@synsci/cli-darwin-x64 1.1.97 → 1.1.99
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bin/synsc +0 -0
- package/package.json +1 -1
- package/bin/skills/accelerate/SKILL.md +0 -332
- package/bin/skills/accelerate/references/custom-plugins.md +0 -453
- package/bin/skills/accelerate/references/megatron-integration.md +0 -489
- package/bin/skills/accelerate/references/performance.md +0 -525
- package/bin/skills/adaptyv/SKILL.md +0 -114
- package/bin/skills/adaptyv/reference/api_reference.md +0 -308
- package/bin/skills/adaptyv/reference/examples.md +0 -913
- package/bin/skills/adaptyv/reference/experiments.md +0 -360
- package/bin/skills/adaptyv/reference/protein_optimization.md +0 -637
- package/bin/skills/aeon/SKILL.md +0 -374
- package/bin/skills/aeon/references/anomaly_detection.md +0 -154
- package/bin/skills/aeon/references/classification.md +0 -144
- package/bin/skills/aeon/references/clustering.md +0 -123
- package/bin/skills/aeon/references/datasets_benchmarking.md +0 -387
- package/bin/skills/aeon/references/distances.md +0 -256
- package/bin/skills/aeon/references/forecasting.md +0 -140
- package/bin/skills/aeon/references/networks.md +0 -289
- package/bin/skills/aeon/references/regression.md +0 -118
- package/bin/skills/aeon/references/segmentation.md +0 -163
- package/bin/skills/aeon/references/similarity_search.md +0 -187
- package/bin/skills/aeon/references/transformations.md +0 -246
- package/bin/skills/alphafold-database/SKILL.md +0 -513
- package/bin/skills/alphafold-database/references/api_reference.md +0 -423
- package/bin/skills/anndata/SKILL.md +0 -400
- package/bin/skills/anndata/references/best_practices.md +0 -525
- package/bin/skills/anndata/references/concatenation.md +0 -396
- package/bin/skills/anndata/references/data_structure.md +0 -314
- package/bin/skills/anndata/references/io_operations.md +0 -404
- package/bin/skills/anndata/references/manipulation.md +0 -516
- package/bin/skills/arboreto/SKILL.md +0 -243
- package/bin/skills/arboreto/references/algorithms.md +0 -138
- package/bin/skills/arboreto/references/basic_inference.md +0 -151
- package/bin/skills/arboreto/references/distributed_computing.md +0 -242
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +0 -97
- package/bin/skills/astropy/SKILL.md +0 -331
- package/bin/skills/astropy/references/coordinates.md +0 -273
- package/bin/skills/astropy/references/cosmology.md +0 -307
- package/bin/skills/astropy/references/fits.md +0 -396
- package/bin/skills/astropy/references/tables.md +0 -489
- package/bin/skills/astropy/references/time.md +0 -404
- package/bin/skills/astropy/references/units.md +0 -178
- package/bin/skills/astropy/references/wcs_and_other_modules.md +0 -373
- package/bin/skills/audiocraft/SKILL.md +0 -564
- package/bin/skills/audiocraft/references/advanced-usage.md +0 -666
- package/bin/skills/audiocraft/references/troubleshooting.md +0 -504
- package/bin/skills/autogpt/SKILL.md +0 -403
- package/bin/skills/autogpt/references/advanced-usage.md +0 -535
- package/bin/skills/autogpt/references/troubleshooting.md +0 -420
- package/bin/skills/awq/SKILL.md +0 -310
- package/bin/skills/awq/references/advanced-usage.md +0 -324
- package/bin/skills/awq/references/troubleshooting.md +0 -344
- package/bin/skills/axolotl/SKILL.md +0 -158
- package/bin/skills/axolotl/references/api.md +0 -5548
- package/bin/skills/axolotl/references/dataset-formats.md +0 -1029
- package/bin/skills/axolotl/references/index.md +0 -15
- package/bin/skills/axolotl/references/other.md +0 -3563
- package/bin/skills/benchling-integration/SKILL.md +0 -480
- package/bin/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/bin/skills/benchling-integration/references/authentication.md +0 -379
- package/bin/skills/benchling-integration/references/sdk_reference.md +0 -774
- package/bin/skills/bigcode-evaluation-harness/SKILL.md +0 -405
- package/bin/skills/bigcode-evaluation-harness/references/benchmarks.md +0 -393
- package/bin/skills/bigcode-evaluation-harness/references/custom-tasks.md +0 -424
- package/bin/skills/bigcode-evaluation-harness/references/issues.md +0 -394
- package/bin/skills/biopython/SKILL.md +0 -443
- package/bin/skills/biopython/references/advanced.md +0 -577
- package/bin/skills/biopython/references/alignment.md +0 -362
- package/bin/skills/biopython/references/blast.md +0 -455
- package/bin/skills/biopython/references/databases.md +0 -484
- package/bin/skills/biopython/references/phylogenetics.md +0 -566
- package/bin/skills/biopython/references/sequence_io.md +0 -285
- package/bin/skills/biopython/references/structure.md +0 -564
- package/bin/skills/biorxiv-database/SKILL.md +0 -483
- package/bin/skills/biorxiv-database/references/api_reference.md +0 -280
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +0 -445
- package/bin/skills/bioservices/SKILL.md +0 -361
- package/bin/skills/bioservices/references/identifier_mapping.md +0 -685
- package/bin/skills/bioservices/references/services_reference.md +0 -636
- package/bin/skills/bioservices/references/workflow_patterns.md +0 -811
- package/bin/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +0 -378
- package/bin/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +0 -408
- package/bin/skills/bitsandbytes/SKILL.md +0 -411
- package/bin/skills/bitsandbytes/references/memory-optimization.md +0 -521
- package/bin/skills/bitsandbytes/references/qlora-training.md +0 -521
- package/bin/skills/bitsandbytes/references/quantization-formats.md +0 -447
- package/bin/skills/blip-2/SKILL.md +0 -564
- package/bin/skills/blip-2/references/advanced-usage.md +0 -680
- package/bin/skills/blip-2/references/troubleshooting.md +0 -526
- package/bin/skills/brenda-database/SKILL.md +0 -719
- package/bin/skills/brenda-database/references/api_reference.md +0 -537
- package/bin/skills/brenda-database/scripts/brenda_queries.py +0 -844
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +0 -772
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +0 -1053
- package/bin/skills/cellxgene-census/SKILL.md +0 -511
- package/bin/skills/cellxgene-census/references/census_schema.md +0 -182
- package/bin/skills/cellxgene-census/references/common_patterns.md +0 -351
- package/bin/skills/chembl-database/SKILL.md +0 -389
- package/bin/skills/chembl-database/references/api_reference.md +0 -272
- package/bin/skills/chembl-database/scripts/example_queries.py +0 -278
- package/bin/skills/chroma/SKILL.md +0 -406
- package/bin/skills/chroma/references/integration.md +0 -38
- package/bin/skills/cirq/SKILL.md +0 -346
- package/bin/skills/cirq/references/building.md +0 -307
- package/bin/skills/cirq/references/experiments.md +0 -572
- package/bin/skills/cirq/references/hardware.md +0 -515
- package/bin/skills/cirq/references/noise.md +0 -515
- package/bin/skills/cirq/references/simulation.md +0 -350
- package/bin/skills/cirq/references/transformation.md +0 -416
- package/bin/skills/citation-management/SKILL.md +0 -1109
- package/bin/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/bin/skills/citation-management/assets/citation_checklist.md +0 -386
- package/bin/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/bin/skills/citation-management/references/citation_validation.md +0 -794
- package/bin/skills/citation-management/references/google_scholar_search.md +0 -725
- package/bin/skills/citation-management/references/metadata_extraction.md +0 -870
- package/bin/skills/citation-management/references/pubmed_search.md +0 -839
- package/bin/skills/citation-management/scripts/doi_to_bibtex.py +0 -182
- package/bin/skills/citation-management/scripts/extract_metadata.py +0 -570
- package/bin/skills/citation-management/scripts/format_bibtex.py +0 -349
- package/bin/skills/citation-management/scripts/search_google_scholar.py +0 -251
- package/bin/skills/citation-management/scripts/search_pubmed.py +0 -348
- package/bin/skills/citation-management/scripts/validate_citations.py +0 -494
- package/bin/skills/clinical-decision-support/README.md +0 -129
- package/bin/skills/clinical-decision-support/SKILL.md +0 -506
- package/bin/skills/clinical-decision-support/assets/biomarker_report_template.tex +0 -380
- package/bin/skills/clinical-decision-support/assets/clinical_pathway_template.tex +0 -222
- package/bin/skills/clinical-decision-support/assets/cohort_analysis_template.tex +0 -359
- package/bin/skills/clinical-decision-support/assets/color_schemes.tex +0 -149
- package/bin/skills/clinical-decision-support/assets/example_gbm_cohort.md +0 -208
- package/bin/skills/clinical-decision-support/assets/recommendation_strength_guide.md +0 -328
- package/bin/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +0 -529
- package/bin/skills/clinical-decision-support/references/biomarker_classification.md +0 -719
- package/bin/skills/clinical-decision-support/references/clinical_decision_algorithms.md +0 -604
- package/bin/skills/clinical-decision-support/references/evidence_synthesis.md +0 -840
- package/bin/skills/clinical-decision-support/references/outcome_analysis.md +0 -640
- package/bin/skills/clinical-decision-support/references/patient_cohort_analysis.md +0 -427
- package/bin/skills/clinical-decision-support/references/treatment_recommendations.md +0 -521
- package/bin/skills/clinical-decision-support/scripts/biomarker_classifier.py +0 -383
- package/bin/skills/clinical-decision-support/scripts/build_decision_tree.py +0 -417
- package/bin/skills/clinical-decision-support/scripts/create_cohort_tables.py +0 -509
- package/bin/skills/clinical-decision-support/scripts/generate_survival_analysis.py +0 -441
- package/bin/skills/clinical-decision-support/scripts/validate_cds_document.py +0 -326
- package/bin/skills/clinical-reports/IMPLEMENTATION_SUMMARY.md +0 -641
- package/bin/skills/clinical-reports/README.md +0 -236
- package/bin/skills/clinical-reports/SKILL.md +0 -1127
- package/bin/skills/clinical-reports/assets/case_report_template.md +0 -352
- package/bin/skills/clinical-reports/assets/clinical_trial_csr_template.md +0 -353
- package/bin/skills/clinical-reports/assets/clinical_trial_sae_template.md +0 -359
- package/bin/skills/clinical-reports/assets/consult_note_template.md +0 -305
- package/bin/skills/clinical-reports/assets/discharge_summary_template.md +0 -453
- package/bin/skills/clinical-reports/assets/hipaa_compliance_checklist.md +0 -395
- package/bin/skills/clinical-reports/assets/history_physical_template.md +0 -305
- package/bin/skills/clinical-reports/assets/lab_report_template.md +0 -309
- package/bin/skills/clinical-reports/assets/pathology_report_template.md +0 -249
- package/bin/skills/clinical-reports/assets/quality_checklist.md +0 -338
- package/bin/skills/clinical-reports/assets/radiology_report_template.md +0 -318
- package/bin/skills/clinical-reports/assets/soap_note_template.md +0 -253
- package/bin/skills/clinical-reports/references/case_report_guidelines.md +0 -570
- package/bin/skills/clinical-reports/references/clinical_trial_reporting.md +0 -693
- package/bin/skills/clinical-reports/references/data_presentation.md +0 -530
- package/bin/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -629
- package/bin/skills/clinical-reports/references/medical_terminology.md +0 -588
- package/bin/skills/clinical-reports/references/patient_documentation.md +0 -744
- package/bin/skills/clinical-reports/references/peer_review_standards.md +0 -585
- package/bin/skills/clinical-reports/references/regulatory_compliance.md +0 -577
- package/bin/skills/clinical-reports/scripts/check_deidentification.py +0 -332
- package/bin/skills/clinical-reports/scripts/compliance_checker.py +0 -78
- package/bin/skills/clinical-reports/scripts/extract_clinical_data.py +0 -97
- package/bin/skills/clinical-reports/scripts/format_adverse_events.py +0 -97
- package/bin/skills/clinical-reports/scripts/generate_report_template.py +0 -149
- package/bin/skills/clinical-reports/scripts/terminology_validator.py +0 -126
- package/bin/skills/clinical-reports/scripts/validate_case_report.py +0 -323
- package/bin/skills/clinical-reports/scripts/validate_trial_report.py +0 -88
- package/bin/skills/clinicaltrials-database/SKILL.md +0 -507
- package/bin/skills/clinicaltrials-database/references/api_reference.md +0 -358
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +0 -215
- package/bin/skills/clinpgx-database/SKILL.md +0 -638
- package/bin/skills/clinpgx-database/references/api_reference.md +0 -757
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +0 -518
- package/bin/skills/clinvar-database/SKILL.md +0 -362
- package/bin/skills/clinvar-database/references/api_reference.md +0 -227
- package/bin/skills/clinvar-database/references/clinical_significance.md +0 -218
- package/bin/skills/clinvar-database/references/data_formats.md +0 -358
- package/bin/skills/clip/SKILL.md +0 -253
- package/bin/skills/clip/references/applications.md +0 -207
- package/bin/skills/cobrapy/SKILL.md +0 -463
- package/bin/skills/cobrapy/references/api_quick_reference.md +0 -655
- package/bin/skills/cobrapy/references/workflows.md +0 -593
- package/bin/skills/colab-finetuning/SKILL.md +0 -153
- package/bin/skills/colab-finetuning/references/bridge-setup.md +0 -68
- package/bin/skills/colab-finetuning/references/gpu-tiers.md +0 -54
- package/bin/skills/colab-finetuning/references/troubleshooting.md +0 -79
- package/bin/skills/constitutional-ai/SKILL.md +0 -290
- package/bin/skills/cosmic-database/SKILL.md +0 -336
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +0 -220
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +0 -231
- package/bin/skills/crewai/SKILL.md +0 -498
- package/bin/skills/crewai/references/flows.md +0 -438
- package/bin/skills/crewai/references/tools.md +0 -429
- package/bin/skills/crewai/references/troubleshooting.md +0 -480
- package/bin/skills/dask/SKILL.md +0 -456
- package/bin/skills/dask/references/arrays.md +0 -497
- package/bin/skills/dask/references/bags.md +0 -468
- package/bin/skills/dask/references/best-practices.md +0 -277
- package/bin/skills/dask/references/dataframes.md +0 -368
- package/bin/skills/dask/references/futures.md +0 -541
- package/bin/skills/dask/references/schedulers.md +0 -504
- package/bin/skills/datacommons-client/SKILL.md +0 -255
- package/bin/skills/datacommons-client/references/getting_started.md +0 -417
- package/bin/skills/datacommons-client/references/node.md +0 -250
- package/bin/skills/datacommons-client/references/observation.md +0 -185
- package/bin/skills/datacommons-client/references/resolve.md +0 -246
- package/bin/skills/datamol/SKILL.md +0 -706
- package/bin/skills/datamol/references/conformers_module.md +0 -131
- package/bin/skills/datamol/references/core_api.md +0 -130
- package/bin/skills/datamol/references/descriptors_viz.md +0 -195
- package/bin/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/bin/skills/datamol/references/io_module.md +0 -109
- package/bin/skills/datamol/references/reactions_data.md +0 -218
- package/bin/skills/deepchem/SKILL.md +0 -597
- package/bin/skills/deepchem/references/api_reference.md +0 -303
- package/bin/skills/deepchem/references/workflows.md +0 -491
- package/bin/skills/deepchem/scripts/graph_neural_network.py +0 -338
- package/bin/skills/deepchem/scripts/predict_solubility.py +0 -224
- package/bin/skills/deepchem/scripts/transfer_learning.py +0 -375
- package/bin/skills/deepspeed/SKILL.md +0 -141
- package/bin/skills/deepspeed/references/08.md +0 -17
- package/bin/skills/deepspeed/references/09.md +0 -173
- package/bin/skills/deepspeed/references/2020.md +0 -378
- package/bin/skills/deepspeed/references/2023.md +0 -279
- package/bin/skills/deepspeed/references/assets.md +0 -179
- package/bin/skills/deepspeed/references/index.md +0 -35
- package/bin/skills/deepspeed/references/mii.md +0 -118
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- package/bin/skills/deepspeed/references/tutorials.md +0 -6554
- package/bin/skills/deeptools/SKILL.md +0 -531
- package/bin/skills/deeptools/assets/quick_reference.md +0 -58
- package/bin/skills/deeptools/references/effective_genome_sizes.md +0 -116
- package/bin/skills/deeptools/references/normalization_methods.md +0 -410
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- package/bin/skills/deeptools/references/workflows.md +0 -474
- package/bin/skills/deeptools/scripts/validate_files.py +0 -195
- package/bin/skills/deeptools/scripts/workflow_generator.py +0 -454
- package/bin/skills/denario/SKILL.md +0 -215
- package/bin/skills/denario/references/examples.md +0 -494
- package/bin/skills/denario/references/installation.md +0 -213
- package/bin/skills/denario/references/llm_configuration.md +0 -265
- package/bin/skills/denario/references/research_pipeline.md +0 -471
- package/bin/skills/diffdock/SKILL.md +0 -483
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- package/bin/skills/diffdock/scripts/analyze_results.py +0 -334
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +0 -254
- package/bin/skills/diffdock/scripts/setup_check.py +0 -278
- package/bin/skills/dnanexus-integration/SKILL.md +0 -383
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# DPO & Preference Learning
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## Direct Preference Optimization (DPO)
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DPO trains models to prefer chosen responses over rejected ones using a classification loss, without needing a separate reward model.
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### Quick Start
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dataset=hhh \
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renderer_name=role_colon \
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learning_rate=1e-5 \
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dpo_beta=0.1
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```
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### Key Parameters
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| `model_name` | Base model (also used as reference policy) | Start with 1B-8B |
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| `dataset` | Preference dataset name | `hhh`, `helpsteer3`, `ultrafeedback` |
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| `renderer_name` | Chat format renderer | Match model family |
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| `learning_rate` | LR for optimization | 1e-5 to 1e-6 (lower than SFT) |
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| `dpo_beta` | Preference strength | Start with 0.1 |
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| `log_path` | Output directory | Required |
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### Available Datasets
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| Dataset | Source | Description |
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| `hhh` | Anthropic | Helpful-Harmless-Honest pairwise comparisons |
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| `helpsteer3` | NVIDIA | HelpSteer3 preference dataset |
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| `ultrafeedback` | UltraFeedback | Binarized preferences |
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Custom datasets: implement `DPODatasetBuilder` from `tinker_cookbook.preference.preference_datasets`.
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### Training Metrics
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| Metric | Description | Watch For |
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| `dpo_loss` | DPO classification loss | Should decrease |
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| `accuracy` | Implicit reward model accuracy | Should increase |
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| `margin` | Chosen - rejected reward gap | Should increase |
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| `chosen_reward` | Average reward for chosen responses | Higher is better |
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| `rejected_reward` | Average reward for rejected responses | Lower is better |
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### Tips
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### Evaluating DPO Models
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tasks=inspect_evals/ifeval,inspect_evals/mmlu_0_shot
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```bash
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### Collect and Visualize
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# Evaluations
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## Inline Evals (During Training)
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Add evaluations that run periodically during training.
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### Supervised Fine-Tuning
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### RL Training
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})
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## Offline Evals with Inspect AI
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Run standard evaluations on checkpoints using the Inspect AI library:
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```bash
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renderer_name=RENDERER_NAME
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```
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### Creating Custom Inspect AI Tasks
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```python
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import tinker
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from inspect_ai.model import GenerateConfig as InspectAIGenerateConfig
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from inspect_ai.model import Model as InspectAIModel
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from inspect_ai.scorer import model_graded_qa
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from inspect_ai.solver import generate
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from tinker_cookbook.eval.inspect_utils import InspectAPIFromTinkerSampling
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QA_DATASET = MemoryDataset(
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name="qa_dataset",
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samples=[
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Sample(input="What is the capital of France?", target="Paris"),
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Sample(input="What is the capital of Italy?", target="Rome"),
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],
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)
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service_client = tinker.ServiceClient()
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sampling_client = service_client.create_sampling_client(
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base_model="meta-llama/Llama-3.1-8B-Instruct"
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)
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api = InspectAPIFromTinkerSampling(
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renderer_name="llama3",
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model_name="meta-llama/Llama-3.1-8B-Instruct",
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sampling_client=sampling_client,
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verbose=False,
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)
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GRADER_MODEL = InspectAIModel(api=api, config=InspectAIGenerateConfig())
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@task
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def example_lm_as_judge() -> Task:
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return Task(
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name="llm_as_judge",
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|
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dataset=QA_DATASET,
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solver=generate(),
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scorer=model_graded_qa(
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instructions="Grade strictly. Respond 'GRADE: C' if correct or 'GRADE: I' otherwise.",
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partial_credit=False,
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model=GRADER_MODEL,
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),
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|
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)
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90
|
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```
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|
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92
|
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Inspect also supports any OpenAI-compatible API (e.g., openrouter) as the grader model.
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93
|
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|
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94
|
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## Custom SamplingClientEvaluator
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Lower-level abstraction with fine-grained control:
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98
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```python
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from typing import Any, Callable
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|
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import tinker
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from tinker import types
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from tinker_cookbook import renderers
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|
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from tinker_cookbook.evaluators import SamplingClientEvaluator
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from tinker_cookbook.tokenizer_utils import get_tokenizer
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|
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|
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106
|
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class CustomEvaluator(SamplingClientEvaluator):
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def __init__(
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self,
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dataset: Any,
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grader_fn: Callable[[str, str], bool],
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model_name: str,
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renderer_name: str,
|
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):
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self.dataset = dataset
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|
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self.grader_fn = grader_fn
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|
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tokenizer = get_tokenizer(model_name)
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|
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self.renderer = renderers.get_renderer(name=renderer_name, tokenizer=tokenizer)
|
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|
-
|
|
119
|
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async def __call__(self, sampling_client: tinker.SamplingClient) -> dict[str, float]:
|
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120
|
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sampling_params = types.SamplingParams(
|
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121
|
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max_tokens=100,
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|
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temperature=0.7,
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|
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top_p=1.0,
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|
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stop=self.renderer.get_stop_sequences(),
|
|
125
|
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)
|
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|
-
|
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127
|
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num_correct = 0
|
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|
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for datum in self.dataset:
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129
|
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model_input = self.renderer.build_generation_prompt(
|
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130
|
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[renderers.Message(role="user", content=datum["input"])]
|
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|
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)
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132
|
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r = await sampling_client.sample_async(
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133
|
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prompt=model_input, num_samples=1, sampling_params=sampling_params
|
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134
|
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)
|
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135
|
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tokens = r.sequences[0].tokens
|
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136
|
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response = self.renderer.parse_response(tokens)[0]
|
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137
|
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if self.grader_fn(response["content"], datum["output"]):
|
|
138
|
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num_correct += 1
|
|
139
|
-
|
|
140
|
-
return {"accuracy": num_correct / len(self.dataset)}
|
|
141
|
-
```
|
|
142
|
-
|
|
143
|
-
### Usage
|
|
144
|
-
|
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145
|
-
```python
|
|
146
|
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import asyncio
|
|
147
|
-
|
|
148
|
-
QA_DATASET = [
|
|
149
|
-
{"input": "What is the capital of France?", "output": "Paris"},
|
|
150
|
-
{"input": "What is the capital of Germany?", "output": "Berlin"},
|
|
151
|
-
]
|
|
152
|
-
|
|
153
|
-
def grader_fn(response: str, target: str) -> bool:
|
|
154
|
-
return target.lower() in response.lower()
|
|
155
|
-
|
|
156
|
-
evaluator = CustomEvaluator(
|
|
157
|
-
dataset=QA_DATASET,
|
|
158
|
-
grader_fn=grader_fn,
|
|
159
|
-
renderer_name="llama3",
|
|
160
|
-
model_name="meta-llama/Llama-3.1-8B-Instruct",
|
|
161
|
-
)
|
|
162
|
-
|
|
163
|
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service_client = tinker.ServiceClient()
|
|
164
|
-
sampling_client = service_client.create_sampling_client(
|
|
165
|
-
base_model="meta-llama/Llama-3.1-8B-Instruct"
|
|
166
|
-
)
|
|
167
|
-
|
|
168
|
-
async def main():
|
|
169
|
-
result = await evaluator(sampling_client)
|
|
170
|
-
print(result) # {"accuracy": 1.0}
|
|
171
|
-
|
|
172
|
-
asyncio.run(main())
|
|
173
|
-
```
|
|
174
|
-
|
|
175
|
-
## Evaluation Strategy
|
|
176
|
-
|
|
177
|
-
| Stage | Method | When |
|
|
178
|
-
|-------|--------|------|
|
|
179
|
-
| During SFT | `evaluator_builders` | Every N training steps |
|
|
180
|
-
| During RL | `evaluator_builders` (SamplingClientEvaluator) | Every N iterations |
|
|
181
|
-
| After training | `run_inspect_evals` CLI | On final checkpoint |
|
|
182
|
-
| Custom tasks | Custom `SamplingClientEvaluator` | Any time with sampling client |
|
|
183
|
-
| LLM-as-judge | Inspect AI with `model_graded_qa` | When automated grading needed |
|
|
@@ -1,157 +0,0 @@
|
|
|
1
|
-
# Getting Started with Tinker
|
|
2
|
-
|
|
3
|
-
## Creating Clients
|
|
4
|
-
|
|
5
|
-
```python
|
|
6
|
-
import tinker
|
|
7
|
-
service_client = tinker.ServiceClient()
|
|
8
|
-
|
|
9
|
-
# Check available models
|
|
10
|
-
for item in service_client.get_server_capabilities().supported_models:
|
|
11
|
-
print("- " + item.model_name)
|
|
12
|
-
|
|
13
|
-
# Create training client
|
|
14
|
-
training_client = service_client.create_lora_training_client(
|
|
15
|
-
base_model="Qwen/Qwen3-VL-30B-A3B-Instruct",
|
|
16
|
-
rank=32,
|
|
17
|
-
)
|
|
18
|
-
|
|
19
|
-
# Get tokenizer
|
|
20
|
-
tokenizer = training_client.get_tokenizer()
|
|
21
|
-
```
|
|
22
|
-
|
|
23
|
-
## Preparing Training Data
|
|
24
|
-
|
|
25
|
-
```python
|
|
26
|
-
import numpy as np
|
|
27
|
-
from tinker import types
|
|
28
|
-
|
|
29
|
-
def process_example(example: dict, tokenizer) -> types.Datum:
|
|
30
|
-
prompt = f"English: {example['input']}\nPig Latin:"
|
|
31
|
-
prompt_tokens = tokenizer.encode(prompt, add_special_tokens=True)
|
|
32
|
-
|
|
33
|
-
completion_tokens = tokenizer.encode(f" {example['output']}\n\n", add_special_tokens=False)
|
|
34
|
-
tokens = prompt_tokens + completion_tokens
|
|
35
|
-
weights = np.array(([0] * len(prompt_tokens)) + ([1] * len(completion_tokens)), dtype=np.float32)
|
|
36
|
-
target_tokens = np.array(tokens[1:], dtype=np.int64)
|
|
37
|
-
|
|
38
|
-
return types.Datum(
|
|
39
|
-
model_input=types.ModelInput.from_ints(tokens=tokens[:-1]),
|
|
40
|
-
loss_fn_inputs=dict(weights=weights[1:], target_tokens=target_tokens)
|
|
41
|
-
)
|
|
42
|
-
```
|
|
43
|
-
|
|
44
|
-
## Vision Inputs
|
|
45
|
-
|
|
46
|
-
```python
|
|
47
|
-
import requests
|
|
48
|
-
|
|
49
|
-
image_data = requests.get("https://example.com/image.png").content
|
|
50
|
-
model_input = tinker.ModelInput(chunks=[
|
|
51
|
-
types.EncodedTextChunk(tokens=tokenizer.encode("<|im_start|>user\n<|vision_start|>")),
|
|
52
|
-
types.ImageChunk(data=image_data, format="png"),
|
|
53
|
-
types.EncodedTextChunk(tokens=tokenizer.encode("<|vision_end|>What is this?<|im_end|>\n<|im_start|>assistant\n")),
|
|
54
|
-
])
|
|
55
|
-
```
|
|
56
|
-
|
|
57
|
-
## Training Loop
|
|
58
|
-
|
|
59
|
-
```python
|
|
60
|
-
import numpy as np
|
|
61
|
-
|
|
62
|
-
for _ in range(6):
|
|
63
|
-
fwdbwd_future = training_client.forward_backward(processed_examples, "cross_entropy")
|
|
64
|
-
optim_future = training_client.optim_step(types.AdamParams(learning_rate=2e-4)) # Use get_lr() for production
|
|
65
|
-
|
|
66
|
-
fwdbwd_result = fwdbwd_future.result()
|
|
67
|
-
optim_result = optim_future.result()
|
|
68
|
-
|
|
69
|
-
# Compute loss
|
|
70
|
-
logprobs = np.concatenate([out['logprobs'].tolist() for out in fwdbwd_result.loss_fn_outputs])
|
|
71
|
-
weights = np.concatenate([ex.loss_fn_inputs['weights'].tolist() for ex in processed_examples])
|
|
72
|
-
print(f"Loss per token: {-np.dot(logprobs, weights) / weights.sum():.4f}")
|
|
73
|
-
```
|
|
74
|
-
|
|
75
|
-
## Sampling
|
|
76
|
-
|
|
77
|
-
```python
|
|
78
|
-
# Create sampling client
|
|
79
|
-
sampling_client = training_client.save_weights_and_get_sampling_client(name='my-model')
|
|
80
|
-
|
|
81
|
-
# Sample
|
|
82
|
-
prompt = types.ModelInput.from_ints(tokens=tokenizer.encode("English: coffee break\nPig Latin:", add_special_tokens=True))
|
|
83
|
-
params = types.SamplingParams(max_tokens=20, temperature=0.0, stop=["\n"])
|
|
84
|
-
future = sampling_client.sample(prompt=prompt, sampling_params=params, num_samples=8)
|
|
85
|
-
result = future.result()
|
|
86
|
-
|
|
87
|
-
for i, seq in enumerate(result.sequences):
|
|
88
|
-
print(f"{i}: {repr(tokenizer.decode(seq.tokens))}")
|
|
89
|
-
```
|
|
90
|
-
|
|
91
|
-
## Computing Logprobs
|
|
92
|
-
|
|
93
|
-
```python
|
|
94
|
-
# Get prompt logprobs
|
|
95
|
-
prompt = types.ModelInput.from_ints(tokens=tokenizer.encode("How many r's are in strawberry?", add_special_tokens=True))
|
|
96
|
-
sample_response = sampling_client.sample(
|
|
97
|
-
prompt=prompt,
|
|
98
|
-
num_samples=1,
|
|
99
|
-
sampling_params=tinker.SamplingParams(max_tokens=1),
|
|
100
|
-
include_prompt_logprobs=True,
|
|
101
|
-
).result()
|
|
102
|
-
print(sample_response.prompt_logprobs) # [None, -9.5, -1.6, ...]
|
|
103
|
-
|
|
104
|
-
# Top-k logprobs
|
|
105
|
-
sample_response = sampling_client.sample(
|
|
106
|
-
prompt=prompt,
|
|
107
|
-
num_samples=1,
|
|
108
|
-
sampling_params=tinker.SamplingParams(max_tokens=1),
|
|
109
|
-
include_prompt_logprobs=True,
|
|
110
|
-
topk_prompt_logprobs=5,
|
|
111
|
-
).result()
|
|
112
|
-
print(sample_response.topk_prompt_logprobs) # [None, [(token_id, logprob), ...], ...]
|
|
113
|
-
```
|
|
114
|
-
|
|
115
|
-
## Async and Futures
|
|
116
|
-
|
|
117
|
-
Every method has sync and async versions:
|
|
118
|
-
|
|
119
|
-
| Sync | Async |
|
|
120
|
-
|------|-------|
|
|
121
|
-
| `create_lora_training_client()` | `create_lora_training_client_async()` |
|
|
122
|
-
| `forward()` | `forward_async()` |
|
|
123
|
-
| `sample()` | `sample_async()` |
|
|
124
|
-
|
|
125
|
-
```python
|
|
126
|
-
# Sync
|
|
127
|
-
future = client.forward_backward(data, loss_fn)
|
|
128
|
-
result = future.result() # Blocks
|
|
129
|
-
|
|
130
|
-
# Async (double await)
|
|
131
|
-
future = await client.forward_backward_async(data, loss_fn)
|
|
132
|
-
result = await future
|
|
133
|
-
```
|
|
134
|
-
|
|
135
|
-
### Overlap Requests for Performance
|
|
136
|
-
|
|
137
|
-
```python
|
|
138
|
-
# Submit both before waiting - runs in same clock cycle
|
|
139
|
-
fwd_bwd_future = await client.forward_backward_async(batch, loss_fn)
|
|
140
|
-
optim_future = await client.optim_step_async(adam_params)
|
|
141
|
-
|
|
142
|
-
# Now retrieve results
|
|
143
|
-
fwd_bwd_result = await fwd_bwd_future
|
|
144
|
-
optim_result = await optim_future
|
|
145
|
-
```
|
|
146
|
-
|
|
147
|
-
## Saving and Loading
|
|
148
|
-
|
|
149
|
-
```python
|
|
150
|
-
# Save weights for sampling (fast, smaller)
|
|
151
|
-
sampling_path = training_client.save_weights_for_sampler(name="0000").result().path
|
|
152
|
-
sampling_client = service_client.create_sampling_client(model_path=sampling_path)
|
|
153
|
-
|
|
154
|
-
# Save full state for resuming training
|
|
155
|
-
resume_path = training_client.save_state(name="0010").result().path
|
|
156
|
-
training_client.load_state(resume_path)
|
|
157
|
-
```
|
|
@@ -1,163 +0,0 @@
|
|
|
1
|
-
# Loss Functions
|
|
2
|
-
|
|
3
|
-
## Built-in Loss Functions
|
|
4
|
-
|
|
5
|
-
Pass as string to `forward_backward(data, loss_fn)`.
|
|
6
|
-
|
|
7
|
-
## Supervised Learning
|
|
8
|
-
|
|
9
|
-
### cross_entropy
|
|
10
|
-
|
|
11
|
-
Standard next-token prediction loss.
|
|
12
|
-
|
|
13
|
-
$$\mathcal{L}(\theta) = -\mathbb{E}_x[\log p_\theta(x)]$$
|
|
14
|
-
|
|
15
|
-
```python
|
|
16
|
-
fwd_bwd = training_client.forward_backward(data, loss_fn="cross_entropy")
|
|
17
|
-
```
|
|
18
|
-
|
|
19
|
-
**Inputs:**
|
|
20
|
-
- `target_tokens: array[(N,), int]` - Target token IDs
|
|
21
|
-
- `weights: array[(N,), float]` - Loss weights (0 = ignore, 1 = train)
|
|
22
|
-
|
|
23
|
-
**Outputs:**
|
|
24
|
-
- `logprobs: array[(N,), float]` - Log probabilities
|
|
25
|
-
- `loss:sum` (scalar) - Total weighted loss
|
|
26
|
-
|
|
27
|
-
## Policy Gradient Methods
|
|
28
|
-
|
|
29
|
-
### importance_sampling
|
|
30
|
-
|
|
31
|
-
Policy gradient with importance weighting for off-policy correction:
|
|
32
|
-
|
|
33
|
-
$$\mathcal{L}_{IS}(\theta) = \mathbb{E}_{x\sim q}\left[\frac{p_\theta(x)}{q(x)}A(x)\right]$$
|
|
34
|
-
|
|
35
|
-
```python
|
|
36
|
-
fwd_bwd = training_client.forward_backward(data, loss_fn="importance_sampling")
|
|
37
|
-
```
|
|
38
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-
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39
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**Inputs:**
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40
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- `target_tokens: array[(N,), int]` - Target tokens
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41
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- `logprobs: array[(N,), float]` - Sampling logprobs (from q)
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42
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- `advantages: array[(N,), float]` - Advantage values
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43
|
-
|
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44
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### ppo
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45
|
-
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46
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Proximal Policy Optimization with clipping:
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47
|
-
|
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48
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-
$$\mathcal{L}_{PPO}(\theta) = -\mathbb{E}_{x \sim q}\left[\min\left(\frac{p_\theta(x)}{q(x)} A(x), \text{clip}\left(\frac{p_\theta(x)}{q(x)}, 1-\epsilon, 1+\epsilon\right) A(x)\right)\right]$$
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49
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-
|
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50
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-
```python
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51
|
-
fwd_bwd = training_client.forward_backward(
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52
|
-
data,
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53
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-
loss_fn="ppo",
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54
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loss_fn_config={"clip_low_threshold": 0.9, "clip_high_threshold": 1.1}
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55
|
-
)
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56
|
-
```
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|
57
|
-
|
|
58
|
-
**Inputs:** Same as `importance_sampling`
|
|
59
|
-
|
|
60
|
-
### cispo
|
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61
|
-
|
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62
|
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Clipped Importance Sampling Policy Optimization:
|
|
63
|
-
|
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64
|
-
$$\mathcal{L}_{CISPO}(\theta) = \mathbb{E}_{x \sim q}\left[\text{sg}\left(\text{clip}\left(\frac{p_\theta(x)}{q(x)}, 1-\epsilon, 1+\epsilon\right)\right) \log p_\theta(x) A(x)\right]$$
|
|
65
|
-
|
|
66
|
-
```python
|
|
67
|
-
fwd_bwd = training_client.forward_backward(
|
|
68
|
-
data,
|
|
69
|
-
loss_fn="cispo",
|
|
70
|
-
loss_fn_config={"clip_low_threshold": 0.8, "clip_high_threshold": 1.2}
|
|
71
|
-
)
|
|
72
|
-
```
|
|
73
|
-
|
|
74
|
-
### dro
|
|
75
|
-
|
|
76
|
-
Direct Reward Optimization with quadratic penalty:
|
|
77
|
-
|
|
78
|
-
$$\mathcal{L}_{DRO}(\theta) = \mathbb{E}_{x \sim q}\left[\log p_\theta(x) A(x) - \frac{1}{2}\beta \left(\log \frac{p_\theta(x)}{q(x)}\right)^2\right]$$
|
|
79
|
-
|
|
80
|
-
```python
|
|
81
|
-
fwd_bwd = training_client.forward_backward(
|
|
82
|
-
data,
|
|
83
|
-
loss_fn="dro",
|
|
84
|
-
loss_fn_config={"beta": 0.05}
|
|
85
|
-
)
|
|
86
|
-
```
|
|
87
|
-
|
|
88
|
-
## Custom Loss Functions
|
|
89
|
-
|
|
90
|
-
For losses not covered above, use `forward_backward_custom`:
|
|
91
|
-
|
|
92
|
-
```python
|
|
93
|
-
def custom_loss(data: list[Datum], logprobs: list[torch.Tensor]) -> tuple[torch.Tensor, dict[str, float]]:
|
|
94
|
-
loss = (logprobs ** 2).sum()
|
|
95
|
-
return loss, {"custom_loss": loss.item()}
|
|
96
|
-
|
|
97
|
-
loss, metrics = training_client.forward_backward_custom(data, custom_loss)
|
|
98
|
-
```
|
|
99
|
-
|
|
100
|
-
### Multi-Sequence Loss
|
|
101
|
-
|
|
102
|
-
```python
|
|
103
|
-
def variance_loss(data: list[Datum], logprobs: list[torch.Tensor]) -> tuple[torch.Tensor, dict[str, float]]:
|
|
104
|
-
flat_logprobs = torch.cat(logprobs)
|
|
105
|
-
variance = torch.var(flat_logprobs)
|
|
106
|
-
return variance, {"variance_loss": variance.item()}
|
|
107
|
-
```
|
|
108
|
-
|
|
109
|
-
### How forward_backward_custom Works
|
|
110
|
-
|
|
111
|
-
1. Forward pass computes logprobs
|
|
112
|
-
2. Custom function computes loss from logprobs
|
|
113
|
-
3. `loss.backward()` computes grad_outputs
|
|
114
|
-
4. Second forward_backward with linear surrogate loss
|
|
115
|
-
|
|
116
|
-
**Note:** Uses 1.5x FLOPs and up to 3x wall time compared to built-in losses.
|
|
117
|
-
|
|
118
|
-
## Implementation Details
|
|
119
|
-
|
|
120
|
-
All losses:
|
|
121
|
-
- Applied at token level with shape `(N,)` where N = sequence length
|
|
122
|
-
- Use sum reduction (not mean)
|
|
123
|
-
- Accept numpy.ndarray or torch.Tensor inputs
|
|
124
|
-
|
|
125
|
-
### cross_entropy Implementation
|
|
126
|
-
```python
|
|
127
|
-
elementwise_loss = -target_logprobs * weights
|
|
128
|
-
loss = elementwise_loss.sum()
|
|
129
|
-
```
|
|
130
|
-
|
|
131
|
-
### importance_sampling Implementation
|
|
132
|
-
```python
|
|
133
|
-
prob_ratio = torch.exp(target_logprobs - sampling_logprobs)
|
|
134
|
-
loss = -(prob_ratio * advantages).sum()
|
|
135
|
-
```
|
|
136
|
-
|
|
137
|
-
### ppo Implementation
|
|
138
|
-
```python
|
|
139
|
-
prob_ratio = torch.exp(target_logprobs - sampling_logprobs)
|
|
140
|
-
clipped_ratio = torch.clamp(prob_ratio, 1 - eps, 1 + eps)
|
|
141
|
-
unclipped = prob_ratio * advantages
|
|
142
|
-
clipped = clipped_ratio * advantages
|
|
143
|
-
loss = -torch.min(unclipped, clipped).sum()
|
|
144
|
-
```
|
|
145
|
-
|
|
146
|
-
### cispo Implementation
|
|
147
|
-
```python
|
|
148
|
-
prob_ratio = torch.exp(target_logprobs - sampling_logprobs)
|
|
149
|
-
clipped_ratio = torch.clamp(prob_ratio, 1 - eps, 1 + eps)
|
|
150
|
-
loss = -(clipped_ratio.detach() * target_logprobs * advantages).sum()
|
|
151
|
-
```
|
|
152
|
-
|
|
153
|
-
### dro Implementation
|
|
154
|
-
```python
|
|
155
|
-
quadratic_term = (target_logprobs - sampling_logprobs) ** 2
|
|
156
|
-
loss = -(target_logprobs * advantages - 0.5 * beta * quadratic_term).sum()
|
|
157
|
-
```
|
|
158
|
-
|
|
159
|
-
## Notes
|
|
160
|
-
|
|
161
|
-
- KL regularization: Include in reward rather than loss (see `incorporate_kl_penalty` in Cookbook)
|
|
162
|
-
- Aggregation: Token-level losses are summed; for different schemes, modify advantages
|
|
163
|
-
- Reference: [Schulman et al., 2017](https://arxiv.org/abs/1707.06347) for PPO
|