dila model and ablation script#3
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david-dozer merged 7 commits intodict_label_attnfrom Apr 18, 2026
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* rename arg name for chefer * Initial attempts to fix the interpretability target_class_idx * Support negative prediction for interpretability metric. * Fix tests * Fix more tests * Revert "Support negative prediction for interpretability metric." This reverts commit fe8c8ad. * Reapply "Support all samples for interpretability metric" * Initial attempt for the filter * Fixup * Fix sample_class handling * fixup * fix test * Fix arg name * Add example * fix docs
…sunlabuiuc#927) * small fix + bump to pyproject.toml ver. for bug fixed release on pypi * We don't really have someone qualified for a second review, and this broken CI is leading to a lot of issues here. Will revert if it doesn't resolve here.
Add test_rnn.py with 12 test cases covering: TestRNN (8 tests): - Model initialization with correct attributes - Forward pass output structure and shapes - Backward pass gradient propagation - Embedding extraction via embed=True - Custom hyperparameters (embedding_dim, hidden_dim) - LSTM cell type variant - Vanilla RNN cell type variant - Bidirectional RNN variant TestMultimodalRNN (4 tests): - Initialization with correct sequential/non-sequential classification - Forward pass with mixed modalities (sequence + multi_hot + tensor) - Backward pass gradient propagation - Embedding extraction with correct mixed-modality dimensions Follows the established test pattern from test_mlp.py and test_tcn.py using create_sample_dataset with synthetic data. Ref sunlabuiuc#425
* Fixed repo to be able to run TUEV/TUAB + updated example scripts * Args need to be passed correctly * Minor fixes and precomputed STFT logic * Fix the test files to reflect codebase changes * Args update * test script fixes * dataset path update * fix contrawr - small change * divide by 0 error * Incorporate tfm logic * Fix label stuff * tuab fixes * fix metrics * aggregate alphas * Fix splitting and add tfm weights * fix tfm+tuab * updates scripts and haoyu splitter * fix conflict * Remove weightfiles from tracking and add to .gitignore Weight files are large binaries distributed separately; untrack all existing .pth files under weightfiles/ and add weightfiles/ to .gitignore so they are excluded from future commits and the PR. Made-with: Cursor * normalization = 95% * temporarily re-add weight files * 16 workers * tuab sanity check * consistent log outputs * test tuab * change back to multiclass * update conformal scripts * remove weightfiles * oops * fix tests
* feat: migrate GRASP model from PyHealth 1.0 to 2.0 API Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * feat: add GRASP mortality prediction notebook and fix cluster_num Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * Restore code_mapping support in SequenceProcessor for PyHealth 2.0 Adds optional code_mapping parameter to SequenceProcessor that maps granular medical codes to grouped vocabularies (e.g. ICD9CM→CCSCM) before building the embedding table. Resolves the functional gap from the 1.x→2.0 rewrite where code_mapping was removed. Ref sunlabuiuc#535 Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> * Add RNN baseline and code_mapping comparison notebooks for MIMIC-III Two identical notebooks for A/B testing code_mapping impact on mortality prediction. Only difference is the schema override in Step 2. Both use seed=42 for reproducible splits. Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> * fix(tasks): extract NDC codes instead of drug names for prescription mapping event.drug returns drug names (e.g. "Aspirin") which produce zero matches in CrossMap NDC→ATC; event.ndc returns actual NDC codes enabling 3/3 feature mapping for mortality and readmission tasks. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * test(tasks): add tests verifying NDC extraction in drug tasks Checks that mortality and readmission task processors build vocabulary from NDC codes (numeric strings) rather than drug names (e.g. "Aspirin"), confirming the event.drug -> event.ndc fix works correctly. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * fix(tasks): fix missed MortalityPredictionMIMIC4 event.drug and update docs - Fix event.drug -> event.ndc in MortalityPredictionMIMIC4 (line 282) - Update readmission task docstrings to reflect NDC extraction Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * fix(tasks): fix DrugRecommendationMIMIC3 to extract NDC codes DrugRecommendationMIMIC3 used prescriptions/drug (drug names) via Polars column select; changed to prescriptions/ndc to match MIMIC-4 variant and enable NDC->ATC code mapping. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * fix(models): guard RNNLayer and ConCare against zero-length sequences RNNLayer: clamp sequence lengths to min 1 so pack_padded_sequence does not crash on all-zero masks, matching TCNLayer (tcn.py:186). ConCare: guard covariance divisor with max(n-1, 1) to prevent ZeroDivisionError when attention produces single-element features. Both edge cases are triggered when code_mapping collapses vocabularies and some patients have all codes map to <unk>, producing all-zero embeddings and all-zero masks. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * docs: add docstrings to SequenceProcessor class and fit method Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * docs: add docstrings, type hints, and fix test dims for GRASP module Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * feat: add GRASP mortality prediction notebooks for baseline and code_mapping Baseline notebook runs GRASP with raw ICD-9/NDC codes. Code_mapping notebook collapses vocab via ICD9CM→CCSCM, ICD9PROC→CCSPROC, NDC→ATC for trainable embeddings on full MIMIC-III. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * fix(models): guard ConCare and GRASP against batch_size=1 crashes - ConCare FinalAttentionQKV: bare .squeeze() removed batch dim when batch_size=1, causing IndexError in softmax. Use .squeeze(-1) and .squeeze(1) to target only the intended dimensions. - ConCare cov(): division by zero when x.size(1)==1. Guard with max(). - GRASP grasp_encoder: remove stale torch.squeeze(hidden_t, 0) that collapsed [1, hidden] to [hidden] with batch_size=1. Both RNNLayer and ConCareLayer already return [batch, hidden]. - GRASP random_init: clamp num_centers to num_points to prevent ValueError when cluster_num > batch_size. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * feat: add GRASP mortality prediction notebooks for baseline and code_mapping Baseline notebook runs GRASP with raw ICD-9/NDC codes. Code_mapping notebook collapses vocab via ICD9CM→CCSCM, ICD9PROC→CCSPROC, NDC→ATC for trainable embeddings on full MIMIC-III. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * Add code_mapping as task __init__ argument Allow tasks to accept a code_mapping dict that upgrades input_schema entries so SequenceProcessor maps raw codes (e.g. ICD9CM) to grouped vocabularies (e.g. CCSCM) at fit/process time. This avoids manual schema manipulation after task construction. - Add code_mapping parameter to BaseTask.__init__() - Thread **kwargs + super().__init__() through all task subclasses with existing __init__ methods (4 readmission tasks, 1 multimodal mortality task) - Add 17 tests covering SequenceProcessor mapping and task-level code_mapping initialization Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * Update code_mapping notebook to use task init argument Replace manual task.input_schema override with the new code_mapping parameter on MortalityPredictionMIMIC3(). Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * feat(examples): add ConCare hyperparameter grid sweep script Mirrors the GRASP+ConCare mortality notebook pipeline exactly (same tables, split, seed, metrics) but sweeps 72 configurations of embedding_dim, hidden_dim, cluster_num, lr, and weight_decay. Results are logged to sweep_results.csv. Supports --root for pointing at local MIMIC-III, --code-mapping, --dev, and --monitor. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * chore(sweep): increase early stopping patience from 10 to 15 epochs Smaller ConCare configs (embedding_dim=8/16) may learn slower and need more epochs before plateauing. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * Initial plan * fix: filter falsy NDCs, guard None tokens in process(), fix NDC regex Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-authored-by: ddhangdd <43976109+ddhangdd@users.noreply.github.com> * refactor(sweep): rename and generalize sweep script for all backbones Rename sweep_concare_grasp.py → sweep_grasp.py. Now supports --block GRU|ConCare|LSTM with per-backbone default grids, --resume for crash recovery, --grid JSON override, auto-dated output dirs (sweep/{BLOCK}_{YYYYMMDD}_{HHMMSS}_{mapping}/), and config.json saved alongside results for reproducibility. Co-Authored-By: Colton Loew <colton.loew@gmail.com> Co-Authored-By: lookman-olowo <lookmanolowo@hotmail.com> Co-Authored-By: christiana-beard <christyanamarie116@gmail.com> Co-Authored-By: ddhangdd <dfung2@wisc.edu> * test(sweep): add unit and integration tests for sweep_grasp utilities Covers grid building, combo hashing, CSV resume parsing, output directory naming, and end-to-end single-config runs for GRU and ConCare on synthetic data (13 tests, all passing). Co-Authored-By: Colton Loew <loewcx@illinois.edu> Co-Authored-By: lookman-olowo <lookman-olowo@github.com> Co-Authored-By: christiana-beard <christiana-beard@github.com> Co-Authored-By: ddhangdd <ddhangdd@github.com> * docs(sweep): add tmux copy-paste instructions for each paper run Co-Authored-By: Colton Loew <loewcx@illinois.edu> Co-Authored-By: lookman-olowo <lookman-olowo@github.com> Co-Authored-By: christiana-beard <christiana-beard@github.com> Co-Authored-By: ddhangdd <ddhangdd@github.com> * chore(examples): adds cleans examples, removes util script * Delete tests/core/test_grasp.py we removed grasp script from examples, dropped test * Revert "Delete tests/core/test_grasp.py" This reverts commit 0d95758. * fix: remove orphaned sweep test, restore grasp tests * feat(grasp): add static_key support for demographic features with tests * fix(test): add valid NDC to test prescriptions so readmit test produces both labels --------- Co-authored-by: lookman-olowo <lookmanolowo@hotmail.com> Co-authored-by: christiana-beard <christyanamarie116@gmail.com> Co-authored-by: ddhangdd <dfung2@wisc.edu> Co-authored-by: Lookman Olowo <42081779+lookman-olowo@users.noreply.github.com> Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: ddhangdd <43976109+ddhangdd@users.noreply.github.com> Co-authored-by: ddhangdd <desmondfung123@gmail.com> Co-authored-by: Colton Loew <loewcx@illinois.edu> Co-authored-by: lookman-olowo <lookman-olowo@github.com> Co-authored-by: christiana-beard <christiana-beard@github.com> Co-authored-by: ddhangdd <ddhangdd@github.com> Co-authored-by: lookman-olowo <lookman-olowo@users.noreply.github.com>
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