v1.1.0

Author: rickyota

README.md

@@ -1,4 +1,4 @@
-# GenoBoost v1.0.7
+# GenoBoost v1.1.0
 
 [![GenoBoost](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/genoboost.yml)
 [![Release](https://github.com/rickyota/genoboost/actions/workflows/publish.yml/badge.svg)](https://github.com/rickyota/genoboost/actions/workflows/publish.yml)
@@ -51,6 +51,8 @@ $ genoboost train \
 
 ## <a name="news"></a>News
 
+- [v1.1.0](https://github.com/rickyota/genoboost/releases/tag/v1.1.0) (May 23, 2024)
+    - Clean code.
 - [v1.0.7](https://github.com/rickyota/genoboost/releases/tag/v1.0.7) (Nov 25, 2023)
     - Initial version.
 

lib/mylinfa/CHANGELOG.md

@@ -0,0 +1,189 @@
+Version 0.7.0 - 2023-10-15
+========================
+Changes
+-----------
+ * add `array_from_gz_csv` and `array_from_csv` in `linfa-datasets`
+ * make Serde support in `linfa-linear`, `linfa-logistic`, and `linfa-ftrl` optional
+ * bump `argmin` to 0.8.1
+ * add Serde support to `linfa-preprocessing` and `linfa-bayes`
+ * make licenses follow SPDX 2.1 license expression standard
+
+Removals
+-----------
+ * Removed Approximate DBSCAN from `linfa-clustering` due to performance issues. It's now an alias to regular DBSCAN.
+ * Removed `partitions` dependency, which breaks in current versions of Rust.
+
+Version 0.6.1 - 2022-12-03
+========================
+New Algorithms
+-----------
+ * Isotonic regression added to `linfa-linear` by [@wildart]
+ * Mean absolute percentage error (MAPE) added to `linfa` by [@bernado-sb]
+
+Changes
+-----------
+ * add constructor for `LpDist`
+ * add `Send + Sync` to trait objects returned by `linfa-nn`
+ * remove `anyhow <= 1.0.48` version restriction
+ * bump `ndarray` to 0.15
+ * fix `serde` support for `LogisticRegression`
+
+Version 0.6.0 - 2022-06-15
+========================
+
+New Algorithms
+-----------
+ * Multinomial Naive Bayes added to `linfa-bayes` by [@sgrigory]
+ * Follow The Regularized Leader added as `linfa-ftrl` by [@MilaKyr]
+
+Changes
+-----------
+ * **BLAS backend no longer required to build Linfa**
+ * remove `SeedableRng` trait bound from `KMeans` and `GaussianMixture`
+ * replace uses of Isaac RNG with Xoshiro RNG
+
+Breaking Changes
+-----------
+ * parametrize `AsTargets` by the dimensionality of the targets and introduce `AsSingleTargets` and `AsMultiTargets`
+ * `Dataset` and `DatasetView` can now be parametrized by target dimensionality, with 2D being the default
+ * single-target algorithms no longer accept 2D target arrays as input
+ * `cross_validate` changed to `cross_validate_single`, `cross_validate_multi` changed to `cross_validate`
+ * `Pr` has been constrained to `0. <= prob <= 1.` with new constructors
+
+Version 0.5.1 - 2022-02-28
+========================
+
+Note that the commits for this release are in the `0-5-1` branch.
+
+Changes
+-----------
+ * remove `Float` trait bound from many `Dataset` impls, making non-float datasets usable
+ * fix build errors in 0.5.0 caused by breaking minor releases from dependencies
+ * fix bug in k-means where the termination condition of the algorithm was calculated incorrectly
+ * fix build failure when building `linfa` alone, caused by incorrect feature selection for `ndarray`
+
+Version 0.5.0 - 2021-10-20
+========================
+
+New Algorithms
+-----------
+
+ * Nearest neighbour algorithms and traits have been added as `linfa-nn` by [@YuhanLiin]
+ * OPTICS has been added to `linfa-clustering` by [@xd009642]
+ * Multinomial logistic regression has been added to `linfa-logistic` by [@YuhanLiin]
+
+Changes
+-----------
+ * use least squares solver from `ndarray-linalg` in `linfa-linear` (3dc9cb0)
+ * optimized DBSCAN by replacing linear range query implementation with KD-tree (44f91d0)
+ * allow distance metrics other than Euclidean to be used for KMeans (4e58d8d)
+ * enable models to write prediction results into existing memory without allocating (37bc25b)
+ * bumped `ndarray` version to 0.15 and reduced duplicated dependencies (603f821)
+ * introduce `ParamGuard` trait to algorithm parameter sets to enable both explicit and implicit parameter checking (01f912a)
+ * replace uses of HNSW with `linfa-nn` (208a762)
+
+Version 0.4.0 - 2021-04-28
+========================
+
+New Algorithms
+-----------
+
+ * Partial Least Squares Regression has been added as `linfa-pls` by [@relf]
+ * Barnes-Hut t-SNE wrapper has been added as `linfa-tsne` by [@frjnn]
+ * Count-vectorizer and IT-IDF normalization has been added as `linfa-preprocessing` by [@Sauro98]
+ * Platt scaling has been added to `linfa-svm` by [@bytesnake]
+ * Incremental KMeans and KMeans++ and KMeans|| initialization methods added to `linfa-clustering` by [@YuhanLiin]
+
+Changes
+-----------
+ * bumped `ndarray` version to 0.14 (8276bdc)
+ * change trait signature of `linfa::Fit` to return `Result` (a5a479f)
+ * add `cross_validate` to perform K-folding (a5a479f)
+
+Version 0.3.1 - 2021-03-11
+========================
+
+In this release of Linfa the documentation is extended, new examples are added and the functionality of datasets improved. No new algorithms were added.
+
+The meta-issue [#82](https://github.com/rust-ml/linfa/issues/82) gives a good overview of the necessary documentation improvements and testing/documentation/examples were considerably extended in this release. 
+
+Further new functionality was added to datasets and multi-target datasets are introduced. Bootstrapping is now possible for features and samples and you can cross-validate your model with k-folding. We polished various bits in the kernel machines and simplified the interface there.
+
+The trait structure of regression metrics are simplified and the silhouette score introduced for easier testing of K-Means and other algorithms.
+
+Changes
+-----------
+ * improve documentation in all algorithms, various commits
+ * add a website to the infrastructure (c8acc785b)
+ * add k-folding with and without copying (b0af80546f8)
+ * add feature naming and pearson's cross correlation (71989627f)
+ * improve ergonomics when handling kernels (1a7982b973)
+ * improve TikZ generator in `linfa-trees` (9d71f603bbe)
+ * introduce multi-target datasets (b231118629)
+ * simplify regression metrics and add cluster metrics (d0363a1fa8ef)
+
+Version 0.3.0 - 2021-01-21
+=========================
+
+New Algorithms
+-----------
+
+ * Approximated DBSCAN has been added to `linfa-clustering` by [@Sauro98]
+ * Gaussian Naive Bayes  has been added to `linfa-bayes` by [@VasanthakumarV]
+ * Elastic Net linear regression has been added to `linfa-elasticnet` by [@paulkoerbitz] and [@bytesnake]
+
+Changes
+----------
+
+ * Added benchmark to gaussian mixture models (a3eede55)
+ * Fixed bugs in linear decision trees, added generator for TiKZ trees (bfa5aebe7)
+ * Implemented serde for all crates behind feature flag (4f0b63bb)
+ * Implemented new backend features (7296c9ec4)
+ * Introduced `linfa-datasets` for easier testing (3cec12b4f)
+ * Rename `Dataset` to `DatasetBase` and introduce `Dataset` and `DatasetView` (21dd579cf)
+ * Improve kernel tests and documentation (8e81a6d)
+
+Version 0.2.0 - 2020-11-26
+==========================
+
+New algorithms
+-----------
+
+ - Ordinary Linear Regression has been added to `linfa-linear` by [@Nimpruda] and [@paulkoerbitz]
+ - Generalized Linear Models has been added to `linfa-linear` by [VasanthakumarV]
+ - Linear decision trees were added to `linfa-trees` by [@mossbanay]
+ - Fast independent component analysis (ICA) has been added to `linfa-ica` by [@VasanthakumarV]
+ - Principal Component Analysis and Diffusion Maps have been added to `linfa-reduction` by [@bytesnake]
+ - Support Vector Machines has been added to `linfa-svm` by [@bytesnake]
+ - Logistic regression has been added to `linfa-logistic` by [@paulkoerbitz]
+ - Hierarchical agglomerative clustering has been added to `linfa-hierarchical` by [@bytesnake]
+ - Gaussian Mixture Models has been added to `linfa-clustering` by [@relf]
+
+Changes
+----------
+
+ - Common metrics for classification and regression have been added
+ - A new dataset interface simplifies the work with targets and labels
+ - New traits for `Transformer`, `Fit` and `IncrementalFit` standardizes the interface
+ - Switched to Github Actions for better integration
+
+Version 0.1.3
+===========================
+
+New algorithms 
+------------
+
+ - The `DBSCAN` clustering algorithm has been added to `linfa-clustering` ([#12](https://github.com/LukeMathWalker/linfa/pull/12) by [@xd009642])
+   
+Version 0.1.2 (2019-11-25)
+===========================
+
+New algorithms 
+------------
+
+ - First release of `linfa-clustering:v0.1.0` with the `KMeans` algorithm (by [@LukeMathWalker])
+ - First (real) release of `linfa`, re-exporting `linfa-clustering` (by [@LukeMathWalker])
+ 
+
+[@LukeMathWalker]: https://github.com/LukeMathWalker
+[@xd009642]: https://github.com/xd009642