shap-mcp
Enables SHAP-based explainability for PyTorch neural networks using DeepExplainer, allowing SHAP values and visualizations to be computed for PyTorch models.
SHAP MCP Server (shap-mcp)
A lightweight, focused Model Context Protocol (MCP) server that exposes SHAP (SHapley Additive exPlanations) model explainability as agent-callable tools.
Designed for AI assistants (like Claude Desktop) and human data scientists to collaborate seamlessly across a shared in-memory session.
Key Features
Dual Simultaneous Transports: Standard
stdiotransport for Claude Desktop alongside a StarletteHTTPtransport on port8765serving the Web GUI and generated visualisations.Unified In-Memory Session: Run analysis via the Web GUI and ask questions in Claude, or have Claude trigger analysis and view generated plots instantly in the GUI gallery.
Universal Model Support:
tree: Exact TreeExplainer for XGBoost, LightGBM, CatBoost, RandomForest, ExtraTrees.linear: Fast closed-form LinearExplainer for Logistic Regression, Ridge, Lasso.deep: DeepExplainer for PyTorch neural networks.kernel: Model-agnostic KernelExplainer with automatic kmeans clustering.
Publication-Ready Visualisations: Generate and save 6 plot types (
summary,bar,waterfall,force,dependence,heatmap) with pre-formatted clickable browser and local file links.URL & File Ingestion: Ingest models and CSV datasets from local paths or public HTTP/HTTPS URLs with streaming downloads, automatic size caps (
SHAP_MCP_MAX_DOWNLOAD_MB), and temp-file cleanup.Security: Optional API key authentication via
SHAP_MCP_API_KEYfor HTTP endpoints.
Related MCP server: my-mcp-server2
Installation
# Standard installation
pip install shap-mcp
# Optional extra for PyTorch DeepExplainer support
pip install shap-mcp[deep]Claude Desktop Configuration
Add shap-mcp to your claude_desktop_config.json:
Universal Recommended Setup (via uvx)
{
"mcpServers": {
"shap-mcp": {
"command": "uvx",
"args": ["shap-mcp", "--no-ui"]
}
}
}Direct Pip / Pipx Setup
{
"mcpServers": {
"shap-mcp": {
"command": "shap-mcp",
"args": ["--no-ui"]
}
}
}Tool Reference
Tool | Purpose | Key Inputs |
| Load |
|
| Compute SHAP values over dataset |
|
| Global ranking of top features |
|
| Local attribution breakdown for single instance |
|
| Pairwise feature interaction strength (Tree models) |
|
| Render & save PNG visualisation with clickable URL |
|
Runtime Configuration
All runtime configuration is managed via environment variables:
Variable | Default | Description |
|
| HTTP server port (auto-increments if busy; |
| (unset) | Bearer token for HTTP auth; unset = no auth required on localhost |
|
| Root directory for saving generated plot PNGs |
|
| Maximum allowed size cap for URL-based model/dataset downloads |
|
| Structured JSON log level ( |
Web GUI
When started directly via shap-mcp, the server automatically opens the Web GUI at http://localhost:8765/ui/:
Configuration Form: Input local paths or URLs, pick model architecture, and run analysis.
Real-Time Badges: Live model loaded status, rows analyzed count, and active explainer type.
Dynamic Plot Gallery: Thumbnails appear automatically as Claude or the GUI generates visualisations.
Instance Explainer: Interactive table of individual feature contributions.
Upcoming Features & Roadmap
The following capabilities are planned for upcoming releases:
save_analysis/load_analysis: Serialize computed SHAP values to.npzfiles to skip re-computation on reload and share results across teams.Auth-Protected Remote Ingestion: Support for Hugging Face tokens, private S3/GCS buckets, and presigned URLs.
Tabbed GUI & Progressive Disclosure: Redesign the Web GUI into clean, focused tabs with progressive unlocking as analysis completes.
Interactive Visualisations: Pan, zoom, and tooltip hover support on matplotlib charts via
mpld3.Plot-Specific Guided Prompts: Dedicated MCP prompts tailored for each of the 6 visualization types.
Multi-Tenant Session Isolation: Connection-isolated session states for shared multi-user server deployments.
Additional Model Formats: Native support for ONNX runtime, MLflow models, and Weights & Biases model registries.
Fairness & Bias Disaggregation: Per-subgroup demographic parity and slice-based SHAP analysis.
MCP-UI Inline Canvas & Local Drag-and-Drop: Direct in-chat canvas rendering via the MCP-UI / MCP Apps specification with local drag-and-drop file ingestion, eliminating external browser tabs and cloud attachment friction.
License
MIT License. See LICENSE for details.
Available Tools
6 toolsexplain_predictionC
Return SHAP breakdown for a single instance.
Parameters
index : int | None Row index in the analyzed dataset. data : dict[str, Any] | None Inline feature dictionary for explaining an arbitrary instance.
| Name | Required | Description | Default |
|---|---|---|---|
| data | No | ||
| index | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
The description states the tool returns a SHAP breakdown but does not specify the output format (e.g., list, table), any side effects, or error behavior. Since there are no annotations, the description alone fails to convey what the user can expect beyond a vague 'breakdown'. No information on whether the model is retrained or data is modified.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise (one sentence) and well-structured, but it is so brief that it sacrifices necessary information. While there is no fluff, the extreme brevity reduces its utility; a slightly longer description with parameter clarification would be more balanced.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool's simplicity, the description is still incomplete. It lacks any mention of when to use it relative to siblings, what parameters are required, or what the output looks like. The presence of sibling tools (get_feature_importance, get_interaction, etc.) makes contextual guidance essential, but none is provided.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The parameters 'index' and 'data' are not described at all in the description. The schema provides no annotations, and the description adds no explanation of what these parameters mean, their constraints, or how they interact. A user cannot know whether to provide an index, data, or both, or what format 'data' should take.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses a clear verb 'Return' and specifies the resource 'SHAP breakdown for a single instance', distinguishing it from sibling tools like get_feature_importance or get_plot. However, it does not elaborate on what the breakdown contains (e.g., feature contributions), leaving some ambiguity for users unfamiliar with SHAP.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
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 this tool versus the siblings, such as get_feature_importance or get_interaction. It does not mention any conditions, prerequisites, or typical scenarios, leaving the user to guess when this is the appropriate choice.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
get_feature_importanceA
Return global feature importance from stored SHAP values.
Parameters
top_n : int Number of top features to return (default: 10).
| Name | Required | Description | Default |
|---|---|---|---|
| top_n | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries the behavioral burden. It discloses that the tool reads 'stored SHAP values' and returns global importance, implying a read-only operation. It does not mention ordering, error behavior, or what happens if SHAP values are absent, but 'top_n' implies a ranked result.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is compact and front-loaded with the core purpose. The parameter documentation is minimal and directly useful, with no filler or redundant restatement of the tool name.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a simple read-only tool with one optional parameter and an output schema, the description is largely complete. It covers purpose, source, and parameter semantics. It could add explicit usage guidance relative to siblings, but that gap is minor given the clear purpose and available output schema.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The schema provides only the default value for top_n, while the description explains its meaning: 'Number of top features to return'. This adds real semantic value beyond the schema, fully compensating for the 0% schema description coverage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb ('Return') and a specific resource ('global feature importance from stored SHAP values'). The word 'global' distinguishes it from sibling tools like explain_prediction (local) and get_interaction, and the source ('stored SHAP values') clarifies it is a read of precomputed results.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies when to use the tool: when global feature importance from SHAP values is needed. However, it does not explicitly state when not to use it or name alternatives such as explain_prediction or get_interaction, leaving the routing decision to inference.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
get_interactionB
Return SHAP interaction values between two features (Tree models only).
Parameters
feature_a : str Name of the first feature. feature_b : str Name of the second feature.
| Name | Required | Description | Default |
|---|---|---|---|
| feature_a | Yes | ||
| feature_b | Yes |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations, the description carries the full behavioral disclosure burden. It does add a key constraint ('Tree models only') and states that the tool returns SHAP interaction values, but it doesn't disclose prerequisites like having a loaded model, failure behavior for unsupported models, or the exact structure of the returned values.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The core description is one short, front-loaded sentence that delivers the main idea. The parameter section is clear but partially redundant with the schema, which keeps it from being a 5.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The tool appears to have an output schema, so little is needed about return values. However, the description is minimal for a tool with no annotations: it lacks preconditions, error behavior, and sibling distinctions. It is a borderline acceptable definition but could be much more helpful.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, so the description must compensate, but it only restates the obvious: feature_a is the first feature and feature_b is the second. It doesn't explain where these names come from, expected format, or any relationship to model features, leaving the agent with little additional meaning over the schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses a specific verb 'Return' and identifies a distinct resource: SHAP interaction values between two features, with the important 'Tree models only' limitation. This purpose is clear and sufficiently differentiates it from sibling tools like get_feature_importance and explain_prediction, though it doesn't name them.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides no explicit guidance on when to choose this tool over its siblings. 'Tree models only' is a precondition, not a usage selection criterion, and no alternatives or trade-offs are mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
get_plotA
Generate a SHAP visualization, save it as a PNG file, and return file path and URL.
Parameters
plot_type : str One of 'summary', 'bar', 'waterfall', 'force', 'dependence', 'heatmap'. index : int | None Row index in dataset (required for waterfall and force). feature_name : str | None Feature name (required for dependence). top_n : int Max features to show (default: 10). color_feature : str | None Feature to color by for dependence plots. output_path : str | None Override default output directory path.
| Name | Required | Description | Default |
|---|---|---|---|
| index | No | ||
| top_n | No | ||
| plot_type | Yes | ||
| output_path | No | ||
| feature_name | No | ||
| color_feature | No | auto |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description carries the burden. It discloses that the tool saves a PNG file and returns a file path and URL, which is useful. However, it doesn't mention side effects like file system writes, potential overwrites, or any permissions needed. It also doesn't describe the output schema beyond the return of path and URL, though an output schema exists.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is well-structured with a clear summary sentence followed by a parameter list. It's front-loaded with the core action and output. The parameter list is concise and informative, though it could be slightly more compact by merging some lines.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the tool has 6 parameters, an output schema, and no annotations, the description covers the essential usage details: plot types, conditional parameters, and output format. It doesn't mention error cases or edge conditions, but for a visualization tool, this is reasonably complete. The output schema likely covers return structure.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, so the description must compensate. It does well by explaining each parameter's purpose, including conditional requirements (index for waterfall/force, feature_name for dependence) and defaults (top_n=10, color_feature='auto'). This adds significant value beyond the raw schema.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool generates a SHAP visualization, saves it as PNG, and returns file path and URL. It lists the plot types, which helps distinguish it from siblings like get_feature_importance or explain_prediction. However, it doesn't explicitly differentiate from get_interaction, which might also produce plots.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies usage by listing required parameters for certain plot types (e.g., index for waterfall/force, feature_name for dependence), but it doesn't explicitly state when to use this tool versus alternatives like get_feature_importance or explain_prediction. No exclusions or alternative routing is provided.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
load_modelA
Load a model file and instantiate the appropriate SHAP explainer.
Note: Prompt the user to provide local filesystem paths on their machine, public URLs, or upload via http://localhost:8765/ui/. Files attached directly in chat are stored in a cloud container (/mnt/user-data/) that local tools cannot reach.
Parameters
model_path : str | None Path to a local .joblib or .pkl model file. model_url : str | None Public URL to download a model file. model_type : str One of 'tree', 'linear', 'deep', 'kernel'. Default is 'tree'. background_path : str | None Path to background CSV dataset (optional for tree/kernel, required for deep).
| Name | Required | Description | Default |
|---|---|---|---|
| model_url | No | ||
| model_path | No | ||
| model_type | No | tree | |
| background_path | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
No annotations are provided, so the description must carry the weight. It discloses the operational constraint about cloud-container paths, which is a non-obvious behavioral detail. It also implies the tool is a prerequisite for other tools. It doesn't state whether it mutates state or returns the explainer, but the output schema exists, and the description is focused on prerequisites, which is beyond what schema conveys.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is well-organized: a purpose sentence, a critical usage note, then parameter definitions. The warning about cloud paths is space-efficient and high-value. Slightly repetitive in noting upload methods, but overall concise and front-loaded with the most important behavioral caveat.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a 4-parameter tool with zero schema descriptions and no annotations, the description covers the key decision points: which parameter to set, required vs optional, and the path accessibility warning. It doesn't describe return values, but an output schema exists, so that's not required. The description is sufficient for correct invocation.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 0%, but the description explains each parameter's purpose and optionality (model_path vs model_url as alternatives, background_path required for deep, optional for tree/kernel). It adds meaningful semantics beyond raw schema types, which is essential given zero coverage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly states the tool loads a model file and instantiates a SHAP explainer, specifying the model types (tree, linear, deep, kernel) and the input sources (local path, URL, or upload). This distinguishes it from sibling tools that focus on analysis/explanation, not loading.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
It provides explicit guidance on when to use this tool (before running analyses) and, crucially, what not to do: it warns that files attached in chat are stored in a cloud container that local tools cannot reach, so the user must provide accessible paths. It doesn't explicitly mention alternatives (sibling tools are analysis tools, not load alternatives), but the context is clear.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
run_analysisB
Run SHAP explainer against a dataset.
Note: Ask the user for local file paths, public URLs (data_url), or use the Web GUI at http://localhost:8765/ui/. For small CSVs (< 500 rows), you may read the table from chat and pass the rows directly in data.
Parameters
data_path : str | None Path to a local CSV file. data_url : str | None Public URL to download a CSV dataset file. data : list[dict] | None Inline dataset passed as a JSON array. sample_size : int | None Override default auto-cap for dataset row sampling.
| Name | Required | Description | Default |
|---|---|---|---|
| data | No | ||
| data_url | No | ||
| data_path | No | ||
| sample_size | No |
Output Schema
| Name | Required | Description |
|---|---|---|
No output parameters | ||
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
With no annotations provided, the description carries the full burden of behavioral disclosure. It states the tool runs a SHAP explainer, but does not mention whether it is read-only, whether it modifies state, whether a model must be loaded first, or what side effects occur. The sample_size parameter hints at auto-sampling, but the overall behavioral profile is opaque.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is well-organized with a clear purpose statement, a practical note, and a parameter list. Each section is necessary, particularly because the schema lacks parameter descriptions. It is not excessively verbose and is easy to parse.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Although an output schema exists, the description lacks important context. It does not mention whether a model must be loaded first (sibling load_model suggests so), what the default sampling behavior is, or how the tool behaves when conflicting data inputs are provided. These are critical for correct usage.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
The schema description coverage is 0%, so the description's parameter block is essential. It clearly explains each parameter: data_path, data_url, data, and sample_size. The guidance about small CSVs and using data directly in chat adds practical semantics. However, it does not explain mutual exclusivity or precedence when multiple data sources are supplied.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description opens with 'Run SHAP explainer against a dataset', which is a specific verb and resource. It clearly distinguishes this from sibling tools like get_feature_importance or explain_prediction, which have different purposes. The intent is immediately understandable.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides no guidance on when to choose this tool over sibling tools like explain_prediction or get_interaction. The note about sourcing data (local paths, URLs, inline data) is about how to provide input, not which tool to select. No alternatives or exclusions are mentioned.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Tool Schema Changelog
Recent tool additions, removals, and schema changes observed during successful MCP inspections. Dates show when Glama detected each change.
6 tool updates
v0.1.0- First observed
explain_prediction - First observed
get_feature_importance - First observed
get_interaction - First observed
get_plot - First observed
load_model - First observed
run_analysis
TDQS
Each tool has a clearly distinct purpose: model loading, SHAP computation, global importance, local explanation, interaction values, and plotting. There is no overlap or ambiguity in what each tool does, so an agent can reliably select the correct one for a given task.
All tool names follow a consistent verb_noun pattern with lowercase and underscores (load_model, run_analysis, get_feature_importance, etc.). The verbs vary but are semantically appropriate, and the naming style is uniform across the set, making the API predictable.
Six tools provide a well-scoped surface for SHAP analysis. This is an appropriate size that covers the core workflow (load, analyze, query results, plot) without redundancy or unnecessary bloat. Each tool earns its place in the server.
The tool surface covers the full lifecycle of a SHAP analysis: loading a model, running the explainer, retrieving global and local explanations, getting interactions, and generating visualizations. There are no obvious gaps that would block an agent from completing typical analysis tasks.
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