Skip to content

Massive cleanup for paper submission - #87

Merged
StevenSong merged 33 commits into
mainfrom
large-user-study
Oct 10, 2026
Merged

StevenSong merged 33 commits into
mainfrom
large-user-study

Conversation

@StevenSong

Copy link
Copy Markdown
Owner

Alot of things drifted between initial experimentation, initial paper submission, rebuttal experiments, and paper resubmission. This PR aims to clean all that up and also adds in some extended experiments we're conduction. A high level list of changes is below:

  • add protossl/models/_protoecgnet.py and protossl/protoecgnet_trainer.py which enables multiarm ProtoECGNet (1D-global, 2D-global, 2D-partial arms), a fusion classifier, a fusion-embedding stage, tuning, and bootstrapped evaluation, all trained over HEEDB. Configs, scripts, and notebooks are under large-user-study/.
  • adds heedb_split_type to split HEEDB other than by year, and drop_blank_overread to drop ECGs with no physician overread.
  • add USE_HEEDB_150 env var toggle to switch to the 150-label HEEDB target set. Adds pretraining configs and scripts for ProtoSSL and supervised prototypes on this set
  • add BlackboxContraster model and train-contraster stage for baseline PCLR pretraining over HEEDB. Adds PCLR embedding extraction and a logistic-regression probe on those embeddings (5-3-run-pclr-logreg.sh, queue-pclr-logreg.sh).
  • add data_wrapper_kwargs to LitData in trainer for the contrastive wrapper datasets, and data_kwargs now goes to the base dataset
  • rename experiments to match the paper: labsup-proto/prosup → supproto and pass → protossl across scripts and run directories
  • better modularization for ECG waveform plotting (full and segment views, baseline-wander removal, axis layout).
  • cleanup of README (new paper title, bibtex citation, repo layout table, data sources, steps to reproduce, experiment naming scheme, environment variables, license)

@StevenSong
StevenSong merged commit c96c1b3 into main Oct 10, 2026
2 checks passed
@StevenSong
StevenSong deleted the large-user-study branch October 10, 2026 21:55
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant