Issues

• exp: what contacts-v1 computes (representations, neurons, circuit)

  Open-Athena/MarinFold#372 · Filter by author jsilter opened on Oct 27, 2026
  1

• exp: default-model contact spiking, length dependence, and AFDB error preference

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#369 · Filter by author timodonnell opened on Oct 21, 2026

• exp: proofreader guided inference for accurate contact maps

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#368 · Filter by author timodonnell opened on Oct 21, 2026

• exp: ProteinMPNN-only training for two epochs with a learning-rate sweep

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#364 · Filter by author timodonnell opened on Oct 13, 2026
  9

• exp: double the channel width of the default exp277 model

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#363 · Filter by author timodonnell opened on Oct 13, 2026
  16

• exp: smaller-model scaling on the full default corpus

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#362 · Filter by author timodonnell opened on Oct 13, 2026

• exp: diagnose training versus AFDB validation contact accuracy

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#357 · Filter by author timodonnell opened on Oct 9, 2026

• exp: bidirectional proofreading of MarinFold rollouts on experimental PDB structures

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#356 · Filter by author timodonnell opened on Oct 9, 2026

• exp: eval-val contact precision and historical CASP context

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#352 · Filter by author timodonnell opened on Oct 8, 2026

• exp: curate 30%-held-out experimental complexes and evaluate contacts plus Helico structures

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#350 · Filter by author timodonnell opened on Oct 5, 2026
  8

• exp: fine-tune Qwen3.5 base models for protein contacts

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#347 · Filter by author timodonnell opened on Oct 2, 2026
  19

• exp: qualitative contact-map errors on eval-val

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#345 · Filter by author timodonnell opened on Sep 30, 2026

• exp: train 1.5B on the exp277 corpus plus the predicted-complex corpus

  agent-generatedexperimentkind/models
  Open-Athena/MarinFold#343 · Filter by author timodonnell opened on Sep 28, 2026
  4

• exp: Interpretability of contacts-v1: chain reconstruction, contact heads, and memorization vs coevolution

  experiment
  Open-Athena/MarinFold#341 · Filter by author jsilter opened on Sep 28, 2026
  3

• exp: diagnose prediction diversity and accuracy bottlenecks

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#339 · Filter by author timodonnell opened on Sep 26, 2026

• exp: quantify structure-aware sequence deduplication of the training corpus

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#336 · Filter by author timodonnell opened on Sep 25, 2026
  3

• exp: Helico confidence for Rosetta decoy ranking

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#335 · Filter by author timodonnell opened on Sep 25, 2026
  5

• exp: random alanine masking for oracle rollouts

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#333 · Filter by author timodonnell opened on Sep 24, 2026
  2

• exp: geometry-aware whole-map medoid branching

  agent-generatedexperiment
  Open-Athena/MarinFold#328 · Filter by author timodonnell opened on Sep 24, 2026
  2

• exp: coherent contact-cluster branching for oracle rollouts

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#326 · Filter by author timodonnell opened on Sep 23, 2026
  3

• exp: analyses for a writeup

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#325 · Filter by author timodonnell opened on Sep 23, 2026

• exp: analyze MarinFold vs ESMFold2 performance across PDB-deduped monomers

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#324 · Filter by author znichols opened on Sep 23, 2026
  1

• exp: null-sequence contrastive guidance for contacts-v1 rollouts

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#321 · Filter by author timodonnell opened on Sep 23, 2026
  2

• exp: Helico confidence selection across top-0 to top-L exp277 contacts

  agent-generatedexperimentkind/evals
  Open-Athena/MarinFold#311 · Filter by author timodonnell opened on Sep 22, 2026
  6

• exp: contact biophysics annotations for MarinFold eval contacts

  agent-generatedexperimentkind/data
  Open-Athena/MarinFold#310 · Filter by author znichols opened on Sep 22, 2026
  1