diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..454a82120b690a5bf19382177b73d04712480283 --- /dev/null +++ b/README.md @@ -0,0 +1,61 @@ +--- +license: apache-2.0 +tags: + - protein + - biology + - protein-language-model + - continual-learning +library_name: transformers +--- + +# CoPeP Continual Learning Checkpoints + +This repository contains **90 checkpoints** from continual +learning experiments with the [AMPLIFY](https://huggingface.co/chandar-lab/AMPLIFY_120M) +protein language model (120M parameters). + +## Loading a checkpoint + +```python +from transformers import AutoModel + +model = AutoModel.from_pretrained( + "chandar-lab/copep-checkpoints", + subfolder="replay/task_5", + trust_remote_code=True, +) +``` + +## Available checkpoints + +| Method | Tasks | +|--------|-------| +| `continual` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `gradient_ascent` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `hare_tortoise` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `joint` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `match` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `random_labels` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `replay` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `shrink_perturb` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | +| `single_year` | task_0, task_1, task_2, task_3, task_4, task_5, task_6, task_7, task_8, task_9 | + + +Each `task_N` subfolder contains a `config.json` and `model.safetensors`. + +### Task mapping + +- **task_0** : pre-2004 (base model) +- **task_1** – **task_9** : successive temporal splits of UniRef data + +For methods that start from task_1 (continual, gradient_ascent, match, +random_labels, replay, shrink_perturb), `task_0` is the same checkpoint as +`single_year/task_0` (the base pre-trained model). + +## Model architecture + +- **Architecture:** Transformer encoder with RoPE + SwiGLU +- **Parameters:** ~120M +- **Config:** hidden_size=640, num_hidden_layers=24, num_attention_heads=10, intermediate_size=2560 +- **Vocab size:** 32 (amino acid tokens + special tokens) +- **Max length:** 512 (training), 50000 (inference with RoPE extrapolation) diff --git a/continual/task_1/config.json b/continual/task_1/config.json new file mode 100644 index 0000000000000000000000000000000000000000..b24d7784e2767e08cfd410d465fecae1070aeb00 --- /dev/null +++ b/continual/task_1/config.json @@ -0,0 +1,26 @@ +{ + "architectures": [ + "AMPLIFY" + ], + "auto_map": { + "AutoConfig": "modeling_amplify.AMPLIFYConfig", + "AutoModel": "modeling_amplify.AMPLIFY", + "AutoModelForMaskedLM": "modeling_amplify.AMPLIFY" + }, + "base_scale": 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