Improved PhiX174 Phage Design Plausibility

[jstjohn]

Description

Addresses the following

• Genome lengths were not realistically sampled due to a lack of EOD token sampling.
• Picked genome length bounds that are biologically informed for PhiX174 based on observations of capsid packing and population frequency.
• Some key capsid genes were often removed from the genome while others were sometimes duplicated due to gene function-level ambiguity in the reward.
• Very large batched generations without model parallelism overflow the kv-cache addressing, limiting the ability to make use of gpus with large memory.
• PhiX174 is a circular genome, and the original prompts at position 0 overlap a particularly gene-dense region with genes A, A* and B all encoded there. This version picks rotated prompts at other less gene dense regions of the assembly.
• Skill text updated with information about various genome structures observed in phages which will hopefully help agents make smart decisions about prompting and assembly verification in other design tasks.

Usage

TODO: Add code snippet

Type of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Refactor
• Documentation update
• Other (please describe):

CI Pipeline Configuration

Configure CI behavior by applying the relevant labels. By default, only basic unit tests are run.

• ciflow:skip - Skip all CI tests for this PR
• ciflow:notebooks - Run Jupyter notebooks execution tests
• ciflow:slow - Run slow single GPU integration tests marked as @pytest.mark.slow
• ciflow:all - Run all tests, including unit tests, slow tests, notebooks, and every recipe/model directory.

Unit tests marked as @pytest.mark.multi_gpu or @pytest.mark.distributed are not run in the PR pipeline.

For more details, see CONTRIBUTING

Note

By default, only basic unit tests are run. Add appropriate labels to enable an additional test coverage.

Authorizing CI Runs

We use copy-pr-bot to manage authorization of CI
runs on NVIDIA's compute resources.

• If a pull request is opened by a trusted user and contains only trusted changes, the pull request's code will
  automatically be copied to a pull-request/ prefixed branch in the source repository (e.g. pull-request/123)
• If a pull request is opened by an untrusted user or contains untrusted changes, an NVIDIA org member must leave an
  /ok to test comment on the pull request to trigger CI. This will need to be done for each new commit.

Triggering Code Rabbit AI Review

To trigger a code review from code rabbit, comment on a pull request with one of these commands:

• @coderabbitai review - Triggers a standard review
• @coderabbitai full review - Triggers a comprehensive review

See https://docs.coderabbit.ai/reference/review-commands for a full list of commands.

Pre-submit Checklist

• I have tested these changes locally
• I have updated the documentation accordingly
• I have added/updated tests as needed
• All existing tests pass successfully

[copy-pr-bot]

Auto-sync is disabled for draft pull requests in this repository. Workflows must be run manually.

Contributors can view more details about this message here.

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: Repository: NVIDIA-BioNeMo/bionemo-recipes/.coderabbit.yaml

Review profile: CHILL

Plan: Enterprise

Run ID: 0ee2c422-30c1-4ce3-95da-4b6464f6885e

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

---

_{Comment @coderabbitai help to get the list of available commands.}

[copy-pr-bot]

This pull request requires additional validation before any workflows can run on NVIDIA's runners.

Pull request vetters can view their responsibilities here.

Contributors can view more details about this message here.