Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / NVIDIA/bionemo-framework issues and pull requests

#468 - Add release notes for v2.1

Pull Request - State: open - Opened by tshimko-nv 1 day ago - 2 comments
Labels: documentation, SKIP_CI

#467 - expose the ESM2 data random seed via CLI

Pull Request - State: open - Opened by pstjohn 1 day ago - 1 comment

#466 - Refactor SCDL Row Feature Index for Performance Improvement (Rebased)

Pull Request - State: open - Opened by savitha-eng 2 days ago - 2 comments

#465 - Pillow version bump into main

Pull Request - State: open - Opened by polinabinder1 2 days ago - 3 comments

#464 - Remove batch size multiple requirement for inference

Pull Request - State: open - Opened by jstjohn 2 days ago - 2 comments

#463 - Implement elementary bond featurizers

Pull Request - State: open - Opened by sveccham 2 days ago - 1 comment

#462 - Cache dev build from our nightly public container

Pull Request - State: closed - Opened by jstjohn 2 days ago - 1 comment
Labels: SKIP_CI

#461 - set num_workers to 1 for esm2 tests

Pull Request - State: closed - Opened by pstjohn 2 days ago - 2 comments

#460 - Dealing with CVE for bionemo1

Pull Request - State: closed - Opened by polinabinder1 3 days ago - 2 comments

#459 - refactor ppl callback calculation

Pull Request - State: open - Opened by pstjohn 3 days ago - 1 comment

#458 - hillst/bionemo noodles

Pull Request - State: open - Opened by skothenhill-nv 3 days ago

#457 - bump version for pillow to avoid the CVE

Pull Request - State: closed - Opened by polinabinder1 3 days ago

#456 - Update pytorch_lightning to pytorch.lightning when bumping NeMo version

Issue - State: open - Opened by jstjohn 3 days ago
Labels: enhancement

#455 - Update error prone stop/go atol to more stable setting

Pull Request - State: closed - Opened by jstjohn 3 days ago - 1 comment
Labels: bug

#453 - Atom and bond features

Pull Request - State: open - Opened by sveccham 4 days ago - 2 comments
Labels: enhancement

#451 - Launchable notebooks in docs!

Pull Request - State: closed - Opened by jstjohn 4 days ago - 2 comments

#450 - Explore esm2 training instability 20241119

Pull Request - State: open - Opened by sichu2023 4 days ago

#449 - BugFix: fix bugs on bionemo-size-aware-batching

Pull Request - State: open - Opened by guoqing-zhou 4 days ago - 4 comments
Labels: bug

#448 - Use torch.finfo settings for eps optionally

Pull Request - State: open - Opened by jstjohn 5 days ago - 5 comments

#447 - Add documentation and release info to README

Pull Request - State: closed - Opened by sirelkhatim 5 days ago - 2 comments
Labels: documentation, SKIP_CI

#446 - Update the title for DSMBind doc

Pull Request - State: closed - Opened by mengliu-nvidia 5 days ago - 1 comment
Labels: SKIP_CI

#445 - Turn off all fusion to test ESM2 pretraining stability

Pull Request - State: open - Opened by sichu2023 5 days ago

#444 - Bump 3rdparty/Megatron-LM from `aded519` to `5438d15`

Pull Request - State: closed - Opened by dependabot[bot] 5 days ago - 2 comments
Labels: dependencies, submodules

#443 - Refactor SCDL Row Feature Index for Performance Improvement

Pull Request - State: open - Opened by savitha-eng 7 days ago - 1 comment

#442 - Amgen's AMPLIFY Port

Pull Request - State: open - Opened by ynashed 8 days ago
Labels: SKIP_CI, contribution

#441 - eliminate the need for NGC login - bionemo1

Pull Request - State: closed - Opened by dorotat-nv 8 days ago - 1 comment

#440 - eliminate the need for NGC login - bionemo2

Pull Request - State: closed - Opened by dorotat-nv 8 days ago - 2 comments

#439 - Update docs to remove NGC config requirements

Pull Request - State: open - Opened by tshimko-nv 8 days ago - 2 comments
Labels: documentation, SKIP_CI

#438 - Initial compatibility testing images

Pull Request - State: open - Opened by malcolmgreaves 8 days ago

#437 - [WIP] hillst/noodles bionemo

Pull Request - State: closed - Opened by skothenhill-nv 8 days ago - 2 comments

#436 - JSON -> YAML for CLI

Pull Request - State: open - Opened by skothenhill-nv 8 days ago - 2 comments

#435 - Mg/bionemo noodles py o3

Pull Request - State: open - Opened by malcolmgreaves 8 days ago - 1 comment

#434 - Revert "re-enable merge groups to trigger blossom-ci"

Pull Request - State: closed - Opened by pstjohn 8 days ago

#433 - add pre-emption callback to esm2 train

Pull Request - State: closed - Opened by pstjohn 9 days ago - 3 comments

#432 - add rdkit dependency to bionemo-geometric

Pull Request - State: closed - Opened by sveccham 9 days ago - 4 comments

#431 - re-enable merge groups to trigger blossom-ci

Pull Request - State: closed - Opened by pstjohn 9 days ago - 1 comment
Labels: SKIP_CI

#430 - Updated notebook, and nemo2 checkpoint with geneformer

Pull Request - State: closed - Opened by jstjohn 10 days ago - 6 comments

#429 - WAR: sets checkpoint filename to be more unique

Pull Request - State: closed - Opened by skothenhill-nv 10 days ago - 1 comment

#428 - initial config for partial conv in JET of esm2 in bionemo2

Pull Request - State: open - Opened by dorotat-nv 10 days ago - 1 comment

#427 - MolMIM checkpoint files ckpt to nemo conversion

Issue - State: open - Opened by xinyu-dev 10 days ago
Labels: bug

#426 - ESM2 Tutorial Updates

Pull Request - State: open - Opened by farhadrgh 10 days ago - 6 comments

#425 - initial attempt to bump the pytorch base image

Pull Request - State: closed - Opened by pstjohn 11 days ago

#424 - Update NeMo and Megatron to TOT

Pull Request - State: closed - Opened by pstjohn 11 days ago - 2 comments

#423 - add fname parameter for pooch downloads

Pull Request - State: closed - Opened by pstjohn 12 days ago - 1 comment

#422 - Bump 3rdparty/Megatron-LM from `0bda578` to `acf4855`

Pull Request - State: closed - Opened by dependabot[bot] 12 days ago - 1 comment
Labels: dependencies, submodules

#421 - Fix geneformer training instability bug

Pull Request - State: closed - Opened by jstjohn 14 days ago - 10 comments

#420 - Update Geneformer modelcard performance comparison note

Pull Request - State: closed - Opened by jstjohn 14 days ago - 3 comments
Labels: documentation, SKIP_CI

#419 - adding scdl dependency + proper notebook output

Pull Request - State: closed - Opened by polinabinder1 15 days ago - 6 comments

#418 - Update minimum driver version

Pull Request - State: closed - Opened by tshimko-nv 15 days ago - 2 comments
Labels: documentation, SKIP_CI

#417 - Update command to pull latest BioNeMo1 tag

Pull Request - State: closed - Opened by tshimko-nv 15 days ago - 1 comment
Labels: documentation, SKIP_CI

#416 - fix: remove text key with custom font value (solves stylesheet verify…

Pull Request - State: closed - Opened by jwilber 15 days ago - 2 comments
Labels: documentation, SKIP_CI

#415 - small bug fix

Pull Request - State: closed - Opened by polinabinder1 15 days ago - 3 comments

#414 - remove every_n_train_steps from ModelCheckpoint

Pull Request - State: closed - Opened by sichu2023 15 days ago - 1 comment

#413 - Fix release notes links from v1.x and update broken `site:` links

Pull Request - State: closed - Opened by tshimko-nv 15 days ago - 3 comments
Labels: documentation, SKIP_CI

#412 - Refactored `load` & `download_bionemo_data` into bionemo-core

Pull Request - State: closed - Opened by malcolmgreaves 15 days ago - 3 comments

#410 - Fix incorrect types for WandbConfig

Pull Request - State: closed - Opened by skothenhill-nv 15 days ago - 4 comments

#409 - adds nbval test for ngc download

Pull Request - State: closed - Opened by pstjohn 16 days ago - 7 comments

#408 - Training cluster performance boost for bert models part 2

Pull Request - State: closed - Opened by jstjohn 16 days ago - 8 comments

#407 - Introducing trt_compile() and example how to use it

Pull Request - State: open - Opened by borisfom 16 days ago

#406 - Move ESM2 scripts to sub-packages

Pull Request - State: closed - Opened by farhadrgh 17 days ago - 2 comments

#405 - Try skipping esm2 test_infer

Pull Request - State: closed - Opened by pstjohn 17 days ago - 2 comments

#404 - [QA BUG] apply batch_collator to predict results

Pull Request - State: closed - Opened by farhadrgh 17 days ago - 2 comments

#403 - Geneformer + ESM2 train script and pydantic config equivalence check

Issue - State: open - Opened by jstjohn 17 days ago - 1 comment

#401 - Write test for `geneformer_mlm_loss_eval` script.

Issue - State: open - Opened by jstjohn 17 days ago

#399 - Update transformer engine commit

Pull Request - State: closed - Opened by pstjohn 18 days ago - 1 comment

#398 - Pstjohn/main/bump nemo megatron

Pull Request - State: closed - Opened by pstjohn 18 days ago

#397 - Polinabinder/profiling

Pull Request - State: open - Opened by polinabinder1 19 days ago

#396 - Refactored `load` & `download_bionemo_data` into bionemo-core

Pull Request - State: closed - Opened by malcolmgreaves 19 days ago - 4 comments

#395 - Small performance improvement to `process_item`

Pull Request - State: closed - Opened by jstjohn 19 days ago - 5 comments

#394 - Savitha/geneformer profiling

Pull Request - State: open - Opened by savitha-eng 19 days ago

#393 - Bump 3rdparty/Megatron-LM from `0bda578` to `8539eba`

Pull Request - State: closed - Opened by dependabot[bot] 19 days ago - 1 comment
Labels: dependencies, submodules

#392 - Geneformer modelcard and loss eval script

Pull Request - State: closed - Opened by jstjohn 21 days ago - 4 comments

#391 - artefacts republished on NGC: revert changes

Pull Request - State: closed - Opened by dorotat-nv 22 days ago - 1 comment

#390 - Polinabinder/scdl document

Pull Request - State: closed - Opened by polinabinder1 22 days ago - 1 comment
Labels: documentation, SKIP_CI

#389 - Savitha/integrate scdl into geneformer megatron compatible

Pull Request - State: open - Opened by savitha-eng 23 days ago - 2 comments

#388 - Revert "Savitha/integrate scdl into geneformer megatron compatible"

Pull Request - State: closed - Opened by pstjohn 23 days ago - 1 comment
Labels: SKIP_CI

#387 - Skip image and data lines in jupyter notebooks in detect-secrets

Pull Request - State: closed - Opened by pstjohn 23 days ago - 1 comment
Labels: SKIP_CI

#386 - Manually pin pypi versions

Pull Request - State: open - Opened by pstjohn 23 days ago - 1 comment

#385 - Geneformer Inference Notebook and Scripts from CLI refactor.

Pull Request - State: closed - Opened by jstjohn 23 days ago - 4 comments

#384 - ESM2 Inference

Pull Request - State: closed - Opened by farhadrgh 24 days ago - 10 comments

#383 - Polinabinder/model document

Pull Request - State: closed - Opened by polinabinder1 24 days ago - 8 comments

#382 - use torchmetrics ppl logging

Pull Request - State: open - Opened by pstjohn 24 days ago - 1 comment

#381 - mount netrc file for wandb inside devcontainer

Pull Request - State: closed - Opened by pstjohn 24 days ago - 1 comment
Labels: SKIP_CI

#380 - Update default mike config

Pull Request - State: closed - Opened by tshimko-nv 24 days ago - 4 comments
Labels: documentation, SKIP_CI

#379 - Savitha/integrate scdl into geneformer megatron compatible

Pull Request - State: closed - Opened by savitha-eng 24 days ago - 3 comments

#378 - move esm2 stop and go test to sanity dataset

Pull Request - State: closed - Opened by pstjohn 25 days ago - 3 comments

#377 - Add docs on MegatronDataModule and WrappedDataLoader

Pull Request - State: closed - Opened by sichu2023 25 days ago - 2 comments
Labels: documentation, SKIP_CI

#376 - Remove tensor_dict_hash in favor of recursive approx_equal

Pull Request - State: closed - Opened by pstjohn 25 days ago - 1 comment

#375 - Move Geneformer dataset to MultiEpochDatasetResampler

Pull Request - State: closed - Opened by pstjohn 25 days ago - 2 comments

#374 - Export FUSED_ATTN in release container and fix geneformer stop and go

Pull Request - State: closed - Opened by pstjohn 25 days ago - 5 comments

#373 - Changes to get toward better training perf in geneformer

Pull Request - State: closed - Opened by jstjohn 25 days ago - 10 comments

#372 - Add FAQ

Pull Request - State: closed - Opened by tshimko-nv 25 days ago - 2 comments
Labels: documentation, SKIP_CI

#371 - better error handling in SCDL collections.

Pull Request - State: closed - Opened by polinabinder1 25 days ago - 3 comments

#370 - Refactor stop and go test suite

Pull Request - State: closed - Opened by pstjohn 26 days ago - 2 comments

#369 - Draft: GH200 support

Pull Request - State: open - Opened by gagank1 26 days ago