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Change Log

All notable changes to this project will be documented in this file. This change log follows the conventions of keepachangelog.com.

[3.0.0 (alpha)]

First release without SMILE dependency. Also a lot of refactoring [breaking] was done.

Added

  • kringing interpolation is enhanced to work with various variograms
  • semi-variograms for kringing
  • rbf interpolation accepts polynomial term
  • barycentric interpolation
  • :frequencies and :bins-maps data in histogram result
  • JTransform fft,dct,dst,dht transformations
  • Data transformations (Power/Box-Cox/Yeo-Johnson)
  • all *mean functions accept optional weights
  • skewness-test, kurtosis-test, normality-test
  • durbin-watson stat
  • shifting and scaling matrix columns/rows
  • lm and glm in fastmath.ml.regression with full analysis
  • fastmath.ml.clustering - (fuzzy) kmeans++ and dbscan clustering algorithms
  • dissimilarity and similarity can accept data for histograms
  • bessel-j0, bessel-j1, bessel-j, bessel-i0, bessel-i1, bessel-i, bessel-y0, bessel-y1, bessel-y, bessel-k0, bessel-k1, bessel-k add to fastmath.special
  • ince-C and ince-S (with radial versions) polynomials

Changed

Removed all functions based on SMILE library, most of them are replaced/rewritten.

  • [breaking] fastmath.clustering namespace is moved to the separate fastmath-clustering library.
  • [breaking] fastmath.gp moved to the fastmath.interpolation.gp
  • [breaking] fastmath.kernel is rewritten with changed API for rbf and kernel
  • [breaking] fastmath.interpolation is rewritten with changed API, part of the methods are implemented directly in Clojure, names are unified
  • [breaking] fastmath.distance rewritten
  • integrate-pdf rewritten to use :gauss-kronrod integration (safer and faster)
  • fastmath.core functionality based on functions with inline code not macros
  • [breaking] polynomial funcitons moved to fastmath.polynomials
  • [breaking] special funcitons (gamma, beta, erf, kummers, bessel, Si/Ci etc) moved to fastmath.special

[2.4.0]

Added

  • Power divergence tests can work on histograms / distribution
  • dissimilarity and similarity distance function of PDF (stats)

Changed

  • SMILE downgraded to 2.6.0 due to licence issue (3.0.2 is GPL, 2.6.0 is LGPL)
  • [breaking] correlation-matrix can use only correlation methods (:pearson, :kendall and :spearman)
  • some SMILE based methods are rewritten to Java or Clojure

Deprecated

  • kullback-leibler-divergence and jensen-shannon-divergence, use dissimilarity function instead.

Fixed

  • stats distances type inconsistency on some cases

[2.3.0]

Added

  • Apache Commons Math RealMatrix and double[][] matrix interfaces
  • vec->array converts any vector to double array
  • Rotation matrix, quaternions, vectors consistency

Changed

  • SMILE deps updated

[2.2.2-SNAPSHOT]

Added

  • mat->float-array2d, mat->array, mat->float-array - row-wise matrix representations as arrays
  • debug? option for :lbfgsb optimizer
  • rint accepts scale argument (same as floor and ceil)
  • roll-a-dice to simulate dice rolling
  • double-exponent, double-significand and ulp functions
  • fastmath.solver/quadratic solver of quadratic equation ax^2+bx+c=0
  • fastmath.quaternion namespace
  • Cholesky decomposition for fixed size matrices
  • Eigenvectors and eigenvalues for matrices
  • negative-zero? tests for -0.0 value
  • linear-optimizer - linear optimization
  • mat, rows->mat and cols->mat - additional matrix creators
  • norm - various matrix norms (0, 1, Inf, max, generalized L_pq, Shatten p-norm, Frobenius)
  • condition - condition number of the matrix
  • smooth-maximum - boltzmann operator, lse, smu, p-norm, mellowmax
  • fastmath.calculus - integration (VEGAS+ MC, h-adaptive Cubature and Gauss-Kronrod, ACM wrappers) and differentiations: derivative, gradient and hessian + Richardson extrapolation

Changed

  • fastmath.complex reimplemented

Fixed

  • matrix object name in printing, indentation
  • speed of element matrix accessing is improved
  • eastwood boxed math and reflection warnings (removed problematic macros, shadowing global vars, etc.)
  • ensuring working with Clojure 1.10.3
  • problem with field methods propagation in uberjar #25, thanks @pfeodrippe

[2.2.1]

Added

  • :lbfgsb java implementation of L-BFGS-B optimization algorithm, use it instead of :bfgs (buggy SMILE implementation)

[2.2.0]

2.1.9-SNAPSHOT renamed to be 2.2.0 - see changes below

[2.1.9-SNAPSHOT]

Added

  • fma - fused multiply and add (+ (* x y) z) (for java 9+)
  • fastmath.efloat - floating point operations with error bounds
  • project - vector projection
  • Apache Commons Math ArrayRealVector extended with VectorProto
  • fastmath.matrix - matrix 2x2, 3x3 and 4x4 basic operations (unrolled)
  • fields refactored
  • binomial-ci - confidence interval methods for binomial distribution
  • new distributions (based on R package gamlss.dist):
    • :zaga - zero adjusted gamma distribution
    • :nbi - negative binomial type I
    • :zinbi - zero inflated negative binomial type I
    • :zanbi - zero altered negative binomial type I
    • :zip - poisson zero inflated
    • :zip2 - zero inflated poisson 2
    • :exgaus - ex-Gaussian, exponentially modified gaussian
    • :zabi - zero adjusted binomial
    • :zibi - binomial zero inflated
    • :bb - beta binomial
    • :zabb - zero adjusted beta binomial
    • :zibb - zero inflated beta binomial
  • other distributions
    • :kolmogorov - Kolmogorov distribution
    • :half-normal - half-normal distribution
    • :truncated and :mixture distributions
    • :multinomial distribution
  • hpdi-extent and pi-extent - new extents based on HPDI and PI from rethinking R package
  • distribution-parameters accept a keyword additionally
  • fastmath.solver/find-root - root solver for univariate functions
  • delta-eq and delta= for checking eqality with given accuracy.
  • coefficient-matrix and correlation-matrix
  • grid functions accept separate coordinates
  • many additional log-exp functions
  • weighted mean (wmean), median (wmedian) and quantiles (wquantile,wquantiles)
  • Vec2/3/4 implement IReduce and IReduceInit
  • historical trigonometric functions (versine with variants, chord, exsec/excsc) with their inverses
  • Clerk notebook for: fastmath.core
  • Added PDF to :cramer-von-misses distribution (based on finite difference)
  • integrate-pdf converted from private to public
  • contingency-2x2-measures - selection of 2x2 contingency measures
  • clj-kondo hooks
  • fastmath.stats.bootstrap introduced as the replacement of fastmath.stats/bootstrap function (now deprecated)

Tests

  • p-value - helper for calculating p-value
  • contingency-table - calculate frequencies
  • binomial-test
  • t-test-one-sample, t-test-two-samples (more information returned)
  • z-test-one-sample, z-test-two-samples
  • f-test
  • power-divergence-test + special cases
    • chisq-test
    • multinomial-likelihood-ratio-test
    • minimum-discrimination-information-test
    • neyman-modified-chisq-test
    • freeman-tukey-test
    • cressie-read-test
  • distribution tests
    • ad-test-one-sample - Anderson Darling test
    • ks-test-one-sample, ks-test-two-samples - Kolmogorov Smirnov test
  • ANOVA tests
    • one-way-anova-test
    • levene-test
    • brown-forsythe-test
    • fligner-killeen-test
  • kruskal-test - Kruskal-Wallis rank sum test

Changed

  • (set! *warn-on-reflection* true) removed (motivation)
  • names changed: ttest- -> t-test-
  • RidgedMulti.java refactored
  • effect size functions revisited

Fixed

  • a nasty bug with primitive macro generation, how could I missed that?
  • :histogram issues with low number of samples
  • fast-max and fast-min had wrong inline operation
  • wrong primitive hinting and protocol extensions
  • set-seed calls protocol for PRNGs
  • integrate-pdf accuracy increased
  • nrd fixed when bandwidth was 0
  • kde estimator revisited

[2.1.8]

Added

  • use-primitive-operators accepts optional set of symbols which shouldn't be imported

Fixed

  • abs redefinition in vector was not properly implemented (problem was visible when vector was precompiled with javac for Clojure2d)

[2.1.7 - do not use]

Added

  • ball-random - unit ball random vector
  • sequence-generator :ball added - unit ball random sampling
  • some more fields
  • ceil and floor can snap to the nearest multiply of scale parameter (optional)

Fixed

  • Vec3 rotation
  • [breaking] ensure proper behaviour for Clojure interfaces for fastmath.vector custom types (see: https://github.com/nextjournal/clerk/issues/64)
  • next-double and prev-double to properly cross 0.0
  • Clojure 1.11.0 fixes (abs)

[2.1.6]

Added

  • jinc - besselj1(x)/x
  • muladd macro
  • evalpoly and mevalpoly - evaluate polynomial (from Julia)
  • makepoly create polynomial function
  • Si and Ci - https://dlmf.nist.gov/6.2#ii
  • much more types of skewness and kurtosis
  • much more effect size functions: r2-determination, eta-sq, omega-sq, epsilon-sq, cohens-f2, cohens-q, cramers-v, cohens-w, tschuprows-t
  • trim and winsor data based on quantiles
  • distances:
    • dist-ang - angular distance
    • sim-cos - cosine similarity
    • angular - refers to angular distance
  • ->seq in fastmath.random can accept sampling scheme (:uniform, :stratified and :systematic)
  • new vector functions: softmax, logsoftmax, logsumexp, logmeanexp, shift (adds a value to all elements), average (mean / weighted average)

Fixed

  • moment didn't work properly for certain cases
  • effect-size methods fixed
  • [breaking] fixes around cosine distance and similarity

Changed

  • fastmath.distance/cosine - refers to cosine similarity now
  • changes around data based distributions:
    • continuous-distribution is the same as kde
    • integer-discrete-distribution and real-discrete-distribution are sorted version of enumerated-int and enumerated-real

Removed

  • [breaking] fastmath.vector/dist-cos - wrong implementation

[2.1.5]

Fixed

  • grid: rhombus is now a real rhombus, triangle is equilateral now (cont. #8)

[2.1.4]

Fixed

  • cell->mid for :triangle grid returned wrong mid point for down triangles (#8)

Changed

  • [breaking] :triangle grid anchor is 3d now, last coordinate indicates triangle position (up/down)

[2.1.3]

Fixed

  • better histogram split

[2.1.2]

Added

  • bias corrected and accelerated percentile method for boostrap (PR7)

[2.1.1]

Added

  • bias corrected percentile method for boostrap (PR6)

[2.1.0]

Added

  • l-bfgs-b optimizer as :bfgs

Changed

  • SMILE version bump to 2.6.0
  • fastmath.gp relies now on SMILE backend (openblas/mkl)

[2.0.5]

Added

  • set-seed! accept :smile RNG which calls smile.math.MathEx/setSeed function. Also, without RNG function will set seed to both: Smile and default-rng.

[2.0.4]

Added

  • :kde distribution - create distribution based on kernel density estimation

[2.0.3]

Changed

  • SMILE version bumped to 2.5.0
  • netlib replaced by mkl (smile)

[2.0.2]

Added

  • moving-average-filter - moving average smoothing
  • kernel-smoothing-filter - signal smoothing filter using kernel methods

[2.0.1]

Added

  • savgol-filter - Savitzky-Golay smoothing filter

[2.0.0-alpha1]

Breaking change: due to significant change of SMILE API I decided to remove three ML namespaces: classification and regression. They probably be back as a separated bindings or incorporeted into SMILE directly.

Added

  • lloyd k-means variants
  • spectral clustering
  • gp namespace (GaussianProcesses) - moved from regression namespace

Removed

  • neural-gas clustering

Changed

  • [breaking] removed namespaces: classification and regression
  • :outliers? key is removed from regrouped data for clusters, now :outliers key is created when outliers are present

[1.5.3]

Added

  • round-even - even (or IEEE/IEC) rounding
  • cut - cut range into even intervals
  • slice-range - cut range into even steps
  • :dense rank ties method

Changed

  • R2 sequence is able to generate up to dimensions=15
  • [breaking] rank and order chagned to be zero based.
  • Licence changed to MIT

Fixed

  • co-intervals works the same as in R now
  • group-by-intervals checks all intervals instead the first one

[1.5.2]

Fixed

  • moment when center is nil should use mean

[1.5.1]

Added

  • moment function

Removed

  • second-moment (invalid implementation)

[1.5.0]

Changed

  • removed slf4j deps

[1.5.0-alpha4]

Changed

  • some defaults for scan optimization

[1.5.0-alpha3]

Added

  • B-Spline and polynomial interpolation
  • cb as cube of the number

[1.5.0-alpha2]

Added

  • mnorm - macro version of norm

Changed

  • protocol's wrapping functions shouldn't have primitive math hints (to avoid too many primitive->boxed conversions)

[1.5.0-alpha1]

Cleaned documentation with more usage examples.

Added

  • demean function
  • seq->vec2, seq->vec3 and seq->vec4
  • warp-noise
  • fastmath.signal - audio signal processing with effects + oscillators

Changed

  • [possibly breaking] all protocols put in separate namespace, wrapping functions introduced (with type hints where possible)
  • binary measure parameters

Fixed

  • acf calculation
  • MAD SMILE bindings replaced (SMILE mutates an array)

Removed

  • TOLERANCE constant in fastmath.vector

[1.4.0 SNAPSHOT]

Added

  • optimization package with various optimization methods
  • BayesianOptimization
  • NegativeBinomial distribution
  • bunch of SSJ based distributions
  • bootstrap datasets
  • t-test

Changed

  • [breaking] classification and regression refactored
  • [breaking] kernel-density moved to kernel namespace

Fixed

  • m/seq->double-array didn't recognize array type properly

[1.3.0 SNAPSHOT]

Added

  • make-vector returns vector for given number of dimensions and optional sequence.
  • vectors implements now IPersistentVector to work with vector?
  • core.matrix protocols for vectors
  • math functions can operate on vectors now (like [[sin]] etc.)
  • new functions for vectors clamp, zero-count, nonzero-count, as-vec
  • classification bindings for SMILE, ~~XGBoost~~ and LIBLINEAR
  • expm1 function
  • monotone interpolation
  • various extent stats funcions
  • haversine and haversine-dist (distance)
  • predicates nan?, inf?, valid-double?, invalid-double?, between?
  • calculate intervals for set of values co-intervals (same as R's function). Also group-by-intervals.
  • various kernel-density methods and kernel-density-ci for kernel density with confidence interval
  • various effect size functions
  • binary measures like fn, tp, etc... (around 30 statistics)
  • multivariate normal distribution added
  • gaussian processes reimplemented
  • kernels consolidated in one namespace

Changed

  • use fmap instead of applyf (now deprecated)
  • outliers are samples which are outside inner fence instead of outer fence
  • Vectors are associative now
  • [breaking] kernel-density is now multimethod
  • [breaking] histogram :bins contain starting point and sample counts only

Removed

  • rbf-obj converter
  • rbf and mercer namespaces (use fastmath.kernel instead)

[1.2.0]

Added

  • Various grid operations
  • hashCode for vectors

Changed

  • Breaking: sequence generator creatators return lazy sequence now (instead of function returning sequence)

[1.1.4]

Added

  • lcm - least common multiplier
  • Vec types implement Reversible Indexed ILookup
  • negative values for some constants (PI, E etc.)

Fixed

  • GAMMA constant name clash

Changed

  • stats-map returns list of outliers rather than number of outliers

Removed

  • :bessel vector field removed (hard to limit input range)

[1.1.3]

Added

  • sample can now return pairs of [x,(f x)].

[1.1.2]

Added

  • estimators for number of bins in histogram
  • kernel-density function

[1.1.1]

Changed

  • histogram data enhanced

[1.1.0]

Added

  • fastmath.clustering namespace

Changed

  • removed k-means from fastmath.stats

[1.0.3]

Fixed

  • norm when domain is a point, returns range start when value is less or equal domain, range end otherwise
  • small fix in one field

[1.0.2]

Added

  • curl for 2d vector fields

[1.0.1]

Added

  • :default (:jdk) rng is added

Fixed

  • MersenneTwister is not synchronized, default RNG is :jdk now

[1.0.0]

Added

  • easings namespace
  • sample function
  • extent stat ([min,max] pair)
  • histgram
  • vector field functions moved from clojure2d, api changed

Changed

  • interpolator have shorter names now (without -interpolator suffix)
  • rbf functions are moved to separate namespace
  • changed parameters order in interpolators (xs and ys are last)
  • next-float-up -> next-double
  • next-float-down -> prev-double

[0.1.1]

Added

  • BesselJ
  • all Gamma function variants (regularized, etc)
  • regularized Beta
  • log1p
  • estimation-strategy can be passed to any function calculating quantiles/percentiles
  • ->seq can accept number of samples now
  • low-exp, high-exp to find lower/greater exponent for given base and number

Changed

  • stats-map doesn't contain select keys option anymore

[0.1.0]

Initial version created from Clojure2d library.

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