# Episteme (StemeDB) Roadmap > **Goal:** Build the "Git for Truth" substrate for autonomous AI research. > **Current Phase:** Phase 4 (The Hive) > **Target Vertical:** BioTech/Pharma ("The Living Review") --- ## High-Level Timeline | Phase | Codename | Focus | Key Deliverable | | :--- | :--- | :--- | :--- | | **1** | **The Spine** | Storage & Safety | Append-only WAL + KV Store | | **2** | **The Lattice** | Indexing & Async | Materialized Views + Ballot Box | | **2.5** | **Hardening** | Camp 2 Fixes | MV staleness, epoch behavior, lens cleanup | | **3** | **The Pilot** | Vertical Integration | Pharma Ingestion + Living Review Agent | | **4** | **The Hive** | Trust & Learning | The Simulator + Super Curator | --- ## Detailed Milestones ### Phase 1: The Spine (Foundation) *Goal: Securely ingest assertions and persist them without data loss.* - [x] **Project Scaffold**: Initialize Rust workspace, set up linting/CI (clippy, fmt). - [x] **Assertion Schema**: Define the `Assertion` struct with `rkyv` serialization. - [x] Add dependencies: `rkyv`, `blake3`, `ed25519-dalek`, `image_hasher`. - [x] Define `Assertion` struct (Subject, Predicate, Object, Confidence, SourceHash). - [x] **Multi-Sig Expansion**: Implement `SignatureEntry` struct and `signatures: Vec` field. - [x] **Visual Expansion**: Add `visual_hash: Option` field for image provenance. - [x] Test serialization round-trips. - [x] **Ballot Schema**: Define the `Vote` struct for multi-agent consensus. - [x] Add `Vote` struct: `assertion_hash`, `agent_id`, `weight`, `signature`. - [x] Test serialization round-trips. - [x] **Paradigm Schema (Epochs)**: Define the `Epoch` and `SupersessionType` structs. - [x] Add `epoch: Option` to `Assertion`. - [x] Implement `Epoch` struct with `supersedes` and `SupersessionType`. - [x] Test serialization round-trips. - [x] **WAL Integration**: Implement the Quarantine Pattern for write-ahead logging. - [x] Create `stemedb-wal` crate. - [x] Port `FsyncGuard` and `Record` logic from established durability patterns. - [x] Implement Record format with BLAKE3 checksums and Headers. - [x] Verify `fsync` behavior with tests. - [x] **Storage Engine**: Implement the `Store` trait using `sled` (embedded KV). - [x] Add `sled` dependency. - [x] Define `KVStore` trait (put, get, delete, scan_prefix, flush). - [x] Implement `SledStore` wrapper. - [x] **Basic Ingestor**: Background worker that tails WAL and writes to KV. - [x] Implement async loop reading from WAL. - [x] Write deserialized assertions, votes, and epochs to `sled`. - [x] Ed25519 signature verification during ingestion. - [x] Maintains S: and SP: indexes on ingest. - [x] Persistent cursor/checkpoint (resumes from `__CURSOR__:ingest` in KV store). - [x] **Verification**: Crash recovery tests (write -> crash -> restart -> read). - [x] Single and multi-record crash recovery. - [x] Multiple crash cycles tested. ### Phase 2: The Lattice (Connectivity) *Goal: Query data with sub-millisecond latency using Materialized Views.* - [x] **Lifecycle Schema**: Add `LifecycleStage` to Assertion. - [x] Define enum: `Proposed`, `UnderReview`, `Approved`, `Deprecated`, `Rejected`. - [x] Update `Assertion` struct and serialization tests. - [x] **The Ballot Box**: Implement high-velocity vote ingestion. - [x] `VoteStore` trait and implementation. - [x] `VoteAwareConsensusLens` for real vote-based resolution. - [x] **Index Infrastructure**: Compound indexes for O(1) queries. - [x] `IndexStore` trait with S: and SP: indexes. - [x] `QueryEngine` smart routing (SP -> S -> scan). - [x] **Materializer**: Background worker for O(1) Read Performance. - [x] `MaterializedView` type in `stemedb-core`. - [x] `Materializer` worker in `stemedb-query` with `step()` and `run()`. - [x] Aggregates Votes via `VoteAwareConsensusLens` (or any `AsyncLens`). - [x] Updates `MV:{Subject}:{Predicate}` with the winning Assertion + metadata. - [x] Event-driven mode via `run_notified()` with `tokio::sync::Notify`. - [x] Fast-path MV lookup in `QueryEngine::try_fast_path()`. - [x] **The Meter**: Implement Economic Throttling (TAN). - [x] `QuotaStore` trait and `GenericQuotaStore` implementation. - [x] Token Bucket algorithm with per-agent per-hour quotas. - [x] `MeterLayer` tower middleware for request cost tracking. - [x] Cost model: Assert=10, Vote=1, Query=5+lens, +1/KB payload. - [x] `GET /v1/meter/quota` endpoint to check remaining quota. - [x] `POST /v1/meter/quota/limit` admin endpoint to set custom limits. - [x] **API Surface**: `axum` HTTP server with OpenAPI (utoipa). - [x] `POST /v1/assert` -> Accepts JSON, writes to WAL. - [x] `POST /v1/vote` -> High-throughput vote endpoint. - [x] `POST /v1/epoch` -> Create epoch with optional supersession. - [x] `GET /v1/query` -> Subject/Predicate/Lens/Lifecycle/Epoch filtering. - [x] `GET /v1/health` -> Health check with assertion count. - [x] `GET /swagger-ui` -> Interactive API docs. - [x] 5 lens types available: Recency, Consensus, Authority, VoteAwareConsensus, TrustAwareAuthority. - [x] **Query Audit**: Log every read with provenance. - [x] Define `QueryAudit` struct: query_id, agent_id, timestamp, params, result_hash, contributing_assertions. - [x] Storage at `AUD:{query_id}` with agent index at `AUDA:{agent_id}:{timestamp}:{query_id}`. - [x] `GET /v1/audit/queries` -> Returns history of agent decisions. - [x] `GET /v1/audit/query/{id}` -> Full reasoning trace for a single query. - [x] Auto-logging on every query via `X-Agent-Id` header. ### Phase 2.5: Hardening (Camp 2 Fixes) *Goal: Close the gaps between "built" and "works right." Every item here addresses a feature that exists but doesn't fully deliver on its promise.* - [x] **2.1 MV Staleness Detection**: Make the fast-path aware of stale materialized views. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `max_stale: Option` to `Query` struct in `crates/stemedb-query/src/query.rs`. - [x] Added `.max_stale(secs)` builder method to `QueryBuilder`. - [x] In `try_fast_path()`: if `query.max_stale` is set and MV age exceeds threshold, falls through to slow path with `debug!` log. - [x] Added `max_stale` to API `QueryParams` DTO in `crates/stemedb-api/src/dto.rs`. - [x] Wired through query handler in `crates/stemedb-api/src/handlers/query.rs`. - **Tests:** - [x] `test_fast_path_stale_view_falls_back`: MV 1000 seconds old, `max_stale = 60` → slow path used. - [x] `test_fast_path_fresh_view_used`: Fresh MV, `max_stale = 300` → fast path used. - [x] `test_fast_path_no_max_stale_always_uses_mv`: No `max_stale` → any MV age accepted (backward compatible). - [x] `test_fast_path_max_stale_zero_rejects_old_mv`: `max_stale = 0`, MV 1 second old → slow path. - [x] `test_fast_path_max_stale_zero_accepts_brand_new_mv`: `max_stale = 0`, brand new MV → fast path. - [x] **2.2 AuthorityLens -> ConfidenceLens Rename**: Eliminate the misleading name. - **Problem:** `AuthorityLens` selects by `confidence` field, not by agent reputation. `TrustAwareAuthorityLens` is the real authority lens. The name creates confusion about what "Authority" means. - **Solution implemented:** - [x] Renamed `authority.rs` → `confidence.rs`, `AuthorityLens` → `ConfidenceLens` - [x] Added `LensDto::Confidence` for the confidence-field selector - [x] Changed `LensDto::Authority` to route to `TrustAwareAuthorityLens` (the real authority lens) - [x] Updated query handler routing - [x] Updated ai-lookup/services/lens.md and skill documentation - [x] **2.3 EpochAwareLens**: Give epoch supersession runtime behavior. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `EpochAwareLens` in `crates/stemedb-lens/src/epoch_aware.rs` - [x] Decorator pattern wrapping any inner lens (default: RecencyLens) - [x] Walks supersession chain from `E:{epoch_id}` keys - [x] Cycle detection + max depth guard (100) - [x] Fail-open on missing epochs - [x] `LensDto::EpochAware` added to API - [x] 11 tests: excludes_superseded, chain_supersession, no_epochs_passes_all, missing_epoch_includes, cycle_detection, consensus_lens_inner, mixed_epochs, etc. - [x] Documentation updated in `ai-lookup/services/lens.md` - **Known Limitation:** Filtering only occurs when assertions from the superseding epoch are present in candidates. If all candidates are from old epoch (no new epoch assertions), they pass through (fail-open behavior). - [x] **2.4 Visual Hash Query Support**: Make the stored `visual_hash` queryable. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `hamming_distance(a: &PHash, b: &PHash) -> u32` in `crates/stemedb-query/src/query.rs` (lines 26-28) - [x] `visual_near: Option` and `visual_threshold: Option` in `Query` struct (lines 84-90) - [x] `.visual_near(hash, threshold)` builder method - [x] `Query::matches()` computes hamming distance when `visual_near` is set - [x] API `QueryParams` DTO has `visual_near` and `visual_threshold` - [x] 10+ tests: exact_match, within_threshold, exceeds_threshold, skips_without_hash, invalid_hex, wrong_length, combines_with_subject, default_threshold, max_threshold, threshold_63_rejects - **Note:** Brute-force O(N) scan. VP-tree/BK-tree index is Phase 3+. - [x] **2.5 Vector Field**: No changes needed. Already roadmapped for Phase 3. - **Status:** ✅ N/A (No Phase 2 work required) - **Current state:** `vector: Option>` on `Assertion`. Stored and returned by API. No index, no search. - **Phase 3 plan:** Integrate `hnsw-rs` or `lance` for k-NN search. - [x] **2.6 E2E Integration Test (Write -> Materialize -> Read)**: Prove the full pipeline works end-to-end. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `crates/stemedb-query/tests/e2e_pipeline.rs` with 5 comprehensive tests: - `test_e2e_write_materialize_read` - Basic happy path - `test_e2e_vote_consensus` - Vote-weighted resolution - `test_e2e_update_winner` - Winner changes on re-materialize - `test_e2e_cursor_persistence` - Cursor survives worker restart - `test_e2e_notify_integration` - Event-driven notification channel - [x] `stemedb-wal` and `stemedb-ingest` added as dev-dependencies - [x] Helper functions: `create_signed_assertion()`, `compute_assertion_hash()`, `create_vote()` - [x] Uses Ed25519 signing for authentic signature verification - [x] Also: `crates/stemedb-api/tests/e2e_flow_test.rs` tests the HTTP API layer end-to-end. ### Phase 3: The Pilot (BioTech/Pharma) *Goal: Prove value in the "High-Liability" beachhead. Close every Camp 4 gap that blocks a credible demo.* #### 3A. Schema Expansion (Prerequisite for everything below) - [x] **3A.1 Source-Class Field**: Add `source_class: SourceClass` to Assertion. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `SourceClass` enum in `crates/stemedb-core/src/types.rs` (lines 68-88). - [x] 6-tier system: `Regulatory` (0), `Clinical` (1), `Observational` (2), `Expert` (3), `Community` (4), `Anecdotal` (5). - [x] `tier()` method returns tier number for ordering. - [x] `default_decay_days()` method for tier-specific confidence decay. - [x] `authority_weight()` method for conflict resolution weighting. - [x] Field on `Assertion` struct at line 152. - [x] Full serialization and indexing support. - [x] **3A.2 Conflict Score on Resolution**: Add `conflict_score: f32` to Resolution. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `conflict_score: f32` field to `Resolution` in `crates/stemedb-lens/src/traits.rs`. - [x] Updated `Resolution::empty()` to set `conflict_score: 0.0`. - [x] Updated `Resolution::with_winner()` to accept `conflict_score` parameter. - [x] Added `compute_conflict_score(candidates: &[Assertion]) -> f32` utility function: - Uses normalized variance of confidence values. - 0 or 1 candidates → 0.0 (no conflict possible). - All same confidence → 0.0 (unanimous). - Max variance (0.0 vs 1.0) → 1.0 (maximum conflict). - Defensive NaN handling (returns 0.0 for malformed data). - [x] Updated all lens implementations to compute and pass conflict score: - `crates/stemedb-lens/src/recency.rs` - `crates/stemedb-lens/src/consensus.rs` - `crates/stemedb-lens/src/confidence.rs` - `crates/stemedb-lens/src/vote_aware_consensus.rs` - `crates/stemedb-lens/src/trust_aware_authority.rs` - [x] Added `conflict_score: f32` to `MaterializedView` in `crates/stemedb-core/src/types.rs`. - [x] Updated `Materializer::materialize_pair()` to write `conflict_score` from resolution. - [x] Added `conflict_score: Option` and `resolution_confidence: Option` to `QueryResponse` DTO in `crates/stemedb-api/src/dto.rs` (only present when lens is applied). - [x] Wired through query handler in `crates/stemedb-api/src/handlers/query.rs`. - **Tests:** - [x] `test_conflict_score_zero_for_empty`: Empty candidates → 0.0. - [x] `test_conflict_score_zero_for_single`: 1 candidate → 0.0. - [x] `test_conflict_score_zero_for_agreement`: All same confidence → near 0.0. - [x] `test_conflict_score_high_for_disagreement`: Candidates at 0.1, 0.5, 0.9 → score > 0.3. - [x] `test_conflict_score_max_for_extremes`: 0.0 vs 1.0 → score ≈ 1.0. - [x] `test_conflict_score_handles_nan_defensively`: NaN confidences → 0.0 (fail-safe). - [x] **3A.3 Rich Source Metadata**: Add structured provenance beyond `source_hash`. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `source_metadata: Option>` field to `Assertion` in `crates/stemedb-core/src/types.rs` (after `epoch`, before `lifecycle`). - [x] Uses `Vec` (not `String`) for rkyv zero-copy compatibility. Callers encode/decode JSON on their side. - [x] Added `source_metadata: Option>` to `AssertionBuilder` in `crates/stemedb-core/src/testing.rs`. - [x] Added `.source_metadata_json(json: &str)` and `.source_metadata(bytes)` builder methods. - [x] Added `source_metadata: Option` to `CreateAssertionRequest` DTO (JSON string in API, converted to bytes internally). - [x] Added `source_metadata: Option` to `AssertionResponse` DTO (bytes converted to JSON string with defensive UTF-8 handling). - [x] Wired through create handler (`dto_to_assertion()`) and query handler (`assertion_to_dto()`). - **Tests:** - [x] `test_serialize_deserialize_assertion_with_metadata`: Serialization roundtrip with metadata present. - [x] `test_serialize_deserialize_assertion_without_metadata`: Serialization roundtrip with metadata absent. - **Note:** Metadata is stored but NOT indexed in Phase 3. Indexing individual metadata fields is Phase 4+. #### 3B. Time & Decay (Core Query Features) - [x] **3B.1 Time-Travel Engine**: `as_of` parameter for historical queries. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `as_of: Option` to `Query` struct in `crates/stemedb-query/src/query.rs:92-99`. - [x] Added `.as_of(timestamp: u64)` to `QueryBuilder`. - [x] In `Query::matches()`: if `as_of` is `Some(ts)`, check `assertion.timestamp <= ts`. Assertions created after `as_of` are excluded. - [x] In `QueryEngine::execute()`: if `query.as_of` is set, **skip the fast path entirely** (MVs reflect current state, not historical). - [x] Added `as_of: Option` to `QueryParams` DTO in `crates/stemedb-api/src/dto.rs`. - [x] Wired through query handler. - **Tests:** - [x] `test_as_of_excludes_future_assertions`: Assertions filtered by timestamp. - [x] `test_as_of_bypasses_fast_path`: MV exists, but `as_of` is set. Slow path used. - [x] `test_as_of_none_uses_fast_path`: Normal query still uses fast path (backwards-compatible). - [x] `test_as_of_with_lens_resolves_among_historical_candidates`: Time-travel + lens = resolve only among pre-as_of candidates. - [x] `test_as_of_returns_empty_when_all_assertions_are_future`: All assertions are future, returns empty. - [x] `test_as_of_with_exact_timestamp_match`: Edge case where assertion.timestamp == as_of. - [x] **3B.2 Semantic Decay**: Confidence Half-Life at query time. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `decay_halflife: Option` to `Query` struct in `crates/stemedb-query/src/query.rs`. - [x] Added `.decay_halflife(seconds: u64)` and `.source_class_decay(enabled: bool)` to `QueryBuilder`. - [x] Added `decay_halflife` and `source_class_decay` to `QueryParams` DTO. - [x] Created new `crates/stemedb-query/src/decay.rs` module with: - `apply_decay()`: Uniform decay using formula `confidence * 2^(-(age / halflife))`. - `apply_source_class_decay()`: Tier-specific decay (Regulatory=none, Clinical=2yr, Anecdotal=30d). - `compute_decayed_confidence()`: Core decay calculation with clamping. - [x] Integrated in `QueryEngine::execute()`: decay applied after filtering, before lens resolution. - [x] Time-travel compatible: uses `as_of` timestamp if set, otherwise current time. - [x] Source-class-aware decay fully implemented using `SourceClass::default_decay_days()`. - **Tests:** (11 unit tests in decay.rs + 1 E2E test) - [x] `test_decay_reduces_old_assertion_confidence`: 1yr old, 1yr halflife → ~50% confidence. - [x] `test_decay_preserves_fresh_assertions`: 1hr old, 1yr halflife → ~100% confidence. - [x] `test_decay_interacts_with_lens`: Older high-confidence loses to newer low-confidence after decay. - [x] `test_source_aware_decay_tier0_no_decay`: Regulatory never decays. - [x] `test_source_aware_decay_tier5_rapid_decay`: Anecdotal decays rapidly (30-day halflife). - [x] `test_source_aware_decay_mixed_tiers`: Clinical vs Anecdotal tier comparison. - [x] `test_decay_zero_halflife_no_change`: Zero halflife skips decay (avoids div-by-zero). - [x] `test_decay_future_assertion_no_change`: Future assertions don't decay. - [x] `test_decay_empty_assertions`: Empty input returns empty output. - [x] `test_decay_confidence_clamps_to_valid_range`: Very old assertions clamp to [0.0, 1.0]. - [x] `test_decay_preserves_other_fields`: Only confidence changes; other fields preserved. - [x] `test_e2e_decay_reduces_old_confidence`: Full pipeline E2E test in e2e_pipeline.rs. - **Note:** When decay is enabled, materialized views (fast path) are bypassed because MVs store pre-computed winners without decay applied. #### 3C. New Lenses - [x] **3C.1 Skeptic Lens**: Surface disagreement, not winners. ✅ **COMPLETED** - **Status:** ✅ COMPLETE - **Implementation:** - [x] `crates/stemedb-lens/src/skeptic.rs` - Full implementation. - [x] `AnalysisLens` trait for lenses that analyze conflict instead of resolving it. - [x] `SkepticLens` uses normalized Shannon entropy for conflict scoring. - [x] Returns `ConflictAnalysis` with: - `conflict_score: f32` (0.0 = unanimous, 1.0 = chaos) - `status: ResolutionStatus` (Unanimous, Agreed, Contested) - `claims: Vec` - all claims ranked by weight - [x] `SkepticResolver` + `SkepticView` in `stemedb-query/src/skeptic.rs`. - [x] `GET /v1/skeptic?subject=X&predicate=Y` API endpoint. - [x] Core types in `stemedb-core/src/types.rs`: - `ResolutionStatus` enum - `ConflictAnalysis` struct - `ClaimSummary`, `SourceSummary`, `AgentSummary` - [x] Comprehensive test coverage (21 test cases). - [x] **3C.2 Layered Consensus Lens**: Per-source-class consensus. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `crates/stemedb-lens/src/layered_consensus.rs` - Full implementation. - [x] `TierResolution` struct: per-tier result with tier, source_class, winner, candidates_count, conflict_score, resolution_confidence. - [x] `LayeredResolution` struct: multi-tier result with tiers vec, overall_winner, overall_conflict_score, total_candidates. - [x] `LayeredLens` trait: `resolve_layered(&[Assertion]) -> LayeredResolution`, `name() -> &'static str`. - [x] `LayeredConsensusLens` implements both `LayeredLens` and `Lens` traits. - [x] Cross-tier conflict score uses normalized Shannon entropy of tier winner object values. - [x] `LensDto::LayeredConsensus` variant (redirects to `/v1/layered` endpoint). - [x] `GET /v1/layered?subject=X&predicate=Y` API endpoint with `LayeredQueryResponse`. - [x] Exported from `crates/stemedb-lens/src/lib.rs`. - **Tests:** - [x] `test_layered_empty_candidates`: Empty input returns empty resolution. - [x] `test_layered_single_tier`: All same source_class, returns one tier result. - [x] `test_layered_multi_tier_agreement`: Tier 0 and Tier 5 agree, low cross-tier conflict. - [x] `test_layered_multi_tier_disagreement`: Tier 1 vs Tier 5 disagree, high conflict, Tier 1 wins. - [x] `test_layered_overall_winner_from_highest_authority`: Tier 0 wins despite fewer assertions. - [x] `test_layered_lens_trait_compatibility`: Standard Lens trait works. - [x] `test_layered_within_tier_conflict`: High internal conflict within a tier. - [x] `test_layered_all_tiers_present`: One assertion from each tier. - [x] `test_layered_lens_name`: Both trait names work. - [x] `test_layered_numeric_values`: Works with numeric object values. - [x] **3C.3 Constraints Lens**: Pre-flight check for must_use/forbidden. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `crates/stemedb-lens/src/constraints.rs` - Full implementation. - [x] `ConstraintSet` struct: holds categorized assertions (must_use, forbidden, prefer) with conflict_score. - [x] `ConstraintsLens` struct with `resolve_constraints(&[Assertion]) -> ConstraintSet` method. - [x] Categorizes by predicate pattern: `must_use:*`, `forbidden:*`, `prefer:*`. - [x] Implements `Lens` trait for compatibility (priority: must_use > forbidden > prefer). - [x] Sorted by confidence (highest first), with timestamp as tiebreaker. - [x] `LensDto::Constraints` added (redirects to `/v1/constraints` endpoint). - [x] `GET /v1/constraints?subject=X` API endpoint with `ConstraintsResponse`. - [x] DTOs: `ConstraintsQueryParams`, `ConstraintEntryDto`, `ConstraintsResponse`. - [x] Exported from `crates/stemedb-lens/src/lib.rs`. - **Tests:** (16 test cases) - [x] `test_constraints_categorizes_by_predicate`: Mixed predicates sorted into must_use/forbidden/prefer. - [x] `test_constraints_empty_categories`: Only prefer, no must_use/forbidden. - [x] `test_constraints_non_constraint_predicates_ignored`: Regular predicates filtered out. - [x] `test_constraints_sorted_by_confidence`: Within-category confidence ordering. - [x] `test_constraints_empty_candidates`: Empty input returns empty set. - [x] `test_constraints_has_constraints_true`: Helper method works. - [x] `test_constraints_all_regular_predicates`: All non-constraint predicates returns no constraints. - [x] `test_lens_trait_picks_must_use_winner`: Standard Lens trait picks must_use first. - [x] `test_lens_trait_falls_back_to_forbidden`: Falls back to forbidden when no must_use. - [x] `test_lens_trait_falls_back_to_prefer`: Falls back to prefer when no must_use/forbidden. - [x] `test_lens_trait_empty_for_no_constraints`: Returns empty when no constraint predicates. - [x] `test_lens_name`: Name returns "Constraints". - [x] `test_lens_empty_candidates`: Empty input to Lens trait returns empty resolution. - [x] `test_multiple_must_use_picks_highest_confidence`: Multiple must_use picks highest confidence. - [x] `test_confidence_tiebreaker_uses_timestamp`: Same confidence uses newer timestamp. - [x] `test_predicate_pattern_exact_prefix`: `must_use_something` not matched (only `must_use:*`). #### 3D. Epoch Enhancement - [x] **3D.1 Epoch Cascade Logic** (enhancement of Phase 2.5 EpochAwareLens): - **Status:** ✅ COMPLETE - **Implementation:** - [x] `write_supersession_cascade()` in `crates/stemedb-ingest/src/worker.rs`: - Writes `SUPERSEDED:{old_epoch_id}` markers for full transitive closure. - All markers point to the LATEST superseding epoch. - Max depth guard (100 levels) and cycle detection via visited set. - [x] `is_epoch_superseded()` in `crates/stemedb-lens/src/epoch_aware.rs`: - O(1) marker lookup instead of O(chain_length) chain walks. - Fail-open semantics: missing marker = not superseded. - [x] `compute_superseded_epochs()` uses marker lookups for filtering. - **Tests:** - [x] `test_cascade_writes_superseded_marker`: Epoch B supersedes A → `SUPERSEDED:A` exists. - [x] `test_cascade_transitive`: C→B→A chain → both `SUPERSEDED:A` and `SUPERSEDED:B` point to C. - [x] `test_cascade_cycle_detection`: Mutual supersession handled gracefully. - [x] `test_epoch_aware_uses_marker`: EpochAwareLens uses O(1) marker lookup. - [x] `test_superseded_epoch_filtered_even_without_new_assertions`: Marker-based filtering works. #### 3E. Similarity Search - [x] **3E.1 Vector Search**: Semantic k-NN queries via embeddings. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Added `hnsw_rs = "0.3"` and `parking_lot = "0.12"` to `stemedb-storage/Cargo.toml`. - [x] New module: `crates/stemedb-storage/src/vector_index.rs`. - [x] `VectorIndex` trait: `insert(hash: &Hash, vector: &[f32])`, `search(query: &[f32], k: usize) -> Vec<(Hash, f32)>`, `dimension()`, `len()`, `is_empty()`. - [x] `HnswVectorIndex` implementation with HNSW graph, RwLock protection, hash↔ID mappings. - [x] Input validation: dimension mismatch, NaN, Infinite values rejected. - [x] Idempotent insert (same hash twice = no-op). - [x] `Arc` trait object support for sharing. - [x] `IngestWorker::with_vector_index()` builder method for index attachment. - [x] IngestWorker: if assertion has `vector`, inserts into vector index after KV write. - [x] Added `vector_near: Option>` and `k: Option` to `Query` struct in `crates/stemedb-query/src/query.rs`. - [x] Added `.vector_near(vector, k)` builder method to `QueryBuilder`. - [x] Added `vector_near` and `k` to API `QueryParams` DTO. - [x] `QueryEngine::with_vector_index()` builder method for index attachment. - [x] QueryEngine: if `vector_near` is set and index configured, uses O(log N) HNSW lookup for candidates. - [x] Falls back to standard path if no index configured (with debug log). - **Tests:** (12 unit tests for VectorIndex + 4 integration tests in engine.rs) - [x] `test_create_index`, `test_insert_and_search`, `test_dimension_mismatch`. - [x] `test_idempotent_insert`, `test_search_empty_index`, `test_search_k_zero`. - [x] `test_nan_rejection`, `test_infinite_rejection`, `test_contains`. - [x] `test_larger_scale` (100 vectors, exact match first), `test_custom_params`, `test_zero_dimension_panics`. - [x] `test_vector_search_returns_nearest_neighbors`, `test_vector_search_with_subject_filter`. - [x] `test_vector_search_without_index_falls_back`, `test_vector_search_with_as_of_filter`. - **Note:** Index is in-memory only. Persistence is Phase 4+. - [x] **3E.2 Visual Hash Index**: BK-tree for O(log N) visual similarity. - **Status:** ✅ COMPLETE - **Implementation:** - [x] New module: `crates/stemedb-storage/src/visual_index.rs`. - [x] `VisualIndex` trait: `insert(hash: &Hash, phash: &PHash)`, `search(query: &PHash, threshold: u32) -> Vec<(Hash, u32)>`, `len()`, `is_empty()`. - [x] `BkTreeVisualIndex` implementation using BK-tree over hamming distance. - [x] `hamming_distance(a: &PHash, b: &PHash) -> u32` utility function. - [x] Threshold clamped to 0-64 range (max 64 bits). - [x] Results sorted by distance ascending. - [x] Idempotent insert (same hash twice = no-op). - [x] `Arc` trait object support for sharing. - [x] `IngestWorker::with_visual_index()` builder method for index attachment. - [x] IngestWorker: if assertion has `visual_hash`, inserts into BK-tree after KV write. - [x] `QueryEngine::with_visual_index()` builder method for index attachment. - [x] QueryEngine: if `visual_near` is set and index configured, uses O(log N) BK-tree lookup. - [x] Falls back to brute-force scan (via `query.matches()`) if no index configured. - [x] Invalid hex input returns `QueryError::InvalidInput` with clear message. - **Tests:** (14 unit tests for VisualIndex + 6 integration tests in engine.rs) - [x] `test_hamming_distance_zero`, `test_hamming_distance_max`, `test_hamming_distance_partial`. - [x] `test_create_index`, `test_insert_and_search_exact`, `test_search_within_threshold`. - [x] `test_search_no_matches`, `test_search_empty_index`, `test_idempotent_insert`. - [x] `test_contains`, `test_results_sorted_by_distance`, `test_threshold_clamped_to_64`. - [x] `test_larger_scale` (1000 hashes), `test_default_impl`. - [x] `test_visual_search_returns_similar_images`, `test_visual_search_with_lifecycle_filter`. - [x] `test_visual_search_invalid_hex_returns_error`, `test_visual_search_without_index_uses_brute_force`. - [x] `test_visual_search_with_limit`, `test_vector_search_empty_index`. - **Note:** Index is in-memory only. Persistence is Phase 4+. #### 3F. Provenance - [x] **3F.1 Source Document Storage & Provenance Lookup**: Enable 100% citation recall. - **Status:** ✅ COMPLETE - **Implementation:** - [x] `POST /v1/source` endpoint to store source documents by BLAKE3 content hash. - [x] `GET /v1/provenance/{hash}` endpoint to retrieve source documents by hash. - [x] Source storage at `SRC:{hash}` keys with format: `[content_type_len:4][content_type][content]`. - [x] Base64 encoding for binary-safe JSON transport. - [x] 10MB size limit per document. - [x] Content-addressed storage: same content → same hash (idempotent uploads). - [x] DTOs: `StoreSourceRequest`, `StoreSourceResponse`, `ProvenanceResponse`. - [x] OpenAPI documentation under "provenance" tag. - **Tests:** (5 test cases) - [x] `test_store_and_retrieve_source`: Happy path store + retrieve. - [x] `test_store_source_invalid_base64`: Bad base64 → 400. - [x] `test_get_provenance_not_found`: Unknown hash → 404. - [x] `test_get_provenance_invalid_hash`: Bad hash format → 400. - [x] `test_store_source_idempotent`: Same content twice → same hash. - **Note:** Benchmark utility for verifying all assertions have retrievable sources is future work. #### 3G. API Cleanup - [x] **3G.1 Document epoch supersession via existing endpoint**: No new `/epoch/supersede` endpoint needed. - **Status:** ✅ COMPLETE - **Implementation:** - [x] Updated use case docs (consumer-health-intelligence.md, glp1-living-review.md) to use `POST /v1/epoch` with `supersedes` field. - [x] Added OpenAPI examples showing both new epoch and supersession flows in handlers/epoch.rs. - [x] Documented all 5 supersession types: Invalidate, Temporal, Refinement, RequiresReview, Additive. - **No code change.** Documentation fix only. ### Phase 4: The Hive (Trust & Scale) *Goal: Change tracking, metadata indexing, and the database primitives for training pipelines.* - [x] **TrustRank Engine**: Foundation for trust-based resolution. - [x] `TrustRankStore` for per-agent reputation storage. - [x] `TrustAwareAuthorityLens` for reputation-weighted resolution. - [x] **Confidence Half-Life**: Implement decay calculation engine. - [x] Learning loop: `record_outcome()` for accuracy tracking. - [ ] **4.1 "Since" Parameter**: Change tracking for returning consumers. - **Problem:** Consumer Health shows `GET /query?since=2023-10-01` returning `changes_since_query` with dated change entries. The "returning consumer" story: "What changed since I last looked?" - **Depends on:** Time-Travel (3B.1) and Materializer. - [ ] Add `since: Option` to `Query` struct and `QueryBuilder` in `crates/stemedb-query/src/query.rs`. - [ ] Add `since` to `QueryParams` DTO. - [ ] **MV Changelog**: Track when materialized views change. - [ ] New key pattern: `MVC:{subject}:{predicate}:{timestamp}` storing the previous winner hash and new winner hash. - [ ] In `Materializer::materialize_pair()` at `materializer.rs:164`: before overwriting MV, read the existing MV. If the winner changed (different assertion hash), write a changelog entry. - [ ] In QueryEngine: if `since` is set, scan `MVC:{subject}:{predicate}:*` for entries with timestamp > since. Return these as a `changes_since` list alongside the normal query result. - [ ] New response field on `QueryResponse`: ```rust pub struct ChangeEntry { pub timestamp: u64, pub previous_winner_hash: Option, pub new_winner_hash: String, } ``` Add `changes_since: Option>` to `QueryResponse` DTO. - [ ] Tests: - [ ] `test_since_returns_changes`: Materialize, change winner, re-materialize. Query with `since` returns the change. - [ ] `test_since_no_changes`: No MV changes since timestamp. Empty changes list. - [ ] `test_since_multiple_changes`: 3 winner changes over time. All returned in order. - [ ] **4.2 Source Metadata Indexing** (extension of 3A.3): Index key metadata fields. - **Problem:** Phase 3 stores `source_metadata` as an opaque blob. Phase 4 makes key fields queryable. - **Depends on:** Rich Source Metadata (3A.3). - [ ] Define a set of indexed metadata keys: `journal`, `doi`, `platform`, `study_design`. - [ ] New key pattern: `SM:{field}:{value}:{assertion_hash}` for metadata field indexes. - [ ] IngestWorker: on ingestion, if `source_metadata` is present, parse JSON, extract indexed fields, write index entries. - [ ] Add metadata field filters to `QueryParams` (e.g., `?source_journal=NEJM`). - [ ] Tests: store assertions with metadata, query by journal name, verify correct filtering. - [ ] **4.3 Batch TrustRank Decay API**: Expose scheduled decay for external orchestration. - **Current state:** `decay_all_trust_ranks()` exists on TrustRankStore. No API endpoint. - [ ] Add `POST /v1/admin/decay-trust-ranks` endpoint. - [ ] Accepts `now: u64` parameter (or uses current time). - [ ] Returns count of decayed agents and summary stats. - **Note:** The Gardener (Camp 5.2, app layer) calls this endpoint on a schedule. The database just exposes the primitive. > **Note:** The following items were reclassified as **Application Layer** responsibilities (see `tmp/ambition-vs-reality.md`, Camp 5). They are not Episteme database features. They consume the Episteme API and are built by integrators or vertical-specific teams. > > - **The Simulator** (Training Data Pipeline) -> Camp 5.3 > - **The Super Curator** (Reviewer Agent swarm) -> Camp 5.4 > - **Background Gardener** (Cluster detection, signal processing) -> Camp 5.2 > - **Agent Wallet** (Key management sidecar) -> Camp 5.1 --- ## Tracking ### Active Tasks * [x] **Phase 3 The Pilot**: Consumer Health vertical integration. ✅ COMPLETE * [ ] **Phase 4 The Hive**: Trust & Scale features. ### Next Up (Phase 3 sequencing) * [ ] **Phase 4 Items**: "Since" parameter (4.1), Metadata indexing (4.2), Batch TrustRank decay (4.3). ### Recently Completed * [x] **Source Document Storage** (3F.1): Provenance lookup for 100% citation recall. * `POST /v1/source` stores source documents by BLAKE3 content hash. * `GET /v1/provenance/{hash}` retrieves source documents. * Content-addressed storage at `SRC:{hash}` keys. * Base64 encoding, 10MB limit, idempotent uploads. * 5 unit tests covering happy path and error cases. * [x] **Epoch Cascade Logic** (3D.1): O(1) supersession lookup via pre-computed markers. * `write_supersession_cascade()` writes `SUPERSEDED:` markers for full transitive closure at ingest time. * `is_epoch_superseded()` uses O(1) marker lookup instead of chain walking. * Cycle detection and max depth guard (100 levels). * 5 tests covering markers, transitive closure, cycles, and marker-based filtering. * [x] **Semantic Decay** (3B.2): Confidence half-life at query time. * `decay_halflife: Option` and `source_class_decay: bool` on Query. * New `decay.rs` module with `apply_decay()` and `apply_source_class_decay()`. * Formula: `effective_confidence = confidence * 2^(-(age / halflife))`. * Tier-specific decay: Regulatory=none, Clinical=2yr, Anecdotal=30d. * 11 unit tests + 1 E2E integration test. * [x] **Layered Consensus Lens** (3C.2): Per-source-class consensus with tier-by-tier visibility. * `LayeredConsensusLens` with `LayeredLens` trait. * `TierResolution` and `LayeredResolution` types. * `GET /v1/layered?subject=X&predicate=Y` endpoint. * Cross-tier conflict score using Shannon entropy. * 10 comprehensive tests. * [x] **Time-Travel Engine** (3B.1): `as_of` parameter for historical queries. * `as_of: Option` field on `Query` for querying historical state. * Bypasses fast path (MVs reflect current state). * `Query::matches()` filters by `assertion.timestamp <= as_of`. * 6 tests covering edge cases. * [x] **Rich Source Metadata** (3A.3): Structured provenance beyond `source_hash`. * `source_metadata: Option>` field on `Assertion`. * `Vec` for rkyv zero-copy compatibility, callers handle JSON encoding. * Builder methods: `.source_metadata_json()` and `.source_metadata()`. * API exposes as `Option` with defensive UTF-8 handling. * 2 serialization tests. * [x] **Conflict Score on Resolution** (3A.2): Numeric disagreement metric across all lenses. * `conflict_score: f32` field on `Resolution` (0.0 = unanimous, 1.0 = max conflict). * `compute_conflict_score()` utility using normalized variance. * Updated all 5 lens implementations to compute and propagate conflict score. * `MaterializedView` now stores conflict score. * API `QueryResponse` exposes `conflict_score` and `resolution_confidence` when lens is applied. * 7 unit tests including NaN handling. * [x] **SkepticLens + SkepticView** (3C.1): "Trust but Verify" conflict analysis that surfaces all claims with conflict scores. * `AnalysisLens` trait for lenses that map conflict instead of resolving it. * `SkepticLens` using normalized Shannon entropy for conflict scoring. * `SkepticResolver` + `SkepticView` in stemedb-query. * `GET /v1/skeptic?subject=X&predicate=Y` API endpoint. * Types: `ResolutionStatus`, `ConflictAnalysis`, `ClaimSummary`, `SourceSummary`, `AgentSummary`. * [x] **Source-Class Field** (3A.1): 6-tier `SourceClass` enum with authority weighting and decay rates. * `SourceClass` enum: Regulatory, Clinical, Observational, Expert, Community, Anecdotal. * `tier()`, `default_decay_days()`, `authority_weight()` methods. * Field on Assertion struct with full serialization support. * [x] **The Meter**: Token bucket quota system with MeterLayer middleware (10K tokens/agent/hour). * [x] **Query Audit Trail**: Every query logged with provenance at `AUD:{query_id}`. `X-Agent-Id` header for attribution. * [x] **Event-Driven Materialization**: `run_notified()` + IngestWorker Notify integration. * [x] **Fast-Path MV Lookup**: `QueryEngine::try_fast_path()` for O(1) reads. * [x] **Materializer**: Background worker for O(1) MV reads via `AsyncLens`. * [x] **VoteAwareConsensusLens**: Real vote-based consensus resolution. * [x] **Compound SP Index**: O(1) subject+predicate lookups. * [x] **TrustRank System**: Agent reputation with decay and learning loop. * [x] **API Surface**: axum HTTP server with 7 endpoints + OpenAPI docs. ### Blockers * None. --- ## Dependency Graph ``` Phase 2.5 (Hardening) Phase 3 (The Pilot) Phase 4 (The Hive) ======================== ======================== ================== [2.1 MV Staleness] ---------> [3B.1 Time-Travel] ✅ --+ | | [2.2 Confidence Rename] -----> (API clarity for all) +----------> [4.1 "Since" Param] | [2.3 EpochAwareLens] --------> [3D.1 Epoch Cascade] ✅ |----------> Invalidation Cascades pillar | [2.4 Visual Hash Query] -----> [3E.2 Visual Hash Index] ✅ | [2.6 E2E Integration] -------> (pipeline confidence) | | [3A.1 Source-Class] ✅ --+----------> [3C.2 Layered Consensus] ✅ | [3B.2 Semantic Decay] ✅ +-----------------------------[4.2 Metadata Indexing] | [3A.2 Conflict Score] ✅ --> (enhance Resolution) | [3A.3 Source Metadata] ✅ --> [4.2 Metadata Indexing] | [3C.1 Skeptic Lens] ✅ (standalone, COMPLETE) [3C.3 Constraints Lens] ✅ (standalone, COMPLETE) [3E.1 Vector Search] ✅ (standalone, COMPLETE) [3E.2 Visual Hash Index] ✅ (standalone, COMPLETE) [3F.1 Provenance] ✅ (standalone, COMPLETE) ``` ### Critical Path for Consumer Health Demo ``` [3A.1 Source-Class] ✅ --> [3A.2 Conflict Score] ✅ --> [3C.2 Layered Consensus] ✅ | +----> CONSUMER HEALTH MVP ✅ | [3B.1 Time-Travel] ✅ ---------------------------------------+ | [3A.3 Source Metadata] ✅ -----------------------------------+ | [3C.1 Skeptic Lens] ✅ --------------------------------------+ ``` ### Critical Path for Financial DD Demo ``` [3A.2 Conflict Score] ✅ --> [3C.1 Skeptic Lens] ✅ ---+ | [3B.1 Time-Travel] ✅ ----------------------------------+----> FINANCIAL DD MVP | [2.3 EpochAwareLens] --> [3D.1 Epoch Cascade] ✅ -------+ | [3B.2 Semantic Decay] ✅ -------------------------------+ ``` ### Critical Path for Agile Agent Team Demo ``` [3C.3 Constraints Lens] (standalone) ------+ | [3B.1 Time-Travel] ✅ --------------------+----> AGENT TEAM MVP | [2.3 EpochAwareLens] ✅ ------------------+ | [Query Audit (Phase 2)] ✅ ----------------+ ```