agentic-ecology-bioacoustics

Bioacoustics Skill

[!CAUTION] DATABASE SAFETY AND INTEGRITY: Do NOT write, modify, or insert test annotations directly into the user's production databases. If you need to test database operations (such as saving annotations or training models), you MUST copy the database to a temporary location in agent_workspace (e.g., agent_workspace/test_db) and test against the copy. Never leave testing data in production databases.

Workflow Overview

Follow these sequential steps:

1. Preprocess: Create and populate a Hoplite database from the user's recordings.
   1. Identify Recordings: Locate the user's recordings. If the location is not provided, ask the user.
   2. Select Embedding Model: Confirm which embedding model to use (e.g., perch_v2, surfperch). Query the user if they have not specified one.
   3. Assess Compute Scale: Follow the compute assessment and execution planning protocol in AGENTS.md to evaluate options (Local vs. Colab vs. GCP Dataflow) and await the user's decision.
   4. Execute Ingestion Strategy:

      [!IMPORTANT] MANDATORY INGESTION PIPELINE: Always use dataflow_embed.py to extract audio embeddings into sharded Apache Parquet files, followed by ingest_embeddings.py to build the Hoplite database. Do NOT use EmbedWorker directly.

      • Option A (Local Ingestion via DirectRunner): For local execution on the local machine:
        1. Extract Embeddings with DirectRunner: Execute the Apache Beam pipeline (dataflow_embed.py) with --runner=DirectRunner, passing local audio paths for --input_glob and a local workspace directory (e.g., agent_workspace/embeddings/<dataset>) for --output_dir.
        2. Convert to Hoplite DB: Ingest the resulting Parquet embeddings into a Hoplite database in databases/<dataset> using ingest_embeddings.py.
      • Option B (Remote Ingestion via Colab): For intermediate batches benefiting from GPU/TPU acceleration:
        1. Stage Audio: Transfer recordings to the Colab environment following the storage evaluation and upload protocols in AGENTS.md.
        2. Remote Embedding with DirectRunner: Run dataflow_embed.py with --runner=DirectRunner on the Colab GPU/TPU runtime to generate sharded Apache Parquet embeddings.
        3. Convert to Hoplite DB: Ingest the Parquet embeddings into an ephemeral Hoplite database using ingest_embeddings.py and sync the database files into the local databases/ directory. Ensure the database audio source metadata points to the local recordings path so the local web app can resolve and stream audio.
      • Option C (Cloud-Scale Ingestion via GCP Dataflow): For large recording corpora (hundreds of GBs to TBs):
        1. Stage Audio to GCS: Stage recordings to Cloud Storage following the GCP storage architecture and staging protocols in AGENTS.md.
        2. Distributed Dataflow Embedding: Execute the Apache Beam pipeline (dataflow_embed.py) on Google Cloud Dataflow with DataflowRunner to extract embeddings and generate sharded Apache Parquet files on GCS.
        3. Convert to Hoplite DB: Ingest the resulting Parquet embeddings into a Hoplite database using ingest_embeddings.py.
        4. Mount with GCS FUSE: Mount the audio bucket via GCS FUSE (google-cloud-storage-fuse) so the web app can stream audio windows on demand without downloading full recordings. Refer to GCP Dataflow Audio Embedding for complete instructions and commands.
2. Build a Bioacoustics Web App: Create an interactive webpage for the user to browse, search, and annotate audio snippets associated with the Hoplite database created in the previous step. Make sure the web app supports the following:
   • Browsing: Design the UI so that the user can inspect rows in the database and listen to their associated audio.
   • Annotating: Empower the user to attach annotations to rows in the database. Save, update, and clear user annotations (positive, negative, or uncertain) directly in the database under the "user" provenance tag as they interact.
   • Searching: Empower the user to reorder rows in the database according to various criteria:
     • Vector Search: Allow the user to present a search query in the form of a URI pointing to an audio clip. Embed it with the selected model and perform a search operation in the database. Use the result to rerank all rows in the database. Ensure that the query URI is only used for ranking, and any annotations submitted are saved under the active label (e.g., species name), NOT under the query URI itself.
     • Trained Classifier: Once enough annotations are provided for a particular label (at least two positives and one negative, or two negatives and one positive), allow the user to search with a classifier trained on those annotations. Train a linear classifier using perch-hoplite APIs, and use the classifier's weights to score database rows and rerank them.

Technical Reference

For detailed API usage, implementation instructions, and code examples, see:

• Bioacoustics Technical Reference
• GCP Dataflow Audio Embedding Technical Reference

This reference covers:

• Hoplite Database initialization and loading
• Audio embedding extraction via dataflow_embed.py (with DirectRunner locally or DataflowRunner on GCP)
• Ingesting Parquet embeddings into Hoplite DB using ingest_embeddings.py
• Distributed audio embedding on Google Cloud Dataflow with Apache Beam
• Ingesting Dataflow embeddings with ingest_embeddings.py
• GCS FUSE audio streaming without breaking changes
• Resolving physical audio files from database records
• Agile Modeling setup and search implementation
• Serving search results via the interactive UI
• Processing user annotations (saving, clearing, and restoring state)