origami-ml 0.1.0__tar.gz

origami_ml-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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origami_ml-0.1.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: origami-ml
+Version: 0.1.0
+Summary: An ML classifier model to make predictions from semi-structured data.
+Home-page: https://github.com/yourusername/origami-ml
+Author: Thomas Rueckstiess
+Author-email: thomas.rueckstiess@mongodb.com
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click>=8.1.7
+Requires-Dist: click-option-group>=0.5.6
+Requires-Dist: guildai>=0.9.0
+Requires-Dist: lightgbm>=4.5.0
+Requires-Dist: matplotlib>=3.9.2
+Requires-Dist: mdbrtools>=0.1.1
+Requires-Dist: numpy>=1.26.4
+Requires-Dist: omegaconf>=2.3.0
+Requires-Dist: openml>=0.15.1
+Requires-Dist: pandas>=2.2.3
+Requires-Dist: pymongo>=4.8.0
+Requires-Dist: python-dotenv>=1.0.1
+Requires-Dist: scikit_learn>=1.5.2
+Requires-Dist: torch>=2.4.1
+Requires-Dist: tqdm>=4.66.4
+Requires-Dist: xgboost>=2.1.3
+Provides-Extra: dev
+Requires-Dist: jupyter>=1.1.1; extra == "dev"
+Requires-Dist: jupyter_contrib_nbextensions>=0.7.0; extra == "dev"
+Requires-Dist: pytest>=8.3.3; extra == "dev"
+Requires-Dist: ruff>=0.9.3; extra == "dev"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+<p align="center">
+  <img src="assets/origami_logo.jpg" style="width: 100%; height: auto;">
+</p>
+
+# ORiGAMi - Object Representation through Generative Autoregressive Modelling
+
+<p align="center">
+| <a href="https://arxiv.org/abs/2412.17348"><b>ORiGAMi Paper on Arxiv</b></a> |
+</p>
+
+## Disclaimer
+
+Please note: This tool is not officially supported or endorsed by MongoDB, Inc. The code is released for use "AS IS" without any warranties of any kind, including, but not limited to its installation, use, or performance. Do not run this tool against critical production systems.
+
+## Overview
+
+ORiGAMi is a transformer-based Machine Learning model to directly process semi-structured data such as MongoDB documents or JSON files and make predictions from this data.
+
+Typically, when working with semi-structured data in a Machine Learning context, the data needs to be flattened
+into a tabular form first. This flattening can be lossy, especially in the presence of arrays and nested objects, and often requires domain expertise to extract meaningful higher-order features from the raw data. This feature extraction step is manual, slow and expensive and doesn't scale well.
+
+ORiGAMi is a transformer model and follows the trend of many other deep learning models by operating directly on the raw data and discovering meaningful features itself. Preprocessing is fully automated (apart from some hyper-parameters that can improve the model performance).
+
+
+## Installation
+
+ORiGAMi requires Python version 3.10 or higher. We recommend using a virtual environment, such as
+Python's native [`venv`](https://docs.python.org/3/library/venv.html).
+
+To install ORiGAMi with `pip`, use
+
+```shell
+pip install origami-ml
+```
+
+You can also clone the repository to your local machine and install the dependencies manually:
+
+```shell
+git clone https://github.com/mongodb-labs/origami.git
+cd origami
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Usage
+
+ORiGAMi comes with a command line interface (CLI) and a Python SDK.
+
+### Usage from the Command Line
+
+The CLI allows to train a model and make predictions from a trained model. After installation, run `origami` from your shell to see an overview of available commands.
+
+Help for specific commands is available with `origami <command> --help`, where `<command>` is currently one of `train` or `predict`.
+
+Detailed documentation for the CLI and available options can be found in [`CLI.md`](CLI.md).
+
+### Usage with Python
+
+To see an example on how to use ORiGAMi from Python, take a look at the provided [./notebooks](./notebooks/) folder, e.g. the [`example_origami_dungeons.ipynb`](./notebooks/example_origami_dungeons.ipynb) notebook.
+
+## Experiment Reproduction
+
+This code is released alongside our paper, which can be found on Arxiv: [ORIGAMI: A generative transformer architecture for predictions from semi-structured data](https://arxiv.org/abs/2412.17348). To reproduce the experiments in the paper, see the instructions in the [`./experiments/`](./experiments/) directory.

origami_ml-0.1.0/README.md

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+<p align="center">
+  <img src="assets/origami_logo.jpg" style="width: 100%; height: auto;">
+</p>
+
+# ORiGAMi - Object Representation through Generative Autoregressive Modelling
+
+<p align="center">
+| <a href="https://arxiv.org/abs/2412.17348"><b>ORiGAMi Paper on Arxiv</b></a> |
+</p>
+
+## Disclaimer
+
+Please note: This tool is not officially supported or endorsed by MongoDB, Inc. The code is released for use "AS IS" without any warranties of any kind, including, but not limited to its installation, use, or performance. Do not run this tool against critical production systems.
+
+## Overview
+
+ORiGAMi is a transformer-based Machine Learning model to directly process semi-structured data such as MongoDB documents or JSON files and make predictions from this data.
+
+Typically, when working with semi-structured data in a Machine Learning context, the data needs to be flattened
+into a tabular form first. This flattening can be lossy, especially in the presence of arrays and nested objects, and often requires domain expertise to extract meaningful higher-order features from the raw data. This feature extraction step is manual, slow and expensive and doesn't scale well.
+
+ORiGAMi is a transformer model and follows the trend of many other deep learning models by operating directly on the raw data and discovering meaningful features itself. Preprocessing is fully automated (apart from some hyper-parameters that can improve the model performance).
+
+
+## Installation
+
+ORiGAMi requires Python version 3.10 or higher. We recommend using a virtual environment, such as
+Python's native [`venv`](https://docs.python.org/3/library/venv.html).
+
+To install ORiGAMi with `pip`, use
+
+```shell
+pip install origami-ml
+```
+
+You can also clone the repository to your local machine and install the dependencies manually:
+
+```shell
+git clone https://github.com/mongodb-labs/origami.git
+cd origami
+pip install -r requirements.txt
+pip install -e .
+```
+
+## Usage
+
+ORiGAMi comes with a command line interface (CLI) and a Python SDK.
+
+### Usage from the Command Line
+
+The CLI allows to train a model and make predictions from a trained model. After installation, run `origami` from your shell to see an overview of available commands.
+
+Help for specific commands is available with `origami <command> --help`, where `<command>` is currently one of `train` or `predict`.
+
+Detailed documentation for the CLI and available options can be found in [`CLI.md`](CLI.md).
+
+### Usage with Python
+
+To see an example on how to use ORiGAMi from Python, take a look at the provided [./notebooks](./notebooks/) folder, e.g. the [`example_origami_dungeons.ipynb`](./notebooks/example_origami_dungeons.ipynb) notebook.
+
+## Experiment Reproduction
+
+This code is released alongside our paper, which can be found on Arxiv: [ORIGAMI: A generative transformer architecture for predictions from semi-structured data](https://arxiv.org/abs/2412.17348). To reproduce the experiments in the paper, see the instructions in the [`./experiments/`](./experiments/) directory.

origami_ml-0.1.0/origami/cli/__init__.py

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+from .main import main

origami_ml-0.1.0/origami/cli/generate.py

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+import click
+
+
+@click.command()
+def generate():
+    """Generate synthetic data from a trained ORIGAMI model."""
+    pass

origami_ml-0.1.0/origami/cli/main.py

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+import click
+
+from origami.cli.generate import generate
+from origami.cli.predict import predict
+from origami.cli.train import train
+
+CONTEXT_SETTINGS = dict(max_content_width=120)
+
+
+@click.group(context_settings=CONTEXT_SETTINGS)
+def main():
+    pass
+
+
+main.add_command(train)
+main.add_command(generate)
+main.add_command(predict)

origami_ml-0.1.0/origami/cli/predict.py

@@ -0,0 +1,118 @@
+import json
+import pathlib
+
+import click
+from click_option_group import optgroup
+from omegaconf import OmegaConf
+
+from origami.cli.utils import create_projection, load_data
+from origami.inference import Predictor
+from origami.model import ORIGAMI
+from origami.model.vpda import ObjectVPDA
+from origami.preprocessing import DFDataset, TargetFieldPipe
+from origami.utils import Symbol, count_parameters, load_origami_model
+from origami.utils.config import GuardrailsMethod
+
+
+@click.command()
+@click.argument("source", type=str)
+@click.option(
+    "--model-path",
+    "-m",
+    type=click.Path(dir_okay=False, exists=True, path_type=pathlib.Path, resolve_path=True),
+    default="./model.origami",
+    show_default=True,
+    help="path to trained model",
+)
+@click.option("--target-field", "-t", type=str, required=True, help="target field name to predict")
+@optgroup.group("Source Options")
+@optgroup.option("--source-db", "-d", type=str, help="database name, only used when SOURCE is a MongoDB URI.")
+@optgroup.option("--source-coll", "-c", type=str, help="collection name, only used when SOURCE is a MongoDB URI.")
+@optgroup.option("--include-fields", "-i", type=str, help="comma-separated list of field names to include")
+@optgroup.option("--exclude-fields", "-e", type=str, help="comma-separated list of field names to exclude")
+@optgroup.option("--skip", "-s", type=int, default=0, help="number of documents to skip")
+@optgroup.option("--limit", "-l", type=int, default=0, help="limit the number of documents to load")
+@optgroup.group("Output Options")
+@optgroup.option("--json", "-j", is_flag=True, default=False, help="output full JSON objects including target field")
+@click.option("--verbose", "-v", is_flag=True, default=False)
+def predict(source, **kwargs):
+    """Predict target fields with a trained ORIGAMI model."""
+
+    # load model, config and pipelines
+    model_dict = load_origami_model(kwargs.get("model_path"))
+    state_dict = model_dict["state_dict"]
+    config = model_dict["config"]
+    pipelines = model_dict["pipelines"]
+    encoder = pipelines["train"]["encoder"].encoder
+    schema = pipelines["train"]["schema"].schema
+
+    # create model and load weights
+    match config.model.guardrails:
+        case GuardrailsMethod.STRUCTURE_AND_VALUES:
+            if not config.pipeline.path_in_field_tokens:
+                raise Exception("GuardrailsMethod.STRUCTURE_AND_VALUES requires path_in_field_tokens=True")
+            vpda = ObjectVPDA(encoder, schema)
+        case GuardrailsMethod.STRUCTURE_ONLY:
+            vpda = ObjectVPDA(encoder)
+        case GuardrailsMethod.NONE:
+            vpda = None
+
+    model = ORIGAMI(config.model, config.train, vpda=vpda)
+    model.load_state_dict(state_dict)
+
+    # data configs
+    config.data.source = source
+    config.data.db = kwargs["source_db"]
+    config.data.coll = kwargs["source_coll"]
+    config.data.projection = create_projection(kwargs["include_fields"], kwargs["exclude_fields"])
+    config.data.limit = kwargs["limit"]
+    config.data.target_field = kwargs["target_field"]
+
+    # load data
+    df = load_data(source, config.data)
+
+    # update or create new target pipe with new target_field
+    test_pipeline = pipelines["test"]
+
+    # update pipeline parameters and transform data
+    if "target" in test_pipeline.named_steps:
+        test_pipeline["target"].target_field = config.data.target_field
+    else:
+        test_pipeline.steps.insert(0, ["target", TargetFieldPipe(config.data.target_field)])
+    test_df = test_pipeline.transform(df)
+
+    # datasets
+    test_dataset = DFDataset(test_df)
+
+    if kwargs["verbose"]:
+        # report number of parameters (note we don't count the decoder parameters in lm_head)
+        n_params = count_parameters(model)
+        click.echo(f"running on device: {model.device}", err=True)
+        click.echo(f"number of parameters: {n_params / 1e6:.2f}M", err=True)
+        click.echo(f"config:\n {OmegaConf.to_yaml(config)}", err=True)
+
+    # predict target field
+    predictor = Predictor(model, encoder, config.data.target_field, max_batch_size=config.train.batch_size)
+
+    predictions = predictor.predict(test_dataset)
+
+    for i, (pred, doc, target) in enumerate(zip(predictions, test_dataset.df["docs"], test_dataset.df["target"])):
+        if kwargs["json"]:
+            doc[config.data.target_field] = pred
+            line_str = json.dumps(doc)
+        else:
+            line_str = pred
+        if target == Symbol.UNKNOWN:
+            click.echo(line_str)
+        else:
+            if pred == target:
+                # replace with green version
+                click.echo(f"\033[32m{line_str}\033[0m")
+            else:
+                # replace with red version
+                click.echo(f"\033[31m{line_str}\033[0m")
+
+    # if any target field is not None, print accuracy
+    if any(test_dataset.df["target"] != Symbol.UNKNOWN):
+        acc = predictor.accuracy(test_dataset, show_progress=False)
+        click.echo(f"\nTest accuracy: {acc:.4f}", err=True)