AI & LLM

torchdrug @K-Dense-AI

PyTorch-native graph neural networks for molecules and proteins. Use when building custom GNN architectures for drug...

torch-geometric @K-Dense-AI

Graph Neural Networks (PyG). Node/graph classification, link prediction, GCN, GAT, GraphSAGE, heterogeneous graphs,...

sympy @K-Dense-AI

Use this skill when working with symbolic mathematics in Python. This skill should be used for symbolic computation...

string-database @K-Dense-AI

Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG...

stable-baselines3 @K-Dense-AI

Production-ready reinforcement learning algorithms (PPO, SAC, DQN, TD3, DDPG, A2C) with scikit-learn-like API. Use...

simpy @K-Dense-AI

Process-based discrete-event simulation framework in Python. Use this skill when building simulations of systems...

shap @K-Dense-AI

Model interpretability and explainability using SHAP (SHapley Additive exPlanations). Use this skill when explaining...

seaborn @K-Dense-AI

Statistical visualization with pandas integration. Use for quick exploration of distributions, relationships, and...

scvi-tools @K-Dense-AI

Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer...

scikit-survival @K-Dense-AI

Comprehensive toolkit for survival analysis and time-to-event modeling in Python using scikit-survival. Use this...

scikit-learn @K-Dense-AI

Machine learning in Python with scikit-learn. Use when working with supervised learning (classification,...

scikit-bio @K-Dense-AI

Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac),...

scientific-visualization @K-Dense-AI

Meta-skill for publication-ready figures. Use when creating journal submission figures requiring multi-panel...

scientific-schematics @K-Dense-AI

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini...

scholar-evaluation @K-Dense-AI

Systematically evaluate scholarly work using the ScholarEval framework, providing structured assessment across...

scanpy @K-Dense-AI

Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction...

rowan @K-Dense-AI

Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including...

research-lookup @K-Dense-AI

Look up current research information using Perplexity Sonar Pro Search or Sonar Reasoning Pro models through...

research-grants @K-Dense-AI

Write competitive research proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Agency-specific formatting, review...

qutip @K-Dense-AI

Quantum physics simulation library for open quantum systems. Use when studying master equations, Lindblad dynamics,...

qiskit @K-Dense-AI

IBM quantum computing framework. Use when targeting IBM Quantum hardware, working with Qiskit Runtime for production...

pytorch-lightning @K-Dense-AI

Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for...

pytdc @K-Dense-AI

Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits,...

pysam @K-Dense-AI

Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions,...