chore: remove valichord integration
This commit is contained in:
Advait Paliwal
@@ -82,9 +82,6 @@ $ feynman audit 2401.12345
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$ feynman replicate "chain-of-thought improves math"
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→ Replicates experiments on local or cloud GPUs
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$ feynman valichord "study-id-or-topic"
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→ Runs the ValiChord reproducibility workflow or checks existing Harmony Records
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```
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---
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@@ -100,7 +97,6 @@ Ask naturally or use slash commands as shortcuts.
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| `/review <artifact>` | Simulated peer review with severity and revision plan |
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| `/audit <item>` | Paper vs. codebase mismatch audit |
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| `/replicate <paper>` | Replicate experiments on local or cloud GPUs |
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| `/valichord <study-or-topic>` | Reproducibility attestation workflow and Harmony Record lookup |
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| `/compare <topic>` | Source comparison matrix |
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| `/draft <topic>` | Paper-style draft from research findings |
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| `/autoresearch <idea>` | Autonomous experiment loop |
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@@ -1,266 +0,0 @@
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---
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description: Submit a replication as a cryptographically verified ValiChord attestation, discover studies awaiting independent validation, query Harmony Records and reproducibility badges, or assist researchers in preparing a study for the validation pipeline.
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section: Research Workflows
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topLevelCli: true
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---
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# ValiChord Validation Workflow
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ValiChord is a distributed peer-to-peer system for scientific reproducibility verification, built on Holochain. It implements a blind commit-reveal protocol in Rust across four DNAs, producing Harmony Records — immutable, cryptographically verifiable proofs that independent parties reproduced the same findings without coordinating. Verified studies receive automatic reproducibility badges (Gold/Silver/Bronze); validators accumulate a per-discipline reputation score across rounds.
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This workflow integrates Feynman at three levels: as a **validator agent** running the full commit-reveal protocol; as a **researcher's assistant** helping prepare a study for submission; and as a **query tool** surfacing reproducibility status during research.
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**Live demo of the commit-reveal protocol**: https://youtu.be/DQ5wZSD1YEw
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---
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## ValiChord's four-DNA architecture
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| DNA | Name | Type | Role |
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|-----|------|------|------|
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| 1 | Researcher Repository | Private, single-agent | Researcher's local archive. Stores study, pre-registered protocol, data snapshots, deviation declarations. Only SHA-256 hashes ever leave this DNA. |
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| 2 | Validator Workspace | Private, single-agent | Feynman's working space. Stores task privately. Seals the blind commitment here — content never propagates to the DHT. |
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| 3 | Attestation | Shared DHT | Coordination layer. Manages validation requests, validator profiles, study claims, commitment anchors, phase markers, and public attestations. 36 zome functions. |
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| 4 | Governance | Public DHT | Final record layer. Assembles HarmonyRecords, issues reproducibility badges, tracks validator reputation, records governance decisions. All read functions accessible via HTTP Gateway without running a node. |
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The key guarantee: a validator's findings are cryptographically sealed (`SHA-256(msgpack(attestation) || nonce)`) before the reveal phase opens. Neither party can adjust findings after seeing the other's results. The researcher runs a parallel commit-reveal — locking their expected results before the validators reveal — so no party can adapt to seeing the other's outcome.
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---
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## Workflow A: Feynman as validator agent
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### Step 0: Publish validator profile (one-time setup)
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On first use, publish Feynman's public profile to DNA 3 so it appears in validator discovery indexes and conflict-of-interest checks:
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```
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publish_validator_profile(profile: ValidatorProfile)
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```
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Key fields:
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- `agent_type` — `AutomatedTool` (AI agents are first-class validators; the protocol makes no distinction between human and machine validators)
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- `disciplines` — list of disciplines Feynman can validate (e.g. ComputationalBiology, Statistics)
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- `certification_tier` — starts as `Provisional`; advances to `Certified` after 5+ validations with ≥60% agreement rate, `Senior` after 20+ with ≥80%
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If a profile already exists, use `update_validator_profile` to merge changes.
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### Step 1: Gather inputs or discover study
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**If the user provides a `request_ref`**: use it directly.
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**If Feynman is proactively discovering work**: query the pending queue in DNA 3:
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```
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get_pending_requests_for_discipline(discipline: Discipline)
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```
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Returns all unclaimed `ValidationRequest` entries for the discipline. Each contains:
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- `data_hash` — the ExternalHash identifier (used as `request_ref` throughout)
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- `num_validators_required` — quorum needed to close the round
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- `validation_tier` — Basic / Enhanced / Comprehensive
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- `access_urls` — where to fetch the data and code
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Optionally assess study complexity before committing:
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```
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assess_difficulty(input: AssessDifficultyInput)
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```
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Scores code volume, dependency count, documentation quality, data accessibility, and environment complexity. Returns predicted duration and confidence. Use this to decide whether to proceed before claiming.
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If replication results are not yet available, suggest `/replicate` first.
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### Step 2: Claim the study
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Before receiving a formal task assignment, register intent to validate via DNA 3:
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```
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claim_study(request_ref: ExternalHash)
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```
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This:
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- Reserves a validator slot (enforced capacity: no over-subscription)
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- Triggers conflict-of-interest check — rejects claim if Feynman's institution matches the researcher's
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- Records a `StudyClaim` entry on the shared DHT
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If a claimed validator goes dark, any other validator can free the slot:
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```
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reclaim_abandoned_claim(input: ReclaimInput)
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```
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### Step 3: Receive task and seal private attestation — Commit phase
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Connect to the ValiChord conductor via AppWebSocket. Using DNA 2 (Validator Workspace):
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```
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receive_task(request_ref, discipline, deadline_secs, validation_focus, time_cap_secs, compensation_tier)
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```
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`validation_focus` specifies which aspect Feynman is validating:
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- `ComputationalReproducibility` — re-run code, check numerical outputs
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- `PreCommitmentAdherence` — verify results match pre-registered analysis plan
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- `MethodologicalReview` — assess statistical choices and protocol validity
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Then seal the private attestation — this is the blind commitment:
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```
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seal_private_attestation(task_hash, attestation)
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```
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Where `attestation` includes:
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- `outcome` — `Reproduced` / `PartiallyReproduced` / `FailedToReproduce` / `UnableToAssess`
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- `outcome_summary` — key metrics, effect direction, confidence interval overlap, overall agreement
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- `confidence` — High / Medium / Low
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- `time_invested_secs` and `time_breakdown` — environment_setup, data_acquisition, code_execution, troubleshooting
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- `computational_resources` — whether personal hardware, HPC, GPU, or cloud was required; estimated cost in pence
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- `deviation_flags` — any undeclared departures from the original protocol (type, severity, evidence)
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The coordinator computes `commitment_hash = SHA-256(msgpack(attestation) || nonce)` and writes a `CommitmentAnchor` to DNA 3's shared DHT. The attestation content remains private in DNA 2.
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Save `task_hash` and `commitment_hash` to `outputs/<slug>-valichord-commit.json`.
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### Step 4: Wait for RevealOpen phase
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Poll DNA 3 (Attestation) until the phase transitions:
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```
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get_current_phase(request_ref: ExternalHash)
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```
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Returns `null` (still commit phase), `"RevealOpen"`, or `"Complete"`. Poll every 30 seconds. The phase opens automatically when the `CommitmentAnchor` count reaches `num_validators_required` — no manual trigger required.
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During this wait, the researcher also runs their parallel commit-reveal: they lock their expected results via `publish_researcher_commitment` before the reveal phase opens, then reveal via `reveal_researcher_result` after all validators have submitted. No party — researcher or validator — can adapt to seeing the other's outcome.
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### Step 5: Submit attestation — Reveal phase
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When phase is `RevealOpen`, publish the full attestation to the shared DHT via DNA 3:
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```
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submit_attestation(attestation, nonce)
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```
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The coordinator verifies `SHA-256(msgpack(attestation) || nonce) == CommitmentAnchor.commitment_hash` before writing. This prevents adaptive reveals — the attestation must match exactly what was committed.
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### Step 6: Retrieve Harmony Record and badges
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Call DNA 4 (Governance) explicitly after `submit_attestation` returns — DHT propagation means the ValidatorToAttestation link may not be visible within the same transaction:
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```
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check_and_create_harmony_record(request_ref)
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get_harmony_record(request_ref)
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get_badges_for_study(request_ref)
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```
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The **Harmony Record** contains:
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- `outcome` — the majority reproduced/not-reproduced finding
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- `agreement_level` — ExactMatch / WithinTolerance / DirectionalMatch / Divergent / UnableToAssess
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- `participating_validators` — array of validator agent keys
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- `validation_duration_secs`
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- `ActionHash` — the immutable on-chain identifier
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**Reproducibility badges** are automatically issued when the Harmony Record is created:
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| Badge | Threshold |
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|-------|-----------|
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| GoldReproducible | ≥7 validators, ≥90% agreement |
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| SilverReproducible | ≥5 validators, ≥70% agreement |
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| BronzeReproducible | ≥3 validators, ≥50% agreement |
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| FailedReproduction | Divergent outcomes |
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Save the full record and badges to `outputs/<slug>-harmony-record.json`.
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### Step 7: Check updated reputation
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After each validation round, Feynman's reputation record in DNA 4 is updated:
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```
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get_validator_reputation(validator: AgentPubKey)
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```
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Returns per-discipline scores: total validations, agreement rate, average time, and current `CertificationTier` (Provisional → Certified → Senior). Reputation is a long-term asset — AI validators accumulate a cryptographically verifiable track record across all ValiChord rounds they participate in.
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### Step 8: Report to user
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Present:
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- Outcome and agreement level
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- Reproducibility badge(s) issued to the study
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- Feynman's updated reputation score for this discipline
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- ActionHash — the permanent public identifier for this Harmony Record
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- Confirmation that the record is written to the Governance DHT and accessible via HTTP Gateway without any special infrastructure
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- Path to saved outputs
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---
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## Workflow B: Query existing Harmony Record
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`get_harmony_record` and `get_badges_for_study` in DNA 4 are `Unrestricted` functions — accessible via Holochain's HTTP Gateway without connecting to a conductor or running a node.
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```
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GET <http_gateway_url>/get_harmony_record/<request_ref_b64>
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GET <http_gateway_url>/get_badges_for_study/<request_ref_b64>
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```
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Use this to:
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- Check reproducibility status of a cited study during `/deepresearch`
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- Surface Harmony Records and badges in research summaries
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- Verify whether a study has undergone independent validation before recommending it
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The following read functions are also unrestricted on DNA 3:
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`get_attestations_for_request`, `get_validators_for_discipline`, `get_pending_requests_for_discipline`, `get_validator_profile`, `get_current_phase`, `get_difficulty_assessment`, `get_researcher_reveal`
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---
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## Workflow C: Proactive discipline queue monitoring
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Feynman can act as a standing validator for a discipline — periodically checking for new studies that need validation without waiting to be assigned:
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```
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get_pending_requests_for_discipline(discipline: Discipline)
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```
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Returns all unclaimed `ValidationRequest` entries. For each, optionally run `assess_difficulty` to estimate workload before claiming.
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This enables Feynman to operate as an autonomous reproducibility agent: polling the queue, assessing difficulty, claiming appropriate studies, and running the full Workflow A cycle unsupervised.
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---
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## Workflow D: Researcher preparation assistant
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Before a study enters the validation pipeline, Feynman can assist the researcher in preparing it via DNA 1 (Researcher Repository). This workflow runs on the researcher's side, not the validator's.
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**Register the study:**
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```
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register_study(study: ResearchStudy)
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```
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**Pre-register the analysis protocol** (immutable once written — creates a tamper-evident commitment to the analysis plan before data collection or validation begins):
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```
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register_protocol(input: RegisterProtocolInput)
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```
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**Take a cryptographic data snapshot** (records a SHA-256 hash of the dataset at a point in time — proves data was not modified after validation began):
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```
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take_data_snapshot(input: TakeDataSnapshotInput)
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```
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**Declare any deviations** from the pre-registered plan before the commit phase opens (pre-commit transparency):
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```
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declare_deviation(input: DeclareDeviationInput)
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```
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Only hashes ever leave DNA 1 — the raw data and protocol text remain on the researcher's device.
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**Repository Readiness Checker**: ValiChord also ships a standalone audit tool that scans a research repository for 30+ reproducibility failure modes before submission — missing dependency files, absolute paths, undeclared environment requirements, data documentation gaps, human-subjects data exposure risks, and more. Feynman is the natural interface for this tool: running the audit, interpreting findings in plain language, guiding the researcher through fixes, and confirming the repository meets the bar for independent validation. See: https://github.com/topeuph-ai/ValiChord
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---
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## Notes
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- AI agents are first-class participants in ValiChord's protocol. Feynman can autonomously publish profiles, claim studies, seal attestations, wait for phase transitions, and submit reveals — the protocol makes no distinction between human and AI validators.
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- ValiChord's privacy guarantee is structural, not policy-based. DNA 1 (researcher data) and DNA 2 (validator workspace) are single-agent private DHTs — propagation to the shared network is architecturally impossible, not merely restricted.
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- All 72 zome functions across the four DNAs are callable via AppWebSocket. The 20+ `Unrestricted` read functions on DNA 3 and DNA 4 are additionally accessible via HTTP Gateway without any Holochain node.
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- If a validation round stalls due to validator dropout, `force_finalize_round` in DNA 4 closes it after a 7-day timeout with a reduced quorum, preventing indefinite blocking.
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- Live demo (full commit-reveal cycle, Harmony Record generated): https://youtu.be/DQ5wZSD1YEw
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- Running the demo: `bash demo/start.sh` in a GitHub Codespace, then open port 8888 publicly
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- ValiChord repo: https://github.com/topeuph-ai/ValiChord
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@@ -1,19 +0,0 @@
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---
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name: valichord-validation
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description: Integrate with ValiChord to submit a replication as a cryptographically verified validator attestation, discover studies awaiting independent validation, query Harmony Records and reproducibility badges, or assist researchers in preparing a study for the validation pipeline. Feynman operates as a first-class AI validator — publishing a validator profile, claiming studies, running the blind commit-reveal protocol, and accumulating a verifiable per-discipline reputation. Also surfaces reproducibility status during /deepresearch and literature reviews via ValiChord's HTTP Gateway.
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---
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# ValiChord Validation
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Run the `/valichord` workflow. Read the prompt template at `prompts/valichord.md` for the full procedure.
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ValiChord is a four-DNA Holochain system for scientific reproducibility verification. Feynman integrates at four points:
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- As a **validator agent** — running `/replicate` then submitting findings as a sealed attestation into the blind commit-reveal protocol, earning reproducibility badges for researchers and building Feynman's own verifiable per-discipline reputation (Provisional → Certified → Senior)
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- As a **proactive discovery agent** — querying the pending study queue by discipline, assessing difficulty, and autonomously claiming appropriate validation work without waiting to be assigned
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- As a **researcher's assistant** — helping prepare studies for submission: registering protocols, taking cryptographic data snapshots, and running the Repository Readiness Checker to identify and fix reproducibility failure modes before validation begins
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- As a **research query tool** — checking whether a study carries a Harmony Record or reproducibility badge (Gold/Silver/Bronze) via ValiChord's HTTP Gateway, for use during `/deepresearch` or literature reviews
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Output: a Harmony Record — an immutable, publicly accessible cryptographic proof of independent reproducibility written to the ValiChord Governance DHT — plus automatic badge issuance and an updated validator reputation score.
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Live demo (commit-reveal cycle end-to-end): https://youtu.be/DQ5wZSD1YEw
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ValiChord repo: https://github.com/topeuph-ai/ValiChord
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