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README.md

@@ -1,3 +1,124 @@
 ---
 license: apache-2.0
+pipeline_tag: text-generation
+tags:
+- chemistry
+language:
+- en
+- zh
 ---
+# ChemDFM-13B: An LLM-Based Dialogue Foundation Model for Chemistry
+
+ChemDFM is the pioneering open-sourced dialogue foundation model for Chemistry and molecule science, which is build based on LLaMa-13B. ChemDFM outperforms the open-sourced LLMs in all the typical tasks of chemistry, and even reach comparable or higher performances of GPT-4. For more details, please refer to [our paper](https://arxiv.org/abs/2401.14818).
+
+## News
+
+* **2024-03-07**: The parameter of ChemLLM-13B is open-sourced!
+* **2024-01-26**: The paper of ChemLLM-13B is released on arXiv: [ChemDFM: Dialogue Foundation Model for Chemistry](https://arxiv.org/abs/2401.14818)
+
+## Usage Details
+
+The online demo of ChemDFM will be up soon!
+
+### local inference
+
+To load and run ChemDFM locally, here is an example:
+
+```python
+import torch
+from transformers import LlamaTokenizer, LlamaForCausalLM, GenerationConfig
+
+model_name_or_id = "X-LANCE/ChemDFM-13B-v1.0"
+tokenizer = LlamaTokenizer.from_pretrained(model_name_or_id)
+model = LlamaForCausalLM.from_pretrained(model_name_or_id, torch_dtype=torch.float16, device_map="auto")
+
+input_text = "Can you please give detailed descriptions of the molecule below?\nCl.O=C1c2c(O)cccc2-c2nn(CCNCCO)c3ccc(NCCNCCO)c1c23"
+input_text = f"[Round 0]\nHuman: {input_text}\nAssistant:"
+
+inputs = tokenizer(input_text, return_tensors="pt").to("cuda")
+generation_config = GenerationConfig(
+    do_sample=True,
+    top_k=20,
+    top_p=0.9,
+    temperature=0.9,
+    max_new_tokens=1024,
+    repetition_penalty=1.05,
+    eos_token_id=tokenizer.eos_token_id
+)
+
+outputs = model.generate(**inputs, generation_config=generation_config)
+generated_text = tokenizer.batch_decode(outputs, skip_special_tokens=True)[0][len(input_text):]
+print(generated_text.strip())
+```
+
+### input format
+
+To get better responses, we recommend to preprocess your input and history with the dialogue templates which are used during instruction tuning of ChemDFM. Specifically, for an input queries
+```python
+{'current_query': current_query, 'history': [(query1, answer1), (query2, answer2), ...]}
+```
+, you can use the following code to preprocess the input and history:
+```python
+def formatting_input(current_query, history):
+    input_text = ''
+    for idx, (query, answer) in history:
+        input_text += f"[Round {idx}]\nHuman: {query}\nAssistant: {answer}\n"
+    input_text += f"[Round {len(history)}]\nHuman: {current_query}\nAssistant:"
+    return input_text
+```
+
+### SMILES preprocess
+
+When there involves SMILES notation in your input, we recommend to preprocess the SMILES with the `rdkit` package to canonicalize the SMILES. Here is an example:
+```python
+from rdkit import Chem
+def canonicalize_smiles(smiles):
+    mol = Chem.MolFromSmiles(smiles)
+    if mol is None:
+        return None
+    return Chem.MolToSmiles(mol, isomericSmiles=True, kekuleSmiles=False)
+```
+or directly:
+```python
+from rdkit import Chem
+def canonicalize_smiles(smiles):
+    return Chem.CanonSmiles(smiles, useChiral=True)
+```
+
+## Performance
+
+### Chemical Benchmarks
+
+We evaluate the performance of ChemDFM-13B on multiple widely-used benchmarks in chemistry. The detail introduction of the benchmarks can be found in [our paper](https://arxiv.org/abs/2401.14818). The overall performance of ChemDFM-13B is shown below:
+
+![Objective Performance]() 
+
+[//]: # (TODO)
+
+### Human Evaluation
+
+![Human Evaluation of QA]()
+
+![Human Evaluation of Dialogue]()
+
+[//]: # (TODO)
+For more examples and analysis, please refer to [our paper](https://arxiv.org/abs/2401.14818).
+
+## Citation
+```bibtex
+@misc{zhao2024chemdfm,
+    title={ChemDFM: Dialogue Foundation Model for Chemistry},
+    author={Zihan Zhao and Da Ma and Lu Chen and Liangtai Sun and Zihao Li and Hongshen Xu and Zichen Zhu and Su Zhu and Shuai Fan and Guodong Shen and Xin Chen and Kai Yu},
+    year={2024},
+    eprint={2401.14818},
+    archivePrefix={arXiv},
+    primaryClass={cs.CL}
+}
+```
+
+## Disclaimer
+Current version of ChemDFM may generate incorrect or misleading information. Please use it with caution and verify the results with domain experts before making any decisions based on the results.
+
+## Contact
+
+If you have any questions or further requests, please contact [Zihan Zhao](mailto:zhao_mengxin@sjtu.edu.cn) and [Lu Chen](mailto:chenlusz@sjtu.edu.cn).

added_tokens.json

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+{
+  "[PAD]": 39408
+}

config.json

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+{
+  "_name_or_path": "/hpc_stor01/home/su.zhu/workspace/ckpts/chem-chinese-llama-13B-without-chem-tokens",
+  "architectures": [
+    "LlamaForCausalLM"
+  ],
+  "attention_bias": false,
+  "bos_token_id": 1,
+  "end_token_id": 2,
+  "eos_token_id": 2,
+  "hidden_act": "silu",
+  "hidden_size": 5120,
+  "initializer_range": 0.02,
+  "intermediate_size": 13824,
+  "max_position_embeddings": 2048,
+  "model_type": "llama",
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+  "num_hidden_layers": 40,
+  "num_key_value_heads": 40,
+  "pad_token_id": 2,
+  "pretraining_tp": 1,
+  "rms_norm_eps": 1e-06,
+  "rope_scaling": null,
+  "rope_theta": 10000,
+  "tie_word_embeddings": false,
+  "torch_dtype": "float16",
+  "transformers_version": "4.35.0",
+  "use_cache": true,
+  "vocab_size": 39409
+}

generation_config.json

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+{
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+  "bos_token_id": 1,
+  "eos_token_id": 2,
+  "pad_token_id": 0,
+  "transformers_version": "4.35.0"
+}

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+    "single_word": false
+  },
+  "pad_token": {
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+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
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+    "content": "<unk>",
+    "lstrip": false,
+    "normalized": true,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer.model

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+version https://git-lfs.github.com/spec/v1
+oid sha256:0e605041f0df5267b062935be72043a8c8c30d6482aeaf8fe6e067cf4806267f
+size 603435

tokenizer_config.json

@@ -0,0 +1,50 @@
+{
+  "add_bos_token": true,
+  "add_eos_token": false,
+  "added_tokens_decoder": {
+    "0": {
+      "content": "<unk>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
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+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": true,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "39408": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "bos_token": "<s>",
+  "clean_up_tokenization_spaces": false,
+  "eos_token": "</s>",
+  "legacy": true,
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_token": "[PAD]",
+  "sp_model_kwargs": {},
+  "spaces_between_special_tokens": false,
+  "tokenizer_class": "LlamaTokenizer",
+  "unk_token": "<unk>",
+  "use_default_system_prompt": false,
+  "use_fast": true
+}