Results for “pymatgen”

Materials science toolkit. Crystal structures (CIF, POSCAR), phase diagrams, band structure, DOS, Materials Project integration, format conversion, for computational materials science.

Solves single- and multi-objective optimization problems with NSGA-II/III, MOEA/D, and other evolutionary algorithms, including constraint handling, Pareto front analysis, and benchmark problems.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Solve single and multi-objective optimization problems using NSGA-II/III, MOEA/D, and other evolutionary algorithms with customizable operators, constraint handling, and benchmark problems.

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

Analyze proteomics and metabolomics mass spectrometry data with PyOpenMS: read/write MS file formats, process spectra, detect and quantify features, identify peptides and proteins, and run end-to-end LC-MS/MS pipelines using ready-to-run scripts.

Pyright fast Python type checker from Microsoft with VS Code integration and strict type checking modes

Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal processing, feature detection, peptide identification, and quantitative analysis. Apply when working with mass spectrometry data, analyzing proteomics experiments, or processing metabolomics datasets.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Creates multi-agent AI systems with AutoGen, enabling agent conversations, tool use, and group chats.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Multi-objective optimization framework. NSGA-II, NSGA-III, MOEA/D, Pareto fronts, constraint handling, benchmarks (ZDT, DTLZ), for engineering design and optimization problems.

Provides guidance on using the QMT quantitative trading terminal, including strategy development, backtesting, and live trading for Chinese securities markets.

Solve single- and multi-objective optimization problems with NSGA-II/III, MOEA/D, and other evolutionary algorithms, including Pareto front analysis, constraint handling, and benchmarking on standard test problems.

Build conversational multi-agent systems with AutoGen (AG2) — define AssistantAgent and UserProxyAgent, set up GroupChat with GroupChatManager for round-robin or auto routing, enable code execution, and compose nested chats or sequential pipelines.

Comprehensive healthcare AI toolkit for developing, testing, and deploying machine learning models with clinical data. This skill should be used when working with electronic health records (EHR), clinical prediction tasks (mortality, readmission, drug recommendation), medical coding systems (ICD, NDC, ATC), physiological signals (EEG, ECG), healthcare datasets (MIMIC-III/IV, eICU, OMOP), or implementing deep learning models for healthcare applications (RETAIN, SafeDrug, Transformer, GNN).

pytest - Python's most powerful testing framework with fixtures, parametrization, plugins, and framework integration for FastAPI, Django, Flask

Machine learning in Python with scikit-learn. Use for classification, regression, clustering, model evaluation, and ML pipelines.

Use for writing, reviewing, debugging, testing, or optimizing Python SymPy symbolic mathematics. Trigger on Symbol, assumptions, Expr, Eq, solve/solveset, simplify, factor, expand, calculus, matrices, exact arithmetic, lambdify, code generation, or symbolic-to-numeric conversion. Do not use for NumPy-only arrays, mpmath-only arbitrary-precision numerics, CVXPY optimization models, or parsing untrusted mathematical text.

Create, read, edit, and convert .pptx presentations using python-pptx and PptxGenJS, with design guidance for professional slide decks.

Build clinical deep-learning pipelines with PyHealth: load EHR, signal, and imaging datasets, define prediction tasks, instantiate models, train with the PyHealth Trainer, and compute clinical metrics.

Wrapper Pythônico ao redor do RDKit com interface simplificada e padrões sensatos. Preferido para descoberta de fármacos padrão: análise de SMILES, padronização, descritores, fingerprints, clustering, conformadores 3D, processamento paralelo. Retorna objetos nativos rdkit.Chem.Mol. Para controle avançado ou parâmetros customizados, use rdkit diretamente.

Use for writing, reviewing, debugging, testing, or diagnosing Python Bayesian models built directly with PyMC, including Model, coords/dims, Data, random variables, potentials, posterior sampling, prior/posterior predictive checks, and InferenceData output. Trigger on model geometry, shape errors, divergences, sampler choice, mutable prediction data, and probabilistic validation. Do not use for Bambi formula models, NumPyro/JAX programs, ArviZ-only analysis of existing draws, deterministic optimization, or general statistics without PyMC code.

Kit de ferramentas de patologia computacional para análise de imagens de lâminas inteiras (WSI) e dados de imagem multiparamétrica. Use esta habilidade ao trabalhar com lâminas de histopatologia, imagens coradas com H&E, imunofluorescência multiplex (CODEX, Vectra), proteômica espacial, detecção/segmentação de núcleos, construção de gráficos de tecido ou treinamento de modelos ML em dados de patologia. Suporta 160+ formatos de lâmina incluindo Aperio SVS, NDPI, DICOM, OME-TIFF para fluxos de trabalho de patologia digital.

Control liquid handling robots, plate readers, pumps, and other lab equipment through a unified Python interface across platforms.

Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery: SMILES parsing, standardization, descriptors, fingerprints, clustering, 3D conformers, parallel processing. Returns native rdkit.Chem.Mol objects. For advanced control or custom parameters, use rdkit directly.

Build and train graph neural networks with PyTorch Geometric, covering node/link/graph classification, message passing layers, heterogeneous graphs, and custom datasets.

Spectral similarity and compound identification for metabolomics. Use for comparing mass spectra, computing similarity scores (cosine, modified cosine), and identifying unknown compounds from spectral libraries. Best for metabolite identification, spectral matching, library searching. For full LC-MS/MS proteomics pipelines use pyopenms.

Automate multi-turn adversarial conversations against LLM agents using Microsoft PyRIT, including Crescendo and Tree-of-Attacks-with-Pruning (TAP) attack chains with scorer feedback loops.

You are an expert in AG2 (formerly AutoGen), the open-source multi-agent conversation framework. You help developers build systems where multiple AI agents collaborate through structured conversations — with tool use, human-in-the-loop, code execution, group chat orchestration, and nested conversations — for complex tasks like software development, research, and data analysis.

Process and analyze mass spectrometry data with the Matchms Python library, including importing spectra, filtering peaks, calculating similarity scores, and building reproducible analytical workflows.

Build, fit, validate, and compare Bayesian models using PyMC's modern API, including hierarchical models, MCMC sampling, variational inference, posterior predictive checks, and model comparison.

Analyze whole-slide pathology images with Python: load 160+ slide formats, preprocess H&E stains, segment nuclei, construct spatial graphs, train ML models, and process multiplex immunofluorescence data (CODEX, Vectra).

Automates hypothesis generation and testing on tabular datasets using LLMs, combining data-driven discovery with literature integration for scientific research.