NVIDIA BioNeMo Framework v2.4

New Features

• Draft implementation of Evo2 with support for Hyena operators
• bionemo-moco v0.0.1 released for building diffusion-like generative models.

Updates & Improvements

• ESM2 fine-tuning script with CLI (finetune_esm2) that supports sequence-level/token-level classification/regression using a CSV dataset.
• Brev.dev launchable fine-tuning tutorial for ESM2

What's Changed

• bump nemo and remove manual tensorstore install by @pstjohn in #619
• remove the apex and TE build steps from our docker container by @pstjohn in #611
• Adds bionemno-esm2 section to CODEOWNERS by @jomitchellnv in #627
• LR multiplier for ESM2 finetuning layers by @farhadrgh in #609
• fix perplexity logging by @sichu2023 in #622
• Allow finetuning ESM2 with [un]frozen encoder by @farhadrgh in #620
• ESM-2 to NeMo checkpoint conversion by @pstjohn in #537
• remove PerplexityCallback in pydantic api by @sichu2023 in #636
• catch ngc api key validation errors and default to not using an api key by @pstjohn in #635
• New approvals workflow by @pstjohn in #639
• 2.3 (25.01) release notes by @trvachov in #641
• short script to initialize environment for devcontainer by @pstjohn in #625
• Don't upload merge queue results to codecov by @pstjohn in #637
• Pin triton version to avoid import error by @pstjohn in #642
• fix devcontainer initialize script by @pstjohn in #648
• Fix geneformer notebook tests by removing 10m_bnmo2 model by @pstjohn in #649
• ignore labels in inference CSV data by @farhadrgh in #652
• Mark geneformer test_pretrain_cli as slow by @pstjohn in #651
• edit to approval workflow to avoid marking a failed action by @pstjohn in #650
• added slow test label and execute full testing suite before merge by @dorotat-nv in #634
• templates for bugs and feature requests by @dorotat-nv in #647
• Instructions for uploading a package to pypi by @polinabinder1 in #638
• add timing callback by @sichu2023 in #657
• add options for pytest duration logging by @pstjohn in #656
• Bump 3rdparty/NeMo from 0cd990d to 6d90758 by @dependabot in #660
• Bump 3rdparty/Megatron-LM from 4fb4c3d to 0e85db5 by @dependabot in #661
• add back transformer engine install by @pstjohn in #658
• Update MoCo Version and MDLM params by @nvdreidenbach in #632
• Fix nightly container link in README by @pstjohn in #666
• Changes to SCDL and documentation by @polinabinder1 in #643
• update issue templates by @dorotat-nv in #668
• improve readme by @yzhang123 in #665
• Dependency graph by @polinabinder1 in #659
• Bump 3rdparty/NeMo from 6d90758 to 48f10af by @dependabot in #676
• Support NVFlare sequence-level classification fine-tuning by @farhadrgh in #664
• Bump 3rdparty/Megatron-LM from 0e85db5 to 2a9793d by @dependabot in #675
• Update pytorch base image by @pstjohn in #670
• clean up distributed env setup and support multi-device testing by @sichu2023 in #535
• support arbitrary metric logging from torchmetrics by @sichu2023 in #677
• Add scheduled nightly tests on github CI by @pstjohn in #687

Full Changelog: v2.3...v2.4