26 skills found
Lightweight WSI tile extraction and preprocessing. Use for basic slide processing, tissue detection, tile extraction, and stain normalization for H&E images. Best for simple pipelines, dataset preparation, and quick tile-based analysis. For advanced spatial proteomics, multiplexed imaging, or deep learning pipelines use pathml.
DiffDock and DiffDock-L molecular docking. Use for protein-small-molecule pose prediction from PDB or sequence plus SMILES/SDF/MOL2, batch docking, virtual screening, and pose-confidence interpretation. Not for binding affinity prediction.
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI). Best for advanced modeling, batch effects, multimodal data. For standard analysis pipelines use scanpy.
Build clinical/healthcare deep-learning pipelines with PyHealth — loading EHR/signal/imaging datasets (MIMIC-III/IV, eICU, OMOP, SleepEDF, ChestXray14, EHRShot), defining tasks (mortality, readmission, length-of-stay, drug recommendation, sleep staging, ICD coding, EEG events), instantiating models (Transformer, RETAIN, GAMENet, SafeDrug, MICRON, StageNet, AdaCare, CNN/RNN/MLP), training with the PyHealth Trainer, computing clinical metrics, and using medical code utilities (ICD/ATC/NDC/RxNorm l
PyTorch Geometric (PyG) for graph neural networks — node/link/graph classification, message passing (GCN, GAT, GraphSAGE, GIN), heterogeneous graphs, neighbor sampling, and custom datasets. Use when working with torch_geometric, not for general NetworkX analytics or non-graph PyTorch models.
Deep learning framework (PyTorch Lightning / lightning package). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B, TensorBoard, MLflow), distributed training (DDP, FSDP, DeepSpeed), for scalable neural network training.
Mask2Former for universal image segmentation (panoptic, instance, and semantic). Transformer-based with masked attention for high-quality segmentation results. Use when training, evaluating, exporting, quantizing, or running inference for a TAO Mask2Former model. Trigger phrases include "train Mask2Former", "universal segmentation", "panoptic / instance / semantic segmentation", "masked-attention transformer segmenter".
Expert guidance for deep learning, transformers, diffusion models, and LLM development with PyTorch, Transformers, Diffusers, and Gradio.
Deep learning for single-cell analysis using scvi-tools. This skill should be used when users need (1) data integration and batch correction with scVI/scANVI, (2) ATAC-seq analysis with PeakVI, (3) CITE-seq multi-modal analysis with totalVI, (4) multiome RNA+ATAC analysis with MultiVI, (5) spatial transcriptomics deconvolution with DestVI, (6) label transfer and reference mapping with scANVI/scArches, (7) RNA velocity with veloVI, or (8) any deep learning-based single-cell method. Triggers inclu
Deep concept anatomist that deconstructs any concept through 8 exploration dimensions (history, dialectics, phenomenology, linguistics, formalization, existentialism, aesthetics, meta-philosophy) and compresses insights into an epiphany. Use when user asks to explain, dissect, or deeply understand a concept, term, or idea. Triggers on '解剖概念', '概念解剖', 'explain concept', 'learn concept', '/ljg-learn'. Produces org-mode output.
PyTorch deep learning patterns and best practices for building robust, efficient, and reproducible training pipelines, model architectures, and data loading.
Add project repository links to PROJECTS.md when user mentions completing, starting, or sharing a hands-on project. Use when user references external repos or implementation work.
