Improved PhiX174 Phage Design Plausibility - #1722

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jstjohn/phix-loss-improvement

Commits on Sep 10, 2026

Address some issues that lead to dropped key genes and partial key genes in the original implementation
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be3f821
Let PhiX rollouts learn the length boundary
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ad54224
Add observations about the swapping that sometimes happens between closely related phages, as well as notes on genome architecture and linear genomes
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7cd22ce
Add update about keeping filters up to date and synced to rl as well in the skills
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2c68b65
Update the notes on install on gb300 and also skill updates related to the changes
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83626e7
Do not mask EOD from loss for this model so it learns when to terminate genomes naturally
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c2353ac
Adding paged kv cache support for large batches of parallel generations
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983befb
Update paged kv cache to match packed work from another branch
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420345c
Add pointers to where each rl term is implemented in the readme section
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c98e09b
Smoother process for handling partial gene matches
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8110ed2
Add more flexible approach for assigning genes for synteny stage
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044e98b
Fix PhiX rollout controls after packed rebase
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f7d43ee
Let PhiX RL learn EOD termination
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ccfee34
Fix filtered action replay and late CUDA graph setup
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85e439c
Repair subquadratic causal convolution import order
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09a689b
Keep NeMo-RL setup checks CUDA-free
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2f5dd75
Avoid repeated optimizer offload around Evo2 refits
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99f9967
Reject periodic rollout replay mismatches
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8542e84
Treat isolated replay tails as advisory
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829cdf1
Balance PhiX length reward and prompt strata
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cc7bd92
Fix circular RL control comparisons
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281736e
Retune PhiX length shaping reward
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cc996cd
Right-size PhiX 8xH100 GDPO execution
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d31f1b3
Require steady-state Evo2 cache qualification
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fd61f55
Document persist-cache steady-state failures
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3c71220
Use conservative PhiX H100 pilot microbatch
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a4ecb67
Qualify RL capacity after validation
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c6295c2
Clarify RL capacity qualification after validation
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ebae4e4
Refine GB300 RL capacity evidence
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0953501
Clarify GB300 capacity confound
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bf9fe91
Record qualified GB300 cache offload capacity
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ba1f418
Document RL horizon and dirty GPU checks
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1c001ed
Allow evidence-based SFT stop ceilings
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3f88510
Preserve Evo2 SFT resume state
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85b650a
Expose PhiX RL microbatch qualification
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4e5cbbf
Use prepared MMseqs for LoVis4u rewards
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cf31c22
Document dirty GPU capacity checks
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6cfb429
fix(phage-gen): serialize batched QC actor calls
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3947ab6
Preflight Evo2 RL training kernels
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54a29d0
Fix PhiX GDPO W&B entity override
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1185c69
Qualify PhiX GDPO checkpoint recovery
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fcccad9
Clarify PhiX H100 RL batch qualification
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0523f59
Clarify RL candidate versus pipeline failures
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8f559f6
Use durable cache release evidence in RL pilot
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6a73bab
Allow slow W&B initialization in PhiX launcher
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ce3e478
Preserve optimizer state in PhiX GDPO checkpoints
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7f27eff
Clarify dirty-device MBS32 evidence
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9ad6f7b
Handle wrapped checkpoint paths in RL pilot reload
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7c33b77
Match Megatron checkpoint root in reload qualification
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bbfdb37
Parallelize grouped diversity scoring
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35890a2
Detect Ray CPU capacity outside OpenMP limits
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0dd378c
Qualify larger PhiX rollout throughput
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5e19dc2
Use packed batches for final PhiX rollout
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26cc229
Report exact rollout termination
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ba7fb6c
Keep PhiX EOD in sampling support
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aa2b77f
Scope terminal support guidance to each design
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f27437f
Prefer recipe cuDNN runtime after activation
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67b500a
Revert "Prefer recipe cuDNN runtime after activation"
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13b16a9
Use recipe cuDNN on compatible H100 images
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49f4b23
Record qualified H100 RL microbatch
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ddc444f
Keep phage QC actors off policy GPUs
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46813c0
Handle non-DNA calibration novelty samples
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284cd73
Clarify termination reachability qualification
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d4b41ff
Retain authentic EOD placement metrics
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230bf00
Retain complementary PhiX RL checkpoints
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c3429d4
Add optional no-EOD reward gate
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992b858
Zero all RL objectives for no-EOD genomes
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59e195d
Retry truncated external asset downloads
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fb3edae
Clean up unused functions and skill wording
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bc96b24
Updated rewards to be more closely biologically informed, corrected discrepency between AAI definition here and the paper, and fixed bugs with circular genome handling
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130eea4

Commits on Sep 11, 2026

Use fused attention for 26.07 PhiX RL
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6d969ef
Simplify length reward related features, and histogram logging
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7af4f47

Commits on Sep 12, 2026

Remove unused functions and consolidate definitions
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7e45f91

Commits on Sep 14, 2026

Commits on Sep 15, 2026

Consistent naming arch vs synteny
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be6e4a2
More comment updates around synteny vs arch scores
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9a65b77
Fix issue with short no-orf genome score crashing
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926b06e
Handle case of no orf outputs
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3a5ef1b
Terminate exhaustive MMseqs candidate streams safely
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7520765

Commits on Sep 16, 2026

Commits on Sep 17, 2026

Commits on Sep 18, 2026

Fix order for filters
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b14666e
Add another RL term with coverage for arcs synteny one break requirement that was removed
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3edf817

Commits on Sep 19, 2026

Fix bug with setting
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21ba5a1

Commits on Sep 21, 2026

Remove shortcut for adding some mutations to K and calling that passing the accessory gene criteria
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3deb237