dotcausal 0.3.0

Binary Knowledge Graph Format with Embedded Inference for AI Applications

dotcausal

The Knowledge Graph Format for AI

The .causal format is a binary knowledge graph format with embedded deterministic inference. It solves the fundamental problem of AI-assisted discovery: LLMs hallucinate, databases don't reason.

Why .causal?

The Problem

Technology	What it does	What's missing
SQLite	Stores facts	No reasoning - only returns explicit matches
Vector RAG	Finds similar text	No logic - returns relevance, not causality
LLMs	Reasons creatively	Hallucination risk - invents plausible but false connections

Example: If Paper A says "COVID → damages mitochondria" and Paper B says "mitochondrial damage → fatigue", a SQL query for "COVID → fatigue" returns nothing. The connection exists but is invisible.

The Solution

.causal pre-computes all transitive chains at storage time:

COVID → damages → mitochondria  (explicit, Paper A)
mitochondria → causes → fatigue  (explicit, Paper B)
─────────────────────────────────────────────────────
COVID → indirectly causes → fatigue  (INFERRED, deterministic)

Zero hallucination. Every inference has full provenance back to source papers.

Key Features

Feature	Benefit
~30-40x faster queries	1.1ms vs 41.5ms (SQLite) - pre-computed inference
50-200% fact amplification	Weak signals become visible through transitive chains
~60-80% smaller files	MessagePack + entity deduplication
Zero hallucination	Pure deterministic logic, full provenance
Edge AI ready	Small enough for mobile/offline (air-gapped privacy)
Auto-threshold	Self-adapting fuzzy matching based on entity characteristics

Installation

pip install dotcausal

# With LangChain integration
pip install dotcausal[langchain]

Quick Start

Python API

from dotcausal import CausalWriter, CausalReader

# Create a knowledge graph
writer = CausalWriter()
writer.add_triplet(
    trigger="SARS-CoV-2",
    mechanism="damages",
    outcome="mitochondria",
    confidence=0.9,
    source="paper_A.pdf"
)
writer.add_triplet(
    trigger="mitochondrial dysfunction",
    mechanism="causes",
    outcome="chronic fatigue",
    confidence=0.85,
    source="paper_B.pdf"
)
writer.save("knowledge.causal")

# Query with inference amplification
reader = CausalReader("knowledge.causal")
stats = reader.get_stats()
print(f"Explicit: {stats['explicit_triplets']}")
print(f"Inferred: {stats['inferred_triplets']}")
print(f"Amplification: {stats['amplification_percent']}%")

# Search
results = reader.search("fatigue")
for r in results:
    tag = "[INFERRED]" if r['is_inferred'] else "[EXPLICIT]"
    print(f"{tag} {r['trigger']} → {r['mechanism']} → {r['outcome']}")

Command Line

# Show statistics
dotcausal stats knowledge.causal

# Query the graph
dotcausal query knowledge.causal "COVID" --limit 10

# Convert SQLite to .causal
dotcausal convert pipeline.db output.causal

# Export to JSON
dotcausal export knowledge.causal -o output.json

# Validate integrity
dotcausal validate knowledge.causal

The 3-Pass Inference Engine

Pass	Method	What it finds
1	Exact keyword	A→activates→B + B→activates→C = A→activates→C
2	Semantic direction	positive×negative = negative chain
3	Jaro-Winkler fuzzy	"COVID-19" ↔ "SARS-CoV-2" (auto-threshold)

Auto-threshold calibration (v0.2.0+): The fuzzy matching threshold automatically adapts based on entity characteristics:

• Short medical terms → strict (0.88)
• Long scientific phrases → loose (0.72)

LangChain Integration

Use .causal as a drop-in retriever for any LangChain pipeline:

from dotcausal import CausalRetriever
from langchain_openai import ChatOpenAI
from langchain_core.prompts import ChatPromptTemplate
from langchain_core.output_parsers import StrOutputParser

# Load knowledge graph as retriever
retriever = CausalRetriever.from_file("knowledge.causal", top_k=10)

# Build RAG chain
prompt = ChatPromptTemplate.from_template("""
Answer based on these verified facts:
{context}

Question: {question}
""")

chain = (
    {"context": retriever, "question": lambda x: x}
    | prompt
    | ChatOpenAI(model="gpt-4")
    | StrOutputParser()
)

# Query with zero hallucination grounding
response = chain.invoke("What mechanisms connect COVID to chronic fatigue?")

The retriever returns Document objects with rich metadata:

• is_inferred: Whether the fact was derived or explicit
• confidence: Confidence score (0-1)
• provenance: Chain of source triplets for inferred facts

Use Cases

LLM Grounding (GraphRAG)

# Instead of asking an LLM to find connections (hallucination risk),
# query the deterministic graph and feed results to the LLM
chains = reader.search("drug_X", field="trigger")
# LLM now synthesizes based on verified facts, not guessing

Edge AI / Privacy

The format is compact enough (~3-5MB for thousands of papers) to run entirely on-device. No cloud, no data leakage. Perfect for:

• Personal health knowledge graphs
• Offline scientific assistants
• Air-gapped research environments

Hypothesis Discovery

Weak signals (3 mentions) become visible convergence points (21+ mentions) after inference. This revealed 3 new Long COVID hypothesis candidates that were invisible in SQLite.

File Format

┌─────────────────────────────────────┐
│ HEADER (64 bytes)                   │
│ Magic: "CAUSAL01" | Version | CRC   │
├─────────────────────────────────────┤
│ ENTITIES - Deduplicated dictionary  │
├─────────────────────────────────────┤
│ TRIPLETS - Explicit facts + metadata│
├─────────────────────────────────────┤
│ RULES - Inference rules             │
├─────────────────────────────────────┤
│ CLUSTERS - Semantic groupings       │
├─────────────────────────────────────┤
│ GAPS - Identified knowledge gaps    │
└─────────────────────────────────────┘

• Encoding: MessagePack (binary) with JSON fallback
• Integrity: xxhash64 CRC verification
• Compression: ~4.7:1 vs JSON through entity deduplication

Citation

If you use .causal in your research, please cite:

@article{foss2026causal,
  author = {Foss, David Tom},
  title = {The .causal Format: Deterministic Inference for AI-Assisted Hypothesis Amplification},
  journal = {Zenodo},
  year = {2026},
  doi = {10.5281/zenodo.18326222}
}

Links

• Homepage: dotcausal.com
• Whitepaper: Zenodo DOI 10.5281/zenodo.18326222
• GitHub: github.com/DT-Foss/dotcausal
• PyPI: pypi.org/project/dotcausal

License

MIT License - see LICENSE for details.

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"The era of probabilistic guessing is ending; the era of deterministic discovery has begun."