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1 | 1 | # Release Notes |
2 | 2 |
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| 3 | +## BioNeMo Framework v2.7 |
| 4 | + |
| 5 | +### Updates & Improvements |
| 6 | + |
| 7 | +- Adds a header to SCDL archives, providing improved provenance tracking and supporting future releases. Also adds tracking of the AnnData API coverage in SCDL tests. |
| 8 | + This header stores metadata about the archive and its composite arrays, including a version, the array lengths and data types, and information about the RowFeatureIndexes. This adds the features necessary to fix https://github.com/NVIDIA/bionemo-framework/issues/999 as well as implement simple bit-packing of the rowptr, colptr, and data arrays. It also should make SCDL more secure, enable strict compatibility checking, and open the door to more performance improvements. https://github.com/NVIDIA/bionemo-framework/pull/1030 |
| 9 | + |
| 10 | +## BioNeMo Framework v2.6.3 |
| 11 | + |
| 12 | +### Updates & Improvements |
| 13 | + |
| 14 | +- Fixes numerous issues with Evo2 model: |
| 15 | + 1. Inference/Generation issues resolved. https://github.com/NVIDIA/bionemo-framework/issues/890 |
| 16 | + 2. FP8 training resumption issues resolved. https://github.com/NVIDIA/bionemo-framework/issues/973 |
| 17 | + 3. Bug in inference script that concerns checkpoint loading is fixed. https://github.com/NVIDIA/bionemo-framework/pull/950 |
| 18 | +- ESM2 LoRA model inference issue resolved. https://github.com/NVIDIA/bionemo-framework/pull/996 |
| 19 | +- Added experimental evo2-mamba model. https://github.com/NVIDIA/bionemo-framework/pull/888 |
| 20 | +- Updated base Docker image to [nvidia-pytorch 25.06-py3](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch/tags) |
| 21 | +- NCCL issue in ESM2 pretraing resolved. https://github.com/NVIDIA/bionemo-framework/issues/970 |
| 22 | + |
| 23 | +## What's Changed |
| 24 | + |
| 25 | +- Fix test_train_evo2_stops test by @balvisio in https://github.com/NVIDIA/bionemo-framework/pull/965 |
| 26 | +- Enable test_train_evo2_stop_at_max_steps_and_continue. by @balvisio in https://github.com/NVIDIA/bionemo-framework/pull/966 |
| 27 | +- automated benchmarks: esm2 650M training analogous to bionemo-recipes by @dorotat-nv in https://github.com/NVIDIA/bionemo-framework/pull/975 |
| 28 | +- Fix database path in esm2_pretrain_recipes by @pstjohn in https://github.com/NVIDIA/bionemo-framework/pull/978 |
| 29 | +- Add fp8 stop and go test for evo2 by @jwilber in https://github.com/NVIDIA/bionemo-framework/pull/974 |
| 30 | +- Update Docs Banner for GitHub Pages-hosted Docs by @tshimko-nv in https://github.com/NVIDIA/bionemo-framework/pull/981 |
| 31 | +- Add release notes for v2.6.2 (25.06) by @trvachov in https://github.com/NVIDIA/bionemo-framework/pull/971 |
| 32 | +- Evo2 Generation fixes and necessary base dependency and container updates. Large change. by @jwilber in https://github.com/NVIDIA/bionemo-framework/pull/949 |
| 33 | +- Point NeMo submodule back to main repo by @trvachov in https://github.com/NVIDIA/bionemo-framework/pull/984 |
| 34 | +- Use new b2b kernels in evo2 jet tests by @jwilber in https://github.com/NVIDIA/bionemo-framework/pull/985 |
| 35 | +- change where dtype is found in checkpoint export by @pstjohn in https://github.com/NVIDIA/bionemo-framework/pull/989 |
| 36 | +- Evo2 Mamba by @jstjohn in https://github.com/NVIDIA/bionemo-framework/pull/888 |
| 37 | +- Adding inference CDS length tests by @jstjohn in https://github.com/NVIDIA/bionemo-framework/pull/991 |
| 38 | +- Fix PIL CVE by @trvachov in https://github.com/NVIDIA/bionemo-framework/pull/992 |
| 39 | +- \[BIONEMO-2334\] Patch TE to fix Evo2 stop and go training by @balvisio in https://github.com/NVIDIA/bionemo-framework/pull/987 |
| 40 | +- Fix bug in evo2-mamba train and add test by @jstjohn in https://github.com/NVIDIA/bionemo-framework/pull/994 |
| 41 | +- Fix esm2 lora inference by @yzhang123 in https://github.com/NVIDIA/bionemo-framework/pull/996 |
| 42 | +- Reset parameters for the ESM-2 contact head on HF export by @pstjohn in https://github.com/NVIDIA/bionemo-framework/pull/983 |
| 43 | + |
3 | 44 | ## BioNeMo Framework v2.6.2 |
4 | 45 |
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5 | 46 | ### Updates & Improvements |
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