Skip to content

Isaac #8

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
isaacdonnell wants to merge 13 commits into
base: main
Choose a base branch
from
Open

Isaac #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
a2323f6
WIP: Isaac branch snapshot
isaacdonnell Jan 8, 2026
9eafc95
Add E1 MSA context support and batching updates
isaacdonnell Jan 9, 2026
a709bac
added ESM3/C dynamic batching
isaacdonnell Jan 9, 2026
96322c0
Add benchmark outputs and pretrain naturalness updates
isaacdonnell Feb 24, 2026
dedb2d7
Add ParEGO multi-objective acquisition and DMS replay harness
isaacdonnell Jul 30, 2026
6c9a073
Register KCNE1/RASK/OXDA datasets and add ESM job submission scripts
isaacdonnell Jul 30, 2026
8c13781
Stop dropping multi-mutants from multi-objective datasets
isaacdonnell Jul 30, 2026
b1f9253
Land SPG1_Wu embeddings and the 10-sim KCNJ2 sweep result
isaacdonnell Jul 30, 2026
be6e2ef
Add survey of ProteinGym multi-mutant datasets by positional spread
isaacdonnell Jul 30, 2026
c865ff5
Submit long-range multi-mutant datasets (Sarkisyan, Somermeyer x3, PHOT)
isaacdonnell Jul 30, 2026
ddfa5dc
Add paired Wilcoxon to the multi-objective analysis; record PTEN sweep
isaacdonnell Jul 30, 2026
79f7456
Add low-N multi-objective acquisition results and pre-registration
isaacdonnell Jul 31, 2026
63cdeb9
Add RASK results; n=6 Tier-1 test fails on the primary comparison
isaacdonnell Jul 31, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions .gitignore
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -148,9 +148,10 @@ backend/notebooks/jacob/flip-aav.csv
backend/folde/data/*
backend/foldydata/*
.boltz/

E1/
backend/EvolveTest

AGENTS.md
SPEC.md
CLAUDE.md
CLAUDE_NOTES.md

Expand Down
1 change: 1 addition & 0 deletions .vscode/settings.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -18,5 +18,6 @@
"editor.detectIndentation": false,
"docker.enableDockerComposeLanguageService": false,
"cursor.general.disableHttp2": true,
"containers.enableComposeLanguageService": false,
}
// BasedPyright settings in vscode are ignored when using pyrightconfig.json is provided.
1,025 changes: 1,025 additions & 0 deletions 2026-07-21-moce-folde-hybrid-spec.md
View file
Open in desktop

Large diffs are not rendered by default.

20 changes: 20 additions & 0 deletions backend/app/api_fields.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -107,13 +107,23 @@ class NullableInteger(fields.Integer):
"logit_model": fields.String(required=True),
"use_structure": fields.Boolean(required=False),
"get_depth_two_logits": fields.Boolean(required=False),
"use_msa_context": fields.Boolean(required=False),
"msa_a3m_path": fields.String(required=False),
"output_fpath": fields.String(required=False),
"output_fpath_computed": fields.String(required=False),
"invokation_id": fields.Integer(required=False),
"date_created": fields.DateTime(required=False),
},
)

naturalness_input_fields = type_ns.inherit(
"NaturalnessInputFields",
naturalness_fields,
{
"msa_a3m": fields.String(required=False),
},
)

embedding_fields = type_ns.model(
"EmbeddingFields",
{
Expand All @@ -126,13 +136,23 @@ class NullableInteger(fields.Integer):
"homolog_fasta": fields.String(required=False),
"extra_layers": fields.String(required=False),
"domain_boundaries": fields.String(required=False),
"use_msa_context": fields.Boolean(required=False),
"msa_a3m_path": fields.String(required=False),
"output_fpath": fields.String(required=False),
"output_fpath_computed": fields.String(required=False),
"invokation_id": fields.Integer(required=False),
"date_created": fields.DateTime(required=False),
},
)

embedding_input_fields = type_ns.inherit(
"EmbeddingInputFields",
embedding_fields,
{
"msa_a3m": fields.String(required=False),
},
)


# =============================================================================
# FEW-SHOT FIELDS (defined early since fold_fields references it)
Expand Down
Loading
Loading