compbio
claudeComputational biology — perturbation analysis, single-cell, spatial omics, databases, project continuity
38 skills
AI/ML — VI methodology, PyTorch, Transformers, PEFT, TRL, distributed training
Plugin ai-ml from marketplace ai-skills in CHENyiru3/AI-Skills-Collections. Commands read from the repo's manifest — 3 days ago.
jepa-pytorch-developmentDesign, implement, adapt, or debug JEPA representation learners and latent world models in PyTorch. Use for masked EMA-teacher JEPA, V-JEPA dense/deep supervision, teacher-free LeJEPA/SIGReg, or action-conditioned latent prediction, including token and mask contracts, gradient flow, collapse diagnos
pytorchImplement or debug PyTorch tensor operations, nn.Module models, autograd, custom training loops, checkpoints, and device or precision issues. Use for concrete PyTorch development; prefer a project-specific model skill when its contracts apply.
bitsandbytesConfigure or debug bitsandbytes 4-bit/8-bit model loading, quantization settings, supported hardware, and PEFT/QLoRA preparation. Use for an actual bitsandbytes integration rather than generic model optimization.
browser-useConfigure or debug the browser-use Python agent, its model provider, and Chromium/CDP browser session. Use when browser-use is explicitly requested or already used in the project; not for general browser tasks with an available browser tool.
huggingface-hubDownload, inspect, version, or publish model/dataset/Space repositories using huggingface_hub or the hf CLI. Use for Hub repository operations, access, cache handling, and model-card metadata.
peftConfigure, train, load, switch, merge, or debug Hugging Face PEFT adapters such as LoRA, QLoRA, prompt tuning, and prefix tuning. Use when an actual PEFT adapter workflow is requested.
transformersImplement or debug Hugging Face Transformers model/tokenizer loading, task heads, generation, feature extraction, or Trainer fine-tuning. Use in a Transformers codebase or when that library is requested.
trlImplement or debug TRL supervised fine-tuning, preference optimization, reward modeling, or reinforcement-learning trainers, including their dataset schemas and evaluation. Use for a specific TRL workflow.
latent-identifiabilityDevelop, prove, or audit identifiability claims for latent-variable and representation-learning models, including VAEs, nonlinear ICA, and spatial or multi-view biological models. Use to turn a model idea into a quantified theorem, identify the remaining symmetries, construct a lemma-based proof, or
vi-methodology-developmentFormulate, implement, or review a variational-inference or VAE research method, from generative assumptions and ELBO to posterior queries and validation. Use for method development or scvi-tools model integration; not routine use of an existing model.
accelerateConfigure or debug Hugging Face Accelerate launchers, Accelerator training loops, mixed precision, accumulation, distributed metrics, and checkpoint resume. Use when the project uses Accelerate.
datasetsLoad, transform, split, stream, cache, or export data with Hugging Face Datasets. Use for Dataset/DatasetDict/IterableDataset workflows and their schema, batching, or reproducibility issues.
deepspeedConfigure or debug DeepSpeed engines, ZeRO stages, offloading, mixed precision, checkpointing, or a supported Transformers/Accelerate integration. Use for an actual DeepSpeed workload.
pytorch-lightningImplement, migrate, or debug LightningModule, LightningDataModule, Trainer configuration, callbacks, logging, checkpoint resume, and distributed training in a PyTorch Lightning project.
Computational biology — perturbation analysis, single-cell, spatial omics, databases, project continuity
38 skills
Document processing — OfficeCLI, Excel, Word, PowerPoint, PDF, web design, and collaboration
20 skills
Academic writing, literature review, Marp presentations, LaTeX, Obsidian, and knowledge management
14 skills
Python library development — project setup, testing, packaging, performance, security, API design
13 skills
Platform integrations — GitHub workflows and Google Workspace CLI/Drive transfers
10 skills
Coding agents — Claude Code, Codex, MCP, handoffs, engineering guidelines
8 skills
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