# Phoebe Domain - Feature Reference

> Partially implemented (TODO Phase 181, in progress). Phoebe is the
> brain-and-mind science platform of the Oshun ecosystem, pursuing fundamental
> breakthroughs across brain-computer interfaces, neuroscience, clinical
> psychology/psychiatry, the AI-driven design and running of experiments, and a
> unified brain-mind knowledge graph. Most capabilities below describe the
> planned envelope, but an initial slice already ships under `libs/phoebe/` —
> `core`, `assessment`, `mbc`, and `comp-psychiatry` (~1,992 non-test LOC). In
> particular the validated-assessment engine (PHQ-9 / GAD-7 / PCL-5 / C-SSRS
> with canonical scoring bands and crisis hard-triggers) is real, shipping code.

Phoebe's mission is to turn passive observation of brains and behaviour into
causal, model-driven discovery and care — with AI integrated at every layer,
honest uncertainty everywhere, and a qualified human in the loop wherever a
living brain or a patient is on the other end.

## Pillar 1 — Neural Interfaces & Signal Intelligence (BCI)

- **Multimodal acquisition** across EEG, MEG (incl. OPM-MEG), ECoG,
  intracortical spikes (Neuropixels 1.0/2.0/Ultra, Connexus-class), sEMG
  (Meta-Neural-Band class), fNIRS, and functional ultrasound — with
  sub-millisecond time-sync over Lab Streaming Layer and XDF recording/replay.
- **Real-time signal processing**: filtering, ICA artifact removal, Common
  Spatial Patterns, xDAWN, and Riemannian/SPD-covariance featurization on a
  bounded-latency Rust hot path.
- **Decoding & neural foundation models**: hot-swappable Kalman/RNN/transformer
  decoders, spike foundation models (POYO/POYO+), masked-population models
  (NDT2/NEDS), EEG/SEEG models (LaBraM), LLM-coupled Brain-to-Text, and
  fMRI/EEG-to-image — with a benchmarking harness (WER, bits/s, co-bps, ITR).
- **Cross-session / cross-subject adaptation** (Riemannian/manifold alignment,
  meta-learning) that targets the daily-recalibration problem.
- **Closed-loop neuromodulation**: adaptive DBS (beta-LFP-driven), responsive
  neurostimulation, transcranial focused ultrasound and temporal-interference
  control, biomimetic ICMS sensory feedback, and a thermal/charge safety
  governor.

## Pillar 2 — Computational & Systems Neuroscience

- **Spike sorting & imaging** via SpikeInterface & Kilosort 4 with drift
  correction and QC; calcium/voltage pipelines at acquisition speed.
- **Connectomics**: flood-filling-network segmentation, ML-driven proofreading,
  CAVE-style versioned annotation, and Neuroglancer/TensorStore petascale
  serving with a synapse-graph query API and function↔structure fusion.
- **Multi-scale simulation**: managed NEST/NEURON/CoreNEURON/Arbor/Brian2
  backends over the SONATA interchange, Arbor↔TVB co-simulation, and GPU/HPC
  scheduling — seeded from Open Brain Institute / Allen reconstructions.
- **Brain foundation models & digital twins**: fMRI/multimodal foundation
  models, topographic priors, function→structure twins, in-silico optogenetics /
  MEI stimulus synthesis, and patient-specific virtual-brain twins that **report
  calibrated uncertainty and refuse to overstate**.
- **Latent dynamics & representation**: LFADS/AutoLFADS/CEBRA/pi-VAE,
  manifold-native APIs, a unified RSA≈CKA≈CCA comparison module, and first-class
  identifiability/degeneracy reporting.

## Pillar 3 — Clinical Psychology & Psychiatry

- **Validated assessment engine**: PHQ-9, GAD-7, PCL-5, C-SSRS with exact
  scoring/banding and computable DSM-5-TR / ICD-11 coding; crisis items
  hard-trigger escalation.
- **Measurement-based & collaborative care**: scheduled re-administration,
  symptom-trajectory dashboards, treat-to-target alerting, and a caseload
  registry (IMPACT/CoCM pattern).
- **Digital phenotyping & JITAI**: EMA, passive sensing (sleep, mobility,
  typing, voice acoustics), relapse/anomaly detection with honest uncertainty,
  and a contextual-bandit just-in-time adaptive-intervention engine
  (MRT-evaluable).
- **Computational psychiatry & treatment matching**: RDoC/HiTOP dimensional
  models, RL/drift-diffusion/active-inference analyses, circuit-biotype and
  EEG-biomarker ingestion, and treatment-matching decision support
  (research-use, advisory to a clinician — never autonomous prescribing).
- **Regulated therapeutics & clinician copilot**: CBT/DBT/ACT/MI content with
  anti-sycophancy guardrails delivered through Psyche, crisis detection, and a
  behavioural-health ambient scribe (SOAP/GIRP/BIRP/DAP) — all clinician-signed.

## Pillar 4 — Experiment Design & Autonomous Discovery

- **Hypothesis engine**: multi-agent generate/debate/rank/evolve over the
  knowledge graph (Co-Scientist pattern, on the Phase 178 & Kalika substrate),
  with graph-derived novelty and GNN-derived feasibility scoring.
- **Optimal experimental design**: Bayesian OED (expected information gain),
  amortized DAD/iDAD policies, ADO/QUEST+ for psychophysics, Bayesian adaptive
  trials (response-adaptive randomization, group-sequential boundaries,
  BOIN/CRM, master protocols), and SMART/offline-RL dynamic-treatment-regime
  design.
- **Experiment runtime**: a frame-precise authoring tool compiling to a WebGPU
  browser runtime and a native lab runtime, a closed-loop layer over LSL for
  brain-state-dependent stimulation, and robotic/wet-lab execution backends
  (Opentrons, Emerald Cloud Lab/Strateos, automated patch-clamp, DeepLabCut/
  SLEAP).
- **Subject & panel management**: Prolific/MTurk/Gorilla/SONA connectors, a
  data-quality firewall (incl. LLM-agent contamination detection), and
  eligibility/patient↔trial matching.
- **Analysis & reproducibility**: containerized BIDS-App/MNE pipelines with
  enforced multiple-comparison correction, a DoWhy/causal-learn discover→
  identify→estimate→refute flow, machine-readable auto-preregistration,
  multiverse analysis by default, and an end-to-end provenance ledger.

## Pillar 5 — Brain-Mind Knowledge & Evidence

- **Knowledge graph & ontology service**: a Biolink-typed store ingesting
  SPOKE/PrimeKG/Hetionet/Monarch/NeuroKG, hosting Cognitive Atlas, NIFSTD,
  Uberon, NeuroNames, NBO, MFOEM, MeSH, SNOMED CT, DSM-5-TR, and ICD-11 — plus
  **the canonical machine-readable RDoC ontology and the DSM↔ICD-11↔MeSH↔SNOMED
  ↔Cognitive-Atlas↔RDoC crosswalk that do not exist anywhere today**.
- **Literature & evidence**:
  PubMed/OpenAlex/Semantic-Scholar/Europe-PMC/preprint ingestion, SciFact-style
  claim/evidence extraction, smart-citation typing, living systematic reviews,
  and GraphRAG with KGARevion-style KG verification to suppress hallucination.
- **FAIR dataset catalog**: UK Biobank, HCP, ABCD, ENIGMA, OpenNeuro, IBL, Allen
  ABC Atlas, ABIDE, ADNI, PPMI, AnswerALS, NDA, DANDI, BIL, EBRAINS — with
  modality, scale, and access-tier metadata and native NWB/BIDS/DICOM I/O.

## Cross-Cutting — Neuroethics, Governance, Safety & the AI Engine

- **Governance**: neural-data governance to the
  Chile/Colorado/California/Montana/ Connecticut neurorights laws & UNESCO 2025
  standard, HIPAA/GDPR, mandatory neuroimaging defacing, federated learning and
  differential privacy, and dbGaP-style controlled access with immutable audit.
- **Regulatory**: FDA SaMD lifecycle (510(k)/De Novo/PMA), Predetermined Change
  Control Plans, bias/equity and model-drift testing, post-market monitoring,
  and a clinical-evidence/RCT & registration pipeline.
- **Crisis-safety backbone**: 988/Samaritans routing, suicidality escalation,
  age-gating, AI-disclosure, and jurisdiction-aware feature gating (Illinois
  WOPR / Nevada AB 406 / Utah HB 452).
- **Autonomous closed-loop neuroscientist**: hypothesis → adaptive design →
  fail-closed AI-IRB ethics gate → execution → analysis → theory update →
  re-rank, with hallucination/fabrication guardrails and human checkpoints on
  every human-subjects action.

## Application Suite

- **Researcher Workbench** — hypothesis → design → run → analyze → preregister/
  reproduce.
- **Clinician Console** — assessment, MBC dashboards, treatment-matching, and
  the copilot/scribe, all with human sign-off gates.
- **Neural-Interface Control Room** — live BCI decode/stim, signal-quality and
  device-health telemetry, latency SLAs.
- **Knowledge Explorer** — KG / literature / evidence browsing with
  verified-citation answers.
- **Participant/Patient app** — consent, EMA, phenotyping opt-ins, and
  therapeutic content with crisis safety.