cehrgpt 0.0.2__py3-none-any.whl → 0.1.1__py3-none-any.whl
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- cehrgpt/analysis/irregularity.py +36 -0
- cehrgpt/data/hf_cehrgpt_dataset.py +25 -4
- cehrgpt/data/hf_cehrgpt_dataset_collator.py +635 -97
- cehrgpt/data/hf_cehrgpt_dataset_mapping.py +308 -95
- cehrgpt/data/sample_packing_sampler.py +181 -0
- cehrgpt/generation/generate_batch_hf_gpt_sequence.py +12 -9
- cehrgpt/generation/omop_converter_batch.py +32 -2
- cehrgpt/gpt_utils.py +20 -2
- cehrgpt/models/config.py +35 -0
- cehrgpt/models/hf_cehrgpt.py +470 -106
- cehrgpt/models/hf_modeling_outputs.py +1 -0
- cehrgpt/models/special_tokens.py +1 -0
- cehrgpt/models/tokenization_hf_cehrgpt.py +358 -71
- cehrgpt/runners/data_utils.py +358 -0
- cehrgpt/runners/gpt_runner_util.py +0 -10
- cehrgpt/runners/hf_cehrgpt_finetune_runner.py +181 -283
- cehrgpt/runners/hf_cehrgpt_pretrain_runner.py +288 -112
- cehrgpt/runners/hf_gpt_runner_argument_dataclass.py +90 -0
- cehrgpt/runners/hyperparameter_search_util.py +10 -8
- cehrgpt/runners/sample_packing_trainer.py +185 -0
- cehrgpt/simulations/generate_plots.py +95 -0
- cehrgpt/simulations/run_simulation.sh +24 -0
- cehrgpt/simulations/time_embedding_simulation.py +250 -0
- cehrgpt/simulations/time_token_simulation.py +177 -0
- cehrgpt/time_to_event/config/1_year_cabg.yaml +23 -0
- cehrgpt/time_to_event/time_to_event_model.py +2 -13
- cehrgpt/time_to_event/time_to_event_prediction.py +27 -13
- cehrgpt/tools/linear_prob/__init__.py +0 -0
- cehrgpt/tools/linear_prob/compute_cehrgpt_features.py +495 -0
- cehrgpt/tools/linear_prob/train_with_cehrgpt_features.py +152 -0
- {cehrgpt-0.0.2.dist-info → cehrgpt-0.1.1.dist-info}/METADATA +11 -8
- {cehrgpt-0.0.2.dist-info → cehrgpt-0.1.1.dist-info}/RECORD +36 -32
- {cehrgpt-0.0.2.dist-info → cehrgpt-0.1.1.dist-info}/WHEEL +1 -1
- cehrgpt/data/hf_cehrgpt_dpo_collator.py +0 -71
- cehrgpt/data/hf_cehrgpt_dpo_dataset_mapping.py +0 -61
- cehrgpt/generation/generate_paired_cehrgpt_sequence.py +0 -224
- cehrgpt/rl_finetune/cehrgpt_dpo_trainer.py +0 -586
- cehrgpt/rl_finetune/cehrgpt_ppo_trainer.py +0 -464
- cehrgpt/rl_finetune/ppo_finetune.py +0 -394
- cehrgpt/rl_finetune/ppo_finetune_v2.py +0 -373
- cehrgpt/runners/hf_cehrgpt_dpo_runner.py +0 -119
- /cehrgpt/{rl_finetune → simulations}/__init__.py +0 -0
- {cehrgpt-0.0.2.dist-info → cehrgpt-0.1.1.dist-info/licenses}/LICENSE +0 -0
- {cehrgpt-0.0.2.dist-info → cehrgpt-0.1.1.dist-info}/top_level.txt +0 -0
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@@ -85,6 +85,7 @@ class CehrGptCausalLMOutput(ModelOutput):
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time_token_loss: Optional[torch.FloatTensor] = None
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time_to_visit_loss: Optional[torch.FloatTensor] = None
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token_value_loss: Optional[torch.FloatTensor] = None
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motor_tte_loss: Optional[torch.FloatTensor] = None
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@dataclass
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