ImmunoGraph MCP

calibrate_confidence

Read-onlyIdempotent

Fit Platt or isotonic calibration to labeled scores and evaluate calibrated probabilities on held-out outcomes, or emit rule-based confidence when measured reliability is unavailable.

Instructions

Fit Platt or isotonic calibration on labeled samples and evaluate on separate labeled outcomes, or emit rule-based confidence. Use fitted modes only with real calibration and evaluation labels; rule-based mode has no measured reliability. Returns calibrated probabilities and metrics only where the input labels support them.

Input Schema

Name	Required	Description
`runId`	Yes	Caller-chosen identifier linking this call to one research run.
`method`	Yes	Algorithm or provider method selected for this operation; inspect allowed schema values.
`predictions`	Yes	Predicted values to calibrate or score using the selected method.
`evaluationSamples`	No	Held-out labeled samples used to evaluate fitted calibration.
`calibrationSamples`	No	Labeled examples used only to fit a calibration model.

Output Schema

Name	Required	Description
`ok`	Yes	Whether execution completed successfully.
`data`	No	Tool-specific result fields on success.
`meta`	Yes	Run identifiers, timings, and input/output hashes.
`error`	No	Structured failure on unsuccessful execution.

Schema Changelog

Changes observed during successful MCP inspections.

Changed6 schema fields changedv0.2.1Oct 31, 2026

addedInput schema / properties / calibrationSamples / description

Added value: +"Labeled examples used only to fit a calibration model."

addedInput schema / properties / evaluationSamples / description

Added value: +"Held-out labeled samples used to evaluate fitted calibration."

addedInput schema / properties / method / description

Added value: +"Algorithm or provider method selected for this operation; inspect allowed schema values."

addedInput schema / properties / predictions / description

Added value: +"Predicted values to calibrate or score using the selected method."

addedInput schema / properties / runId / description

Added value: +"Caller-chosen identifier linking this call to one research run."

changedOutput schema / (root)

Previous value: -nullNew value: +{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "additionalProperties": {},
+  "properties": {
+    "data": {
+      "additionalProperties": {},
+      "description": "Tool-specific result fields on success.",
+      "properties": {},
+      "type": "object"
+    },
+    "error": {
+      "additionalProperties": false,
+      "description": "Structured failure on unsuccessful execution.",
+      "properties": {
+        "category": {
+          "type": "string"
+        },
+        "code": {
+          "type": "string"
+        },
+        "details": {
+          "additionalProperties": {},
+          "properties": {},
+          "type": "object"
+        },
+        "message": {
+          "type": "string"
+        },
+        "retryable": {
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "code",
+        "category",
+        "message",
+        "retryable"
+      ],
+      "type": "object"
+    },
+    "meta": {
+      "additionalProperties": {},
+      "description": "Run identifiers, timings, and input/output hashes.",
+      "properties": {
+        "completedAt": {
+          "type": "string"
+        },
+        "durationMs": {
+          "type": "number"
+        },
+        "inputHash": {
+          "type": "string"
+        },
+        "outputHash": {
+          "type": "string"
+        },
+        "requestId": {
+          "type": "string"
+        },
+        "runId": {
+          "type": "string"
+        },
+        "startedAt": {
+          "type": "string"
+        },
+        "toolName": {
+          "type": "string"
+        },
+        "toolVersion": {
+          "type": "string"
+        }
+      },
+      "required": [
+        "requestId",
+        "runId",
+        "toolName",
+        "toolVersion",
+        "startedAt",
+        "inputHash"
+      ],
+      "type": "object"
+    },
+    "ok": {
+      "description": "Whether execution completed successfully.",
+      "type": "boolean"
+    }
+  },
+  "required": [
+    "ok",
+    "meta"
+  ],
+  "type": "object"
+}

First observedv0.2.0Oct 31, 2026

TDQS

A4.1/5.0

Behavior4/5

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

Annotations already establish that this is a read-only, idempotent operation. The description adds meaningful behavioral context: fitted modes depend on real labels, rule-based output is not measured reliability, and metrics are only returned where labels support them. It does not contradict the annotations.

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

Conciseness5/5

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

The description is three tight sentences with the purpose front-loaded and the critical method caveat immediately following. Every sentence adds actionable information with no repetition or filler.

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

Completeness4/5

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

Given the 5-parameter schema, full schema description coverage, output schema, and read-only annotations, the description covers the key mode-selection and label requirements well. It omits sample-size details, but those are already documented in the schema.

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

Parameters4/5

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

Schema coverage is 100%, so the schema already documents all parameters. The description adds semantic meaning for the method enum by distinguishing fitted Platt/isotonic behavior from rule-based confidence and by tying fitted modes to calibration and evaluation labels.

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

Purpose4/5

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

The description states a specific verb and resource: fitting Platt or isotonic calibration, evaluating on labeled outcomes, or emitting rule-based confidence. It is clear what the tool does, but it does not explicitly differentiate this tool from nearby siblings such as normalize_scores or rank_candidates.

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

Usage Guidelines4/5

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

It gives clear conditional guidance: fitted modes require real calibration and evaluation labels, while rule-based mode has no measured reliability. That is useful when-to-use context, though it does not name sibling alternatives or state explicit when-not-to-use conditions beyond the reliability caveat.

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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