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pretraining_config/data_config.json

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+{"transcript_save_dir": "/data1/morrisq/ian/rna_contrast/transcripts", "n_tracks": 6, "proportion_to_mask": 0.15, "short_transcript_map_path": "/data1/morrisq/ian/rna_contrast/maps/COMB-eutheria-splice_all_basic_shorter.pkl", "long_transcript_map_path": "/data1/morrisq/ian/rna_contrast/maps/COMB-eutheria-splice_all_basic_longer.pkl", "transcript_type": "all"}

pretraining_config/model_config.json

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+{"model_class": "ssm", "ssm_model_dim": 512, "ssm_n_layers": 6, "n_tracks": 4, "predict_splice_codon": false, "predict_masked": false, "bidirectional": false, "gradient_checkpointing": false}

pretraining_config/optimizer_config.json

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+{"model_lr": 0.001, "model_weight_decay": 5e-05, "projection_head_lr": 0.001, "projection_head_weight_decay": 0.0001, "max_weight_decay": -1, "loss_fn": "dcl", "clipnorm": 5, "warmup_steps": 2000.0}

pretraining_config/projector_config.json

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+{"projection_body": 512, "projection_head_size": 128, "projection_norm_type": "batchnorm", "representation_dim": 512}

pretraining_config/train_config.json

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+{"rand_seed": 0, "number_steps": 20000, "mixed_precision": true, "wandb_run_dir": "/home/dalalt1/compute/Orthrus/runs", "split_by_length": true, "gpu_batch_sizes": [50, 150, 50], "mask_prop": 0.0, "note": ""}