# linkedparticles

**[linkedparticles.org](https://linkedparticles.org)** ·
**[docs.linkedparticles.org](https://docs.linkedparticles.org)** ·
[PyPI](https://pypi.org/project/linkedparticles/) ·
[Apache-2.0](https://github.com/LinkedParticles/particles-engine-py/blob/main/LICENSE)

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> **Particles is shared memory for humans and AI agents.** Each particle is one
> claim, plus what you need to judge it: who said it, where, when, and how
> confident they were. Facts, opinions, and memories are all claims, recorded
> the same way as particles. Particles are not edited or deleted. Particles are
> superseded, retracted, or disputed in the open. How much to trust it is a
> perspective applied at query time, never baked into the record.

`linkedparticles` is the **Engine** of the Particles reference implementation:
the package you install to actually run a belief store. Give it documents,
pages, chat logs, or an agent's own session notes; get back claim-granularity
beliefs, each carrying calibrated confidence, an uncertainty kind, a resolved
subject, and provenance back to the exact source bytes. Ask a question and the
answer cites the beliefs it was built from. Nothing is ever overwritten, so you
can ask the store what it believed a year ago and why it stopped.

**When your agent is wrong, you can see exactly why, and fix it at the source.**

The Engine is a library first. The HTTP API, the CLI, the read-only MCP server,
and the resident daemon are all *surfaces* over it.

## Install

```bash
pip install linkedparticles
```

Python 3.11+. `linkedparticles-core`, the store-free Client layer, is pulled
in automatically.

Extraction and the written answers call a language model. The quickstart below
uses Anthropic, and any OpenAI-compatible endpoint works too, hosted or local
(Ollama, llama.cpp, vLLM): each purpose names its provider in `config.yaml`
([named providers](https://docs.linkedparticles.org/operator-guide/configuration/#named-providers-any-openai-compatible-endpoint)).
Deposit, the session digest and structural queries make no model call at all.

## Sixty seconds

```bash
export ANTHROPIC_API_KEY=sk-ant-...
particles db init

# Deposit a source (file, URL, or literal text) into the append-only corpus
particles deposit https://en.wikipedia.org/wiki/Pluto

# Extract claim-granularity beliefs with confidence, subjects, and provenance
particles extract --all-pending

# Ask in natural language; the answer cites the particles behind it
particles query "Why is Pluto not a planet?"

# Health-check the store: contradictions, staleness, orphaned links
particles lint
```

Because nothing is overwritten, the store can replay its own history. `--as-of`
is the **assertion-time** lens. It answers *what did the store believe at T, and
why did it stop*, not what was true of the world at T:

```bash
particles query "How many planets are in the Solar System?" --as-of 2000-01-01
# → the belief as it stood then, and why it no longer stands: SUPERSEDED,
#   retired 2006-08-24, superseded by "Pluto is a dwarf planet."
```

There is a clickable version of that belief history on the
[front door](https://linkedparticles.org). Step by step:
[getting started](https://docs.linkedparticles.org/user-guide/getting-started/),
then [as-of time travel](https://docs.linkedparticles.org/user-guide/as-of/).

### Wiring it into an agent

```bash
particles mcp serve                 # read-only MCP server (stdio), any MCP client
particles init claude-code          # session-start digest, session-end harvest
particles engine serve              # HTTP API, for a shared or remote engine
particles export obsidian ./vault   # also: anki, wiki, logseq, notion, graph, jsonl
```

It can also stand in for the reference memory server, and it plugs into
LangChain as a retriever and a tool set. See
[Claude Code memory](https://docs.linkedparticles.org/user-guide/claude-code/),
[swapping in for the reference memory server](https://docs.linkedparticles.org/user-guide/memory-server-swap/),
and [using from LangChain](https://docs.linkedparticles.org/user-guide/integrations/).

## Does it hold up?

Measured on **LongMemEval**, the multi-session agent-memory benchmark, with a
full-context oracle and a no-memory floor run as controls in the same harness:

| | Recall@40 | End-to-end QA |
|---|---:|---:|
| **Particles memory** (shipped default, `top_k` 40) | **0.969** | **0.804** |
| Full-context oracle (baseline, n=148) | — | 0.878 |
| No memory (floor) | — | 0.047 |

The oracle and floor rows come from a separate control run in the same harness,
the day before the three runs the Particles row averages; the benchmarks page
names the report of record for each row.

Method, per-question-type breakdowns, comparator memories, and the
budget-matched arm (including the arms where Particles *loses*) are on the
[benchmarks page](https://docs.linkedparticles.org/benchmarks/), with the
report JSONs of record beside them.

## Security posture

A memory layer is an *input-shaping* attack surface: it does not merely hold
data, it shapes what the agent believes and does next, so a poisoned claim is
an instruction on a delay timer.

**Three adversarial audits have covered this code, and each returned
GO-WITH-FIXES.** The verdicts are quoted as given.

| Audit | Code audited | Verdict | Fixes shipped in |
|---|---|---|---|
| June 2026, before the code was opened: the HTTP, CLI and MCP surfaces, the filesystem writers, the egress layer, the CI and wheel build | `v1.62.0` | GO-WITH-FIXES | `1.62.1` to `1.63.0`; the last open finding closed in `1.128.0` |
| 2026-10-23: everything changed since `v1.62.0`, including the release and publication pipeline the first audit predates, and the claims on this page | `v1.210.2` | GO-WITH-FIXES | `1.210.3` to `1.211.0` |
| 2026-10-24: everything changed since the second audit, every earlier finding, and the claims on this page again | `v1.211.0` | GO-WITH-FIXES | `1.211.1` to `1.214.0` |

Since those fixes, a cloned repository can no longer configure Particles or
supply the store an MCP server reads, an HTTP caller can no longer make the
engine read a file on its own disk, and a web page can no longer send writes to
an engine on loopback or read from one that runs without a key. The job that
holds the PyPI publishing identity runs no code from a package index: it
downloads the built files, checks them against the digests the build job
recorded, and runs the pinned upload action. Not every finding is
fixed: part of the second audit's finding on automatic retirements remains
open, and SECURITY.md describes it and the other limits that remain.

What holds today, and what does not:

- **Prompt injection is contained, not eliminated.** Outside the benchmark
  harness, every model prompt that carries deposited, stored or harvested text
  keeps its instructions in the system turn and wraps that text in a per-call
  fence marked with a 128-bit random nonce. A test finds every call to the
  model's entry points, including calls through a wrapper that passes a system
  turn on, and fails the build on one that has not been classified and, if it
  carries such text, fenced. A call reached another way, such as through a
  function passed as a value, is outside what that test can find. Behind the
  fence sit structural checks: a JSON contract enforced at the parser, and a
  gate that rejects synthesized prose citing a claim it was not given. This
  raises the bar materially. It is hardening, not immunity.
- **The model has no tools, but its verdicts change what is stored.** The
  model is never offered function calling, and nothing it emits is run as code
  or SQL or used as a fetch destination. Its output still has effects: subject
  names it extracts become Wikidata search terms; its verdicts retire claims
  (an older value a newer claim updates, a claim from the same passage that
  the re-anchor pass restates in words the model wrote, the less trusted side
  of a contradiction between sources of different trust) and return held
  claims to active, each recorded in the event log; and the beliefs it extracts
  are written into Claude Code's `MEMORY.md`, which an agent with tools reads
  as instructions. An injection can distort claims, and a distorted claim can
  steer an agent.
- **Fetches of URLs from deposited content are checked on every hop.** The
  host is resolved, each address is checked against a blocklist, and the
  connection goes to that vetted address, again on every redirect, which closes
  DNS rebinding and redirect SSRF. The two fetches that run as subprocesses are
  pinned to addresses this process vetted, neither follows a redirect on its
  own, and the git clone runs under no system or global git config, so no
  filter driver (git-lfs among them) runs for the cloned files. Endpoints you configure yourself (a model
  provider, a remote engine, a telemetry collector) are held to the
  `network.egress` setting but not to the blocklist, since a LAN or local model
  server is a legitimate target.
- **Fail-closed auth, and no SQL built from input.** With no bearer key set,
  the engine refuses to start on a non-loopback bind, reading the bind from the
  `uvicorn` command line when it is started that way and refusing a launch by
  another ASGI server whose bind it cannot read. On every path it then serves
  only a loopback client that names a loopback host or one listed in
  `api.allowed_hosts`, which turns away a DNS-rebinding page. Routes that act
  with the operator's authority (subject merges, operator retractions, review
  rulings, trust policy) need a real key even from loopback. The token
  comparison is constant-time. The data layer issues typed ORM statements with
  bound parameters; its few literal SQL statements (a schema-version read and
  the change-journal triggers) are constants that take no input.
- **Local by default, with three outbound defaults you should know.** The
  engine binds to loopback, stores to a local SQLite file, keeps telemetry
  off, and serves MCP as a locally spawned stdio child. Out of the box it also
  contacts the model provider you configure, Wikidata for subject lookups
  during extraction (these carry extracted entity names), and the Hugging Face
  Hub, to download the embedding model and, while outbound traffic is open, to
  check for a newer copy when a process loads it. Settings come only from the
  file `PARTICLES_CONFIG` names or `~/.particles/config.yaml`, never from the
  directory a command runs in. The store is a different matter: when nothing
  names one, the `particles` command line and `engine serve` open
  `./particles.db` in the directory they run in, while an MCP server opens
  `~/.particles/particles.db`. Set `network.egress` to `none` or `allowlist`
  to restrict outbound traffic.

The real answer to the residual is epistemic rather than technical: every
particle carries its provenance, source trust is a read-time lens that
discounts a distrusted source without rewriting anything, and `lint` / `review`
turn your rulings on contradictions into a reusable trust policy. The store is
a record of *what sources said, weighted by how much you trust them*, not an
oracle, so a poisoned source is something you can see, discount, and retract
with the audit trail intact.

The limitations we ask you to read before relying on any of this are in
[SECURITY.md](https://github.com/LinkedParticles/particles-engine-py/blob/main/SECURITY.md):
the read surface left open by default, verbatim storage of whatever you
deposit (secrets included), model verdicts that retire claims, project scope
as a relevance filter rather than isolation, the single-operator trust model,
and the MCP write boundary. SECURITY.md is also where to report a
vulnerability; please report privately.

## Why Particles?

<!-- BEGIN PROJECTED: what-is (manifest: docs/projection/readme.yaml) -->
Most Retrieval-Augmented Generation systems re-derive knowledge from scratch on every query, operating over raw text chunks without any persistent record of what was learned, how confidently it was held, or where it came from. Particles takes a different approach: rather than retrieving passages, it stores discrete, citable, revisable claims (natural-language sentences paired with structured metadata for confidence, provenance, and uncertainty) so that an agent's knowledge accumulates as an auditable ledger rather than evaporating between sessions. Corpus-entry-level provenance is required at Core, meaning every belief can be traced back to the source that produced it, and the particle store itself is a derived view that can be rebuilt from the corpus by re-running extractors, giving the system both durability and reproducibility.

The Particles standard defines the particle schema, the source-corpus model, the extraction protocol, and a set of operations (deposit, extract, query, lint, review, and reindex) that together form the spine along which an agent's knowledge is built, queried, audited, and revised one belief at a time. A developer working with this loop deposits a source into the append-only corpus, extracts claim-granularity particles with resolved subjects, queries by effective-confidence ranking, lints for contradictions and staleness, and reviews inconsistencies into a reusable trust policy. Because particles carry explicit confidence and provenance, Particles can answer queries that require finding relevant claims about a subject and synthesising them with provenance intact, rather than returning a ranked list of chunks whose epistemic status is opaque.

Particles is a minimal interoperable substrate for claim-granularity agent knowledge: narrower than a formal-ontology knowledge graph such as RDF/SPARQL and more structured than augmented markdown. Anchoring every particle to a subject is what makes this precision possible: the Subject store is the standard's catalogue of real-world entities against which particles are indexed, aligning beliefs to canonical entities that can, in principle, be mapped to external ontologies. A developer choosing Particles is therefore choosing a substrate where each belief is a first-class object with an identity, a confidence score, a source, and a subject, not a position in a vector space.

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## Design rationale

<!-- BEGIN PROJECTED: design-rationale (manifest: docs/projection/readme.yaml) -->
The foundation of Particles is the guarantee that nothing already written is ever overwritten. The Source Corpus is constituted as an append-only archive of all materials from which particles have been or may be extracted, meaning that every ingested source and every derived claim accumulates in place rather than displacing what came before. Provenance is carried by each particle from the moment of its creation, and when a source must be handled in a mutable mode rather than a purely append-only one, the system does not silently absorb the change: particles whose provenance location falls within the changed regions are flagged with `PROVENANCE_STALE`, making the disturbance visible rather than burying it. Supersession and retraction therefore propagate deterministically through the provenance graph, touching every claim whose origin is implicated, so the ledger remains a faithful record of what was asserted and when, never a quietly revised version of the past.

Trust in Particles is not a property baked into a stored record but a lens applied at the moment of reading. The raw confidence value is stored immutably, calibrated at the time a particle is created and never subsequently altered; what changes with each query is the effective confidence, which is computed at query time rather than stored. Trust weighting, recency decay, and the as-of instant are all applied per observer at query time, never written back into the record. This means that a belief does not need to be retracted or rewritten to sink in the rankings as its source ages or as the extractor that produced it loses credibility: the stored particle remains intact while the effective confidence computed over it falls, allowing stale beliefs to recede naturally without any mutation of the underlying ledger. When `as_of` is set to a past instant T, the query evaluates the store on the assertion-time axis (what the store believed at T) rather than on any world-time validity dimension, so the same immutable corpus can answer questions about present belief and historical belief without ambiguity.

Contradictions in Particles are treated as first-class citizens of the knowledge graph rather than anomalies to be suppressed. When two sources or two principals disagree, the conflict-resolution ladder surfaces an `INCONSISTENCY` record for review instead of silently overwriting either side, preserving both competing claims in the ledger and making the disagreement legible to any downstream consumer. Contestedness, the property that marks a particle as being in tension with one or more others, must be computed at read time and is never stored; like effective confidence, it is a read-time lens rather than a durable annotation, which means that as new particles arrive or old ones are superseded, the contested status of any given claim is always freshly derived from the current state of the graph rather than from a stale flag written at some earlier moment.

Memory in Particles maintains itself through a periodic, automated health discipline. The Lint operation performs health checks for contradictions, stale claims, orphan pages, and missing cross-references, scanning the corpus on a scheduled basis so that problems accumulate into visible findings rather than silently degrading the quality of the belief store. Because nothing is overwritten and contradictions are surfaced rather than resolved by fiat, Lint operates on a stable substrate: it traverses the same immutable record that queries read, and its findings feed back into the trust-policy review cycle, closing the loop between ingestion, querying, and the ongoing stewardship of the ledger's integrity.

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## Architecture

<!-- BEGIN PROJECTED: architecture (manifest: docs/projection/readme.yaml) -->
A Particles deployment is organized around two distinct storage subsystems: a Source Corpus store and a Particle store. The Source Corpus store is an append-only object store, compatible with a local filesystem, an S3-compatible backend, or a content-addressed store, while corpus entries and snapshot metadata are held in queryable form, either relational or document store. Together these two subsystems form the durable foundation on which all operations act.

The Core SDK exposes both a clean Python API and a CLI, and the six core operations (Deposit, Extract, Query, Lint, Reindex, and Review) each map to a CLI subcommand and a `POST` API endpoint in the reference SDK. A developer therefore has two symmetric surfaces for every operation: a scriptable command line suitable for pipelines and a programmatic endpoint suitable for application integration.

The journey from a raw source to a set of particles begins with Deposit, which writes the source into the append-only corpus, and continues with Extract, which drives the extraction pipeline. That pipeline selects the most specific registered extractor whose applicability specification matches the deposited source; the general extractor is used if and only if no domain-specific extractor applies. Once particles exist in the Particle store, Query retrieves them ranked by effective confidence, Lint checks for contradictions and staleness, Reindex rebuilds derived indexes, and Review consolidates inconsistencies into a reusable trust policy. Each step in this sequence is a discrete, named operation rather than an implicit side effect, which means a developer can invoke any stage independently and observe its inputs and outputs in isolation.

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> The *Why Particles?*, *Design rationale*, and *Architecture* sections are
> **cited projections of a particle store**, not hand-authored prose. Each
> marked block is rendered from
> [`docs/projection/readme.yaml`](https://github.com/LinkedParticles/particles-engine-py/blob/main/docs/projection/readme.yaml)
> and the corpus bundle committed beside it, and the trailer under each block
> names the exact claims it was built from. Edit the manifest or the underlying
> particles and re-render, never the prose between the sentinels. Check it
> yourself: `python scripts/projection_drift.py` restores the bundle into a
> throwaway store, re-derives the deterministic render, and fails if any block
> has drifted from the claims it cites.
>
> This is the project eating its own dogfood: the README argues for
> claim-granularity knowledge with provenance, and is itself assembled that way.

## Documentation

Everything below is served at
**[docs.linkedparticles.org](https://docs.linkedparticles.org)**.

| Guide | What it covers |
|---|---|
| [User guide](https://docs.linkedparticles.org/user-guide/) | Depositing, extracting, querying, as-of time travel, exporting, agent integrations |
| [Operator guide](https://docs.linkedparticles.org/operator-guide/) | Configuration, tuning, lint and review, remote engines, containers, observability, troubleshooting |
| [Plugin-author guide](https://docs.linkedparticles.org/plugin-author-guide/) | Writing extractors, exporters, and benchmark suites |
| [CLI reference](https://docs.linkedparticles.org/cli-reference/) | Every verb and flag |
| [HTTP API](https://docs.linkedparticles.org/api/http/) | The OpenAPI contract |
| [Benchmarks](https://docs.linkedparticles.org/benchmarks/) | LongMemEval results, method, and comparators |

The standard itself (whitepaper, technical specification, and the normative
schema, context, and vocabulary artifacts) lives at
**[linkedparticles.org](https://linkedparticles.org)**.

## The three repositories

| Repo | What it is |
|---|---|
| [`particles-standard`](https://github.com/LinkedParticles/particles-standard) | The standard: whitepaper, technical specification, normative schema + SHACL artifacts, conformance fixtures |
| [`particles-core-py`](https://github.com/LinkedParticles/particles-core-py) | The Python Client layer ([`linkedparticles-core`](https://pypi.org/project/linkedparticles-core/)) |
| [`particles-engine-py`](https://github.com/LinkedParticles/particles-engine-py) | **This repo**: the Python Engine layer + surfaces (`linkedparticles`) |

## Deployment

Container and chart artifacts live under
[`deploy/`](https://github.com/LinkedParticles/particles-engine-py/tree/main/deploy).
The engine ships as a single-writer service; see
[running in a container](https://docs.linkedparticles.org/operator-guide/container-deployment/).

## Contributing

See
[CONTRIBUTING.md](https://github.com/LinkedParticles/particles-engine-py/blob/main/CONTRIBUTING.md)
and
[ARCHITECTURE.md](https://github.com/LinkedParticles/particles-engine-py/blob/main/ARCHITECTURE.md).
Contributions are accepted under a Developer Certificate of Origin sign-off;
there is no CLA.

## License

Apache-2.0. See
[LICENSE](https://github.com/LinkedParticles/particles-engine-py/blob/main/LICENSE)
and
[NOTICE](https://github.com/LinkedParticles/particles-engine-py/blob/main/NOTICE).