数据与 AI技能

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

Process mass spectrometry data using scripts for format conversion, signal cleanup, peak detection, and quantification across samples. Prepare protein and metabolite analyses with identification filtering, candidate annotations, data tables, and plots.

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• Inspect, convert, and preprocess mass spectrometry files
• Build quantitative tables across multiple samples
• Find metabolite candidates from accurate mass

Process paired-end 16S sequencing reads in QIIME 2 to produce ASVs, distinct sequence variants, and taxonomic assignments. Check input files, primer settings, and read retention while preserving artifacts that record the processing history.

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• Validate paired FASTQ files and sample metadata
• Remove primers and denoise reads with DADA2
• Assign taxonomy using a compatible classifier

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

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

Build Python workflows for filtering, grouping, joining, and reshaping table data with Polars. Get guidance on migrating pandas code and using lazy evaluation, which optimizes a processing plan before execution, for large datasets.

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• Filtering and summarizing large CSV files
• Migrating pandas processing code to Polars
• Joining and reshaping multiple tables

Read, query, filter, and write genomic files with pysam in Python. Extract regions, summarize variants, and count aligned bases while handling coordinate conventions, file indexes, headers, and the reference sequences needed to decode CRAM files.

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• Inspect genomic file formats, headers, and indexes
• Filter alignment records by quality and flags
• Summarize variants and genotypes in a genomic region

Analyze gene-expression differences in bulk RNA-seq data using PyDESeq2. Validate count tables and experimental designs, test explicit comparisons, adjust for multiple testing, shrink effect estimates, and export statistical results with volcano and MA plots.

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• Compare gene expression between treatment and control groups
• Analyze expression differences while accounting for batch effects
• Validate count tables against sample metadata

Build and optimize quantum circuits with PennyLane, including models that combine quantum circuits with PyTorch or JAX. Explore molecular energy estimation and optimization problems, validate values and gradients in simulation, and prepare tested circuits for provider plugins.

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• Check quantum circuit values and gradients in simulation
• Train hybrid quantum and PyTorch or JAX models
• Estimate molecular energies with VQE

Explore public pathogen genome data to verify lineage names, summarize weekly sequence proportions, examine reporting delays, and compare mutation frequencies. Results include filters and denominators, with clear limits on what submitted sequences reveal about infections.

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• Tracking weekly lineage proportions in submitted sequences
• Verifying current Pango lineage names
• Examining delays between sample collection and reporting

Solve optimization problems in Python with one or several competing goals. Define constraints, compare search algorithms, visualize trade-offs, and assess candidate solutions before choosing an option that fits your priorities.

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• Comparing designs with competing cost and performance goals
• Searching for solutions under explicit constraints
• Benchmarking optimization algorithms

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

Analyze drug concentration and response data to calculate exposure, fit models of drug movement and effects, and simulate dosing schedules. Produces exploratory research results with explicit assumptions and diagnostic checks.

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• Calculate exposure and half-life from concentration data
• Compare models of drug concentration over time
• Simulate dosing schedules for research

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.

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

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

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

Use PyTDC to discover therapeutic machine-learning datasets, create task-appropriate training and test splits, and evaluate predictions against curated benchmarks. Also score selected molecules with supported scoring functions, with explicit download plans and bounded outputs.

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• Find datasets for therapeutic machine-learning tasks
• Plan and create task-appropriate data splits
• Evaluate predictions with benchmark-specific metrics

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.

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

Organize PyTorch models and data pipelines with PyTorch Lightning, automate training, save checkpoints, and track experiments. Includes templates and guidance for configuring training across multiple GPUs or TPUs.

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• Restructure PyTorch training code into LightningModules
• Build reusable data preparation and loading pipelines
• Configure checkpoints, early stopping, and experiment logs

Plan and audit HypoGeniC workflows that use language models to propose patterns from labeled text. Check configurations, dataset splits, cost limits, and saved predictions while keeping candidate hypotheses separate from scientific confirmation.

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• Reviewing task settings before a HypoGeniC run
• Checking duplicates across training and test data
• Estimating token and cost limits before model calls

Process calibrated one-dimensional NMR signals into spectra, candidate peaks, and signed integration results. Supports manual phase adjustment, baseline correction, and recorded processing settings so results can be reviewed and reproduced.

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• Convert raw one-dimensional NMR signals into spectra
• Check peak positions against reference signals
• Review phase and baseline corrections

Prepare and analyze genomic intervals, regions defined by chromosome coordinates, with Gtars. Validate BED files, compare overlaps and coverage, combine region sets, and plan tokenization or reference storage while tracking data provenance and resource limits.

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• Validating BED coordinates and reference assemblies
• Counting overlaps and comparing genomic region sets
• Converting genomic intervals into token IDs

Match scientific labels to ontology identifiers, standardized IDs for concepts such as tissues, cell types, and diseases. Checks existing IDs, labels, obsolete terms, and prefixes to support metadata annotation, submission preparation, and table audits.

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• Annotating tissue, cell type, or disease fields with standard IDs
• Auditing metadata tables for incorrect IDs and labels
• Checking obsolete terms and available replacements

Work with geographic points, lines, and areas in Python using GeoPandas. Guidance and local audit tools help check coordinate systems, geometry validity, spatial join matches, and export settings before trusting or sharing analysis results.

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• Checking geographic data before analysis
• Reviewing coordinate systems and transformations
• Auditing matches between points and areas