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umap

Reduce high-dimensional single-cell RNA sequencing data to 2D or 3D visualizations for pattern discovery and cluster analysis using UMAP dimensionality reduction.

Instructions

Uniform Manifold Approximation and Projection (UMAP) for visualization

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
min_distNoMinimum distance between embedded points.
spreadNoScale of embedded points.
n_componentsNoNumber of dimensions of the embedding.
maxiterNoNumber of iterations (epochs) of the optimization.
alphaNoInitial learning rate for the embedding optimization.
gammaNoWeighting applied to negative samples.
negative_sample_rateNoNumber of negative samples per positive sample.
init_posNoHow to initialize the low dimensional embedding.spectral
random_stateNoRandom seed for reproducibility.
aNoParameter controlling the embedding.
bNoParameter controlling the embedding.
methodNoImplementation to use ('umap' or 'rapids').umap
neighbors_keyNoKey for neighbors settings in .uns.
Behavior2/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries full burden for behavioral disclosure but offers minimal information. It mentions 'for visualization' which suggests a read/transform operation rather than destructive modification, but doesn't clarify computational requirements, memory usage, typical runtime, or what the output actually contains. For a complex tool with 13 parameters, this leaves significant behavioral unknowns.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is extremely concise - a single phrase that identifies the algorithm and its purpose. There's no wasted language or redundancy. However, given the tool's complexity (13 parameters, no output schema), this brevity borders on under-specification rather than optimal conciseness.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness2/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

For a complex dimensionality reduction tool with 13 parameters, no annotations, and no output schema, the description is inadequate. It doesn't explain what the tool returns (embeddings? plots? transformed data?), doesn't mention typical input data formats, and provides no context about how UMAP differs from other available methods. The agent would struggle to use this tool effectively based solely on this description.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, with all 13 parameters well-documented in the schema itself. The description adds no parameter-specific information beyond the generic mention of UMAP. This meets the baseline of 3 since the schema does the heavy lifting, but the description doesn't provide any higher-level guidance about which parameters are most important or typical configurations.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose3/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states 'Uniform Manifold Approximation and Projection (UMAP) for visualization' which identifies the algorithm and its purpose (dimensionality reduction for visualization). However, it's somewhat vague about what the tool actually does - it doesn't specify whether it creates embeddings, transforms data, or generates plots. Among siblings like 'tsne', 'pca', and 'diffmap', it doesn't clearly differentiate UMAP's specific use cases or advantages.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines2/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides no guidance on when to use UMAP versus alternative dimensionality reduction methods like 'tsne', 'pca', or 'diffmap' that are available as sibling tools. There's no mention of typical use cases, prerequisites, or performance characteristics that would help an agent choose between these visualization/dimensionality reduction options.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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