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Tribuo - A Java machine learning library
https://github.com/oracle/tribuo

classification clustering deep-learning java machine-learning ml nlp regression

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Tribuo - A Java machine learning library

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README 

        
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# Tribuo - A Java prediction library (v4.3)



[Tribuo](https://tribuo.org) is a machine learning library in Java that

provides multi-class classification, regression, clustering, anomaly detection

and multi-label classification. Tribuo provides implementations of popular ML

algorithms and also wraps other libraries to provide a unified interface.

Tribuo contains all the code necessary to load, featurise and transform data.

Additionally, it includes the evaluation classes for all supported prediction

types. Development is led by [Oracle Labs](https://labs.oracle.com)' Machine

Learning Research Group;  we welcome community contributions.



All trainers are configurable using the

[OLCUT](https://github.com/oracle/olcut) configuration system. This allows a

user to define a trainer in an xml or json file and repeatably build models.

Example configurations for each of the supplied Trainers can be found in the

config folder of each package. These configuration files can also be written in

json or edn by using the appropriate OLCUT configuration dependency. Models and

datasets are serializable using Java serialization. 



All models and evaluations include a serializable provenance object which

records the creation time of the model or evaluation, the identity of the data

and any transformations applied to it, as well as the hyperparameters of the

trainer. In the case of evaluations, this provenance information also includes

the specific model used. Provenance information can be extracted as JSON, or

serialised directly using Java serialisation. For production deployments,

provenance information can be redacted and replaced with a hash to provide

model tracking through an external system.  Many Tribuo models can be exported

in ONNX format for deployment in other languages, platforms or cloud services.



Tribuo runs on Java 8+, and we test on LTS versions of Java along with the

latest release.  Tribuo itself is a pure Java library and is supported on all

Java platforms;  however, some of our interfaces require native code and are

thus supported only where there is native library support. We test on x86\_64

architectures on Windows 10, macOS and Linux (RHEL/OL/CentOS 7+), as these are

supported platforms for the native libraries with which we interface. If you're

interested in another platform and wish to use one of the native library

interfaces (ONNX Runtime, TensorFlow, and XGBoost), we recommend reaching out

to the developers of those libraries. Note the model card and reproducibility

packages require Java 17, and as such are not part of the `tribuo-all` Maven

Central deployment.



## Documentation



* [Library Architecture](docs/Architecture.md)

* [Package Overview](docs/PackageOverview.md)

* Javadoc [4.3](https://tribuo.org/learn/4.3/javadoc), [4.2](https://tribuo.org/learn/4.2/javadoc), [4.1](https://tribuo.org/learn/4.1/javadoc/), [4.0](https://tribuo.org/learn/4.0/javadoc/)

* [Helper Programs](docs/HelperPrograms.md)

* [Developer Documentation](docs/Internals.md)

* [Roadmap](docs/Roadmap.md)

* [Frequently Asked Questions](docs/FAQs.md)



## Tutorials



Tutorial notebooks, including examples of Classification, Clustering,

Regression, Anomaly Detection, TensorFlow, document classification, columnar

data loading, working with externally trained models, and the configuration

system, can be found in the [tutorials](tutorials). These use the

[IJava](https://github.com/SpencerPark/IJava) Jupyter notebook kernel, and work

with Java 10+, except the model card & reproducibility tutorials which require

Java 17.  To convert the tutorials' code back to Java 8, in most cases simply

replace the `var` keyword with the appropriate types.



## Algorithms



### General predictors



Tribuo includes implementations of several algorithms suitable for a wide range 

of prediction tasks:



|Algorithm|Implementation|Notes|

|---|---|---|

|Bagging|Tribuo|Can use any Tribuo trainer as the base learner|

|Random Forest|Tribuo|For both classification and regression|

|Extra Trees|Tribuo|For both classification and regression|

|K-NN|Tribuo|Includes options for several parallel backends, as well as a single threaded backend|

|Neural Networks|TensorFlow|Train a neural network in TensorFlow via the Tribuo wrapper. Models can be deployed using the ONNX interface or the TF interface|



The ensembles and K-NN use a combination function to produce their output.

These combiners are prediction task specific, but the ensemble & K-NN 

implementations are task agnostic. We provide voting and averaging combiners

for multi-class classification, multi-label classification and regression tasks.



### Classification



Tribuo has implementations or interfaces for:



|Algorithm|Implementation|Notes|

|---|---|---|

|Linear models|Tribuo|Uses SGD and allows any gradient optimizer|

|Factorization Machines|Tribuo|Uses SGD and allows any gradient optimizer|

|CART|Tribuo||

|SVM-SGD|Tribuo|An implementation of the Pegasos algorithm|

|Adaboost.SAMME|Tribuo|Can use any Tribuo classification trainer as the base learner|

|Multinomial Naive Bayes|Tribuo||

|Regularised Linear Models|LibLinear||

|SVM|LibSVM or LibLinear|LibLinear only supports linear SVMs|

|Gradient Boosted Decision Trees|XGBoost||



Tribuo also supplies a linear chain CRF for sequence classification tasks. This

CRF is trained via SGD using any of Tribuo's gradient optimizers.



Tribuo has a set of information theoretic feature selection algorithms which

can be applied to classification tasks. Feature inputs are automatically

discretised into equal width bins. At the moment this includes implementations

of mutual information maximisation (MIM), Conditional Mutual Information

Maximisation (CMIM), minimum Redundancy Maximum Relevancy (mRMR) and Joint

Mutual Information (JMI).



To explain classifier predictions there is an implementation of the LIME

algorithm. Tribuo's implementation allows the mixing of text and tabular data,

along with the use of any sparse model as an explainer (e.g., regression trees,

lasso etc), however it does not support images.



### Regression



Tribuo's regression algorithms are multidimensional by default. Single 

dimensional implementations are wrapped in order to produce multidimensional

output.



|Algorithm|Implementation|Notes|

|---|---|---|

|Linear models|Tribuo|Uses SGD and allows any gradient optimizer|

|Factorization Machines|Tribuo|Uses SGD and allows any gradient optimizer|

|CART|Tribuo||

|Lasso|Tribuo|Using the LARS algorithm|

|Elastic Net|Tribuo|Using the co-ordinate descent algorithm|

|Regularised Linear Models|LibLinear||

|SVM|LibSVM or LibLinear|LibLinear only supports linear SVMs|

|Gradient Boosted Decision Trees|XGBoost||



### Clustering



Tribuo includes infrastructure for clustering and also supplies two 

clustering algorithm implementations. We expect to implement additional

algorithms over time.



|Algorithm|Implementation|Notes|

|---|---|---|

|HDBSCAN\*|Tribuo|A density-based algorithm which discovers clusters and outliers|

|K-Means|Tribuo|Includes both sequential and parallel backends, and the K-Means++ initialisation algorithm|



### Anomaly Detection



Tribuo offers infrastructure for anomaly detection tasks. 

We expect to add new implementations over time.



|Algorithm|Implementation|Notes|

|---|---|---|

|One-class SVM|LibSVM||

|One-class linear SVM|LibLinear||



### Multi-label classification



Tribuo offers infrastructure for multi-label classification, along

with a wrapper which converts any of Tribuo's multi-class classification

algorithms into a multi-label classification algorithm. We expect to add 

more multi-label specific implementations over time.



|Algorithm|Implementation|Notes|

|---|---|---|

|Independent wrapper|Tribuo|Converts a multi-class classification algorithm into a multi-label one by producing a separate classifier for each label|

|Classifier Chains|Tribuo|Provides classifier chains and randomized classifier chain ensembles using any of Tribuo's multi-class classification algorithms|

|Linear models|Tribuo|Uses SGD and allows any gradient optimizer|

|Factorization Machines|Tribuo|Uses SGD and allows any gradient optimizer|



### Interfaces



In addition to our own implementations of Machine Learning algorithms, Tribuo

also provides a common interface to popular ML tools on the JVM. If you're

interested in contributing a new interface, open a GitHub Issue, and we can

discuss how it would fit into Tribuo.



Currently we have interfaces to:



* [LibLinear](https://github.com/bwaldvogel/liblinear-java) - via the LibLinear-java port of the original [LibLinear](https://www.csie.ntu.edu.tw/~cjlin/liblinear/) (v2.44).

* [LibSVM](https://www.csie.ntu.edu.tw/~cjlin/libsvm/) - using the pure Java transformed version of the C++ implementation (v3.25).

* [ONNX Runtime](https://onnxruntime.ai) - via the Java API contributed by our group (v1.12.1).

* [TensorFlow](https://tensorflow.org) - Using [TensorFlow Java](https://github.com/tensorflow/java) v0.4.2 (based on TensorFlow v2.7.4). This allows the training and deployment of TensorFlow models entirely in Java.

* [XGBoost](https://xgboost.ai) - via the built in XGBoost4J API (v1.6.2).



## Binaries



Binaries are available on Maven Central, using groupId `org.tribuo`. To pull

all the Java 8 compatible components of Tribuo, including the bindings for

TensorFlow, ONNX Runtime and XGBoost (which are native libraries), use:



Maven:

```xml



    org.tribuo

    tribuo-all

    4.3.1

    pom



```

or from Gradle:

```groovy

implementation ("org.tribuo:tribuo-all:4.3.1@pom") {

    transitive = true // for build.gradle (i.e., Groovy)

    // isTransitive = true // for build.gradle.kts (i.e., Kotlin)

}

```



The `tribuo-all` dependency is a pom which depends on all the Tribuo

subprojects except for the model card and reproducibility projects which

require Java 17.



Most of Tribuo is pure Java and thus cross-platform, however some of the

interfaces link to libraries which use native code. Those interfaces

(TensorFlow, ONNX Runtime and XGBoost) only run on supported platforms for the

respective published binaries, and Tribuo has no control over which binaries

are supplied. If you need support for a specific platform, reach out to the

maintainers of those projects. As of the 4.1 release these native packages all

provide x86\_64 binaries for Windows, macOS and Linux. It is also possible to

compile each package for macOS ARM64 (i.e., Apple Silicon), though there are no

binaries available on Maven Central for that platform for TensorFlow or

XGBoost. As of the 4.3 release Tribuo now depends on a version of ONNX Runtime

which includes support for macOS ARM64 and Linux aarch64 platforms.  When

developing on an ARM platform you can select the `arm` profile in Tribuo's

`pom.xml` to disable the native library tests.



Individual jars are published for each Tribuo module. It is preferable to

depend only on the modules necessary for the specific project. This prevents

your code from unnecessarily pulling in large dependencies like TensorFlow.



## Compiling from source



Tribuo uses [Apache Maven](https://maven.apache.org/) v3.5 or higher to build.

Tribuo is compatible with Java 8+, and we test on LTS versions of Java along

with the latest release. To build, simply run `mvn clean package`. All Tribuo's

dependencies should be available on Maven Central. Please file an issue for

build-related issues if you're having trouble (though do check if you're

missing proxy settings for Maven first, as that's a common cause of build

failures, and out of our control). Note if you're building using Java 16 or

earlier the model card and reproducibility packages will be disabled.



## Repository Layout



Development happens on the `main` branch, which has the version number of the

next Tribuo release with "-SNAPSHOT" appended to it. Tribuo major and minor

releases will be tagged on the `main` branch, and then have a branch named

`vA.B.X-release-branch` (for release `vA.B.0`) branched from the tagged release

commit for any point releases (i.e., `vA.B.1`, `vA.B.2` etc) following from

that major/minor release. Those point releases are tagged on the specific

release branch e.g., `v4.0.2` is tagged on the `v4.0.X-release-branch`.



## Contributing



We welcome contributions! See our [contribution guidelines](./CONTRIBUTING.md).



We have a discussion mailing list

[[email protected]](mailto:[email protected]), archived

[here](https://oss.oracle.com/pipermail/tribuo-devel/). We're investigating

different options for real time chat, check back in the future. For bug

reports, feature requests or other issues, please file a [Github

Issue](https://github.com/oracle/tribuo/issues).



## Security



Please consult the [security guide](./SECURITY.md) for our responsible security vulnerability disclosure process.



## License



Tribuo is licensed under the [Apache 2.0 License](./LICENSE.txt).



## Release Notes:



- [v4.3.1](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-3-1-release-notes.md) - Small bug fixes, notably to CART trees and Example.densify, bumps dependencies to more secure versions.

- [v4.3.0](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-3-release-notes.md) - Model card support, feature selection for classification, protobuf serialization format, kd-tree for distance computations, speed improvements for sparse linear models. Version bumps for most dependencies, and various other small fixes and improvements.

- [v4.2.2](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-2-2-release-notes.md) - Small bug fixes, bump TF-Java to 0.4.2, jackson to 2.13.4, protobuf-java to 3.19.6, OpenCSV to 5.7.1.

- [v4.2.1](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-2-1-release-notes.md) - Bug fixes for KMeans' multithreading, nondeterministic iteration orders affecting ONNX export and K-Means initialization, and upgraded TF-Java to 0.4.1.

- [v4.2.0](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-2-release-notes.md) - Added factorization machines, classifier chains, HDBSCAN. Added ONNX export and OCI Data Science integration. Added reproducibility framework. Various other small fixes and improvements, including the regression fixes from v4.1.1. Filled out the remaining javadoc, added 4 new tutorials (onnx export, multi-label classification, reproducibility, hdbscan), expanded existing tutorials.

- [v4.1.1](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-1-1-release-notes.md) - Bug fixes for multi-output regression, multi-label evaluation, KMeans & KNN with SecurityManager, and update TF-Java 0.4.0.

- [v4.1.0](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-1-release-notes.md) - Added TensorFlow training support, a BERT feature extractor, ExtraTrees, K-Means++, many linear model & CRF performance improvements, new tutorials on TF and document classification. Many bug fixes & documentation improvements.

- [v4.0.2](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-0-2-release-notes.md) - Many bug fixes (CSVDataSource, JsonDataSource, RowProcessor, LibSVMTrainer, Evaluations, Regressor serialization). Improved javadoc and documentation. Added two new tutorials (columnar data and external models).

- [v4.0.1](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-0-1-release-notes.md) - Bugfix for CSVReader to cope with blank lines, added IDXDataSource to allow loading of native MNIST format data.

- [v4.0.0](https://github.com/oracle/tribuo/blob/main/docs/release-notes/tribuo-v4-0-release-notes.md) - Initial public release.

- v3 - Added provenance system, the external model support and onnx integrations.

- v2 - Expanded beyond a classification system, to support regression, clustering and multi-label classification.

- v1 - Initial internal release. This release only supported multi-class classification.