query_index = index %}
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+ {%- endif %}
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+ {%- endif %}
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+ {%- endfor %}
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+ {%- for message in messages %}
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+ {%- set content = render_content(message.content, True) %}
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+ {%- if (message.role == "user") or (message.role == "system" and not loop.first) %}
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+ {{- '<|im_start|>' + message.role + '\n' + content + '<|im_end|>' + '\n' }}
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+ {%- elif message.role == "assistant" %}
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+ {%- set reasoning_content = '' %}
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+ {%- set reasoning_content = message.reasoning_content %}
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+ {%- else %}
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+ {%- if '</think>' in content %}
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+ {%- set reasoning_content = content.split('</think>')[0].rstrip('\n').split('<think>')[-1].lstrip('\n') %}
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+ {%- set content = content.split('</think>')[-1].lstrip('\n') %}
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+ {%- endif %}
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+ {%- endif %}
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+ {%- if loop.index0 > ns.last_query_index %}
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+ {%- if loop.last or (not loop.last and reasoning_content) %}
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+ {{- '<|im_start|>' + message.role + '\n<think>\n' + reasoning_content.strip('\n') + '\n</think>\n\n' + content.lstrip('\n') }}
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+ {%- else %}
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+ {{- '<|im_start|>' + message.role + '\n' + content }}
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+ {%- endif %}
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+ {%- else %}
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+ {{- '<|im_start|>' + message.role + '\n' + content }}
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+ {%- endif %}
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+ {%- if message.tool_calls %}
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+ {%- for tool_call in message.tool_calls %}
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+ {%- if (loop.first and content) or (not loop.first) %}
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+ {{- '\n' }}
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+ {%- endif %}
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+ {%- if tool_call.function %}
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+ {%- set tool_call = tool_call.function %}
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+ {%- endif %}
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+ {{- '<tool_call>\n{"name": "' }}
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+ {{- tool_call.name }}
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+ {{- '", "arguments": ' }}
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+ {%- if tool_call.arguments is string %}
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+ {{- tool_call.arguments }}
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+ {%- else %}
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+ {{- tool_call.arguments | tojson }}
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+ {%- endif %}
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+ {{- '}\n</tool_call>' }}
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+ {%- endfor %}
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+ {%- endif %}
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+ {{- '<|im_end|>\n' }}
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+ {%- elif message.role == "tool" %}
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+ {%- if loop.first or (messages[loop.index0 - 1].role != "tool") %}
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+ {{- '<|im_start|>user' }}
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+ {%- endif %}
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+ {{- '\n<tool_response>\n' }}
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+ {{- content }}
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+ {{- '\n</tool_response>' }}
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+ {%- if loop.last or (messages[loop.index0 + 1].role != "tool") %}
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+ {{- '<|im_end|>\n' }}
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+ {%- endif %}
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+ {%- endif %}
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+ {%- endfor %}
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+ {%- if add_generation_prompt %}
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+ {{- '<|im_start|>assistant\n<think>\n' }}
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+ {%- endif %}
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+ {
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+ "architectures": [
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+ "Qwen3VLForConditionalGeneration"
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+ ],
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+ "hidden_size": 5120,
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+ "image_token_id": 151655,
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+ "model_type": "qwen3_vl",
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+ "pad_token_id": 151643,
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+ "text_config": {
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+ "attention_bias": false,
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+ "attention_dropout": 0.0,
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+ "bos_token_id": 151643,
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+ "dtype": "bfloat16",
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+ "eos_token_id": 151645,
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+ "head_dim": 128,
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+ "hidden_act": "silu",
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+ "hidden_size": 5120,
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+ "initializer_range": 0.02,
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+ "intermediate_size": 25600,
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+ "max_position_embeddings": 262144,
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+ "model_type": "qwen3_vl_text",
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+ "num_attention_heads": 64,
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+ "num_hidden_layers": 64,
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+ "num_key_value_heads": 8,
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+ "pad_token_id": 151643,
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+ "rms_norm_eps": 1e-06,
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+ "rope_scaling": {
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+ "mrope_interleaved": true,
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+ "mrope_section": [
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+ 24,
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+ 20,
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+ 20
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+ ],
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+ "rope_type": "default"
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+ },
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+ "rope_theta": 5000000,
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+ "use_cache": false,
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+ "vocab_size": 151936
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+ },
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+ "tie_word_embeddings": false,
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+ "transformers_version": "4.57.6",
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+ "video_token_id": 151656,
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+ "vision_config": {
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+ "deepstack_visual_indexes": [
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+ 8,
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+ 16,
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+ 24
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+ ],
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+ "depth": 27,
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+ "dtype": "bfloat16",
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+ "hidden_act": "gelu_pytorch_tanh",
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+ "hidden_size": 1152,
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+ "in_channels": 3,
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+ "initializer_range": 0.02,
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+ "intermediate_size": 4304,
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+ "model_type": "qwen3_vl",
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+ "num_heads": 16,
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+ "num_position_embeddings": 2304,
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+ "out_hidden_size": 5120,
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+ "pad_token_id": 151643,
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+ "patch_size": 16,
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+ "spatial_merge_size": 2,
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+ "temporal_patch_size": 2
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+ },
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+ "vision_end_token_id": 151653,
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+ "spec2mol_v2": {
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+ "format": "spec2mol_v2_hf_inline_safetensors",
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+ "tensor_prefix": "spec2mol.",
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+ "small_modules": {
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+ "format": "spec2mol_small_modules_v2",
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+ "tensor_prefix": "spec2mol.",
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+ "modules": {
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+ "s1_omni_ir_linear": {
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+ "prefix": "s1_omni_ir_linear.",
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+ "modality": "ir",
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+ "num_classes": 20,
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+ "vocab": [
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+ "alkane",
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+ "alkene",
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+ "alkyne",
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+ "amine",
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+ "imine",
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+ "nitrile",
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+ "alcohol",
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+ "ether",
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+ "haloalkane",
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+ "aldehyde",
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+ "ketone",
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+ "ester",
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+ "amide",
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+ "arene",
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+ "imidazole",
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+ "pyrazole",
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+ "oxazole",
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+ "isoxazole",
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+ "cyclopropane",
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+ "epoxide"
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+ ],
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+ "threshold_source": "0.5",
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+ "thresholds": [
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+ 0.5,
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+ "n_heads": 8,
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+ "ffn_mult": 2,
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+ "dropout": 0.1,
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+ "num_queries": 4,
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+ "num_classes": 20,
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+ "feat_dim": 0,
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+ "head_dropout": 0.1
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+ },
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+ "hf_prefix": "spec2mol.s1_omni_ir_linear.",
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+ "tensor_count": 46
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+ },
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+ "s1_omni_raman_linear": {
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+ "prefix": "s1_omni_raman_linear.",
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+ "modality": "raman",
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+ "num_classes": 20,
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+ "vocab": [
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+ "alkane",
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+ "alkene",
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+ "alkyne",
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+ "amine",
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+ "imine",
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+ "nitrile",
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+ "alcohol",
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+ "ether",
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+ "haloalkane",
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+ "aldehyde",
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+ "ketone",
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+ "ester",
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+ "amide",
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+ "arene",
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+ "imidazole",
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+ "pyrazole",
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+ "oxazole",
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+ "isoxazole",
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+ "cyclopropane",
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+ "epoxide"
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+ ],
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+ "threshold_source": "0.5",
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+ "thresholds": [
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+ 0.5,
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+ 0.5,
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+ "proj_dim": 768,
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+ "n_heads": 8,
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+ "num_queries": 4,
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+ "num_classes": 20,
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+ "feat_dim": 0,
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+ "head_dropout": 0.1
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+ },
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+ "hf_prefix": "spec2mol.s1_omni_raman_linear.",
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+ "tensor_count": 46
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+ },
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+ "s1_omni_uv_linear": {
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+ "prefix": "s1_omni_uv_linear.",
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+ "modality": "uv",
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+ "num_classes": 20,
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+ "vocab": [
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+ "alkane",
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+ "alkene",
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+ "alkyne",
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+ "amine",
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+ "imine",
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+ "nitrile",
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+ "alcohol",
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+ "ether",
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+ "haloalkane",
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+ "aldehyde",
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+ "ketone",
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+ "ester",
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+ "amide",
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+ "arene",
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+ "imidazole",
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+ "pyrazole",
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+ "oxazole",
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+ "isoxazole",
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+ "cyclopropane",
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+ "epoxide"
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+ ],
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+ "threshold_source": "0.5",
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+ "thresholds": [
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+ "feat_dim": 0,
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+ "build_args": {
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+ "hidden": [
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+ 512,
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+ 256
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+ ],
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+ "dropout": 0.1,
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+ "out_dim": 27
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+ },
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+ "hf_prefix": "spec2mol.atomcount.",
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+ "tensor_count": 8
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+ },
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+ "motif": {
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+ "prefix": "motif.",
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+ "build_args": {
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+ "in_dim": 256,
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+ "num_classes": 20,
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+ "hidden": [
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+ 512,
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+ 256
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+ ],
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+ "dropout": 0.1,
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+ "vocab": [
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+ "alkane",
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+ "alkene",
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+ "alkyne",
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+ "amine",
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+ "imine",
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+ "nitrile",
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+ "alcohol",
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+ "ether",
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+ "haloalkane",
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+ "aldehyde",
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+ "ketone",
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+ "ester",
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+ "amide",
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+ "arene",
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+ "imidazole",
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+ "pyrazole",
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+ "oxazole",
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+ "isoxazole",
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+ "cyclopropane",
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+ "epoxide"
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+ ],
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+ "thresholds_default": [
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+ "<|object_ref_start|>",
274
+ "<|object_ref_end|>",
275
+ "<|box_start|>",
276
+ "<|box_end|>",
277
+ "<|quad_start|>",
278
+ "<|quad_end|>",
279
+ "<|vision_start|>",
280
+ "<|vision_end|>",
281
+ "<|vision_pad|>",
282
+ "<|image_pad|>",
283
+ "<|video_pad|>",
284
+ "<image_gen>",
285
+ "<image_edit>",
286
+ "<linear_cla>",
287
+ "<linear_pre>",
288
+ "<prot_st>",
289
+ "<prot_cla>",
290
+ "<spectra_st>"
291
+ ],
292
+ "bos_token": null,
293
+ "clean_up_tokenization_spaces": false,
294
+ "eos_token": "<|im_end|>",
295
+ "errors": "replace",
296
+ "extra_special_tokens": {},
297
+ "model_max_length": 262144,
298
+ "pad_token": "<|endoftext|>",
299
+ "processor_class": "Qwen3VLProcessor",
300
+ "split_special_tokens": false,
301
+ "tokenizer_class": "Qwen2Tokenizer",
302
+ "unk_token": null
303
+ }
video_preprocessor_config.json ADDED
@@ -0,0 +1,41 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
2
+ "crop_size": null,
3
+ "data_format": "channels_first",
4
+ "default_to_square": true,
5
+ "device": null,
6
+ "do_center_crop": null,
7
+ "do_convert_rgb": true,
8
+ "do_normalize": true,
9
+ "do_rescale": true,
10
+ "do_resize": true,
11
+ "do_sample_frames": true,
12
+ "fps": 2,
13
+ "image_mean": [
14
+ 0.5,
15
+ 0.5,
16
+ 0.5
17
+ ],
18
+ "image_std": [
19
+ 0.5,
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+ 0.5,
21
+ 0.5
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+ ],
23
+ "input_data_format": null,
24
+ "max_frames": 768,
25
+ "merge_size": 2,
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+ "min_frames": 4,
27
+ "num_frames": null,
28
+ "pad_size": null,
29
+ "patch_size": 16,
30
+ "processor_class": "Qwen3VLProcessor",
31
+ "resample": 3,
32
+ "rescale_factor": 0.00392156862745098,
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+ "return_metadata": false,
34
+ "size": {
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+ "longest_edge": 25165824,
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+ "shortest_edge": 4096
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+ },
38
+ "temporal_patch_size": 2,
39
+ "video_metadata": null,
40
+ "video_processor_type": "Qwen3VLVideoProcessor"
41
+ }
vocab.json ADDED
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