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Generate embeddings, numerical representations of text or images, for meaning-based search, similarity comparisons, and document grouping. The skill guides model selection, multilingual processing, local execution, and integration with retrieval workflows.
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Generate embeddings, numerical representations of text or images, for meaning-based search, similarity comparisons, and document grouping. The skill guides model selection, multilingual processing, local execution, and integration with retrieval workflows.
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Build JavaScript or TypeScript applications that run text, image, and audio models in browsers or server runtimes. Guides compatible model selection, GPU or CPU execution, caching, and memory cleanup without requiring a Python server.
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Build this skill automates the adaptation of pre-trained machine learning models using transfer learning techniques. it is triggered when the user requests assistance with fine-tuning a model, adapting a pre-trained model to a new dataset, or performing... Use when appropriate context detected. Trigger with relevant phrases based on skill purpose.
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Work with state-of-the-art machine learning models for NLP, computer vision, audio, and multimodal tasks using HuggingFace Transformers. This skill should be used when fine-tuning pre-trained models, performing inference with pipelines, generating text, training sequence models, or working with BERT, GPT, T5, ViT, and other transformer architectures. Covers model loading, tokenization, training with Trainer API, text generation strategies, and task-specific patterns for classification, NER, QA, summarization, translation, and image tasks. (plugin:scientific-packages@claude-scientific-skills)
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Extend the amount of text a language model can process at once. Compares RoPE, YaRN, ALiBi, and position interpolation, with implementation examples, additional training guidance, and memory optimization approaches for long document processing.
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Helps extend how much text a language model can process at once. Covers choosing RoPE, YaRN, ALiBi, or position interpolation, implementing position information, fine-tuning on longer documents, and managing memory during inference.
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This skill should be used when working with pre-trained transformer models for natural language processing, computer vision, audio, or multimodal tasks. Use for text generation, classification, question answering, translation, summarization, image classification, object detection, speech recognition, and fine-tuning models on custom datasets.
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Maps query single-cell data to reference atlases using scArches transfer learning with scVI and scANVI models. Transfers cell type labels without retraining on combined data. Use when annotating new single-cell datasets using pre-trained reference models.
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Analyze pre-trained generative diffusion models (Stable Diffusion, DALL-E, Flux) by computing quality metrics (FID, IS, CLIP score, precision/recall), inspecting noise schedules, extracting and visualizing attention maps, and probing latent spaces. Use when evaluating a pre-trained generative diffusion model's output quality, comparing noise schedule variants, analyzing cross-attention patterns for text-conditioned generation, interpolating between latent codes, or detecting out-of-distribution inputs.
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I-A LLMs Large Language Models (LLMs) are extensive, general-purpose models that can be pre-trained and adapted for specific tasks.
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Use Transformers.js to run state-of-the-art machine learning models directly in JavaScript/TypeScript. Supports NLP (text classification, translation, summarization), computer vision (image classification, object detection), audio (speech recognition, audio classification), and multimodal tasks. Works in browsers and server-side runtimes (Node.js, Bun, Deno) with WebGPU/WASM using pre-trained models from Hugging Face Hub.
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Automated scRNA-seq cell type annotation via pre-trained logistic regression. 45+ models: immune, gut, lung, brain, fetal, cancer microenvironments. Input normalized AnnData; outputs per-cell labels, majority-vote cluster labels, confidence scores. Use for fast, reference-backed annotation without manual marker inspection.
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DL cell/nucleus segmentation for fluorescence and brightfield microscopy. Pre-trained models (cyto3, nuclei, tissuenet) and a generalist flow-based algorithm segment cells without retraining. Outputs label masks for morphology and tracking. Use scikit-image watershed for rule-based; Cellpose when DL generalization across staining is needed.
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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For ready-made ADMET numbers without training a model use admet-prediction; for benchmark datasets and task-aware splits use pytdc.
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Identify and exploit vulnerabilities in the AI Supply Chain by injecting malicious models, datasets, or dependencies. Use this skill to simulate advanced persistent threats (APTs) compromising Hugging Face repositories, manipulating pre-trained weights (Model Poisoning), and exploiting insecure deserialization during model loading (e.g., Pickle files).
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Maps query single-cell data onto reference atlases and transfers cell-type labels using scArches surgery (scVI/scANVI), Symphony, Azimuth, CellTypist, scPoli, popV, and foundation models, with explicit out-of-distribution and label-transfer uncertainty. Use when annotating new single-cell datasets against a pre-trained reference, deciding which mapping method fits, or judging whether transferred labels are trustworthy. For de novo clustering and manual annotation see single-cell/cell-annotation; for batch integration without a reference see single-cell/batch-integration.
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PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug discovery, protein modeling, or knowledge graph reasoning. Best for custom model development, protein property prediction, retrosynthesis. For pre-trained models and diverse featurizers use deepchem; for benchmark datasets use pytdc.
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Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks. Best for quick experiments with pre-trained models, diverse molecular representations. For graph-first PyTorch workflows use torchdrug; for benchmark datasets use pytdc.
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