Index

A

ADR AMQP anc2vec Ankh AnnotationSet artifact store

Aspect (class in protea.core.domain.aspect) aspects (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) async job queue audit trail AuPRC axis_tuple_shortid() (in module protea.core.axis_tuple)

B

baseline_scoring_name (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) BatchSpanProcessor (protea.infrastructure.telemetry.SdkBundle attribute) bench-v1-K5-v226-lineage-prostt5 BenchmarkConfig (class in protea.infrastructure.benchmark_config)

BIOLOGICAL_PROCESS (protea.core.domain.aspect.Aspect attribute) BLASTP BPO build_metric_registry() (in module protea.infrastructure.telemetry) build_pair_feature_dict() (in module protea.core._pair_feature_compute)

C

CAFA cafa (protea.core.domain.aspect.Aspect property) canonical accession CANONICAL_AXIS_KEYS (in module protea.core.axis_tuple) categories (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) CCO CELLULAR_COMPONENT (protea.core.domain.aspect.Aspect attribute) chunk pooling chunks() (in module protea.core.utils) code (protea.core.domain.aspect.Aspect property)

column (protea.core._feature_enricher_helpers.LabelConfig attribute) compute() (protea.core._pair_feature_compute.PairAlignmentComputer method) compute_alignment() (in module protea.core.feature_engineering) compute_ia_weight() (in module protea.core._feature_enricher_helpers) compute_nw() (in module protea.core.feature_engineering) compute_sw() (in module protea.core.feature_engineering) compute_taxonomy() (in module protea.core.feature_engineering) configure_logging() (in module protea.infrastructure.logging) configure_telemetry() (in module protea.infrastructure.telemetry) Coordinator

D

Dataset db_pool_in_use (protea.infrastructure.telemetry.MetricRegistry attribute) Deferred deploy-keeper

DIAMOND discover_plugins() (in module protea.core.plugins) DLQ DLX dual-write

E

ECO embedding backend EmbeddingConfig embeddings_batch_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) enabled (protea.infrastructure.telemetry.TelemetryConfig attribute) endpoint (protea.infrastructure.telemetry.TelemetryConfig attribute) ESM-2 ESM-3

ESM-3c ESM-C eval_set_labels (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) evaluation runner EvaluationResult EvaluationSet evidence code EvidenceFilter extract_trace_context() (in module protea.infrastructure.telemetry)

F

FAISS FASTA FeatureRegistry Fmax

format() (protea.infrastructure.logging.JSONFormatter method) format_training_row() (in module protea.services._scoring_training_helpers) from_cafa() (protea.core.domain.aspect.Aspect class method) from_code() (protea.core.domain.aspect.Aspect class method)

G

GAF get_runner_plugins() (in module protea.core.runners) get_tracer() (in module protea.infrastructure.telemetry) GO

GO term GOA golden parquet gate GOPrediction gt_pairs (protea.core._feature_enricher_helpers.LabelConfig attribute)

H

hidden_stages (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) http_request_duration_seconds (protea.infrastructure.telemetry.MetricRegistry attribute)

http_requests_in_flight (protea.infrastructure.telemetry.MetricRegistry attribute) http_requests_total (protea.infrastructure.telemetry.MetricRegistry attribute)

I

IA IC IEA inject_trace_context() (in module protea.infrastructure.telemetry) instrument_sqlalchemy_engine() (in module protea.infrastructure.telemetry)

integration runner intern_string() (in module protea.core.annotation_intern) is_dual_write_enabled() (in module protea.core.schema_sha_v2) is_experimental() (in module protea.core.evidence_codes) is_jsonb_dual_write_enabled() (in module protea.core.jsonb_dual_write) isoform

J

Job job_duration_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) JobEvent jobs_total (protea.infrastructure.telemetry.MetricRegistry attribute)

JSONB JSONB_DUAL_WRITE_ENV (in module protea.core.jsonb_dual_write) JSONFormatter (class in protea.infrastructure.logging) JWT

K

KNN

L

label_for_stage() (protea.infrastructure.benchmark_config.BenchmarkConfig method) LabelConfig (class in protea.core._feature_enricher_helpers) LAFA

LCP leakage-free temporal holdout LK load_benchmark_config() (in module protea.infrastructure.benchmark_config)

M

make_ancestor_closure() (in module protea.core._feature_enricher_helpers) manage.sh maybe_jsonb() (in module protea.core.jsonb_dual_write) maybe_v2() (in module protea.core.schema_sha_v2) MD5 merge_into_existing_leaf() (in module protea.core._feature_enricher_helpers) Method Object MetricRegistry (class in protea.infrastructure.telemetry) MFO MIL MinIO module protea.core._feature_enricher_helpers protea.core._pair_feature_compute protea.core.annotation_intern protea.core.axis_tuple protea.core.disk_cache protea.core.domain.aspect protea.core.evidence_codes protea.core.feature_engineering protea.core.jsonb_dual_write protea.core.plugins protea.core.runners protea.core.schema_sha_v2 protea.core.utils protea.infrastructure.benchmark_config protea.infrastructure.logging protea.infrastructure.telemetry protea.services._embeddings_validation_helpers protea.services._scoring_training_helpers

MOLECULAR_FUNCTION (protea.core.domain.aspect.Aspect attribute)

N

NetGO ngrok tunnel

NK normalize() (in module protea.core.evidence_codes)

O

OBO OntologySnapshot OOM Operation

OperationConsumer OperationRegistry ORM OTel OTLPSpanExporter (protea.infrastructure.telemetry.SdkBundle attribute)

P

PairAlignmentComputer (class in protea.core._pair_feature_compute) Parameter Object ParentBased (protea.infrastructure.telemetry.SdkBundle attribute) pgvector PK PLM plugin registry dispatch pool_size() (in module protea.core.annotation_intern) precompute_alignment_features() (in module protea.core._pair_feature_compute) predictions_batch_seconds (protea.infrastructure.telemetry.MetricRegistry attribute) PredictionSet preferred_default_stages (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) present (protea.core._feature_enricher_helpers.LabelConfig attribute) ProstT5 PROTEA protea.core._feature_enricher_helpers module protea.core._pair_feature_compute module protea.core.annotation_intern module protea.core.axis_tuple module protea.core.disk_cache module protea.core.domain.aspect module

protea.core.evidence_codes module protea.core.feature_engineering module protea.core.jsonb_dual_write module protea.core.plugins module protea.core.runners module protea.core.schema_sha_v2 module protea.core.utils module protea.infrastructure.benchmark_config module protea.infrastructure.logging module protea.infrastructure.telemetry module protea.services._embeddings_validation_helpers module protea.services._scoring_training_helpers module Protein ProtT5

Q

q_acc (protea.core._feature_enricher_helpers.LabelConfig attribute)

qualifier QueueConsumer

R

RabbitMQ Redis refresh_db_pool_gauge() (in module protea.infrastructure.telemetry) registry (protea.infrastructure.telemetry.MetricRegistry attribute) release-please render_metrics() (in module protea.infrastructure.telemetry) reranker_cache

RerankerModel reset_plugin_cache() (in module protea.core.plugins) resolve_runner() (in module protea.core.runners) resolve_telemetry_config() (in module protea.infrastructure.telemetry) resolve_workers() (in module protea.core._pair_feature_compute) Resource (protea.infrastructure.telemetry.SdkBundle attribute) RetryLaterError

S

sample_ratio (protea.infrastructure.telemetry.TelemetryConfig attribute) schema_sha SdkBundle (class in protea.infrastructure.telemetry) SemVer Sequence

service_name (protea.infrastructure.telemetry.TelemetryConfig attribute) SHORTID_HEX_LEN (in module protea.core.axis_tuple) smell budget Smin stage_labels (protea.infrastructure.benchmark_config.BenchmarkConfig attribute) study_v9

T

t0 t1 TelemetryConfig (class in protea.infrastructure.telemetry) TraceIdRatioBased (protea.infrastructure.telemetry.SdkBundle attribute)

TracerProvider (protea.infrastructure.telemetry.SdkBundle attribute) TSV TTFB two-session worker pattern

U

update_synth_entry() (in module protea.core._feature_enricher_helpers)

utcnow() (in module protea.core.utils)

V

validate_embedding_config_body() (in module protea.services._embeddings_validation_helpers)

W

warmup_taxonomy_db() (in module protea.core.feature_engineering)