pragma-ai 1.0.6

Atomic-fact reasoning over a knowledge graph. A RAG alternative that needs no vector database.

pragma

Atomic-fact reasoning over a knowledge graph. A RAG alternative that needs no vector database.

Quickstart · Why · Benchmarks · How it works · Colab demo

---

Why pragma

Vector RAG has predictable failure modes: keyword mismatch, irrelevant chunks in the prompt, no multi-hop reasoning, no citations, no temporal awareness.

pragma stores documents as a graph of atomic (subject, predicate, object) facts in a single SQLite file. Queries traverse the graph, surface only the relevant facts, and return cited reasoning paths.

	Vector RAG	GraphRAG	LightRAG	pragma
Vector DB required	Yes	Yes	No	No
Multi-hop reasoning	Manual	Yes	Yes	Yes
Reasoning trace	No	Partial	Yes	Full + fact IDs
Temporal queries	No	No	No	Yes (as_of)
Storage	Vector DB	Vector DB	LMDB	SQLite
Infra to operate	Server	Server	Server	None
Token efficiency	bounded by chunk count × chunk size	similar	low	scales with relevant facts, not corpus size

Token budget — measured, not claimed

All numbers are true LLM tokens as reported by the model's tokenizer (prompt_eval_count / eval_count), not internal approximations. Captured by benchmarks_run/run.py against a real Ollama model on a 4-paragraph corpus.

Metric (per-query average over 2 representative queries)	Vector-RAG baseline	pragma
tokens_used — relevant-facts prompt size	n/a	192 ✓
Prompt tokens (full LLM input)	346	234 (−32 %)
Completion tokens	61	model-dependent
LLM calls / query	1	1 (decompose auto-skipped)
Cited reasoning steps	✗	✓

The tokens_used figure is what the original ~280-token claim referred to — the size of the curated fact prompt pragma builds, which is bounded by graph structure, NOT by corpus size. We measured an average of 192 tokens — 31 % below the ~280 headline across two representative queries:

• "Who founded Apple?" → answered correctly with tokens_used = 265.
• "Where was Tim Cook born?" → answered correctly with tokens_used = 120 (the direct-answer fast path even skipped the LLM call entirely on a previous run).

Both answers cite the exact fact_id they used. Vector-RAG also answered both correctly but spent 32 % more prompt tokens overall.

Honest caveats so you don't get burned reproducing this:

1. Completion tokens are model-dependent. The benchmark above was run against minimax-m2.7:cloud, a reasoning model that emits ~250 completion tokens regardless of prompt size. Switch to Groq Llama-3.3-70B and completions drop to ~80, putting pragma's measured total around 380 tokens vs vector-RAG's 553 — a real ~30 % win.
2. On tiny corpora (≤ ~2 k tokens) vector-RAG wins on absolute token count because it can stuff the whole corpus in one prompt. pragma pays off when the corpus grows past roughly 5 k tokens — at that point vector-RAG must include 3 k+ retrieved tokens regardless of relevance, while pragma's prompt stays bounded at the size of the relevant facts.
3. Fact-extraction quality affects answer quality. If the extractor truncated an object value at ingestion time (rare, but happens on long predicates), pragma will honestly answer "unknown" rather than hallucinate. Vector-RAG, working from raw text, may guess correctly. We consider the honest behaviour the right default; you can re-ingest with a stronger model to fix the underlying facts.

Realistic-scale benchmark — 50 documents, 12 queries (new in 1.0.2)

The 4-paragraph numbers above are honest but unconvincing on their own. The realistic-scale harness ingests 50 cross-referenced documents (~9,000 tokens of corpus, 1,084 atomic facts, 484 entities extracted) and runs a mix of single-hop, multi-hop, and aggregation queries against pragma vs a BM25 top-k baseline — i.e. the right enemy for vector-RAG, not "stuff the whole corpus in the prompt".

Both systems use the same Ollama model (deepseek-v3.1:671b-cloud); tokens are counted by the model's own tokenizer (prompt_eval_count / eval_count).

Metric (avg over 12 ground-truth-scored queries)	BM25 top-3 RAG	pragma
Accuracy (substring match)	12/12	12/12
Multi-hop accuracy (2–3 hop)	6/6	6/6
Prompt tokens	614	0 (12/12 zero-LLM)
Completion tokens	8	0 (12/12 zero-LLM)
Latency-zero answers (deterministic resolver)	0	12

Honest read of these numbers:

• 12/12 accuracy, matching RAG — with zero LLM calls. The deterministic MultiHopResolver walks the graph directly for all query types: single-entity lookups, multi-hop chains (founder→education, acquired_by→founder), reverse lookups (product→company), and aggregation (companies in a city).
• Zero prompt + completion tokens. Every query is answered by graph traversal alone; the LLM is never invoked. This is the latency ceiling: answers return as fast as a SQLite query.

Per-query JSON with answers + token counts + which docs RAG retrieved is written to benchmarks_run/results_large.json so anyone can audit the run.

Reproduce these numbers yourself:

ollama pull deepseek-v3.1:671b-cloud   # or any chat model

# Small honesty harness (4-paragraph corpus, 2 queries, very fast):
python benchmarks_run/run.py        # writes results.json + prints summary

# Realistic-scale benchmark (50 documents, 12 queries, ~10-25 minutes
# depending on the model -- ingestion is one-shot and can be reused
# with --no-ingest on subsequent runs):
python benchmarks_run/large_corpus.py     # (re-)materialise corpus
python benchmarks_run/run_large.py --model deepseek-v3.1:671b-cloud
# subsequent runs skip ingestion:
python benchmarks_run/run_large.py --no-ingest

The large benchmark is deterministic: the corpus is regenerated byte-for-byte from the data tables in benchmarks_run/large_corpus.py on every run, and a unit test pins this so future changes can't silently shrink the signal. See tests/unit/test_large_benchmark.py.

Quickstart

pip install "pragma-ai[pdf]"
pragma connect          # one-time interactive setup, see below
pragma ingest ./paper.pdf
pragma query "what is the main contribution of this paper?"

PDF support requires the [pdf] extra (pip install "pragma-ai[pdf]"), which installs pdfplumber and pymupdf for robust extraction including LaTeX-generated papers with pattern fills.

pragma connect — interactive setup (new in 1.0.2)

The first thing to run after install. The wizard walks you through:

1. Picking a provider — Ollama (local, no API key), OpenAI, Anthropic, Groq, or Inception.
2. Pasting your API key (input is hidden) for cloud providers, or confirming the URL for Ollama.
3. Picking a model from the live list — pragma calls the provider's own /v1/models (or /api/tags for Ollama) endpoint to discover what your account / local install actually offers, so you do not have to memorise model names.

The result is saved to a private local config file (~/.pragma/config.json on POSIX, %USERPROFILE%\.pragma\config.json on Windows, mode 0600 where supported). Subsequent pragma ingest and pragma query commands pick it up automatically. Re-run any time to switch provider; pragma connect --reset deletes the saved config.

If you prefer environment variables (CI, servers, secret managers) they still work as a fallback: INCEPTION_API_KEY, OPENAI_API_KEY, GROQ_API_KEY, ANTHROPIC_API_KEY.

Programmatic usage

from pragma import KnowledgeBase
from pragma.llm import get_provider

llm = get_provider("groq")            # or "openai", "anthropic", "inception", "ollama"
kb = KnowledgeBase(llm=llm, kb_dir="./my_kb")

# Ingest anything: pdf, csv, json/jsonl, txt, md, docx, html, URL, dict, or directory
kb.ingest("./docs/")

# Query with full reasoning trace
result = kb.query("Which company did Steve Jobs co-found in 1976?")
print(result.answer)
print(f"confidence={result.confidence:.2f}  tokens={result.tokens_used}")
for step in result.reasoning_path:
    print(f"  [{step.fact_id[:8]}] {step.explanation}")

kb.close()

Streaming:

async for token in kb.stream("Who is the CEO of Apple?"):
    print(token, end="", flush=True)

CLI:

pragma connect                      # one-time: pick provider + model
pragma ingest                       # no path? ingests every supported file in cwd
pragma ingest ./paper.pdf           # one file
pragma ingest ./docs/               # whole directory (recursive)
pragma query "What does pragma do?"
pragma stats
pragma facts --entity "Apple"
pragma entities
pragma connect --reset              # forget saved config

Try it without installing: Open the Colab quickstart →

How it works

┌──────────────  INGESTION  ──────────────┐    ┌──────────────  QUERY  ──────────────┐
│  Documents → Segment                    │    │  Question → Decompose                │
│            → Extract atomic facts (LLM) │    │           → BM25 seed entities       │
│            → Resolve entities (fuzzy)   │    │           → Multi-hop graph traversal│
│            → Build NetworkX graph       │    │           → Assemble facts (budget)  │
│            → BM25 index + SQLite        │    │           → Synthesize + citations   │
└─────────────────────────────────────────┘    └──────────────────────────────────────┘

Storage: A single SQLite file (pragma_kb/pragma.db) holds entities, facts, edges, and a query cache. The graph lives in NetworkX; BM25 powers seed retrieval. Nothing else to run.

Reasoning: Every answer comes with reasoning_path: List[ReasoningStep] — each step cites the exact fact_id it depends on, so users (and you) can audit why the model said what it said.

Deterministic resolver (1.0.2+): Canonical question shapes (founder, education, industry, headquarters, etc.) are answered by graph traversal alone — zero LLM calls, sub-millisecond latency. 1.0.3 adds research-paper intents (core idea, problem caused by, difference, purpose, performance, drop-in replacement) so academic queries like "What is the core idea behind AttnRes?" resolve without invoking the LLM.

Benchmarks

The honest end-to-end harness lives in benchmarks_run/run.py and uses real LLM token counts. See Token budget above for the latest measured numbers.

# Token / answer-quality harness against a live Ollama model
python benchmarks_run/run.py

# Internal unit-style benchmarks (mocked LLM, no network)
pytest tests/benchmarks -q

We have not validated the often-quoted "vector RAG accuracy on HotpotQA" numbers ourselves. If you produce a clean comparison on a real public benchmark with this codebase, a PR adding the harness + results to tests/benchmarks/ is very welcome.

Providers

Provider	Env var	Free tier	Notes
Groq	GROQ_API_KEY	Yes	Fast, recommended for getting started
OpenAI	OPENAI_API_KEY	$5 credit	gpt-4o-mini default
Anthropic	ANTHROPIC_API_KEY	$5 credit	Claude Haiku default
Inception (Mercury)	INCEPTION_API_KEY	Yes	Diffusion LLM
Ollama	—	Local	Offline, requires ollama serve

All providers implement complete, acomplete, and stream_complete. Add your own in 30 lines — see CONTRIBUTING.md.

Supported document formats

.pdf · .csv · .json · .jsonl · .md · .txt · .docx · .html · URLs · Python dict · List[Path | str | dict] · directories (recursive)

Add a new loader in ~50 lines — see CONTRIBUTING.md.

API reference (essentials)

kb = KnowledgeBase(llm, kb_dir="./kb")           # or pass config=PragmaConfig(...)

kb.ingest(source, show_progress=False)           # IngestResult(documents, facts, entities, skipped)
kb.query(q, hop_depth=2, min_confidence=0.5,
         as_of=None, top_k=5)                    # PragmaResult
kb.stream(q)                                     # AsyncIterator[str]
kb.stats()                                       # KBStats(documents, facts, entities, relationships)
kb.close()                                       # or use as a context manager

PragmaResult fields: answer, reasoning_path: List[ReasoningStep], source_facts: List[AtomicFact], confidence, tokens_used, latency_ms, subgraph_size.

Configuration

from pragma import PragmaConfig
config = PragmaConfig(
    kb_dir="./pragma_kb",
    default_hop_depth=2,
    max_subgraph_nodes=50,    # 1.0.2: bumped from 5 (see CHANGELOG)
    fact_confidence_threshold=0.6,
    llm_provider="groq",
)

Env var	Default
PRAGMA_KB_DIR	./pragma_kb
PRAGMA_DEFAULT_HOP_DEPTH	2
PRAGMA_MAX_SUBGRAPH_NODES	50 (was 5 in 1.0.1; floor is 5)
PRAGMA_FACT_CONFIDENCE_THRESHOLD	0.6
PRAGMA_PROMPT_<NAME>	path to override built-in prompt
GROQ_API_KEY / OPENAI_API_KEY / ANTHROPIC_API_KEY / INCEPTION_API_KEY	—

Evaluation harness

from pragma.eval import Evaluator, TestCase
report = Evaluator(kb, [
    TestCase(query="Who founded Apple?",
             expected_answer_contains=["Steve Jobs"],
             expected_entities=["Apple", "Steve Jobs"]),
]).run()
print(report.summary())

Status

• 379 tests passing locally (Windows / Python 3.12)
• ruff clean, type-annotated (py.typed shipped)
• Stable public API at v1.0 — see CHANGELOG.md

Run the suite yourself:

pip install -e ".[dev]"
pytest tests -q
ruff check pragma tests

Contributing

Bug reports, loaders, providers, and benchmark contributions welcome. See CONTRIBUTING.md.

git clone https://github.com/kbpr21/pragma-ai
cd pragma-ai
pip install -e ".[dev]"
pytest tests -q
ruff check pragma tests

License

MIT — see LICENSE.

---

_{Built because vector search is the wrong primitive for reasoning. Star ⭐ the repo if pragma earned it.}