Release of v1.0 of BioNeMo Modular Co-Design (MoCo)

[nvdreidenbach]

Release of v1.0 of BioNeMo Modular Co-Design (MoCo)

Introduces modular interpolants for various popular generative model frameworks including continuous and discrete diffusion and flow matching.

Summary

Introduces MoCo.

Details

See documentation.md for details.

Usage

pip install bionemo-moco

from bionemo.moco.interpolants import ContinuousFlowMatcher
from bionemo.moco.distributions.time import UniformTimeDistribution
from bionemo.moco.distributions.prior import GaussianPrior

uniform_time = UniformTimeDistribution()
moon_prior = GaussianPrior()
sigma = 0.1
cfm = ContinuousFlowMatcher(time_distribution=uniform_time, 
                            prior_distribution=moon_prior, 
                            sigma=sigma, 
                            prediction_type="velocity")

see examples directory for notebook tutorials

Testing

Unit tests for all key functions.

Tests for these changes can be run via:

pytest -v tests

[jstjohn]

/build-ci

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 78.73232% with 406 lines in your changes missing coverage. Please review.

Project coverage is 86.01%. Comparing base (7960ada) to head (cd6b7a3).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
...oco/interpolants/continuous_time/continuous/vdm.py	47.51%	95 Missing ⚠️
...inuous_time/continuous/continuous_flow_matching.py	64.86%	65 Missing ⚠️
...moco/interpolants/discrete_time/continuous/ddpm.py	70.40%	58 Missing ⚠️
...bionemo/moco/schedules/inference_time_schedules.py	76.72%	37 Missing ⚠️
.../moco/schedules/noise/continuous_snr_transforms.py	63.29%	29 Missing ⚠️
...us_time/continuous/optimal_transport/ot_sampler.py	82.05%	14 Missing ⚠️
...o/moco/schedules/noise/discrete_noise_schedules.py	73.07%	14 Missing ⚠️
...inuous/optimal_transport/equivariant_ot_sampler.py	85.55%	13 Missing ⚠️
.../src/bionemo/moco/interpolants/base_interpolant.py	84.41%	12 Missing ⚠️
...rc/bionemo/moco/interpolants/batch_augmentation.py	41.17%	10 Missing ⚠️
... and 16 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #575      +/-   ##
==========================================
- Coverage   88.78%   86.01%   -2.77%     
==========================================
  Files          81      116      +35     
  Lines        5027     6936    +1909     
==========================================
+ Hits         4463     5966    +1503     
- Misses        564      970     +406     

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[nvdreidenbach]

/build-ci

[jstjohn]

Ship