| { | |
| "training_wkdir": "RESULTS_transformer-TKF", | |
| "rng_seednum": 75, | |
| "data_dir": "example_data", | |
| "train_dset_splits": ["sevenSamp"], | |
| "dev_dset_splits": ["sevenSamp"], | |
| "test_dset_splits": ["sevenSamp"], | |
| "toss_alignments_longer_than": null, | |
| "chunk_length": 512, | |
| "batch_size": 7, | |
| "num_epochs": 3, | |
| "optimizer_config": { | |
| "init_value": 1e-4, | |
| "peak_value": 1e-4, | |
| "end_value": 1e-4, | |
| "warmup_steps": 0, | |
| "weight_decay": 1e-4, | |
| "every_k_schedule": 1 | |
| }, | |
| "early_stop_cond1_atol": 1e-3, | |
| "early_stop_cond2_gap": 0.5, | |
| "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": 20, | |
| "num_blocks": 1, | |
| "num_heads": 2, | |
| "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": 20, | |
| "num_blocks": 1, | |
| "num_heads": 2, | |
| "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": [20], | |
| "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": [20], | |
| "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" | |
| } | |
| } | |