Update README.md

README.md

@@ -2,10 +2,124 @@
 configs:
 - config_name: ChemProt
   data_files:
-    - split: train
-      path: "train.json"
-    - split: validation
-      path: "dev.json"
-    - split: test
-      path: "test.json"
----
+  - split: train
+    path: train.jsonl
+  - split: validation
+    path: dev.jsonl
+  - split: test
+    path: test.jsonl
+task_categories:
+- text-classification
+- question-answering
+- zero-shot-classification
+language:
+- en
+tags:
+- medical
+- chemistry
+- biology
+---
+
+# Domain Adaptation of Large Language Models
+This repo contains the **ChemProt dataset** used in our **ICLR 2024** paper [Adapting Large Language Models via Reading Comprehension](https://huggingface.co/papers/2309.09530).
+
+We explore **continued pre-training on domain-specific corpora** for large language models. While this approach enriches LLMs with domain knowledge, it significantly hurts their prompting ability for question answering. Inspired by human learning via reading comprehension, we propose a simple method to **transform large-scale pre-training corpora into reading comprehension texts**, consistently improving prompting performance across tasks in biomedicine, finance, and law domains. **Our 7B model competes with much larger domain-specific models like BloombergGPT-50B**. 
+
+### 🤗 We are currently working hard on developing models across different domains, scales and architectures! Please stay tuned! 🤗
+
+**************************** **Updates** ****************************
+* 2024/4/2: Released the training and testing splits of all the evaluation datasets: [ChemProt](https://huggingface.co/datasets/AdaptLLM/ChemProt)
+* 2024/1/16: 🎉 Our [research paper](https://huggingface.co/papers/2309.09530) has been accepted by ICLR 2024!!!🎉
+* 2023/12/19: Released our [13B base models](https://huggingface.co/AdaptLLM/law-LLM-13B) developed from LLaMA-1-13B.
+* 2023/12/8: Released our [chat models](https://huggingface.co/AdaptLLM/law-chat) developed from LLaMA-2-Chat-7B.
+* 2023/9/18: Released our [paper](https://huggingface.co/papers/2309.09530), [code](https://github.com/microsoft/LMOps), [data](https://huggingface.co/datasets/AdaptLLM/law-tasks), and [base models](https://huggingface.co/AdaptLLM/law-LLM) developed from LLaMA-1-7B.
+
+
+## Domain-Specific LLaMA-1
+### LLaMA-1-7B
+In our paper, we develop three domain-specific models from LLaMA-1-7B, which are also available in Huggingface: [Biomedicine-LLM](https://huggingface.co/AdaptLLM/medicine-LLM), [Finance-LLM](https://huggingface.co/AdaptLLM/finance-LLM) and [Law-LLM](https://huggingface.co/AdaptLLM/law-LLM), the performances of our AdaptLLM compared to other domain-specific LLMs are:
+
+<p align='center'>
+    <img src="https://cdn-uploads.huggingface.co/production/uploads/650801ced5578ef7e20b33d4/6efPwitFgy-pLTzvccdcP.png" width="700">
+</p>
+
+### LLaMA-1-13B
+Moreover, we scale up our base model to LLaMA-1-13B to see if **our method is similarly effective for larger-scale models**, and the results are consistently positive too: [Biomedicine-LLM-13B](https://huggingface.co/AdaptLLM/medicine-LLM-13B), [Finance-LLM-13B](https://huggingface.co/AdaptLLM/finance-LLM-13B) and [Law-LLM-13B](https://huggingface.co/AdaptLLM/law-LLM-13B).
+
+## Domain-Specific LLaMA-2-Chat
+Our method is also effective for aligned models! LLaMA-2-Chat requires a [specific data format](https://huggingface.co/blog/llama2#how-to-prompt-llama-2), and our **reading comprehension can perfectly fit the data format** by transforming the reading comprehension into a multi-turn conversation. We have also open-sourced chat models in different domains: [Biomedicine-Chat](https://huggingface.co/AdaptLLM/medicine-chat), [Finance-Chat](https://huggingface.co/AdaptLLM/finance-chat) and [Law-Chat](https://huggingface.co/AdaptLLM/law-chat)
+
+For example, to chat with the finance-chat model:
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+
+model = AutoModelForCausalLM.from_pretrained("AdaptLLM/finance-chat")
+tokenizer = AutoTokenizer.from_pretrained("AdaptLLM/finance-chat")
+
+# Put your input here:
+user_input = '''Use this fact to answer the question: Title of each class Trading Symbol(s) Name of each exchange on which registered
+Common Stock, Par Value $.01 Per Share MMM New York Stock Exchange
+MMM Chicago Stock Exchange, Inc.
+1.500% Notes due 2026 MMM26 New York Stock Exchange
+1.750% Notes due 2030 MMM30 New York Stock Exchange
+1.500% Notes due 2031 MMM31 New York Stock Exchange
+
+Which debt securities are registered to trade on a national securities exchange under 3M's name as of Q2 of 2023?'''
+
+# Apply the prompt template and system prompt of LLaMA-2-Chat demo for chat models (NOTE: NO prompt template is required for base models!)
+our_system_prompt = "\nYou are a helpful, respectful and honest assistant. Always answer as helpfully as possible, while being safe.  Your answers should not include any harmful, unethical, racist, sexist, toxic, dangerous, or illegal content. Please ensure that your responses are socially unbiased and positive in nature.\n\nIf a question does not make any sense, or is not factually coherent, explain why instead of answering something not correct. If you don't know the answer to a question, please don't share false information.\n" # Please do NOT change this
+prompt = f"<s>[INST] <<SYS>>{our_system_prompt}<</SYS>>\n\n{user_input} [/INST]"
+
+# # NOTE:
+# # If you want to apply your own system prompt, please integrate it into the instruction part following our system prompt like this:
+# your_system_prompt = "Please, check if the answer can be inferred from the pieces of context provided."
+# prompt = f"<s>[INST] <<SYS>>{our_system_prompt}<</SYS>>\n\n{your_system_prompt}\n{user_input} [/INST]"
+
+inputs = tokenizer(prompt, return_tensors="pt", add_special_tokens=False).input_ids.to(model.device)
+outputs = model.generate(input_ids=inputs, max_length=4096)[0]
+
+answer_start = int(inputs.shape[-1])
+pred = tokenizer.decode(outputs[answer_start:], skip_special_tokens=True)
+
+print(f'### User Input:\n{user_input}\n\n### Assistant Output:\n{pred}')
+```
+
+## Domain-Specific Tasks
+
+### Pre-templatized/Formatted Datasets
+To easily reproduce our prompting results, we have uploaded the filled-in zero/few-shot input instructions and output completions of each domain-specific task: [biomedicine-tasks](https://huggingface.co/datasets/AdaptLLM/medicine-tasks), [finance-tasks](https://huggingface.co/datasets/AdaptLLM/finance-tasks), and [law-tasks](https://huggingface.co/datasets/AdaptLLM/law-tasks).
+
+**Note:** those filled-in instructions are specifically tailored for models before alignment and do NOT fit for the specific data format required for chat models.
+
+### Raw Datasets
+We have also uploaded all the raw datasets, for fine-tuning or other usage: [ChemProt](https://huggingface.co/datasets/AdaptLLM/ChemProt)
+
+
+## Citation
+If you find our work helpful, please cite us:
+```bibtex
+@inproceedings{
+cheng2024adapting,
+title={Adapting Large Language Models via Reading Comprehension},
+author={Daixuan Cheng and Shaohan Huang and Furu Wei},
+booktitle={The Twelfth International Conference on Learning Representations},
+year={2024},
+url={https://openreview.net/forum?id=y886UXPEZ0}
+}
+```
+
+And the original dataset:
+```bibtex
+@article{ChemProt,
+  author    = {Jens Kringelum and
+               Sonny Kim Kj{\ae}rulff and
+               S{\o}ren Brunak and
+               Ole Lund and
+               Tudor I. Oprea and
+               Olivier Taboureau},
+  title     = {ChemProt-3.0: a global chemical biology diseases mapping},
+  journal   = {Database J. Biol. Databases Curation},
+  volume    = {2016},
+  year      = {2016}
+}
+```