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LoRA supervised fine-tuning vs the frozen linear probe on Mendelian-missense VEP (motivated by #341)
agent-generatedCreated by an agentCreated by an agentedaType: bounded exploratory analysis of data/results; no preregistered hypothesisType: bounded exploratory analysis of data/results; no preregistered hypothesisevalsArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricStatus: Open.#369 In Open-Athena/marin-dna;Blog: explanatory schematics — model→data provenance, data-generation paths, eval apparatus (mermaid-first)
agent-generatedCreated by an agentCreated by an agentcommunicationType: external-facing dissemination — blog posts, papers, talks, publication figuresType: external-facing dissemination — blog posts, papers, talks, publication figuresStatus: Open.#368 In Open-Athena/marin-dna;Blog hand-off: swap redone SVGs into PR #59 + reconcile captions
agent-generatedCreated by an agentCreated by an agentcommunicationType: external-facing dissemination — blog posts, papers, talks, publication figuresType: external-facing dissemination — blog posts, papers, talks, publication figuresStatus: Open.#367 In Open-Athena/marin-dna;Blog: Genomic LM Optimization — analysis & figures
agent-generatedCreated by an agentCreated by an agentcommunicationType: external-facing dissemination — blog posts, papers, talks, publication figuresType: external-facing dissemination — blog posts, papers, talks, publication figuresepicEngineering decomposition only — a build split into parts (not for organizing research)Engineering decomposition only — a build split into parts (not for organizing research)Status: Open.#361 In Open-Athena/marin-dna;Migrate experiment launch.py to marin's new marin.execution API (old-API pin window closes ~mid-July)
agent-generatedCreated by an agentCreated by an agentinfrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbingmarinChange really belongs upstream in marin/levanterChange really belongs upstream in marin/levanterStatus: Open.#358 In Open-Athena/marin-dna;marin/iris launches blocked: freshness floor (06-18) exceeds the only [tpu]-resolvable build (0.2.19/06-17)
agent-generatedCreated by an agentCreated by an agentbugType: something is brokenType: something is brokenmarinChange really belongs upstream in marin/levanterChange really belongs upstream in marin/levanterStatus: Open.#356 In Open-Athena/marin-dna;Add OpenSplice benchmark
evalsArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricinfrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbingStatus: Open.#346 In Open-Athena/marin-dna;Pre-existing mypy + snakefmt failures block a full lint/typecheck CI gate
agent-generatedCreated by an agentCreated by an agentinfrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbingStatus: Open.#323 In Open-Athena/marin-dna;Build bolinas-dna/evals_prime_editing — a saturation-prime-editing variant-effect dataset
agent-generatedCreated by an agentCreated by an agentevalsArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricArea: work on the eval apparatus — new eval dataset, scoring protocol, or metricinfrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbingStatus: Open.#290 In Open-Athena/marin-dna;Sparse autoencoders
infrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbinginterpretationArea: model interpretation — UMAP, nucleotide-dependency maps, SAEs, TF-MoDIScoArea: model interpretation — UMAP, nucleotide-dependency maps, SAEs, TF-MoDIScoStatus: Open.#288 In Open-Athena/marin-dna;Does conditioning on species/clade help?
modelingArea: core gLM recipe — architecture, objective, tokenization, loss weighting, contextArea: core gLM recipe — architecture, objective, tokenization, loss weighting, contextresearch-questionType: durable, revisitable question pursued across many experiments over time (a north-star)Type: durable, revisitable question pursued across many experiments over time (a north-star)Status: Open.#287 In Open-Athena/marin-dna;TF-MoDISco
infrastructureType: tooling, pipelines, CI, migrations, compute plumbingType: tooling, pipelines, CI, migrations, compute plumbinginterpretationArea: model interpretation — UMAP, nucleotide-dependency maps, SAEs, TF-MoDIScoArea: model interpretation — UMAP, nucleotide-dependency maps, SAEs, TF-MoDIScoStatus: Open.#286 In Open-Athena/marin-dna;