K-Dense

Build and check clinical machine learning workflows with PyHealth, from loading electronic health records, signals, or images to training and evaluation. Includes patient-level data splits, prediction task checks, model checkpoints, and medical code mapping.

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• Prototype mortality and readmission prediction models
• Check patient splits and data leakage
• Train and evaluate sleep staging models

Inspect and transform local DICOM medical imaging files, including metadata, image frames, and compression formats. Generate technical inventories and preview images, check installed codecs, and review pseudonymized derivatives without treating those checks as proof of de-identification.

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• Create a technical inventory of local DICOM files
• Check compression support and frame memory needs
• Export a frame as a non-diagnostic preview

Analyze biological sequences and microbial communities in Python. Process and align DNA, RNA, or proteins, build evolutionary trees, calculate diversity, visualize sample differences, test group differences, and convert common biological file formats.

中文简介正在准备中。当前显示英语简介。

• Calculate and compare microbiome diversity
• Align DNA, RNA, or protein sequences
• Build and compare evolutionary trees

Build quantum circuits with Qiskit, test them locally, and prepare them for IBM quantum hardware. The skill covers hardware-specific circuit conversion, sampling, expectation values, and analysis of measurement results, uncertainty, and resource usage.

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• Building and simulating quantum circuits locally
• Adapting circuits to IBM quantum hardware
• Comparing sampled results and expectation values

Combine laboratory animal welfare measurements into reference-relative RELSA severity scores. Analyze individual trajectories, explore forecasts for specified observation times, and derive candidate score zones, with explicit checks on normalization, reference selection, prediction intervals, and evaluation limits.

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• Combine animal welfare measurements into daily scores
• Compare group severity using a shared reference
• Explore severity forecasts at specified observation times

Validate particle data and run RELION refinement for single-particle cryo-electron microscopy. Check independently refined half maps, calculate diagnostic map correlations, and perform soft-mask postprocessing while preserving execution logs and restart information.

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• Check particle metadata and image-stack consistency
• Run refinement on a selected particle population
• Inspect agreement between independent half maps

Find biological pathways and functions enriched in gene lists or ranked gene data. Choose an appropriate statistical method, align gene identifiers, define comparison backgrounds, and turn results into interpretable tables and plots with multiple-testing corrections.

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• Finding enriched pathways among differentially expressed genes
• Running GSEA on a complete ranked gene list
• Calculating gene-set scores for individual samples or cells

Calculate equilibrium phases, their molar fractions, and compositions from a local thermodynamic database using pycalphad. Compare temperatures, check material balance and sampling stability, and export results with recorded conditions and database identifiers.

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• Calculate equilibrium phase fractions for an alloy composition
• Compare stable phases across specified temperatures
• Check material balance and sampling stability

Explore gene, drug, disease, and phenotype associations in a downloaded PrimeKG CSV. Retrieve direct relationships, disease summaries, and paths through one intermediate node while preserving relationship types and data provenance for reproducible research and hypothesis generation.

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• Checking associations between genes, drugs, and diseases
• Summarizing genes, drugs, and phenotypes linked to a disease
• Exploring short paths between two entities

Manage Zotero reference libraries through Python: search, create, update, and delete references, organize collections and tags, upload PDF attachments, and export citation data. Guidance covers both remote libraries and access through a running local Zotero app.

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• Searching references in a Zotero library
• Organizing references with collections and tags
• Uploading PDF attachments to references

Gather scholarly evidence for a scientific manuscript or research brief. Organize supporting and conflicting findings into references, study comparison tables, and claim-to-source maps, with search records and coverage reports that help identify gaps requiring further review.

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• Gather background literature for a manuscript
• Compare supporting, conflicting, and null findings
• Build study comparison tables and claim-to-source maps

Work with genomic regions in Polars tables to find overlaps, nearby regions, covered bases, and gaps. Read and write bioinformatics files, query data with SQL, and check coordinate conventions when joining datasets or migrating from bioframe.

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• Finding variants that overlap genomic regions
• Merging regions and measuring covered bases
• Summarizing sequencing read depth

Create research presentation slides with clear structure, concise text, figures, and timing guidance. The skill supports PowerPoint, LaTeX Beamer, and image-based PDFs, with workflows for preserving original research charts and reviewing slide layouts.

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• Prepare slides for a conference research talk
• Build a thesis or dissertation defense presentation
• Adapt paper content for a seminar presentation

Research current web information with Parallel CLI and organize findings with supporting sources. The skill covers search, page extraction, detailed reports, adding sourced fields to existing lists, finding matching entities, and recurring monitoring of web changes.

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• Research current information and locate academic sources
• Extract content from public webpages and PDFs
• Add sourced information to company or product lists

Build Bayesian models in PyMC to estimate effects and quantify uncertainty. Fit regression or hierarchical models, check sampling diagnostics, assess predictions against observed data, predict new groups, and compare models using predictive performance.

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• Estimate regression effects with uncertainty
• Model differences across patients or groups
• Inspect sampling diagnostics and predictive checks

Prepare and review research funding proposals for NSF, NIH, DOE, DARPA, and Taiwan NSTC. Maps application requirements to draft sections, identifies gaps, and helps refine research aims, budgets, impact statements, and responses to reviewers.

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• Map funding-call requirements to proposal sections
• Review research aims against evaluation criteria
• Align budgets and timelines with the research plan

Simulate lithium-ion battery charging, discharging, and rest with PyBaMM. Track voltage and capacity, record parameter sources, check how numerical settings affect predictions, and compare simulated curves with measured cycling data.

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• Predicting voltage changes during charge, discharge, and rest
• Comparing simulation results with measured cycling data
• Checking how numerical settings affect predictions

Analyze single-cell RNA-seq data with Scanpy, from quality checks and normalization to cell grouping, exploratory marker genes, and plots. Bundled scripts also prepare sample-level count summaries and support conversion of R objects to h5ad.

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• Check data quality and normalize single-cell measurements
• Visualize cell groups with UMAP or t-SNE
• Explore marker genes and review cell-type labels

Review papers, drafts, and research ideas with evidence-linked feedback focused on improvement. Audit low-stakes assessment rubrics, trace supporting evidence, and check rater agreement and uncertainty without ranking people or recommending consequential decisions.

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• Prepare evidence-linked feedback on a paper draft
• Review strengths and limitations of a research idea
• Check assessment criteria and evidence traceability

Plan and review PufferLib reinforcement learning workflows, where agents learn through rewards. Covers version-specific environment checks, parallel execution, training and evaluation plans, plus checkpoint inspection before loading saved models.

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• Choose APIs for a specific PufferLib version
• Check environment behavior before training
• Create training and evaluation plans with separate seeds

Use PathML for local pathology image research, from loading whole-slide images and splitting them into tiles to preprocessing and quality checks. Plan multiplex measurements, analyze spatial relationships between cells, and run model inference in bounded batches.

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• Planning tile extraction from whole-slide images
• Reviewing preprocessing and image quality
• Validating multiplex measurements and spatial graphs

Design and review laboratory automation with PyLabRobot, including equipment layouts and liquid transfers. Check planned volumes and tip capacities, draft protocols, and simulate operations in software before a trained operator reviews any physical run.

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• Reviewing liquid-transfer plans
• Checking labware layouts and capacities
• Simulating protocols without physical equipment

Explore recommended papers in Paperzilla projects, search project feeds, and summarize available paper text. The skill also helps explain research relevance, record recommendation feedback, export records as JSON, and retrieve personal feed URLs.

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• Review recent paper recommendations for a research project
• Summarize a paper and explain its relevance to your research
• Export papers or recommendations as JSON

Build Python machine learning workflows for classification, numerical prediction, and grouping similar data. Combine preprocessing with training, compare algorithms, tune model settings, and evaluate performance using data splits suited to the task.

中文简介正在准备中。当前显示英语简介。

• Building classification or numerical prediction models
• Grouping similar records and visualizing the results
• Combining missing-value handling with model training