autoannotate-timeseries 0.1.5

SOTA unsupervised auto-annotation SDK for time series classification

AutoAnnotate-TimeSeries 📊

State-of-the-art unsupervised auto-annotation SDK for time series classification with GUI

AutoAnnotate-TimeSeries automatically clusters and organizes unlabeled time series datasets using cutting-edge Chronos foundation models by Amazon. It features a GUI and interactive HTML preview with Plotly charts for visual cluster inspection, as well as CLI tool.

✨ Features

• 🎨 Graphical User Interface: Easy file browser and visual controls via autoannotate-ts
• 📈 Interactive Plotly Charts: View cluster samples in browser before labeling
• 🤖 SOTA Foundation Models: Chronos-T5, Chronos-2
• 🔬 Multiple Clustering: K-means, HDBSCAN, Spectral, DBSCAN
• 📁 Smart Organization: CSV files named after cluster names for easy identification
• 🕐 Flexible Timestamp Handling: Auto-detect or specify timestamp column (GUI uses indices, CLI uses names)
• 📂 Clean Output: HTML preview files saved in output folder alongside results
• ✂️ Auto Splits: Train/val/test dataset splitting
• 💾 Export: CSV, JSON formats
• 📊 Single CSV Input: All time series in one file
• 🔌 Python API: Full programmatic control

🚀 Installation

pip install autoannotate-timeseries

Optional Dependencies

HDBSCAN Clustering (Optional):

If you want to use the HDBSCAN clustering method:

# Option 1: Install with the package
pip install autoannotate-timeseries[hdbscan]

# Option 2: Install separately before running autoannotate
pip install hdbscan

Note: HDBSCAN is not required for the default K-means, Spectral, or DBSCAN methods. Only install it if you specifically need HDBSCAN clustering.

Development Tools:

pip install -e .[dev]

After Installation

Two commands are available:

• autoannotate-ts - Launch the graphical user interface
• autoannotate-ts-cli - Command-line interface for automation

Check installation:

autoannotate-ts-cli --version
autoannotate-ts-cli --help

📝 Input Data Format

Your CSV Structure

INPUT: One CSV file with multiple time series as columns

timestamp,series_1,series_2,series_3,series_4,series_5
2024-01-01 00:00:00,10.5,20.1,15.3,18.2,22.5
2024-01-01 01:00:00,11.2,19.8,14.9,17.8,23.1
2024-01-01 02:00:00,9.8,21.2,15.7,18.5,21.8
2024-01-01 03:00:00,10.1,19.5,16.1,18.0,22.2
...

Key Points:

• First column can be timestamp (auto-detected or specify explicitly)
• Each column = one time series to be clustered
• Column names are preserved as series identifiers
• Variable length series supported
• Missing values automatically handled

Timestamp Column Handling:

• Auto-detect (recommended): Leave empty in GUI or omit --timestamp-column in CLI
• GUI: Use column index (0 = first column, 1 = second column, etc.)
• CLI: Use column name (e.g., --timestamp-column "timestamp")

Specify timestamp column:

autoannotate-ts-cli annotate data.csv output --timestamp-column "datetime" --n-clusters 5

Output Structure

output/
├── increasing_trend/
│   └── increasing_trend.csv    # Contains series_1, series_4 (all rows)
├── decreasing_trend/
│   └── decreasing_trend.csv    # Contains series_2 (all rows)
├── seasonal/
│   └── seasonal.csv            # Contains series_3, series_5 (all rows)
├── unclustered/
│   └── unclustered.csv         # Outliers/noise
├── splits/                     # Available with a CLI parameter
│   ├── train/
│   │   ├── increasing_trend/
│   │   │   └── increasing_trend.csv
│   │   └── ...
│   ├── val/
│   └── test/
├── cluster_0_preview.html      # HTML preview files (saved in output folder)
├── cluster_1_preview.html
├── cluster_2_preview.html
├── metadata.json
└── labels.csv

Key Points:

• Each class folder contains ONE CSV file named after the class
• CSV file includes timestamp column and all time series belonging to that class
• HTML preview files are saved in the output folder for reference

🎨 Quick Start - GUI

The easiest way to use AutoAnnotate-TimeSeries:

autoannotate-ts

Workflow:

1. 📁 Select input CSV file (with multiple time series as columns)
2. 📂 Select output folder
3. 🔢 Set number of classes
4. 🤖 Choose model
5. 📏 Configure context length (512 for typical series, 1024+ for long series)
6. 📊 [Optional] Specify timestamp column index (e.g., 0 for first column, leave empty for auto-detect)
7. ▶️ Click "Start Auto-Annotation"

The app will:

• Cluster your time series automatically
• Open interactive HTML previews in your browser with Plotly charts for each cluster
• Save all preview files in the output folder (not project root)
• Prompt you to label each cluster interactively

💻 CLI Usage

Basic Command

autoannotate-ts-cli annotate /path/to/data.csv /path/to/output \
    --n-clusters 5 \
    --model chronos-t5-tiny \
    --create-splits

Advanced CLI Options

autoannotate-ts-cli annotate ./data/sensors.csv ./output \
    --n-clusters 8 \
    --method hdbscan \
    --model chronos-2 \
    --context-length 512 \
    --timestamp-column "datetime" \
    --create-splits \
    --export-format json

Available models: chronos-t5-tiny, chronos-t5-small, chronos-2

Note: CLI uses column names for timestamp (e.g., --timestamp-column "timestamp"), while GUI uses column * indices* (e.g., 0 for first column).

CLI Options Reference

autoannotate-ts-cli annotate INPUT_FILE OUTPUT_DIR [OPTIONS]

Options:
  --n-clusters, -n INTEGER        Number of clusters (required for kmeans/spectral)
  --method, -m [kmeans|hdbscan|spectral|dbscan]
                                  Clustering method (default: kmeans)
  --model [chronos-t5-tiny|chronos-t5-small|chronos-2]
                                  Embedding model (default: chronos-2)
  --batch-size, -b INTEGER        Batch size for embedding extraction (default: 16)
  --n-samples INTEGER             Representative samples per cluster (default: 5)
  --context-length INTEGER        Context length for models (default: 512)
  --timestamp-column TEXT         Timestamp column name (auto-detected if not specified)
  --create-splits                 Create train/val/test splits
  --export-format [csv|json]      Export labels format (default: csv)
  --help                          Show this message and exit

Technical Details:

• Batch Size: Default is 16 for both GUI and CLI, optimized for memory efficiency
• Dimensionality Reduction: Automatically applied when dataset has more than 50 time series
• Context Length: Number of time steps processed by the model (512 for typical series, up to 8192 for chrono-2 and long time-series)

🐍 Python API

from autoannotate import AutoAnnotator
from pathlib import Path

annotator = AutoAnnotator(
    input_file=Path("./data/timeseries.csv"),
    output_dir=Path("./output"),
    model="chronos-t5-tiny",
    clustering_method="kmeans",
    n_clusters=5,
    batch_size=16,
    context_length=512,
    timestamp_column="timestamp"  # Optional
)

result = annotator.run_full_pipeline(
    n_samples=7,
    create_splits=True,
    export_format="csv"
)

print(f"Processed {result['n_timeseries']} time series")
print(f"Created {result['n_clusters']} classes")

Manual Pipeline Control

annotator.load_timeseries()
annotator.extract_embeddings()
annotator.cluster()

stats = annotator.get_cluster_stats()
print(f"Found {stats['n_clusters']} clusters")

class_names = {
    0: "increasing_trend",
    1: "decreasing_trend",
    2: "seasonal_pattern",
    3: "stationary"
}

annotator.organize_dataset(class_names)
annotator.export_labels(format="json")

📊 Example: Real-World Sensor Data

Input CSV (sensors.csv):

timestamp,temp_A,temp_B,temp_C,humidity_A,humidity_B
2024-01-01 00:00,22.5,23.1,21.8,65.2,64.8
2024-01-01 01:00,22.8,23.0,21.9,65.5,64.9
2024-01-01 02:00,23.1,22.9,22.1,65.8,65.1
...

Command:

autoannotate-ts-cli annotate sensors.csv ./organized \
    --n-clusters 3 \
    --timestamp-column "timestamp"

Output:

organized/
├── stable_temperature/
│   └── stable_temperature.csv        # Contains: timestamp, temp_A, temp_C
├── variable_temperature/
│   └── variable_temperature.csv      # Contains: timestamp, temp_B
├── high_humidity/
│   └── high_humidity.csv             # Contains: timestamp, humidity_A, humidity_B
├── cluster_0_preview.html
├── cluster_1_preview.html
├── cluster_2_preview.html
├── metadata.json
└── labels.csv

🧠 Model Comparison

Model	Context	Speed	Quality	Best For
chronos-t5-tiny	512	⚡⚡⚡	⭐⭐⭐	Fast inference, small datasets
chronos-t5-small	512	⚡⚡	⭐⭐⭐⭐	Balanced (recommended)
chronos-2	up to 8192	⚡	⭐⭐⭐⭐⭐	Best quality, long series (v2 model)

Important Notes:

• chronos-2 is a completely new architecture (uses Chronos2Pipeline) with support for much longer time series (up to 8192 tokens vs 512)
• chronos-2 requires chronos-forecasting>=2.0.0 (Already installed with pip install autoannotate-timeseries)
• For most use cases, chronos-t5-small offers the best balance of speed and quality

🔬 Clustering Methods

The following methods can be specified when running autoannotate-ts-cli annotate through the --method argument

Method	Auto K	Handles Noise	Best For	Installation
kmeans	❌	❌	Fast, spherical clusters	✅ Included (Default method used in GUI)
hdbscan	✅	✅	Complex shapes, outliers	⚠️ Optional: pip install ...[hdbscan]
spectral	❌	❌	Non-convex shapes	✅ Included
dbscan	✅	✅	Density-based	✅ Included

Note: HDBSCAN requires separate installation. See Optional Dependencies section.

✅ Quick Validation

Test if your CSV file is valid:

autoannotate-ts-cli validate ./your_data.csv

This shows:

• Number of time series columns found
• Column names
• Auto-detected timestamp column (if present)

With explicit timestamp column:

autoannotate-ts-cli validate ./your_data.csv --timestamp-column "timestamp"

🐛 Troubleshooting

Out of Memory?

Reduce batch size and context length for large datasets:

annotator = AutoAnnotator(
    input_file=Path("./data.csv"),
    output_dir=Path("./output"),
    batch_size=8,  # Reduce from default 16 to 8
    context_length=256,  # Reduce from default 512 to 256
    model="chronos-t5-tiny"
)

Or for CLI:

autoannotate-ts-cli annotate data.csv output \
    --batch-size 8 \
    --context-length 256 \
    --model chronos-t5-tiny \
    --n-clusters 5

Too Many/Few Clusters?

Try HDBSCAN for automatic cluster detection:

autoannotate-ts-cli annotate data.csv output --method hdbscan

Note: HDBSCAN must be installed first:

pip install autoannotate-timeseries[hdbscan]

If you try to use HDBSCAN without installing it, you'll get an error: ImportError: HDBSCAN is not installed. Install it with: pip install autoannotate-timeseries[hdbscan]

Need to specify timestamp column?

CLI (uses column name):

autoannotate-ts-cli annotate data.csv output --timestamp-column "datetime" --n-clusters 5

GUI (uses column index):

• Enter 0 for first column, 1 for second column, etc.
• Leave empty to auto-detect

🔄 Data Preparation Tips

If you have separate CSV files per time series:

Merge them first:

import pandas as pd
from pathlib import Path

dfs = []
for csv_file in Path("./separate_files").glob("*.csv"):
    df = pd.read_csv(csv_file)
    series_name = csv_file.stem
    df_renamed = df.rename(columns={"value": series_name})
    dfs.append(df_renamed)

merged_df = pd.concat(dfs, axis=1)
merged_df.to_csv("combined_timeseries.csv", index=False)

If you have wide format with row-based time series:

Transpose it:

import pandas as pd

df = pd.read_csv("wide_format.csv")
df_transposed = df.T
df_transposed.to_csv("column_format.csv")

🤝 Contributing

1. Fork the repository
2. Create feature branch
3. All actions from tests.yml should pass.
4. Push and create PR

📄 License

MIT License - see LICENSE file.

🙏 Acknowledgments

Built with PyTorch, scikit-learn, pandas, numpy and more. Foundation models: Chronos-T5 and Chronos-2 (Amazon)

Made for the RAIDO Project, from MetaMind Innovations

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Sister Project: AutoAnnotate-Vision - For image auto-annotation