The main-header HTML at the top of the page still spelled TRACE
('Trace Recognition and Amortized Conditional Estimation') because
the previous global rename couldn't match the phrase when each
initial letter is individually wrapped in <strong>. Replace with
the correct SPARK expansion: Simulation-based Posterior Amortization
for Reaction Kinetics.
Co-authored-by: Cursor <cursoragent@cursor.com>
The main-header HTML at the top of the page still spelled TRACE
('Trace Recognition and Amortized Conditional Estimation') because
the previous global rename couldn't match the phrase when each
initial letter is individually wrapped in <strong>. Replace with
the correct SPARK expansion: Simulation-based Posterior Amortization
for Reaction Kinetics.
Co-authored-by: Cursor <cursoragent@cursor.com>
- Full name: 'Simulation-based Posterior Amortization for Reaction Kinetics'
- Class TRACEPredictor -> SPARKPredictor; env vars TRACE_* -> SPARK_*
- Updated README, app.py title/info, all docstrings and comments.
- No model architecture or checkpoint format changes.
Co-authored-by: Cursor <cursoragent@cursor.com>
- ec_joint_best.pt + tpd_joint_best.pt now contain the OOD-equipped
joint checkpoints (val AUROC 0.965 EC, 0.967 TPD); From-Image tab
will show OOD warnings under joint mode just like the headline path.
- Add image_encoder.py (imported by multi_mechanism_model.py and
tpd_model.py for the Phase-2 joint encoder) and image_preprocessing.py
(used by app.py for auto-crop + gridline removal preview).
Co-authored-by: Cursor <cursoragent@cursor.com>
- Add EC/TPD Phase-2 joint (image+waveform) checkpoints
- Add EC/TPD Phase-1 image-only checkpoints
- multi_mechanism_model.py / tpd_model.py: add input_mode='image+waveform'
with parallel image + signal encoders fused via joint_fusion MLP
- inference.py: load joint checkpoints, predict_*_joint, hybrid path
routes through new joint result tuple; auto-detect input_mode from
state_dict for older Phase-1 checkpoints
- app.py: From-Image hybrid pipeline (Image-direct / Digitize-then-infer
/ Ensemble / Auto-fallback / Joint Phase-2), method-comparison HTML
panel, preprocessed-image preview, radio default auto-flips to
'Joint image+waveform (Phase 2)' when joint env vars are set
New env vars to set in HF Space:
TRACE_EC_IMAGE_CHECKPOINT=checkpoints/ec_image_best.pt
TRACE_TPD_IMAGE_CHECKPOINT=checkpoints/tpd_image_best.pt
TRACE_EC_JOINT_CHECKPOINT=checkpoints/ec_joint_best.pt
TRACE_TPD_JOINT_CHECKPOINT=checkpoints/tpd_joint_best.pt
Co-authored-by: Cursor <cursoragent@cur…
From-Image: gallery shows the input plots (not pre-rendered outputs); add note that digitized curves often trigger OOD
