Data Science & ML Agent Skills

Expected Value

Calculates probability-weighted outcomes to facilitate rational decision-making under uncertainty for investments, product development, and strategic initiatives.

Symmetry Discovery Questionnaire

Guides machine learning engineers through identifying data symmetries and physical constraints to optimize model architectures.

Design Experiment

Guides the planning, parameter selection, and documentation of LLM fine-tuning and evaluation experiments.

Mojo SIMD Optimization

Optimizes Mojo tensor and array operations using SIMD vectorization to maximize computational throughput on modern hardware.

Algorithm Extraction & Documentation

Extracts and structures algorithm pseudocode from academic research papers into actionable implementation plans.

RDKit Cheminformatics

Performs advanced molecular modeling, chemical property calculation, and substructure analysis using the RDKit toolkit.

FlowIO Cytometry Handler

Parses and creates Flow Cytometry Standard (FCS) files for seamless integration with Python data science workflows.

PDB Database Access

Accesses the RCSB Protein Data Bank to search, retrieve, and analyze 3D structural data for biological macromolecules.

Geniml Genomic Machine Learning

Applies unsupervised machine learning models to genomic interval data for embedding, clustering, and bioinformatics analysis.

RDKit Cheminformatics Toolkit

Performs advanced chemical data analysis, molecular manipulation, and property calculation for drug discovery and computational chemistry.

Datamol Cheminformatics

Simplifies molecular cheminformatics and drug discovery workflows using a Pythonic interface for RDKit.

PathML Computational Pathology

Analyzes whole-slide images and multiparametric imaging data for computational pathology and machine learning workflows.

Histolab Digital Pathology

Processes gigapixel whole slide images for digital pathology, automating tissue detection and tile extraction for deep learning pipelines.

Biomni: Biomedical AI Agent

Executes autonomous multi-step biomedical research tasks across genomics, drug discovery, and clinical analysis using integrated databases and code execution.

LaminDB Biology Data Management

Manages biological datasets with lineage tracking, ontology-based validation, and FAIR data principles using a unified Python API.

PyLabRobot Lab Automation

Automates laboratory liquid handling and equipment control through a hardware-agnostic Python interface.

Astropy Astronomy Toolkit

Provides comprehensive tools for astronomical data analysis, coordinate transformations, and physical unit conversions in Python.

MarkItDown Converter

Converts diverse file formats including PDFs, Office documents, and media into LLM-optimized Markdown for AI processing.

PufferLib High-Performance RL

Accelerates reinforcement learning development with high-speed parallel environment simulation and optimized PPO training.

Zarr Python Array Management

Manages large-scale N-dimensional arrays with efficient chunking, compression, and cloud-native storage integration.

Statsmodels Statistical Analysis

Performs rigorous statistical modeling, econometric analysis, and hypothesis testing using Python's premier inference toolkit.

Bioinformatics Query Toolkit (gget)

Provides unified, high-speed access to 20+ genomic databases and protein structure prediction tools directly from the command line.

scvi-tools for Single-Cell Analysis

Analyzes single-cell omics data using deep generative models and probabilistic frameworks for batch correction and multimodal integration.

Transformers Model Integration

Implements and fine-tunes state-of-the-art machine learning models for natural language processing, computer vision, and audio tasks.

ESM Protein Language Models

Powers protein engineering workflows with state-of-the-art generative design, structure prediction, and high-quality sequence embeddings.

ENA Bioinformatics Database

Accesses and retrieves nucleotide sequence data, raw reads, and genome assemblies from the European Nucleotide Archive.

HMDB Database Access

Accesses the Human Metabolome Database (HMDB) to retrieve detailed information on over 220,000 human metabolites, including chemical properties, clinical biomarkers, and spectral data.

NCBI Gene Database Connector

Queries and retrieves comprehensive genetic data from NCBI using E-utilities and Datasets APIs for biological research and gene annotation.

SymPy Symbolic Math

Performs exact symbolic mathematics, calculus, and algebraic computations in Python to provide precise mathematical results.

ZINC Chemical Database

Accesses the ZINC repository of 230M+ purchasable compounds for virtual screening, drug discovery, and molecular property analysis.