Learnable mask token + Kronecker marker covariance GP - #22

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feat/kronecker-learnmask

Commits on Mar 17, 2026

Add SLURM training scripts and fix Comet.ml logging

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9b343c8
Fix scheduler resumption from checkpoint and set 100 epochs for GP training

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9b1baea

Commits on Mar 23, 2026

Add reset_lr_schedule flag for fresh cosine cycle on resumption

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7a58ad4
Fix empty training loop and total_steps mismatch on fresh LR reset

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a5a42a6

Commits on Apr 3, 2026

feat(logging): add variance-MSE correlation metrics to validation logging
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0fc9385
docs: add design spec for Kronecker marker covariance extension

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880159f
docs: add implementation plan for Kronecker marker covariance

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54a7d00
feat: add marker covariance config fields to TrainingConfig
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7a75fb4
feat: add KroneckerMarkerCovariance with triple Kronecker solver

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ac2d7db
feat: add log_prob_joint and compute_marker_correlation to KroneckerMarkerCovariance

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7cb4381
feat: add KroneckerMarkerGPNLLLoss and HybridKroneckerMarkerGPNLLLoss

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996f14e
feat: wire up KroneckerMarkerCovariance instantiation and optimizer in training script

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6579687
feat: extract marker embeddings and pass to marker GP loss in training loop

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80b7b0a
feat: wire up marker covariance in validation loop and add diagnostics logging

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30deac0
feat: export KroneckerMarkerCovariance from modules and add marker GP config

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049dd3f
test: add end-to-end smoke test for marker covariance training step
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5209b1c
fix: scalar loss shape and loosen float32 solver tolerances in tests
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6fa2249
fix: move KroneckerMarkerCovariance to device after instantiation
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0d462e5

Commits on Apr 4, 2026

Commits on Apr 27, 2026

feat: add use_mask_token and mask_token_init fields to EncoderConfig
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b455490
feat: add learnable mask token to MultiplexImageEncoder

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3615368
fix: remove unused import copy from immuvis.py
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6f41cc8
feat: propagate spatial_mask through MultiplexAutoencoder and add architecture config utilities

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bbde14b
feat: add mask_token param to log_training_metrics

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eac84ff
feat: add train_masked_model_learnmask training script and get_pixel_mask utility

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5c589e3
fix: resolve mypy type errors in train_masked_model_learnmask
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f85668d

Commits on Apr 29, 2026

feat: add learnmask training config and train.sh learnmask mode

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0698fa0

Commits on May 4, 2026

fix: source .bashrc in train.sh to load COMET_API_KEY for SLURM jobs

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7ec853c
fix: extract COMET_API_KEY from .bashrc via grep instead of sourcing

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af8123b
fix: use cut instead of grep -P to extract COMET_API_KEY from .bashrc

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1a4d729

Commits on May 11, 2026

chore: resume from ImVs-29 checkpoint and bump walltime to 7 days

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7cefa19

Commits on May 19, 2026

feat: merge learnmask mask token with Kronecker marker GP training
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e6bc61c
chore: bump learnmask resume checkpoint to ImVs-30
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fb736cc
fix: resolve merge conflict with gp branch in GP config printout

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a1d3b2b
fix: address PR review issues 1-15 (guards, validators, tests)

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f31184a
chore: remove local-only files from tracking (DS_Store, CLAUDE.md, docs/superpowers)

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9f89beb

Commits on May 20, 2026

fix: address Copilot review comments on PR #22

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fbaff70

Commits on Jun 15, 2026

fix: disambiguate parallel run names with SLURM job id

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b52701e

Commits on Jul 22, 2026

feat: add marker covariance (K_C) analysis for kronecker-learnmask

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ffd4edf
feat: add K_C downstream analysis (error-correlation and redundancy tests)

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e5526d2