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README.md

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+# PlasmidGPT Model
+
+This is a GPT-2 based model for engineered plasmid sequence generation, converted from PyTorch `.pt` format to HuggingFace transformers format.
+
+This is a supervised fine-tuned (SFT) version of [PlasmidGPT](https://github.com/lingxusb/PlasmidGPT) for engineered plasmids. This work was done by **Angus Cunningham** while at **Prof. Chris Barnes' lab at UCL**.
+
+## Model Details
+
+- **Architecture**: GPT-2
+- **Vocab Size**: 30,002
+- **Hidden Size**: 768
+- **Number of Layers**: 12
+- **Number of Heads**: 12
+- **Max Position Embeddings**: 2048
+- **Parameters**: ~124M
+
+## Usage
+
+```python
+from transformers import AutoModelForCausalLM, AutoTokenizer
+
+model = AutoModelForCausalLM.from_pretrained("./plasmidgpt-model")
+tokenizer = AutoTokenizer.from_pretrained("./plasmidgpt-model")
+
+# Basic generation
+inputs = tokenizer("ATGC", return_tensors="pt")
+outputs = model.generate(**inputs, max_length=100)
+generated_sequence = tokenizer.decode(outputs[0], skip_special_tokens=True)
+print(generated_sequence)
+
+# With sampling (for more diverse outputs)
+outputs = model.generate(**inputs, max_length=100, do_sample=True, temperature=0.8, top_p=0.9)
+generated_sequence = tokenizer.decode(outputs[0], skip_special_tokens=True)
+print(generated_sequence)
+```
+
+### Example Outputs
+
+**Input:** `ATGCGATCG`  
+**Generated:** `ATGCGATCGGTGGTAGGCACTGGATGATGGCCCTGCAGTGTAGCCGTAGTTATGAGCCTCGGGATTCTTTGATGATTCAGCCACCCTCATCATCCTCCTCCTCC...`
+
+**Input:** `ATGGCC`  
+**Generated:** `ATGGCCTACATACCTTCAATTACCGAAACAAGGTGGTTCATCTCTAACGCTGTCCATAAAACCGCCCAGTCTAGCTATCGCCATTTGCGCATCTAACGTGGTAGGCACTCCGGGTCCGCGCC...`
+
+## Compatible With
+
+This model is compatible with the architecture from [McClain/plasmidgpt-addgene-gpt2](https://huggingface.co/McClain/plasmidgpt-addgene-gpt2), but with different weights from the pretrained model.
+
+## Files
+
+- `config.json`: Model configuration
+- `generation_config.json`: Generation parameters
+- `model.safetensors`: Model weights in SafeTensors format
+- `tokenizer.json`: Fast tokenizer data
+- `tokenizer_config.json`: Tokenizer configuration
+- `special_tokens_map.json`: Special token mappings

config.json

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+{
+  "activation_function": "gelu_new",
+  "architectures": [
+    "GPT2LMHeadModel"
+  ],
+  "attn_pdrop": 0.1,
+  "bos_token_id": 50256,
+  "dtype": "float32",
+  "embd_pdrop": 0.1,
+  "eos_token_id": 50256,
+  "initializer_range": 0.02,
+  "layer_norm_epsilon": 1e-05,
+  "model_type": "gpt2",
+  "n_ctx": 2048,
+  "n_embd": 768,
+  "n_head": 12,
+  "n_inner": null,
+  "n_layer": 12,
+  "n_positions": 2048,
+  "reorder_and_upcast_attn": false,
+  "resid_pdrop": 0.1,
+  "scale_attn_by_inverse_layer_idx": false,
+  "scale_attn_weights": true,
+  "summary_activation": null,
+  "summary_first_dropout": 0.1,
+  "summary_proj_to_labels": true,
+  "summary_type": "cls_index",
+  "summary_use_proj": true,
+  "task_specific_params": {
+    "text-generation": {
+      "do_sample": true,
+      "max_length": 50
+    }
+  },
+  "transformers_version": "4.57.1",
+  "use_cache": true,
+  "vocab_size": 30002
+}

generation_config.json

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+{
+  "_from_model_config": true,
+  "bos_token_id": 50256,
+  "eos_token_id": 50256,
+  "transformers_version": "4.57.1"
+}

model.safetensors

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+version https://git-lfs.github.com/spec/v1
+oid sha256:437b7ecef6996e7c8cc523b59c2aaa492f344e17320551f2b797369f50b881f7
+size 489030728

special_tokens_map.json

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+{
+  "bos_token": {
+    "content": "<s>",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "eos_token": {
+    "content": "[SEP]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "[PAD]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
+}

tokenizer_config.json

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+{
+  "added_tokens_decoder": {
+    "0": {
+      "content": "[UNK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "1": {
+      "content": "[CLS]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "2": {
+      "content": "[SEP]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "3": {
+      "content": "[PAD]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "4": {
+      "content": "[MASK]",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "30000": {
+      "content": "<s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    },
+    "30001": {
+      "content": "</s>",
+      "lstrip": false,
+      "normalized": false,
+      "rstrip": false,
+      "single_word": false,
+      "special": true
+    }
+  },
+  "bos_token": "<s>",
+  "clean_up_tokenization_spaces": false,
+  "eos_token": "[SEP]",
+  "extra_special_tokens": {},
+  "max_length": null,
+  "model_max_length": 1000000000000000019884624838656,
+  "pad_to_multiple_of": null,
+  "pad_token": "[PAD]",
+  "pad_token_type_id": 0,
+  "padding_side": "left",
+  "tokenizer_class": "PreTrainedTokenizerFast"
+}