# Knoten > A research graph that remembers what didn't work. Markdown in git. MCP server so coding agents stop redoing dead experiments. - **Type:** MCP server - **Install:** `agentstack add mcp-by571-knoten` - **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior - **Seller:** [BY571](https://agentstack.voostack.com/s/by571) - **Installs:** 0 - **Category:** [AI & ML](https://agentstack.voostack.com/c/ai-and-ml) - **Latest version:** 0.1.0 - **License:** MIT - **Upstream author:** [BY571](https://github.com/BY571) - **Source:** https://github.com/BY571/knoten ## Install ```sh agentstack add mcp-by571-knoten ``` Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent. ## About A research graph that remembers what didn't work. Each idea is a markdown file in git, marked **alive**, **dead**, or **retracted**. If it died, the node carries the reason, what would bring it back, and the code to reproduce it. ## How it works A graph is a folder. A node is a markdown file: **frontmatter for machines, prose for humans, code to reproduce it.** ````markdown --- id: hyp-self-consistency type: hypothesis status: dead links: - {rel: kn:killedByGate, to: method-compute-matched-baseline} repro: script: experiments/self_consistency.py model: Qwen3-8B-Instruct data: GSM8K test, 1319 questions cmd: python experiments/self_consistency.py --n 5 --temp 0.7 results: acc_greedy: 0.741 acc_self_consistency: 0.792 acc_compute_matched_baseline: 0.788 tokens_per_question: 1420 n_independent: 1319 --- # Self-consistency (sample 5, majority vote) beats greedy decoding ## Verdict: DEAD Sampling 5 chains and taking the majority scored 79.2% vs 74.1% greedy. +5.1 points. It looked like a free win. ## Why it died It is not free. It costs **5x the tokens**, and given the same budget a longer-CoT baseline reaches **78.8%**. The entire gain was compute, not method. ```python # reproduce the kill: python experiments/self_consistency.py --n 5 --compare compute_matched ``` ## What would reopen this A task where the majority-vote *aggregation* does real work, i.e. where the gain survives a compute-matched baseline. Plausible for code execution or theorem proving. GSM8K is not that task. ```` Three months later, when someone proposes self-consistency again: ``` $ knoten query "self-consistency" [✗ DEAD] hyp-self-consistency killed by : method-compute-matched-baseline reopen if : A task where the majority-vote aggregation does real work, i.e. where the gain survives a compute-matched baseline… ``` ## Use it ```bash pip install -e . # add ".[mcp]" for the agent server knoten init my-topic # a new graph (it's a folder) knoten new hypothesis hyp-idea # scaffold a node with whatever the rules demand knoten query # has this been tried? knoten show # edges, results, attachments knoten attach ... # attach a script, plot or notebook knoten detach knoten validate # enforce this graph's own rules knoten path A B # how did we get from A to B? knoten hook # make `git commit` refuse a broken graph ``` Each graph declares its own rules in `graph.yaml`. `knoten` knows nothing about your field. It enforces whatever *you* said matters. The example graph requires every claim to report `tokens_per_question` and to rest on at least 30 independent questions; a different topic would require something else entirely. ```yaml rules: - id: underpowered when_type: hypothesis require_result_min: {n_independent: 30} message: A result on fewer than 30 independent questions is noise, not evidence. ``` Your graph also declares its own vocabulary, and that is enforced too: ```yaml node_types: [hypothesis, experiment, finding, method, source] statuses: [open, alive, dead, retracted, superseded, active] ``` `type: hypthesis` is a typo, not a new type. `status: ded` is worse than wrong — it would silently drop the claim out of every query, which is exactly the sort of quiet rot this tool exists to prevent. Both are now violations. A rule key — or a config key — `knoten` doesn't recognise is a **hard error**, not a shrug. Config that enforces nothing is decoration, and a rule that enforces nothing is worse than no rule, because you think you're covered. `knoten new` reads those rules and pre-fills exactly what they demand — nothing in the scaffold is knoten's opinion, it's your graph's. The values are `TODO` on purpose, so `new` + `validate` is a checklist rather than a guessing game: ``` $ knoten new hypothesis hyp-my-idea --status dead + nodes/hyp-my-idea.md (hypothesis, dead) pre-filled what THIS graph's rules require: ## Why it died, ## What would reopen this, tokens_per_question, n_independent ``` The failure this tool exists to prevent was caused by **friction**, so the write path is where friction hurts most. Write prose, not boilerplate you had to be rejected to discover. ## The gate is a git hook ```bash knoten hook # after `git init` ``` `git commit` now runs `knoten validate` and **refuses a graph that breaks its own rules**: ``` $ git commit -m "self-consistency is a win" ✗ hyp-self-consistency [live-claims-must-cite-their-gates] An unchallenged claim is not a finding, it is a hope. 1 violation(s) — commit REJECTED ``` A rule that only fires when you remember to ask is the rule that let the last attempt rot. Put it somewhere you can't walk past. (`git commit --no-verify` bypasses it — you should have a reason.) ## Attach the code and the plots A node isn't just a claim. It carries what you need to re-run it. ```bash knoten attach hyp-self-consistency experiments/self_consistency.py accuracy_vs_budget.png ``` The files are copied into `attachments//`, listed in the frontmatter, and images are **embedded in the node body** so they render on GitHub: ``` attachments/hyp-self-consistency/ self_consistency.py the script that KILLED it accuracy_vs_budget.png the plot that shows why ``` `knoten validate` then fails if a node lists an attachment that isn't there. A broken repro is a broken node. ```bash knoten show hyp-self-consistency # edges, results, attachments knoten detach hyp-self-consistency accuracy_vs_budget.png ``` ## Two readers, one file **Humans** skim the prose and get the story: what was tried, what killed it, what's still open. No database, no UI, just markdown you can read in any editor or on GitHub. **Agents** traverse the frontmatter: typed edges (`kn:killedByGate`, `kn:survivedGate`), structured `results`, a `repro` block with the exact script/model/data/command, and the paths of any attached scripts and plots, which they can read and re-run directly. An agent answers *"has this been tried?"* and *"how do I reproduce it?"* without reading a word of prose. The same file serves both. That's the whole design. ## For coding agents (MCP) Point Claude Code, or any MCP client, at a graph. It then **accumulates knowledge about a topic across sessions** instead of starting cold every time: ```bash pip install -e ".[mcp]" ``` ```jsonc {"mcpServers": {"knoten": { "command": "knoten-mcp", "env": {"KNOTEN_GRAPH": "/path/to/llm-research"} }}} ``` ``` knoten_query("has anyone tried self-consistency?") ← BEFORE it starts work knoten_get("hyp-self-consistency") ← the full node, post-mortem included knoten_commit(node) ← AFTER it finishes, pass or fail knoten_attach(node, [script, plot]) ← and the code that proves it knoten_path(a, b) ← how did we get from A to B? knoten_validate() ← run the graph's own rules ``` The agent reads the graph before running an experiment and writes back when it's done, **including when the experiment fails.** A dead hypothesis with a documented cause of death is the most valuable node in the graph, and the one that would otherwise be lost. It writes back the *evidence* too, not just the prose: `knoten_attach` puts the script it ran and the plot it made into the node. A claim you can't re-run is a claim nobody trusts in six months — so the agent that killed a hypothesis leaves behind the thing that killed it, ready for the next agent to run. `knoten_commit` **validates before writing and refuses on violation** — the candidate node is parsed and checked in memory, so an invalid node never reaches your filesystem. An agent cannot record a shiny result that cites no test it survived: ```json {"status": "REJECTED", "violations": [{"rule": "live-claims-must-cite-their-gates", "message": "An unchallenged claim is not a finding, it is a hope."}]} ``` ## Why bother **You stop redoing experiments you already ran and forgot.** Dead ends come back with their cause of death and a command to re-run them. **And you can't fool yourself as easily:** a claim can only be marked *alive* if it cites a test it survived, so a good-looking result that was never checked can't quietly become a finding. **And a broken node is a loud failure, not a quiet one.** Unreadable frontmatter, an unknown edge relation (`kn:killdByGate` — one letter dropped), a rule key that doesn't exist: all are errors. A graph that silently drops what it can't parse reports itself healthy while it rots. **And a claim someone later withdrew says so.** `query` surfaces the retraction from both sides, so an agent asking *"has this been tried?"* about a claim that was later retracted is told it was retracted — not just what the claim said: ``` [✓ ALIVE] hyp-few-shot-format survived : method-compute-matched-baseline RETRACTED by : ret-oops ``` See `examples/llm-research/` for a worked graph and [SPEC.md](SPEC.md) for the design. MIT. One dependency (PyYAML). The whole thing is a few files you can read in one sitting. ## Source & license This open-source MCP server is cataloged on AgentStack and links to its original source — we do not rehost the code. - **Author:** [BY571](https://github.com/BY571) - **Source:** [BY571/knoten](https://github.com/BY571/knoten) - **License:** MIT Install and usage instructions live in the source repository linked above. ## Pricing - **Free** — Free ## Security capabilities Automated source analysis of v0.1.0 — what this tool can access: - **Network access:** no - **Filesystem access:** no - **Shell / process execution:** no - **Environment & secrets:** no - **Dynamic code execution:** no *"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.* ## Versions - **0.1.0** — security scan: passed — Imported from the upstream source. ## Links - Listing page: https://agentstack.voostack.com/l/mcp-by571-knoten - Seller: https://agentstack.voostack.com/s/by571 - Browse the marketplace: https://agentstack.voostack.com/browse --- Listed on AgentStack — the marketplace for AI agent skills and MCP servers. 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