TF-DNA Adapters (TRAFICA PEFT tuning)

Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/adapter/adapter_config.json

@@ -1,40 +0,0 @@
-{
-  "config": {
-    "adapter_residual_before_ln": false,
-    "cross_adapter": false,
-    "factorized_phm_W": true,
-    "factorized_phm_rule": false,
-    "hypercomplex_nonlinearity": "glorot-uniform",
-    "init_weights": "bert",
-    "inv_adapter": null,
-    "inv_adapter_reduction_factor": null,
-    "is_parallel": false,
-    "learn_phm": true,
-    "leave_out": [],
-    "ln_after": false,
-    "ln_before": false,
-    "mh_adapter": false,
-    "non_linearity": "relu",
-    "original_ln_after": true,
-    "original_ln_before": true,
-    "output_adapter": true,
-    "phm_bias": true,
-    "phm_c_init": "normal",
-    "phm_dim": 4,
-    "phm_init_range": 0.0001,
-    "phm_layer": false,
-    "phm_rank": 1,
-    "reduction_factor": 16,
-    "residual_before_ln": true,
-    "scaling": 1.0,
-    "shared_W_phm": false,
-    "shared_phm_rule": true,
-    "use_gating": false
-  },
-  "hidden_size": 768,
-  "model_class": "BertModel",
-  "model_name": "Allanxu/TRAFICA",
-  "model_type": "bert",
-  "name": "SingleAdapter",
-  "version": "3.2.1"
-}

Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/adapter/pytorch_adapter.bin

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Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/peripherals/config.json

@@ -1,11 +0,0 @@
-{
-  "add_pooler": true,
-  "architectures": [
-    "TRAFICA_peripherals"
-  ],
-  "hidden_size": 768,
-  "pool_strategy": "mean",
-  "predictor_type": "classification",
-  "torch_dtype": "float32",
-  "transformers_version": "4.26.1"
-}

Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/peripherals/pytorch_model.bin

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Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/test_y.txt

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Adapters/TF_DNA_Adapters/ChIP_seq/ARID3A_HepG2_ARID3A_(NB100-279)_Stanford/test_y_hat.txt

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Adapters/TF_DNA_Adapters/ChIP_seq/ATF1_K562_ATF1_(06-325)_Harvard/peripherals/pytorch_model.bin

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-{
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Adapters/TF_DNA_Adapters/ChIP_seq/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha/adapter/pytorch_adapter.bin

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-{
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Adapters/TF_DNA_Adapters/ChIP_seq/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha/train_loss_epoch.txt

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Adapters/TF_DNA_Adapters/ChIP_seq/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha/training_setting.txt

@@ -1 +0,0 @@
-{"batch_size": 128, "lr": 0.0001, "k": 4, "n_epoch": 50, "n_epoch_tolerancech_": 3, "max_len_tokens": 512, "model_save_dir": "./ChIP_seq_finetuned_adapter/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha", "data_path": "/tmp/csyuxu/processed_ChIP_seq_DeepBind_4mer_finetuneDataFolder/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha", "vocab_path": "/home/comp/csyuxu/aptdrug/vocab_k_mer/vocab_DNA_4_mer.txt", "pretrained_model_path": "./pretrained_models/ATAC_seq_10split_4mer", "use_gpu": true}

Adapters/TF_DNA_Adapters/ChIP_seq/ATF2_H1-hESC_ATF2_(SC-81188)_HudsonAlpha/val_loss_epoch.txt

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Adapters/TF_DNA_Adapters/ChIP_seq/ATF3_H1-hESC_ATF3_HudsonAlpha/adapter/adapter_config.json

@@ -1,40 +0,0 @@
-{
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