File size: 3,625 Bytes
5032722 222dc80 5032722 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | {
"training_wkdir": "RESULTS_neuralTKF_6block_gpu",
"rng_seednum": 9,
"data_dir": "preprocess_data/DATA",
"train_dset_splits": ["CHERRIES_split0"],
"dev_dset_splits": ["CHERRIES_split1"],
"test_dset_splits": ["CHERRIES_split1"],
"toss_alignments_longer_than": 513,
"batch_size": 8,
"chunk_length": 512,
"num_epochs": 30,
"optimizer_config": {
"init_value": 1e-4,
"peak_value": 1e-4,
"end_value": 1e-4,
"warmup_steps": 0,
"weight_decay": 1e-3,
"every_k_schedule": 1
},
"early_stop_cond1_atol": 1e-3,
"early_stop_cond2_gap": 0.1,
"patience": 5,
"update_grads": true,
"use_scan_fns": false,
"interms_for_tboard": {
"sow_outputs": false,
"embeddings": false,
"gradients": false,
"weights": false,
"optimizer": false,
"forward_pass_outputs": false,
"attn_weights": false
},
"save_arrs": false,
"save_per_sample_losses": false,
"record_metrics_every_n_steps": 500,
"checkpoint_every_t_seconds": 1800,
"anc_model_type": "transformer",
"anc_enc_config": {"initial_embed_module": "EmbeddingWithPadding",
"first_block_module": "RoPETransfBlock",
"subsequent_block_module": "RoPETransfBlock",
"hidden_dim": 756,
"num_blocks": 6,
"num_heads": 6,
"dropout": 0.2,
"max_position_embeddings": 3000
},
"desc_model_type": "transformer",
"desc_dec_config": {"initial_embed_module": "EmbeddingWithPadding",
"first_block_module": "RoPETransfBlock",
"subsequent_block_module":"RoPETransfBlock",
"hidden_dim": 756,
"num_blocks": 6,
"num_heads": 6,
"dropout": 0.2,
"max_position_embeddings": 3000
},
"pred_model_type": "neural_hmm",
"pred_config": {
"load_all": false,
"subst_model_type": "f81",
"indel_model_type": "tkf92",
"global_or_local": {"equl_dist": "local",
"rate_mult": "local",
"tkf_rates": "local",
"tkf92_frag_size": "local"},
"emissions_postproc_model_type": "feedforward",
"emissions_postproc_config": {"use_anc_emb": true,
"use_desc_emb": true,
"use_prev_align_info": false,
"layer_sizes": [500],
"dropout": 0.20,
"normalize_seq_embeddings_before_block": true},
"transitions_postproc_model_type": "feedforward",
"transitions_postproc_config": {"use_anc_emb": true,
"use_desc_emb": true,
"use_prev_align_info": true,
"layer_sizes": [500],
"dropout": 0.20,
"normalize_seq_embeddings_before_block": true},
"regularization_rates": {"equl_dist":0,
"rate_mult":0,
"tkf_lambda":0,
"tkf_mu":0,
"tkf92_frag_size":0},
"times_from": "t_per_sample"
}
}
|