STEM BIO-AI Explain Report
Target  : yorkeccak/bio
Policy  : default [ca-policy-1.0; mirror_only; authoritative_release]
Policy Mode: mirror-only in 1.7.8 — selected profile metadata is surfaced in artifacts, but authoritative scan scoring still follows deterministic runtime constants. Preview-only posture changes, including Stage 4 replication emphasis, do not change the formal score until a future read-through phase. Use `stem policy simulate` to preview governed score deltas and posture changes.
Score   : 48 / 100  (T1 Quarantine)
Replic  : 30 / 100  (R1)
========================================================================

S1_readme_bio_terms  [DETECTED]  (37 findings)
  [001]  README.md:2
         finding_id: S1_readme_bio_terms:README.md:2:001
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/stargazers"><img src="https://img.shields.io/github/stars/yorkeccak/bio?style=flat&color=yellow" alt="GitHub Stars"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [002]  README.md:2
         finding_id: S1_readme_bio_terms:README.md:2:002
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/stargazers"><img src="https://img.shields.io/github/stars/yorkeccak/bio?style=flat&color=yellow" alt="GitHub Stars"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [003]  README.md:3
         finding_id: S1_readme_bio_terms:README.md:3:003
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/blob/main/LICENSE"><img src="https://img.shields.io/github/license/yorkeccak/bio" alt="License"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [004]  README.md:3
         finding_id: S1_readme_bio_terms:README.md:3:004
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/blob/main/LICENSE"><img src="https://img.shields.io/github/license/yorkeccak/bio" alt="License"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [005]  README.md:4
         finding_id: S1_readme_bio_terms:README.md:4:005
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/network/members"><img src="https://img.shields.io/github/forks/yorkeccak/bio?style=flat" alt="Forks"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [006]  README.md:4
         finding_id: S1_readme_bio_terms:README.md:4:006
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/network/members"><img src="https://img.shields.io/github/forks/yorkeccak/bio?style=flat" alt="Forks"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [007]  README.md:5
         finding_id: S1_readme_bio_terms:README.md:5:007
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/graphs/contributors"><img src="https://img.shields.io/github/contributors/yorkeccak/bio" alt="Contributors"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [008]  README.md:5
         finding_id: S1_readme_bio_terms:README.md:5:008
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio/graphs/contributors"><img src="https://img.shields.io/github/contributors/yorkeccak/bio" alt="Contributors"></a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [009]  README.md:8
         finding_id: S1_readme_bio_terms:README.md:8:009
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "# Bio"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [010]  README.md:10
         finding_id: S1_readme_bio_terms:README.md:10:010
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Try the hosted version [here](https://bio.valyu.ai) 🙌"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [011]  README.md:14
         finding_id: S1_readme_bio_terms:README.md:14:011
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "> **Enterprise-grade biomedical research behind a chat interface** - Access PubMed, clinical trials, FDA drug labels, and run complex Python analyses through natural language. P..."
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [012]  README.md:16
         finding_id: S1_readme_bio_terms:README.md:16:012
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "![Bio](public/bio-screenshot.png)"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [013]  README.md:16
         finding_id: S1_readme_bio_terms:README.md:16:013
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "![Bio](public/bio-screenshot.png)"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [014]  README.md:18
         finding_id: S1_readme_bio_terms:README.md:18:014
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "## Why Bio?"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [015]  README.md:20
         finding_id: S1_readme_bio_terms:README.md:20:015
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Traditional biomedical research and data is fragmented across dozens of databases and platforms. Bio changes everything by providing:"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [016]  README.md:22
         finding_id: S1_readme_bio_terms:README.md:22:016
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Comprehensive Medical Data** - PubMed articles, ClinicalTrials.gov data, FDA drug labels, and more"
         reason  : README exposes bio/medical vocabulary.
         match      : Medical
  [017]  README.md:25
         finding_id: S1_readme_bio_terms:README.md:25:017
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Interactive Visualizations** - Beautiful charts and dashboards for clinical data"
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [018]  README.md:26
         finding_id: S1_readme_bio_terms:README.md:26:018
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Real-Time Intelligence** - Web search integration for breaking medical news"
         reason  : README exposes bio/medical vocabulary.
         match      : medical
  [019]  README.md:35
         finding_id: S1_readme_bio_terms:README.md:35:019
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Clinical Trials Database** - Search ClinicalTrials.gov for active and completed trials"
         reason  : README exposes bio/medical vocabulary.
         match      : Clinical
  [020]  README.md:38
         finding_id: S1_readme_bio_terms:README.md:38:020
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Interactive Charts** - Visualize clinical data, drug efficacy, patient outcomes"
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [021]  README.md:38
         finding_id: S1_readme_bio_terms:README.md:38:021
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Interactive Charts** - Visualize clinical data, drug efficacy, patient outcomes"
         reason  : README exposes bio/medical vocabulary.
         match      : patient
  [022]  README.md:44
         finding_id: S1_readme_bio_terms:README.md:44:022
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Interactive Charts** - Create publication-ready visualizations of clinical data"
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [023]  README.md:50
         finding_id: S1_readme_bio_terms:README.md:50:023
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Self-hosted mode is the recommended way to run Bio. It provides a complete local environment with:"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [024]  README.md:68
         finding_id: S1_readme_bio_terms:README.md:68:024
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "git clone https://github.com/yorkeccak/bio.git"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [025]  README.md:69
         finding_id: S1_readme_bio_terms:README.md:69:025
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "cd bio"
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [026]  README.md:165
         finding_id: S1_readme_bio_terms:README.md:165:026
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- That's it! Bio will automatically detect and use it"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [027]  README.md:167
         finding_id: S1_readme_bio_terms:README.md:167:027
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "3. **Use in Bio**"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [028]  README.md:216
         finding_id: S1_readme_bio_terms:README.md:216:028
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Try these powerful queries to see what Bio can do:"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [029]  README.md:218
         finding_id: S1_readme_bio_terms:README.md:218:029
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- "What are the latest clinical trials for CAR-T therapy in melanoma?""
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [030]  README.md:222
         finding_id: S1_readme_bio_terms:README.md:222:030
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- "Analyze Phase 3 clinical trial data for immunotherapy drugs""
         reason  : README exposes bio/medical vocabulary.
         match      : clinical
  [031]  README.md:227
         finding_id: S1_readme_bio_terms:README.md:227:031
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- Keep all your medical research completely private"
         reason  : README exposes bio/medical vocabulary.
         match      : medical
  [032]  README.md:228
         finding_id: S1_readme_bio_terms:README.md:228:032
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- Perfect for sensitive patient data analysis"
         reason  : README exposes bio/medical vocabulary.
         match      : patient
  [033]  README.md:243
         finding_id: S1_readme_bio_terms:README.md:243:033
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "The quickest way to get Bio running in production:"
         reason  : README exposes bio/medical vocabulary.
         match      : Bio
  [034]  README.md:260
         finding_id: S1_readme_bio_terms:README.md:260:034
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- No storage of sensitive medical data"
         reason  : README exposes bio/medical vocabulary.
         match      : medical
  [035]  README.md:279
         finding_id: S1_readme_bio_terms:README.md:279:035
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "For bugs or feature requests, [open an issue](https://github.com/yorkeccak/bio/issues) or start a [discussion](https://github.com/yorkeccak/bio/discussions)."
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [036]  README.md:279
         finding_id: S1_readme_bio_terms:README.md:279:036
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "For bugs or feature requests, [open an issue](https://github.com/yorkeccak/bio/issues) or start a [discussion](https://github.com/yorkeccak/bio/discussions)."
         reason  : README exposes bio/medical vocabulary.
         match      : bio
  [037]  README.md:296
         finding_id: S1_readme_bio_terms:README.md:296:037
         pattern : bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "<a href="https://github.com/yorkeccak/bio">GitHub</a>"
         reason  : README exposes bio/medical vocabulary.
         match      : bio

S1_clinical_boundary  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_clinical_boundary:.:0:001
         pattern : clinical_boundary_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_clinical_boundary.

S1_H1_clinical_certainty_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H1_clinical_certainty_hype:.:0:001
         pattern : hype_clinical_certainty_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H1_clinical_certainty_hype.

S1_H2_regulatory_approval_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H2_regulatory_approval_hype:.:0:001
         pattern : hype_regulatory_approval_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H2_regulatory_approval_hype.

S1_H3_autonomous_replacement_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H3_autonomous_replacement_hype:.:0:001
         pattern : hype_autonomous_replacement_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H3_autonomous_replacement_hype.

S1_H4_breakthrough_marketing_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H4_breakthrough_marketing_hype:.:0:001
         pattern : hype_breakthrough_marketing_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H4_breakthrough_marketing_hype.

S1_H5_universal_generalization_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H5_universal_generalization_hype:.:0:001
         pattern : hype_universal_generalization_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H5_universal_generalization_hype.

S1_H6_perfect_accuracy_hype  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_H6_perfect_accuracy_hype:.:0:001
         pattern : hype_perfect_accuracy_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_H6_perfect_accuracy_hype.

S1_R1_limitations_section  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_R1_limitations_section:.:0:001
         pattern : limitations_section_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_R1_limitations_section.

S1_R2_regulatory_framework  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_R2_regulatory_framework:.:0:001
         pattern : regulatory_framework_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_R2_regulatory_framework.

S1_R2_weak_regulatory_self_assertion  [DETECTED]  (1 finding)
  [001]  README.md:262
         finding_id: S1_R2_weak_regulatory_self_assertion:README.md:262:001
         pattern : weak_regulatory_self_assertion_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- HIPAA-compliant architecture (when self-hosted)"
         reason  : Self-asserted privacy/compliance language detected without stronger regulatory-framework evidence.
         match      : HIPAA-compliant

S1_R2_unsupported_legal_or_compliance_claim  [DETECTED]  (1 finding)
  [001]  README.md:262
         finding_id: S1_R2_unsupported_legal_or_compliance_claim:README.md:262:001
         pattern : unsupported_legal_or_compliance_claim_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- HIPAA-compliant architecture (when self-hosted)"
         reason  : Legal, privacy, or compliance claim detected without supporting governance or security-grounding evidence in reviewed sources.
         claim      : HIPAA-compliant
         grounding_present      : False

S1_R4_demographic_bias_boundary  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_R4_demographic_bias_boundary:.:0:001
         pattern : demographic_bias_boundary_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_R4_demographic_bias_boundary.

S1_R5_reproducibility_provisions  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S1_R5_reproducibility_provisions:.:0:001
         pattern : reproducibility_provisions_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S1_R5_reproducibility_provisions.

S3_T1_workflow_files  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_T1_workflow_files:.:0:001
         pattern : workflow_presence_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_T1_workflow_files.

S3_T2_domain_tests  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_T2_domain_tests:.:0:001
         pattern : domain_tests_bio_terms_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_T2_domain_tests.

S3_T3_changelog_release_hygiene  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_T3_changelog_release_hygiene:.:0:001
         pattern : changelog_presence_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_T3_changelog_release_hygiene.

S3_T3_changelog_bugfix_evidence  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_T3_changelog_bugfix_evidence:.:0:001
         pattern : changelog_bugfix_terms_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_T3_changelog_bugfix_evidence.

S3_B1_dependency_manifest  [DETECTED]  (3 findings)
  [001]  package-lock.json
         finding_id: S3_B1_dependency_manifest:package-lock.json:0:001
         pattern : dependency_manifest_presence_v1
         evidence: confirmed_present
         conf    : high
         snippet : "package-lock.json"
         reason  : Dependency or environment manifest exists.
  [001]  package.json
         finding_id: S3_B1_dependency_manifest:package.json:0:001
         pattern : dependency_manifest_presence_v1
         evidence: confirmed_present
         conf    : high
         snippet : "package.json"
         reason  : Dependency or environment manifest exists.
  [001]  pnpm-lock.yaml
         finding_id: S3_B1_dependency_manifest:pnpm-lock.yaml:0:001
         pattern : dependency_manifest_presence_v1
         evidence: confirmed_present
         conf    : high
         snippet : "pnpm-lock.yaml"
         reason  : Dependency or environment manifest exists.

S3_B1_data_source_language  [DETECTED]  (2 findings)
  [001]  README.md:22
         finding_id: S3_B1_data_source_language:README.md:22:001
         pattern : data_source_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Comprehensive Medical Data** - PubMed articles, ClinicalTrials.gov data, FDA drug labels, and more"
         reason  : Data source, dataset citation, IRB, or provenance language detected.
         match      : ClinicalTrials
  [002]  README.md:35
         finding_id: S3_B1_data_source_language:README.md:35:002
         pattern : data_source_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **Clinical Trials Database** - Search ClinicalTrials.gov for active and completed trials"
         reason  : Data source, dataset citation, IRB, or provenance language detected.
         match      : ClinicalTrials

S3_B2_bias_limitations  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_B2_bias_limitations:.:0:001
         pattern : bias_limitations_v2
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_B2_bias_limitations.

S3_B2_measurement_evidence  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S3_B2_measurement_evidence:.:0:001
         pattern : bias_measurement_terms_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S3_B2_measurement_evidence.

S3_B3_coi_funding  [DETECTED]  (1 finding)
  [001]  README.md:281
         finding_id: S3_B3_coi_funding:README.md:281:001
         pattern : coi_funding_v1
         evidence: confirmed_present
         conf    : high
         snippet : "## Acknowledgments"
         reason  : COI, funding, sponsor, or acknowledgement language detected.
         match      : Acknowledgments

S2_package_bio_terms  [DETECTED]  (2 findings)
  [001]  package.json:2
         finding_id: S2_package_bio_terms:package.json:2:001
         pattern : package_bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : ""name": "bio","
         reason  : Package metadata exposes bio/medical vocabulary.
         match      : bio
  [002]  package.json:5
         finding_id: S2_package_bio_terms:package.json:5:002
         pattern : package_bio_terms_v1
         evidence: confirmed_present
         conf    : high
         snippet : ""description": "Enterprise-grade biomedical research AI chatbot with access to PubMed, clinical trials, FDA drug labels, and Python code execution","
         reason  : Package metadata exposes bio/medical vocabulary.
         match      : clinical

R2R_D5_single_external_service_dependency  [DETECTED]  (8 findings)
  [001]  .env.example:24
         finding_id: R2R_D5_single_external_service_dependency:.env.example:24:001
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : medium
         snippet : "VALYU_API_KEY=valyu_your_api_key_here"
         reason  : Required external service API key detected for a named workflow dependency.
         provider      : Valyu
         env_var      : VALYU_API_KEY
         required_signal      : True
  [002]  .env.example:38
         finding_id: R2R_D5_single_external_service_dependency:.env.example:38:002
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : medium
         snippet : "DAYTONA_API_KEY=your_daytona_api_key_here"
         reason  : Required external service API key detected for a named workflow dependency.
         provider      : Daytona
         env_var      : DAYTONA_API_KEY
         required_signal      : True
  [001]  README.md:23
         finding_id: R2R_D5_single_external_service_dependency:README.md:23:001
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **One Unified Search** - Powered by Valyu's specialized biomedical data API"
         reason  : Named external service provider is presented as part of the core repository workflow.
         provider      : Valyu
         line_role      : provider_dependency_claim
  [002]  README.md:60
         finding_id: R2R_D5_single_external_service_dependency:README.md:60:002
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- Valyu API key (get one at [platform.valyu.ai](https://platform.valyu.ai))"
         reason  : Named external service provider is presented as part of the core repository workflow.
         provider      : Valyu
         line_role      : provider_dependency_claim
  [003]  README.md:61
         finding_id: R2R_D5_single_external_service_dependency:README.md:61:003
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- [Daytona](https://www.daytona.io) API key - used for secure sandboxed Python code execution (get one at [app.daytona.io](https://app.daytona.io))"
         reason  : Named external service provider is presented as part of the core repository workflow.
         provider      : Daytona
         line_role      : provider_dependency_claim
  [004]  README.md:48
         finding_id: R2R_D5_single_external_service_dependency:README.md:48:004
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "## Quick Start (Self-Hosted)"
         reason  : Local or self-host claims coexist with required external service dependencies.
         providers      : ['Daytona', 'Valyu']
         line_role      : local_or_self_host_claim
         provider_count      : 2
  [005]  README.md:50
         finding_id: R2R_D5_single_external_service_dependency:README.md:50:005
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Self-hosted mode is the recommended way to run Bio. It provides a complete local environment with:"
         reason  : Local or self-host claims coexist with required external service dependencies.
         providers      : ['Daytona', 'Valyu']
         line_role      : local_or_self_host_claim
         provider_count      : 2
  [006]  README.md:51
         finding_id: R2R_D5_single_external_service_dependency:README.md:51:006
         pattern : single_external_service_dependency_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **No authentication required** - Auto-login as dev user"
         reason  : Local or self-host claims coexist with required external service dependencies.
         providers      : ['Daytona', 'Valyu']
         line_role      : local_or_self_host_claim
         provider_count      : 2

C6_mock_auth_or_fail_open_boundary  [DETECTED]  (6 findings)
  [001]  README.md:51
         finding_id: C6_mock_auth_or_fail_open_boundary:README.md:51:001
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- **No authentication required** - Auto-login as dev user"
         reason  : Mock-auth, auto-login, or no-auth local/self-host boundary surfaced in reviewed sources.
         match      : No authentication required
         local_claim_context      : True
  [002]  README.md:110
         finding_id: C6_mock_auth_or_fail_open_boundary:README.md:110:002
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "You'll be automatically logged in as `dev@localhost` with full access to all features."
         reason  : Mock-auth, auto-login, or no-auth local/self-host boundary surfaced in reviewed sources.
         match      : dev@localhost
         local_claim_context      : True
  [003]  README.md:134
         finding_id: C6_mock_auth_or_fail_open_boundary:README.md:134:003
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "2. **Mock Authentication**"
         reason  : Mock-auth, auto-login, or no-auth local/self-host boundary surfaced in reviewed sources.
         match      : Mock Authentication
         local_claim_context      : True
  [004]  README.md:135
         finding_id: C6_mock_auth_or_fail_open_boundary:README.md:135:004
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "- Auto-login as dev user (`dev@localhost`)"
         reason  : Mock-auth, auto-login, or no-auth local/self-host boundary surfaced in reviewed sources.
         match      : Auto-login
         local_claim_context      : True
  [001]  .env.example:11
         finding_id: C6_mock_auth_or_fail_open_boundary:.env.example:11:001
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "# Set to 'self-hosted' or 'valyu'"
         reason  : Local or self-host claims coexist with mock-auth or auto-login boundary signals.
         line_role      : local_or_self_host_claim
  [002]  .env.example:12
         finding_id: C6_mock_auth_or_fail_open_boundary:.env.example:12:002
         pattern : mock_auth_fail_open_boundary_v1
         evidence: confirmed_present
         conf    : high
         snippet : "# self-hosted = no auth, local SQLite, unlimited queries, Ollama/LM Studio support"
         reason  : Local or self-host claims coexist with mock-auth or auto-login boundary signals.
         line_role      : local_or_self_host_claim

C1_hardcoded_credentials  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: C1_hardcoded_credentials:.:0:001
         pattern : credential_pattern_v2
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No hardcoded credential evidence detected for C1_hardcoded_credentials.

C2_dependency_pinning  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: C2_dependency_pinning:.:0:001
         pattern : loose_dependency_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No loose dependency evidence detected.

C3_dead_or_deprecated_patient_adjacent_paths  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: C3_dead_or_deprecated_patient_adjacent_paths:.:0:001
         pattern : deprecated_patient_metadata_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for C3_dead_or_deprecated_patient_adjacent_paths.

C4_exception_handling_clinical_adjacent_paths  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: C4_exception_handling_clinical_adjacent_paths:.:0:001
         pattern : fail_open_exception_v2
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No fail-open exception handler detected in executable Python code.

BIO_smiles_surface_integrity  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_smiles_surface_integrity:.:0:001
         pattern : bio_smiles_surface_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No malformed or suspicious SMILES-like strings detected by conservative surface checks.

BIO_smiles_rdkit_validation  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_smiles_rdkit_validation:.:0:001
         pattern : bio_smiles_rdkit_invalid_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : RDKit optional validation lane not exercised because no SMILES-like candidates were detected.
         lane      : A1_optional_rdkit

BIO_smiles_parser_guard  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_smiles_parser_guard:.:0:001
         pattern : bio_smiles_parser_guard_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No missing None/invalid guards detected after SMILES parser calls.

BIO_silent_mock_fallback  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_silent_mock_fallback:.:0:001
         pattern : bio_silent_mock_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No silent mock or simulated-data fallback patterns detected in production code paths.

BIO_trace_manifest  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_trace_manifest:.:0:001
         pattern : bio_trace_manifest_file_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No traceability manifest or runtime audit-log schema surface detected.

BIO_run_trace  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: BIO_run_trace:.:0:001
         pattern : bio_run_trace_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No risky subprocess or os.system bio-tool execution patterns detected.

S4_container_environment  [DETECTED]  (1 finding)
  [001]  Dockerfile
         finding_id: S4_container_environment:Dockerfile:0:001
         pattern : container_file_v1
         evidence: confirmed_present
         conf    : high
         snippet : "Dockerfile"
         reason  : Container or compose file exists.

S4_make_reproduce_target  [ABSENT]  (1 finding)
  [001]  (repository)
         finding_id: S4_make_reproduce_target:.:0:001
         pattern : make_reproduce_target_v1
         evidence: confirmed_missing
         conf    : medium
         reason  : No Makefile detected.

S4_environment_lock_evidence  [DETECTED]  (2 findings)
  [001]  package-lock.json
         finding_id: S4_environment_lock_evidence:package-lock.json:0:001
         pattern : environment_lock_file_v1
         evidence: confirmed_present
         conf    : high
         snippet : "package-lock.json"
         reason  : Environment, dependency, or lock manifest detected.
  [001]  pnpm-lock.yaml
         finding_id: S4_environment_lock_evidence:pnpm-lock.yaml:0:001
         pattern : environment_lock_file_v1
         evidence: confirmed_present
         conf    : high
         snippet : "pnpm-lock.yaml"
         reason  : Environment, dependency, or lock manifest detected.

S4_exact_dependency_pins_or_hashes  [DETECTED]  (2 findings)
  [001]  package-lock.json
         finding_id: S4_exact_dependency_pins_or_hashes:package-lock.json:0:001
         pattern : exact_pin_or_hash_v1
         evidence: confirmed_present
         conf    : high
         snippet : "package-lock.json"
         reason  : Lock manifest with exact dependency resolution detected.
  [001]  pnpm-lock.yaml
         finding_id: S4_exact_dependency_pins_or_hashes:pnpm-lock.yaml:0:001
         pattern : exact_pin_or_hash_v1
         evidence: confirmed_present
         conf    : high
         snippet : "pnpm-lock.yaml"
         reason  : Lock manifest with exact dependency resolution detected.

S4_readme_reproducibility_section  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_readme_reproducibility_section:.:0:001
         pattern : readme_repro_heading_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : README exists but no reproducibility or replication section heading was detected.

S4_checksum_files  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_checksum_files:.:0:001
         pattern : checksum_file_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S4_checksum_files.

S4_dataset_url  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_dataset_url:.:0:001
         pattern : dataset_url_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : Documentation exists but no dataset URL or data source URL was detected.

S4_model_weight_url_or_checksum  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_model_weight_url_or_checksum:.:0:001
         pattern : model_weight_url_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : Documentation exists but no model artifact URL/checksum evidence was detected.

S4_citation_cff  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_citation_cff:.:0:001
         pattern : citation_cff_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S4_citation_cff.

S4_license_restriction  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_license_restriction:.:0:001
         pattern : license_restriction_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : License/readme/docs surfaces exist but no restriction language was detected.

S4_cli_entrypoint  [ABSENT]  (1 finding)
  [001]  (repository)
         finding_id: S4_cli_entrypoint:.:0:001
         pattern : cli_entrypoint_v1
         evidence: confirmed_missing
         conf    : medium
         reason  : No package metadata or Python AST surface detected.

S4_seed_setting  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_seed_setting:.:0:001
         pattern : ast_seed_setting_stage4_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No deterministic seed setting evidence detected by AST summary.

S4_runnable_examples  [NOT_DETECTED]  (1 finding)
  [001]  (repository)
         finding_id: S4_runnable_examples:.:0:001
         pattern : runnable_example_file_v1
         evidence: not_found_in_reviewed_sources
         conf    : medium
         reason  : No evidence detected for S4_runnable_examples.

========================================================================
Bio Deterministic Diagnostics

  SMILES Surface Integrity           not_detected=1
  SMILES RDKit Validation            not_detected=1
  SMILES Parser Guard                not_detected=1
  Silent Mock Fallback               not_detected=1
  Traceability Manifest Surface      not_detected=1
  Bio Subprocess Run Trace           not_detected=1

========================================================================
Regulatory Traceability Assistant

  Regulatory basis note
  Aligned to current official source classes as of May 2026: EU AI Act (Regulation (EU) 2024/1689), FDA QMSR, FDA AI-enabled device guidance themes, and IMDRF SaMD/GMLP frameworks.
  This is a traceability aid, not a compliance or clearance determination.

  stage_1                        
    EU_AI_ACT_ARTICLE_13: signal_only (mapping=weak, evidence=weak)
      note: Boundary, intended-use, and limitation language is relevant to transparency scaffolding only.
    COMPLIANCE_CLAIM_GROUNDING_SIGNAL: signal_only (mapping=weak_moderate, evidence=weak)
      note: Legal or compliance claims without supporting governance evidence are relevant to transparency and quality-system review, not compliance proof.
  stage_2r                       
    IMDRF_CLINICAL_CONTEXT_BOUNDARY_SIGNAL: signal_only (mapping=weak_moderate, evidence=moderate)
      note: Repository-local contradiction and boundary signals are relevant to clinical-context traceability, not clinical validation.
  stage_3                        
    EU_AI_ACT_ARTICLE_10: signal_only (mapping=weak, evidence=weak)
      note: Provenance and bias signals are relevant to data-governance review, but do not verify execution quality.
  stage_4                        
    EU_AI_ACT_ARTICLE_12: partially_aligned (mapping=moderate, evidence=moderate)
      note: Reproducibility and trace manifests support record-keeping scaffolding, not operational logging completeness.

  summary                         Structural signals partially align with traceability scaffolding. This remains a pre-audit traceability aid, not a compliance determination.

========================================================================
AIRI Coverage

  covered_count                  7
  detector_scope_total           32
  coverage_rate                  0.219
  bundle_scope                   curated_medical_clinical_subset
  upstream_snapshot              2026-04-23

  covered examples:
    - 24.01.03 | Safe exploration problem with widely deployed AI assistants | covered_by=C5_compliance_boundary_integrity | why=C5_compliance_boundary_integrity: Unsupported legal/compliance claim surfaced in boundary-integrity lane.
    - 24.04.01 | Physical and Psychological Harms | covered_by=C2_dependency_pinning | why=C2_dependency_pinning: External operational dependency signal surfaced in code-integrity lane.
    - 33.01.05 | Privacy and security | covered_by=C2_dependency_pinning | why=C2_dependency_pinning: External operational dependency signal surfaced in code-integrity lane.

  known gaps in bundle:
    - 65.03.03 | Reidentification
    - 70.02.02 | Misinformation — hallucination of clinical knowledge

========================================================================
Audit Freshness

  review_after_days               45
  expires_on                      2026-07-02
  freshness_basis                 clinical_adjacent_short_cycle
  change_triggered_reaudit_now    False
  change_triggered_reasons        none
  trigger_examples                git_commit_changed, readme_or_docs_claim_surface_changed, dependency_manifest_changed, dataset_or_model_reference_changed

========================================================================
AST Signal Summary

  files_total                        0
  files_considered                   0
  files_parsed                       0
  files_skipped_size                 0
  syntax_errors                      0
  file_limit_exceeded                False
  test_functions                     0
  assertion_tests                    0
  public_functions                   0
  docstring_functions                0
  annotated_functions                0
  seed_settings                      0
  argparse_cli                       False
  portable_model_loading             0
  fail_open_handlers                 0

========================================================================
Stage 4 Replication Rubric

  S4_container_environment                    10 / 10   Container or compose file exists.
  S4_make_reproduce_target                     0 / 10   No Makefile detected.
  S4_environment_lock_evidence                10 / 10   Environment, dependency, or lock manifest detected.
  S4_exact_dependency_pins_or_hashes          10 / 10   Exact dependency pin or hash evidence detected.
  S4_readme_reproducibility_section            0 / 10   README exists but no reproducibility or replication section heading was detected.
  S4_checksum_files                            0 / 10   No evidence detected for S4_checksum_files.
  S4_dataset_url                               0 / 10   Documentation exists but no dataset URL or data source URL was detected.
  S4_model_weight_url_or_checksum              0 / 10   Documentation exists but no model artifact URL/checksum evidence was detected.
  S4_citation_cff                              0 / 5    No evidence detected for S4_citation_cff.
  S4_license_restriction                       0 / 0    No license/use restriction language detected.
  S4_cli_entrypoint                            0 / 5    No package metadata or Python AST surface detected.
  S4_seed_setting                              0 / 5    No deterministic seed setting detected.
  S4_runnable_examples                         0 / 5    No evidence detected for S4_runnable_examples.
  stage_4_raw_total                           30 / 100  Raw Stage 4 rubric total. Stage 4 is reported separately and does not alter final score.

========================================================================
Reasoning Diagnostics

  version                         stem-bio-ai-reasoning-v1.3.2
  mode                            diagnostic_only
  final_score_override            False
  weights                         uncalibrated_initial_priors_pending_benchmark_calibration
  evidence_budget                 supported
  confidence_envelope             unknown
  lane_coherence                  heuristic_mixed
  uncertainty_budget              review_advised
  evidence_risk_gate              within_heuristic_gate

========================================================================
DISCLAIMER: Evidence-surface pre-screen only.
Not clinical certification, regulatory clearance, or medical advice.
