Paper Reader MCP
Click on "Install Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type
@followed by the MCP server name and your instructions, e.g., "@Paper Reader MCPAnalyze C:\papers\transformer.pdf and list the key results with page references."
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Paper Reader MCP
Paper Reader MCP is a local, read-only Model Context Protocol server for evidence-first analysis of research papers and slide decks. It supports PDF, DOCX, PPT, and PPTX files while minimizing tool round trips, repeated context, and unnecessary visual tokens.
The server converts a document once, stores a content-addressed local cache, and retrieves compact evidence for an entire question batch in one call. Original PDF regions are rendered only when textual evidence is insufficient for a visual claim.
Highlights
Token-efficient retrieval: one
paper_batch_searchcall handles up to 32 questions and returns a deduplicated evidence bank.Long-document support: adaptive context budgets, ranked chunks, exact numbered-reference routing, and compact wide-table serialization.
Selective visual evidence: exact figure, table, or formula crops are limited to 500,000 pixels each and 1.3 million pixels per batch.
Evidence traceability: results retain source page or slide references and stable evidence identifiers.
Local and read-only: source documents are never modified or uploaded by the server.
Persistent cache: unchanged files reuse Markdown, document structure, evidence indexes, and extracted assets.
Weak-model oriented: the retrieval contract is designed to reduce planning and tool-loop errors in smaller models.
Related MCP server: context-bridge
Supported formats
Format | Pipeline | Notes |
Docling + TableFormer + conditional RapidOCR | Preserves page geometry for exact visual crops | |
DOCX | Docling | Extracts structured text, tables, and embedded assets |
PPTX | Docling | Preserves slide-derived evidence and images |
PPT | PowerPoint or LibreOffice conversion, then Docling | Requires PowerPoint on Windows or LibreOffice |
MCP tools
Tool | Intended use |
| Primary entry point; ingest or reuse a document and retrieve evidence for all questions in one round trip |
| One focused follow-up when the batch result reports a genuine evidence gap |
| Explicit pre-ingestion and outline generation |
| Render one exact region or a batched set of evidence crops for visual verification |
local document
-> content hash and cache lookup
-> Docling conversion
-> Markdown + structured evidence index + assets
-> one batched retrieval call
-> optional single batched visual call
-> page/slide-grounded answerInstallation
Python 3.10–3.12 is required. Python 3.10 is the tested version.
git clone https://github.com/oylx666/paper-reader-mcp.git
cd paper-reader-mcp
py -3.10 -m venv .venv
.\.venv\Scripts\python.exe -m pip install -e .Download the local PDF models once:
.\.venv\Scripts\docling-tools.exe models download layout tableformer rapidocr `
--output-dir "$env:USERPROFILE\.cache\paper-reader-models"The server deliberately fails instead of silently downloading missing models during a paper-reading request. This keeps first-call latency and network behavior predictable.
MCP configuration
Add a STDIO server entry to your MCP client, using absolute paths:
{
"mcpServers": {
"paper-reader": {
"command": "C:\\path\\to\\paper-reader-mcp\\.venv\\Scripts\\paper-reader-mcp.exe",
"env": {
"PAPER_READER_MODELS": "C:\\Users\\YOUR_NAME\\.cache\\paper-reader-models"
}
}
}
}Ask questions naturally and include the local document path. Compatible clients are instructed to batch questions, avoid redundant follow-ups, and request visual evidence only when needed.
Configuration
Variable | Default | Values / purpose |
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| Cache directory |
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| Offline Docling model directory |
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Evaluation results
Tests used gpt-5.6-luna with low reasoning effort so retrieval and tool-use weaknesses could not be hidden by a stronger model.
Fifteen-question paper stress test
Pipeline | Correctness | Gross input tokens | Output tokens | Traceable page coverage | Cold conversion |
Paper Reader MCP | 56/60 (93.33%) | 227,113 | 3,925 | 15/15 | 22.32 s |
Docling Markdown | 54/60 (90.00%) | 30,722 | 2,017 | 0/15 | 85.56 s |
MarkItDown Markdown | 55/60 (91.67%) | 43,646 | 2,651 | 0/15 | 2.40 s |
Raw PDF workflow | 54/60 (90.00%) | 240,665 | 4,221 | 15/15 | 0 s |
The original implementation used 13 retrieval calls. The current batch-first interface reduces the intended path to one retrieval call plus, only when required, one visual call. Gross token counts above therefore describe the conservative pre-batching stress run and are not the optimized lower bound.
TableFormer A/B on 16 manually reviewed paper tables
Mode | Weight size | Exact table shapes | Numeric recall | Total full-document time |
fast | 138.7 MB | 16/16 | 100% | 81.92 s |
accurate | 202.9 MB | 13/16 | 99.76% | 82.87 s |
The reviewed reference was initially produced by the fast model and then manually checked, so this comparison may still favor that model. A fully independent cell-level HTML corpus and TEDS evaluation would be required for an unbiased model benchmark.
Visual input tokens are not reported because the platform did not expose modality-level token usage. Pixel counts were measured instead; missing visual-token telemetry must not be interpreted as zero usage.
Accuracy limits
Reading order on complex multi-column pages is inferred and can be wrong.
OCR output is unsuitable as sole evidence for exact quotations, formulas, subscripts, or very small table cells.
Merged cells, dense tables, and chart markers should be verified against rendered source regions.
Formula decoding is not proof of mathematical correctness; formula evidence remains visually verifiable.
Office slide/page numbers are parser-derived and may differ from application UI numbering.
The
nativePDF pipeline sacrifices layout, table, and OCR quality and is intended only as an emergency fallback.
Development
.\.venv\Scripts\python.exe -m pip install -e . pytest
.\.venv\Scripts\pytest.exe -qThe current suite contains 36 tests covering validation, caching, retrieval, evidence deduplication, long-context limits, table compaction, visual pixel budgets, and supported Office formats.
Status
This is an experimental research tool. Treat its output as retrieval evidence, not as an authoritative interpretation of a paper.
Available Tools
4 toolspaper_batch_searchCRead-onlyIdempotent
Retrieve adaptively bounded evidence for up to 32 questions in one MCP call.
| Name | Required | Description | Default |
|---|---|---|---|
| path | No | Absolute PDF/DOCX path; automatically uses or creates the cache. Omit when paper_id is provided. | |
| paper_id | No | Existing paper_id. Omit when path is provided. | |
| questions | Yes | Focused questions to retrieve in one round trip. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, destructiveHint=false and openWorldHint=false, so the safety profile is fully covered without the description. The description adds one behavioral trait beyond that: batching multiple questions into a single round trip. It says nothing about partial results, failure handling per question, or how "adaptively bounded" retrieval behaves.
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?
A single front-loaded sentence with no padding or restatement of the tool title. It is appropriately sized, though "adaptively bounded" is unexplained shorthand that spends words without adding meaning.
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 search tool with no output schema, the description should at least sketch what comes back per question; it does not, so return format and result structure must be discovered by calling. The input side is fully covered by the schema, leaving the definition minimally adequate rather than complete.
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 coverage is 100% and includes cache behavior for path, the path-vs-paper_id exclusion, and the 32-item maxItems bound. The description only echoes the 32-question limit already enforced by the schema, adding no syntax, format, or selection nuance. Baseline 3 is correct when the schema carries the load.
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 pairs a clear verb ("Retrieve") with a resource ("evidence") and states a scope (up to 32 questions in one call), which is enough to tell it is a batch variant. However, "adaptively bounded evidence" is undefined jargon, and no sibling (paper_search, paper_ingest) is named to anchor the distinction. An agent can guess the purpose but not confidently differentiate it from paper_search.
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?
There is no when-to-use guidance, no statement of when paper_search or paper_ingest is the better choice, and no preconditions (e.g. that a paper must be ingested first). The batch framing implies a use case but nothing is stated explicitly.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
paper_ingestBRead-onlyIdempotent
Parse one research file into cached evidence and referenced images.
| Name | Required | Description | Default |
|---|---|---|---|
| path | Yes | Absolute local path to a .pdf, .docx, .ppt, or .pptx research file. | |
| force | No | Expensive cache invalidation. Keep false unless the user explicitly requests reparsing. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, and destructiveHint=false, so the safety profile is covered. The description adds that the tool materializes cached evidence and images, which is useful outcome context, but it does not explain re-ingest behavior, cache location, or cost beyond what the 'force' parameter text says.
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?
A single front-loaded sentence naming the input, the action, and the two outputs with zero filler. Nothing could be removed without losing information.
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?
With no output schema, the description usefully names the two artifacts produced, but it omits how this tool relates to the search/visual siblings and gives no sense of cost or latency for a parsing operation. Adequate but with clear gaps for a tool sitting in a four-tool family.
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 coverage is 100%, so both 'path' (absolute local path with accepted extensions) and 'force' (expensive cache invalidation) are fully documented in the schema. The description adds nothing beyond that, which is the correct baseline when the schema does the heavy lifting.
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?
States a specific verb (parse), a specific resource (one research file), and the outcome (cached evidence plus referenced images). The word 'one' implicitly scopes it to single-file ingestion, contrasting with paper_batch_search, though no sibling is named explicitly.
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?
There is no explicit when-to-use guidance: nothing says when to ingest versus paper_search, paper_batch_search, or paper_visual, nor whether ingestion is a prerequisite for the other tools. Only the implicit single-file scope hints at usage.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
paper_searchCRead-onlyIdempotent
Return compact, ranked Markdown evidence with page hints and linked image paths.
| Name | Required | Description | Default |
|---|---|---|---|
| query | Yes | Focused topic or question. Empty returns the opening chunks. | |
| paper_id | Yes | paper_id returned by paper_ingest. | |
| max_results | No |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare a safe, idempotent, closed-world read operation, so the safety profile is covered. The description adds useful behavioral context about the return format (Markdown, ranked, page hints, linked images), but says nothing about ranking behavior, limits, or how empty queries behave.
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?
A single front-loaded sentence with no filler. It is efficient, though arguably too terse to carry the missing usage and parameter context.
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?
With no output schema, the description does describe the return shape, which partially compensates. But for a 3-parameter search tool it omits when to choose it over siblings, the meaning of max_results, and any ranking or scope details an agent would need to invoke it confidently.
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 coverage is 67%: query and paper_id are documented (including the 'empty returns the opening chunks' behavior), while max_results has no description. The description adds no parameter-level meaning beyond the schema, so the mid-range baseline of 3 is appropriate.
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 resource ('compact, ranked Markdown evidence with page hints and linked image paths'), which tells the agent what comes back. However, it frames the tool as an output producer rather than stating that it searches a paper's content for a query, and it does not distinguish itself from siblings paper_batch_search or paper_visual.
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?
There is no guidance on when to use this tool versus the clearly related siblings (paper_batch_search for multiple papers, paper_visual for visual content). The mention that paper_id comes from paper_ingest appears only in the schema, not the description, so no explicit sequencing advice is given.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
paper_visualBRead-onlyIdempotent
Return exactly one relevant extracted image or one on-demand original PDF page/crop.
| Name | Required | Description | Default |
|---|---|---|---|
| bbox | No | Optional pixel crop (x0,y0,x1,y1) after rendering; requires page_number. | |
| asset | No | Exact linked asset path/name returned by paper_search. Prefer this for figures. | |
| scale | No | PDF render scale; 3.0 protects small chart markers while oversized crops are pixel-capped. | |
| paper_id | Yes | paper_id returned by paper_ingest. | |
| evidence_id | No | Evidence identifier returned by paper_search. Preferred: crops its source region automatically. | |
| page_number | No | 1-based original PDF page. With evidence_id, selects one page of multi-page evidence. | |
| evidence_ids | No | Two to six evidence IDs returned as one labeled contact sheet; preferred over repeated visual calls. |
TDQS
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true, idempotentHint=true, destructiveHint=false, and openWorldHint=false, so the safety profile is covered and the description need not repeat it. The description adds that output is rendered on demand ('on-demand original PDF page/crop'), which hints at server-side rendering, but it omits cost/latency implications, and the phrase 'exactly one' sits awkwardly against the schema's contact-sheet mode for 2-6 evidence IDs. With annotations covering the behavioral bar, a 3 is appropriate.
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?
A single front-loaded sentence with no filler or redundancy; the core promise (what is returned) leads immediately. It is efficiently sized, though its brevity veers toward under-specification for a 7-parameter tool.
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?
With no output schema, the description partially carries the return-value burden by naming the returned artifact (image, PDF page, or crop), which is useful. However, for a 7-parameter tool with three distinct output modes (single image, PDF page, contact sheet), it never explains how modes are selected or what the contact-sheet return looks like, leaving real gaps.
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 100%, so every parameter (bbox scaling, asset path, scale cap, page_number, evidence_id, evidence_ids) is already documented in the schema itself. The description adds no parameter-level meaning beyond what the schema provides, which is the correct baseline of 3 when the schema does the heavy lifting.
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 gives a specific verb ('Return') and a concrete resource (an extracted image, or an on-demand original PDF page/crop), which is clearer than a bare image-fetch restatement. It does not, however, distinguish the tool from its siblings (paper_ingest, paper_search, paper_batch_search) or state why one would fetch a visual rather than search. Purpose is clear but sibling differentiation is absent.
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?
There is no when-to-use or when-not-to-use guidance in the description; the only routing hints ('Prefer this for figures', 'preferred over repeated visual calls') live in the schema property descriptions, not the tool description. An agent gets no explicit condition for choosing this tool over paper_search or paper_ingest. Usage is only implied by the tool name.
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.
4 tool updates
v0.1.0- First observed
paper_batch_search - First observed
paper_ingest - First observed
paper_search - First observed
paper_visual
TDQS
Scored across 4 tools
The four tools have distinct primary purposes: ingest parses files, search returns ranked evidence, batch_search handles multiple questions in one call, and visual returns a single image or PDF page. The main potential overlap is between search and batch_search, but the batch version is clearly scoped to multi-question retrieval and bounded evidence. Overall, boundaries are clear.
All names use snake_case with a consistent paper_ prefix. Three tools use a verb (ingest, search, batch_search) while paper_visual is a noun/adjective, slightly breaking the verb_noun pattern. The deviation is minor and the prefix keeps the set predictable.
Four tools is well-scoped for a focused paper reader server. Each tool covers a distinct stage: ingestion, single search, batch search, and visual retrieval. No tool feels redundant or missing at this scale.
The surface covers the core lifecycle: parse a paper, search its evidence, batch search, and fetch visual content. Minor gaps include no tool to list or manage already-ingested papers/cache, and no explicit metadata extraction or full-text retrieval beyond search. These are workable around but prevent full lifecycle coverage.
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