Commit Graph

36 Commits

Author SHA1 Message Date
3cd1109249 Add event-free survival evaluation 2026-06-27 11:48:47 +08:00
df6b45b95a Clarify all-future model interpretation 2026-06-27 10:53:55 +08:00
6df0435f65 Refactor DeepHealth indices around disease expression 2026-06-26 16:25:36 +08:00
9ec3921bed Add burden trajectory plotting script 2026-06-26 12:49:21 +08:00
fb873326ee Keep burden landmark query times consistent 2026-06-26 12:24:51 +08:00
7ee29329f5 Write burden CSV shards in workers 2026-06-26 12:06:57 +08:00
263267f583 Use DataLoader for burden readouts 2026-06-26 11:50:12 +08:00
2b0b20d231 Use fork for Linux burden workers 2026-06-26 11:36:52 +08:00
c5ecbb79f2 Keep burden reduction on GPU 2026-06-26 11:27:44 +08:00
63df61e1dd Batch burden index readout computation 2026-06-26 11:15:15 +08:00
ee7d363e3d Support multi-GPU burden index computation 2026-06-26 10:51:56 +08:00
e400dab887 Add burden mapping files and landmark computation 2026-06-26 10:42:36 +08:00
a3bf3a0cd4 Add burden index computation interfaces 2026-06-25 17:15:56 +08:00
0138cbd95b Add calendar-dated event index utilities 2026-06-22 17:36:04 +08:00
56421eb3f5 Add dist_mode parameter to evaluate_landmark_auc for improved flexibility in evaluation 2026-06-22 09:40:08 +08:00
615f395058 Refactor evaluation device handling in AUC scripts for improved clarity and flexibility 2026-06-20 12:13:58 +08:00
e5ecb714ba Refactor loss computation and model input handling for improved clarity and efficiency 2026-06-20 11:26:03 +08:00
c3cac6dcea Refactor dataset.py to remove caching functionality and related methods for improved simplicity 2026-06-18 16:25:55 +08:00
aa8ec5c3ac Refactor code structure for improved readability and maintainability 2026-06-18 13:07:35 +08:00
1ea72e9133 Refactor DeepHealth model to expand extra-info token handling and update output structure 2026-06-17 14:27:07 +08:00
1757bcd25b Refactor DeepHealth model and related components
- Removed BaselineEncoder and CrossAttention classes from models.py.
- Introduced OtherInfoTokenizer for handling additional token types.
- Updated DeepHealth class to integrate OtherInfoTokenizer and manage extra pooling logic.
- Added support for extra_pool_reduce parameter to control pooling behavior.
- Modified forward methods to return structured output using DeepHealthOutput dataclass.
- Updated training scripts to accommodate changes in model architecture and output handling.
- Enhanced error handling and validation for input shapes and types.
2026-06-17 11:05:10 +08:00
27aefb2f90 Refactor run directory creation to use a unique naming function in training scripts 2026-06-15 14:54:06 +08:00
36ec36c8a8 Add time attention mask handling and baseline class time computation to DeepHealth model 2026-06-15 14:35:10 +08:00
c3e49db859 Enhance DeepHealth model to incorporate CHECKUP state tokens in next-step training and evaluation, update dataset cache versioning, and improve handling of observed event histories. 2026-06-15 14:10:09 +08:00
593ecd2e71 Revert cross-attention integration into GPTBlock 2026-06-15 10:05:13 +08:00
c87c3b9f7c Add cross-attention support to GPTBlock and update DeepHealth model integration 2026-06-13 17:02:04 +08:00
58f253d9b6 Implement parallel processing for DOA AUC evaluation and enhance task management 2026-06-13 15:45:07 +08:00
76787d2fb2 Add evaluation split handling and dataset subset size to DOA AUC evaluation 2026-06-13 15:39:31 +08:00
46a3dfe628 Add training scripts for all-future and next-step supervision with DeepHealth
- Implement `train_all_future.py` for training with query-conditioned all-future supervision.
- Implement `train_next_step.py` for training with next-token/next-time-point supervision.
- Introduce `train_util.py` for shared utility functions including logging, dataset splitting, and model checkpointing.
- Enhance argument parsing for both training scripts to accommodate new parameters.
- Update loss functions and model configurations to support the new training paradigms.
2026-06-13 11:42:04 +08:00
034d8065a7 Refactor bias handling in AUC evaluation scripts to improve robustness and prevent errors when bias is not defined 2026-06-12 17:28:22 +08:00
1240766aa9 Enhance training script and evaluation logic to support all-future model target mode and improve error handling for distribution modes 2026-06-12 11:53:35 +08:00
82f70945d9 Enhance training script to support all-future model target mode and update dataset handling 2026-06-12 11:49:44 +08:00
3125b6119f Refactor AUC evaluation scripts to support model target modes and improve distribution handling 2026-06-12 11:33:32 +08:00
0fa8bbbb9a Enhance data parsing and validation, add extra info types files
- Improved `parse_int_list` and `parse_float_list` functions to support JSON list input.
- Introduced `validate_dataset_metadata` function to ensure dataset metadata consistency with training configuration.
- Added multiple new files for extra information types, categorizing them into assessment-only, exposure-only, and combined types.
- Removed deprecated `merge_extra_info_types` function and adjusted related logic in `train.py`.
- Updated `save_config` function to accept additional metadata for training runs.
- Refactored model and training scripts for better clarity and maintainability.
2026-06-12 11:16:19 +08:00
fc8c7b7177 Refactor code structure for improved readability and maintainability 2026-06-12 10:40:48 +08:00
5e979e061b Add target construction and training script for DeepHealth model
- Implemented target construction in `targets.py` for next-token and unique-time set supervision.
- Added validation functions and utility methods for target building.
- Created a comprehensive training script in `train.py` that includes data loading, model building, optimizer setup, and training loop with early stopping and logging.
- Integrated loss functions and readout mechanisms based on target modes.
- Established dataset splitting and DataLoader configurations for training, validation, and testing.
2026-06-12 10:28:16 +08:00