initial commit

README.md

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+# iSEEEK
+Generative pretraining from the rankings of top expressing genes. 
+Finetune on `transcriptome-1024-8-16-128` for 10 epochs with a sequence length of 128.
+

config.json

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+{
+  "activation_function": "gelu_new",
+  "architectures": [
+    "GPT2LMHeadModel"
+  ],
+  "attn_pdrop": 0.1,
+  "bos_token_id": 1,
+  "embd_pdrop": 0.1,
+  "eos_token_id": 2,
+  "gradient_checkpointing": false,
+  "initializer_range": 0.02,
+  "layer_norm_epsilon": 1e-05,
+  "model_type": "gpt2",
+  "n_ctx": 1024,
+  "n_embd": 1024,
+  "n_head": 16,
+  "n_inner": null,
+  "n_layer": 8,
+  "n_positions": 1024,
+  "pad_token_id": 0,
+  "resid_pdrop": 0.1,
+  "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,
+  "torch_dtype": "float32",
+  "transformers_version": "4.10.0",
+  "use_cache": true,
+  "vocab_size": 21150
+}

copy.sh

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+cp /data/ai/gene_expression/gpt2/gpt2-1024-8-16-128/config.json ./
+cp /data/ai/gene_expression/gpt2/gpt2-1024-8-16-128/pytorch_model.bin ./
+cp /data/ai/gene_expression/gpt2/gpt2tokenizer/* ./

pytorch_model.bin

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+version https://git-lfs.github.com/spec/v1
+oid sha256:d0f3c042aaa39eb6f05e5af86b9aacf91ec37e4bbe40bdb264b72a364b19123b
+size 502345283

special_tokens_map.json

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+{"bos_token": "</b>", "eos_token": "</s>", "unk_token": "<unk>", "pad_token": "<pad>"}

tokenizer_config.json

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+{"model_max_length": 1024, "pad_token": "<pad>", "eos_token": "</s>", "bos_token": "</b>", "unk_token": "<unk>", "tokenizer_class": "PreTrainedTokenizerFast"}