Search results

Linear probing of frozen gLM embeddings for VEP — representation design, leak-proof chromosome CV, and transfer across variant types & datasets

agent-generated

evals

experiment

Status: Open.

#314 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 11, 2026

evals_sge: dataset issues to revisit on a rebuild (function_score direction, missing consequence_group, …)

agent-generated

evals

Status: Open.

#297 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 8, 2026

Build bolinas-dna/evals_prime_editing — a saturation-prime-editing variant-effect dataset

agent-generated

enhancementNew feature or requestNew feature or request

evals

Status: Open.

#290 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 7, 2026

Sparse autoencoders

interpretationModel interpretation / mechanistic analysisModel interpretation / mechanistic analysis

Status: Open.

#288 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 7, 2026

Does conditioning on species/clade help?

research-questionOpen research question / hypothesis to investigateOpen research question / hypothesis to investigate

Status: Open.

#287 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 7, 2026

TF-MoDISco

interpretationModel interpretation / mechanistic analysisModel interpretation / mechanistic analysis

Status: Open.

#286 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 7, 2026

exp232 follow-up: why doesn't distal (enhancer) VEP improve with training? — hypotheses to investigate

agent-generated

research-questionOpen research question / hypothesis to investigateOpen research question / hypothesis to investigate

Status: Open.

#283 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 6, 2026

Preemption/crash drops the paired in-training eval + HF-export at the resume step (native checkpoint survives; arm also doesn't auto-resume)

agent-generated

bugSomething isn't workingSomething isn't working

infrastructure

marinChange really belongs upstream in marin/levanterChange really belongs upstream in marin/levanter

Status: Open.

#282 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 6, 2026

Thread per-task add_special_tokens through levanter loglikelihood tokenization (durable BOS fix; supersedes #263 monkeypatch)

agent-generated

enhancementNew feature or requestNew feature or request

marinChange really belongs upstream in marin/levanterChange really belongs upstream in marin/levanter

Status: Open.

#264 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 5, 2026

Regenerate exp135 embedding-UMAP artifacts after the FWD/RC strand-bounds fix (#248)

agent-generated

interpretationModel interpretation / mechanistic analysisModel interpretation / mechanistic analysis

Status: Open.

#251 In Open-Athena/marin-dna;

· gonzalobenegas opened on Jun 4, 2026

S3 bucket rename: migrate oa-bolinas → oa-marin-dna + code sweep

agent-generated

infrastructure

Status: Open.

#207 In Open-Athena/marin-dna;

· gonzalobenegas opened on May 20, 2026

HF org migration: transfer bolinas-dna/* repos to marin-dna + code sweep

agent-generated

infrastructure

Status: Open.

#206 In Open-Athena/marin-dna;

· gonzalobenegas opened on May 20, 2026