Isabelle-Semantic-Embedding 0.1.0

Isabelle Semantic Embedding

Semantic Embedding

Semantic interpretation and vector search for Isabelle entities (constants, theorems, types, type classes, locales). A Claude agent translates formal definitions into plain English, which are then embedded into vectors for similarity search.

Semantic DB

The semantic database (Semantic_DB singleton in semantics.py) stores interpretations in an LMDB file at ~/.cache/Isabelle_Semantic_Embedding/semantics.lmdb.

Entity Records

Each entity is stored as a msgpack tuple keyed by its universal key:

(kind: int, name: str, expr: str, interpretation: str)

• kind: EntityKind value (1=constant, 2=lemma, 3=type, 4=typeclass, 5=locale, 6=named_theorems, 7=proof method; plus 0x12/0x22/0x32/0x42 for intro/elim/induction/case-split rules)
• name: fully qualified name (e.g. "HOL.List.append")
• expr: pretty-printed type signature or proposition
• interpretation: plain English description

Access via Semantic_DB[key] (returns SemanticRecord | None) or Semantic_DB[key] = record.

Theory Status

Theory keys (16-byte theory hashes) store cost tracking and interpretation status as a msgpack dict:

{"input_tokens": int, "output_tokens": int, "cost_usd": float, "finished": bool}

Semantic_DB.is_thy_interpreted(key) checks the finished flag.

Persistent vs WIP Theories

Theory hashes use an LSB convention (defined in Isabelle_RPC/Tools/theory_hash.ML):

• Persistent (LSB=0): from built heap images, content-hashed — stable across sessions
• WIP (LSB=1): theories being edited in jEdit, name-hashed — change on every reload

WIP entities are stored persistently just like persistent ones. However, when source files are edited and entities change semantics, the stored interpretations and embeddings are not automatically updated — they become stale. You must explicitly call clean_wip() (Python) or Semantic_Store.clean_wip() (ML) to purge all WIP data from both the semantic DB and all vector stores, so that subsequent queries regenerate fresh interpretations and embeddings.

WIP theories are never marked as "interpreted" or "embedded finished" — mark_interpreted and mark_thy_embedded silently skip them. This ensures WIP theories are always re-processed on the next request, since their content may have changed.

Skipped Theories

Certain infrastructure theories are never interpreted: Pure, Code_Generator, Code_Evaluation, Typerep. These are defined in _SKIP_THEORY_LONG_NAMES and filtered in both interpretation and entity enumeration.

Semantic Interpretation

semantic_interpretation.py uses a Claude agent (claude-opus-4-6) to translate Isabelle entities into plain English. The flow:

1. ML side (semantic_store.ML:interpret'): extracts constants, theorems, types, classes, locales from a theory, computes universal keys, and calls Python via RPC
2. Python side (interpret_file): checks LMDB cache for existing interpretations, launches Claude agent for uncached entries
3. Agent: receives batches of entities (20 per batch), uses MCP tools (query, definition, hover) to understand dependencies, submits translations via the answer tool
4. Storage: each answer is immediately written to LMDB via Semantic_DB[key] = SemanticRecord(...)

Semantic_Store.interpret(context) interprets all uninterpreted ancestor theories plus the current proof context. interpret_theories_by_names(connection, names) interprets specific theories by name.

Embedding Providers

Embedding_Provider (in semantic_embedding.py) is the abstract base for text embedding services. A provider is selected by three parameters — driver, base_url, model — rather than a per-model registered subclass:

• driver: a registered driver class. OpenAI_Embedding_Provider serves any OpenAI-compatible /v1/embeddings endpoint (Fireworks, OpenAI, Mistral, Aliyun DashScope, …); Gemini_Embedding is the native Google Gemini API. Default OpenAI_Embedding_Provider.
• base_url: the API endpoint. Default https://api.fireworks.ai/inference.
• model: the canonical model name — the HuggingFace name where one exists (e.g. Qwen/Qwen3-Embedding-8B), else the provider's id (e.g. text-embedding-3-large). Default Qwen/Qwen3-Embedding-8B.

Build one with make_embedding_provider(driver, base_url, model). The API key is read only from the EMBEDDING_API_KEY environment variable (Gemini additionally falls back to GEMINI_API_KEY).

YAML config

All model/endpoint specifics live in a YAML config at $ISABELLE_HOME_USER/etc/embedding_config, seeded on first run from the bundled embedding_config_template.yaml. It is keyed by the canonical model name and by the base_url domain (netloc):

• per model: dimension (required — determines the LMDB matrix shape; a missing entry is a hard error), default_scores ({score, local} fallbacks for un-embedded entities), normalize (L2-normalize returned vectors), max_request_size, templates (per-model query/document text wrappers applied before embedding; default identity "{text}", literal str.replace over {text}/{task} so Isabelle { } text is safe)
• providers.<domain>.normalization: maps the canonical name to the id this endpoint expects (e.g. on api.fireworks.ai, Qwen/Qwen3-Embedding-8B → fireworks/qwen3-embedding-8b)
• providers.<domain>.batch: the Batch API shape (dialect: openai | mistral, endpoint, status strings, max_batch_size); its presence is what enables batch for that domain
• task_description: the sentence injected into a query template's {task} slot; its {kinds} slot is filled per query from the EntityKind filter (e.g. "constants and theorems", or "constructs" when unfiltered). Shared across models; must not contain literal {text}/{task}

Add a model by editing the YAML; add a new driver class via @register_embedding_driver("Name") or drivers/{Name}.py. Configs are seeded once and never auto-merged, so a machine that already has etc/embedding_config must add templates/task_description by hand.

Caching

Embedding results are cached per-string (keyed by the canonical model name + text) in a DiskCache database at ~/.cache/Isabelle_Semantic_Embedding/embed_cache/ (2 GB limit, 3-day TTL). Both embed() and embed_batch() use the cache. This cache is purely local and is excluded from the published DB snapshot.

Batch API

When the base_url's domain has a batch entry in the YAML config, OpenAI_Embedding_Provider._embed_batch uses the OpenAI-style Batch API (e.g. for 50% cost reduction on OpenAI). It uploads a JSONL file, creates an async batch job, polls for completion, and downloads results. Large inputs are split into sub-batches of max_batch_size (from the YAML batch config) and submitted in parallel on the server side. The dialect (openai/mistral) selects the request/response shape.

Vector Store & Semantic Vector Store

Vector Store

Vector_Store (in semantic_embedding.py) stores embedding vectors in LMDB, keyed by universal keys. Multiple stores share a global LMDB environment pool (thread-safe).

Key operations:

• store[key] / store.put(key, vector): get/set vectors
• store.topk(query, domain, k): return top-k (key, score) pairs using faiss.knn
• store._auto_embed(missing, matrix, row): hook for subclasses to recover missing vectors

Semantic Vector Store

Semantic_Vector_Store (in semantics.py) extends Vector_Store with:

• Auto-interpretation: when vectors are missing, automatically interprets uninterpreted theories (if auto_interpret_for_embedding is enabled), fetches semantic texts from Semantic_DB, embeds them, and stores the vectors
• Provider resolution: resolves (driver, base_url, model), each by Isabelle config (Semantic_Embedding.embedding_driver / embedding_base_url / embedding_model) → env var (EMBEDDING_DRIVER / EMBEDDING_BASE_URL / EMBEDDING_MODEL) → default (OpenAI_Embedding_Provider / Fireworks / Qwen/Qwen3-Embedding-8B)
• Store identity: the LMDB vector store lives at vector_<canonical model>.lmdb, with the canonical name made filesystem-safe (/ → __), e.g. vector_Qwen__Qwen3-Embedding-8B.lmdb
• Per-connection registry: each Connection maintains a dict of stores by canonical model name, accessed via connection.semantic_vector_store(model_name). NOTE: one run has a single active driver+base_url, so embedding several models at once only works for models served by that same endpoint.

lookup(query, k, kinds, domain) combines entity filtering with k-NN search:

• kinds: filter by EntityKind (e.g. [ConstantK, TheoremK])
• domain=None: search all entities of those kinds (excluding skipped theories)
• Returns list[tuple[float, SemanticRecord]] sorted by similarity

Config Options

Set in Isabelle via declare [[option = value]]:

Option	Type	Default	Description
auto_interpret_for_embedding	bool	true	Auto-trigger interpretation when embeddings are missing
Semantic_Embedding.embedding_driver	string	""	Embedding driver class (empty = env EMBEDDING_DRIVER or OpenAI_Embedding_Provider)
Semantic_Embedding.embedding_base_url	string	""	Embedding endpoint base_url (empty = env EMBEDDING_BASE_URL or the Fireworks endpoint)
Semantic_Embedding.embedding_model	string	""	Canonical (HuggingFace) embedding model name (empty = env EMBEDDING_MODEL or Qwen/Qwen3-Embedding-8B)
Semantic_Embedding.reranker_model	string	""	Reranker model for re-ranking search results (empty = disabled; env var RERANKER_MODEL)

These are accessible from Python via connection.config_lookup("option_name").

Marking entities as infrastructure (excluded from retrieval)

Some entities are plumbing that should never surface in semantic retrieval. Built-in heuristics already drop most of them (concealed/hidden names, ADT/record/BNF machinery, Minilang.*, tool-internal collections, …). To mark additional ones by hand:

declare [[infra_constant Foo.bar Baz.qux]]   (* constants (also cascades to theorems
                                                 whose statement mentions them) *)
declare [[infra_type   Foo.t]]               (* types *)
declare some_lemma[infra_thm]                 (* a theorem — attached fact attribute *)

declare [[infra_constant del Foo.bar]]        (* `del` undoes any of the above *)
declare some_lemma[infra_thm del]

Notes:

• infra_thm matches by proposition (like named_theorems): it stores the theorem itself, so two lemmas with the same statement are treated alike, and a declaration inside a locale correctly suppresses the exported instance at each interpretation. Marking a trivially-shaped lemma (x = x, True) is honoured but warns, since it would suppress every same-statement lemma.
• infra_constant/infra_type resolve their (global) argument at parse time; infra_thm is attached to the fact (lemma[infra_thm], not [[infra_thm name]]).
• Whole named_theorems collections are suppressed via the static blacklist in Tools/infra_filter.ML, not via infra_thm.
• Effect is read at collection time: re-collect to drop entries already written to the DB.

Usage

Isabelle/ML

(* Interpret all ancestor theories *)
Semantic_Store.interpret \<^context>

(* Query semantic interpretation *)
Semantic_Store.query_semantics \<^context> (Universal_Key.Constant "List.append") false

(* k-NN search for similar entities *)
Semantic_Store.query_knn \<^context>
  "concatenation of two lists"
  10
  [Universal_Key.ConstantK, Universal_Key.TheoremK]
  NONE

Python (within RPC handler)

from Isabelle_Semantic_Embedding.semantics import Semantic_DB, SemanticRecord

# Query interpretation
rec = Semantic_DB[some_universal_key]
if rec is not None:
    print(rec.pretty_print)       # "constant List.append: 'a list => ..."
    print(rec.interpretation)     # "Appends two lists together."

# Vector search
store = connection.semantic_vector_store()
results = store.lookup("addition on natural numbers", k=5,
                       kinds=[EntityKind.CONSTANT, EntityKind.THEOREM])
for score, rec in results:
    print(f"{score:.3f} {rec.pretty_print}: {rec.interpretation}")