初始化项目，由ModelHub XC社区提供模型
Model: mims-harvard/bio-posttrain-qwen3-1.7b-rna-sft Source: Original Platform
This commit is contained in:
ModelHub XC
36
.gitattributes
vendored
Normal file
36
.gitattributes
vendored
Normal file
@@ -0,0 +1,36 @@
|
||||
*.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
|
||||
*.npz filter=lfs diff=lfs merge=lfs -text
|
||||
*.onnx filter=lfs diff=lfs merge=lfs -text
|
||||
*.ot filter=lfs diff=lfs merge=lfs -text
|
||||
*.parquet filter=lfs diff=lfs merge=lfs -text
|
||||
*.pb filter=lfs diff=lfs merge=lfs -text
|
||||
*.pickle filter=lfs diff=lfs merge=lfs -text
|
||||
*.pkl filter=lfs diff=lfs merge=lfs -text
|
||||
*.pt filter=lfs diff=lfs merge=lfs -text
|
||||
*.pth filter=lfs diff=lfs merge=lfs -text
|
||||
*.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
|
||||
*.tar.* filter=lfs diff=lfs merge=lfs -text
|
||||
*.tar filter=lfs diff=lfs merge=lfs -text
|
||||
*.tflite filter=lfs diff=lfs merge=lfs -text
|
||||
*.tgz filter=lfs diff=lfs merge=lfs -text
|
||||
*.wasm filter=lfs diff=lfs merge=lfs -text
|
||||
*.xz filter=lfs diff=lfs merge=lfs -text
|
||||
*.zip filter=lfs diff=lfs merge=lfs -text
|
||||
*.zst filter=lfs diff=lfs merge=lfs -text
|
||||
*tfevents* filter=lfs diff=lfs merge=lfs -text
|
||||
tokenizer.json filter=lfs diff=lfs merge=lfs -text
|
||||
46
README.md
Normal file
46
README.md
Normal file
@@ -0,0 +1,46 @@
|
||||
---
|
||||
license: apache-2.0
|
||||
base_model: Qwen/Qwen3-1.7B
|
||||
tags:
|
||||
- biology
|
||||
- bio-posttrain
|
||||
- rna-sft
|
||||
- rna
|
||||
library_name: transformers
|
||||
---
|
||||
|
||||
# Bio-posttrain Qwen3-1.7B RNA SFT
|
||||
|
||||
RNA supervised fine-tuning (SFT) checkpoint from [How Post-Training Shapes Biological Reasoning Models](https://huggingface.co/collections/mims-harvard/bio-posttrain).
|
||||
|
||||
## Model details
|
||||
|
||||
- **Base model:** `Qwen/Qwen3-1.7B`
|
||||
- **RNA embeddings:** Precomputed TranscriptFormer (2048-d), projected via `rna_projection.pt`
|
||||
- **LoRA:** rank 32, alpha 64
|
||||
- **Validation loss:** 0.5394
|
||||
|
||||
## Files
|
||||
|
||||
| File | Description |
|
||||
|------|-------------|
|
||||
| `model.safetensors` | Merged LLM weights |
|
||||
| `rna_projection.pt` | Linear map RNA embed (2048) → text hidden |
|
||||
| `rna_model_config.json` | Architecture metadata |
|
||||
|
||||
## Loading
|
||||
|
||||
```python
|
||||
from transformers import AutoModelForCausalLM, AutoTokenizer
|
||||
import torch
|
||||
|
||||
model = AutoModelForCausalLM.from_pretrained("mims-harvard/bio-posttrain-qwen3-1.7b-rna-sft", trust_remote_code=True)
|
||||
tokenizer = AutoTokenizer.from_pretrained("mims-harvard/bio-posttrain-qwen3-1.7b-rna-sft")
|
||||
proj = torch.load("rna_projection.pt", map_location="cpu")
|
||||
```
|
||||
|
||||
RNA sequence embeddings are supplied offline at inference time. See the `rna_models` code in the BioReason repository.
|
||||
|
||||
## Collection
|
||||
|
||||
Part of the [Bio-posttrain](https://huggingface.co/collections/mims-harvard/bio-posttrain) collection.
|
||||
84
chat_template.jinja
Normal file
84
chat_template.jinja
Normal file
@@ -0,0 +1,84 @@
|
||||
{%- set rna_count = namespace(value=0) %}{%- if tools %}
|
||||
{{- '<|im_start|>system\n' }}
|
||||
{%- if messages[0].role == 'system' %}
|
||||
{{- messages[0].content + '\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' + messages[0].content + '<|im_end|>\n' }}
|
||||
{%- endif %}
|
||||
{%- endif %}
|
||||
{%- set ns = namespace(multi_step_tool=true, last_query_index=messages|length - 1) %}
|
||||
{%- for message in messages[::-1] %}
|
||||
{%- set index = (messages|length - 1) - loop.index0 %}
|
||||
{%- if ns.multi_step_tool and message.role == "user" and not(message.content is string and message.content.startswith('<tool_response>') and message.content.endswith('</tool_response>')) %}
|
||||
{%- set ns.multi_step_tool = false %}
|
||||
{%- set ns.last_query_index = index %}
|
||||
{%- endif %}
|
||||
{%- endfor %}
|
||||
{%- for message in messages %}
|
||||
{%- if (message.role == "user") or (message.role == "system" and not loop.first) %}
|
||||
{{- '<|im_start|>' + message.role + '\n' }} {%- if message.content is string %}{{- message.content + '<|im_end|>' + '\n' }}{%- else %}{%- for content in message.content %}{%- if content.type == 'rna' or 'rna' in content %}{%- set rna_count.value = rna_count.value + 1 %}{%- if add_rna_id %}RNA Sequence {{- rna_count.value }}: {%- endif %}<|rna_start|><|rna_pad|><|rna_end|>{%- elif 'text' in content %}{{- content.text }}{%- endif %}{%- endfor %}{{- '<|im_end|>' + '\n' }}{%- endif %}{%- elif message.role == "assistant" %}
|
||||
{%- set content = message.content[0].text %}
|
||||
{%- set reasoning_content = '' %}
|
||||
{%- if message.reasoning_content is defined and message.reasoning_content is not none %}
|
||||
{%- set reasoning_content = message.reasoning_content %}
|
||||
{%- else %}
|
||||
{%- if '</think>' in message.content %}
|
||||
{%- set content = message.content[0].text.split('</think>')[-1].lstrip('\n') %}
|
||||
{%- set reasoning_content = message.content[0].text.split('</think>')[0].rstrip('\n').split('<think>')[-1].lstrip('\n') %}
|
||||
{%- endif %}
|
||||
{%- endif %}
|
||||
{%- if loop.index0 > ns.last_query_index %}
|
||||
{%- if loop.last or (not loop.last and reasoning_content) %}
|
||||
{{- '<|im_start|>' + message.role + '\n<think>\n' + reasoning_content.strip('\n') + '\n</think>\n\n' + content.lstrip('\n') }}
|
||||
{%- else %}
|
||||
{{- '<|im_start|>' + message.role + '\n' + content }}
|
||||
{%- endif %}
|
||||
{%- else %}
|
||||
{{- '<|im_start|>' + message.role + '\n' + content }}
|
||||
{%- endif %}
|
||||
{%- if message.tool_calls %}
|
||||
{%- for tool_call in message.tool_calls %}
|
||||
{%- if (loop.first and 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' }}
|
||||
{{- message.content }}
|
||||
{{- '\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' }}
|
||||
{%- if enable_thinking is defined and enable_thinking is false %}
|
||||
{{- '<think>\n\n</think>\n\n' }}
|
||||
{%- endif %}
|
||||
{%- endif %}
|
||||
63
config.json
Normal file
63
config.json
Normal file
@@ -0,0 +1,63 @@
|
||||
{
|
||||
"architectures": [
|
||||
"Qwen3ForCausalLM"
|
||||
],
|
||||
"attention_bias": false,
|
||||
"attention_dropout": 0.0,
|
||||
"bos_token_id": 151643,
|
||||
"dtype": "float32",
|
||||
"eos_token_id": 151645,
|
||||
"head_dim": 128,
|
||||
"hidden_act": "silu",
|
||||
"hidden_size": 2048,
|
||||
"initializer_range": 0.02,
|
||||
"intermediate_size": 6144,
|
||||
"layer_types": [
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention",
|
||||
"full_attention"
|
||||
],
|
||||
"max_position_embeddings": 40960,
|
||||
"max_window_layers": 28,
|
||||
"model_type": "qwen3",
|
||||
"num_attention_heads": 16,
|
||||
"num_hidden_layers": 28,
|
||||
"num_key_value_heads": 8,
|
||||
"pad_token_id": null,
|
||||
"rms_norm_eps": 1e-06,
|
||||
"rope_parameters": {
|
||||
"rope_theta": 1000000,
|
||||
"rope_type": "default"
|
||||
},
|
||||
"sliding_window": null,
|
||||
"tie_word_embeddings": false,
|
||||
"transformers_version": "5.1.0",
|
||||
"use_cache": true,
|
||||
"use_sliding_window": false,
|
||||
"vocab_size": 151936
|
||||
}
|
||||
13
generation_config.json
Normal file
13
generation_config.json
Normal file
@@ -0,0 +1,13 @@
|
||||
{
|
||||
"bos_token_id": 151643,
|
||||
"do_sample": true,
|
||||
"eos_token_id": [
|
||||
151645,
|
||||
151643
|
||||
],
|
||||
"pad_token_id": 151643,
|
||||
"temperature": 0.6,
|
||||
"top_k": 20,
|
||||
"top_p": 0.95,
|
||||
"transformers_version": "5.1.0"
|
||||
}
|
||||
3
missing_and_unexpected_keys.txt
Normal file
3
missing_and_unexpected_keys.txt
Normal file
@@ -0,0 +1,3 @@
|
||||
Missing keys:
|
||||
|
||||
Unexpected keys:
|
||||
3
model.safetensors
Normal file
3
model.safetensors
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:324e41cb8ddeb37fc0ead5fdded91dab65ea436f7d20423c7515a4aeb32dcfa5
|
||||
size 8126995136
|
||||
29
rna_model_config.json
Normal file
29
rna_model_config.json
Normal file
@@ -0,0 +1,29 @@
|
||||
{
|
||||
"model_type": "rna_llm",
|
||||
"text_model_name": "Qwen/Qwen3-1.7B",
|
||||
"chat_template_family": "qwen",
|
||||
"rna_embed_dim": 2048,
|
||||
"max_rna_seq_len": 1,
|
||||
"max_length_text": 4096,
|
||||
"lora_rank": 32,
|
||||
"lora_alpha": 64,
|
||||
"lora_dropout": 0.05,
|
||||
"source_checkpoint": "/n/holylfs06/LABS/mzitnik_lab/Lab/lfesser/evo_tfm/hf_upload_models/Qwen3-1.7B-RNA-SFT-paper-e5-val_loss-0.5394.ckpt",
|
||||
"epoch": 2,
|
||||
"global_step": 515,
|
||||
"hyper_parameters": {
|
||||
"text_model_name": "Qwen/Qwen3-1.7B",
|
||||
"rna_embed_dim": 2048,
|
||||
"lora_rank": 32,
|
||||
"lora_alpha": 64,
|
||||
"lora_dropout": 0.05,
|
||||
"max_length_text": 4096,
|
||||
"chat_template_family": "qwen"
|
||||
},
|
||||
"special_tokens": [
|
||||
"<|rna_start|>",
|
||||
"<|rna_pad|>",
|
||||
"<|rna_end|>"
|
||||
],
|
||||
"notes": "RNA embeddings are precomputed offline (TranscriptFormer, 2048-d) and projected via rna_projection.pt. Use the evo_tfm/rna_models inference code to load."
|
||||
}
|
||||
3
rna_projection.pt
Normal file
3
rna_projection.pt
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:187eb2dfaebc9b4d52419542d996d8120cc3c942456e6bfe48df1dadd5ee6e52
|
||||
size 16787357
|
||||
3
tokenizer.json
Normal file
3
tokenizer.json
Normal file
@@ -0,0 +1,3 @@
|
||||
version https://git-lfs.github.com/spec/v1
|
||||
oid sha256:f404de3ab57bf86dc45e79781aa017f200bf28bb699d24eef7bc459b3e71cdfb
|
||||
size 11423216
|
||||
19
tokenizer_config.json
Normal file
19
tokenizer_config.json
Normal file
@@ -0,0 +1,19 @@
|
||||
{
|
||||
"add_prefix_space": false,
|
||||
"backend": "tokenizers",
|
||||
"bos_token": null,
|
||||
"clean_up_tokenization_spaces": false,
|
||||
"eos_token": "<|im_end|>",
|
||||
"errors": "replace",
|
||||
"extra_special_tokens": [
|
||||
"<|rna_start|>",
|
||||
"<|rna_pad|>",
|
||||
"<|rna_end|>"
|
||||
],
|
||||
"is_local": false,
|
||||
"model_max_length": 131072,
|
||||
"pad_token": "<|im_end|>",
|
||||
"split_special_tokens": false,
|
||||
"tokenizer_class": "Qwen2Tokenizer",
|
||||
"unk_token": null
|
||||
}
|
||||
Reference in New Issue
Block a user