1 ;;; GNU Guix --- Functional package management for GNU
2 ;;; Copyright © 2015, 2016, 2017, 2018 Ricardo Wurmus <rekado@elephly.net>
3 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
4 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
6 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
7 ;;; Copyright © 2018 Kei Kebreau <kkebreau@posteo.net>
8 ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
9 ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
10 ;;; Copyright © 2018 Fis Trivial <ybbs.daans@hotmail.com>
11 ;;; Copyright © 2018 Julien Lepiller <julien@lepiller.eu>
12 ;;; Copyright © 2018 Björn Höfling <bjoern.hoefling@bjoernhoefling.de>
14 ;;; This file is part of GNU Guix.
16 ;;; GNU Guix is free software; you can redistribute it and/or modify it
17 ;;; under the terms of the GNU General Public License as published by
18 ;;; the Free Software Foundation; either version 3 of the License, or (at
19 ;;; your option) any later version.
21 ;;; GNU Guix is distributed in the hope that it will be useful, but
22 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
23 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
24 ;;; GNU General Public License for more details.
26 ;;; You should have received a copy of the GNU General Public License
27 ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
29 (define-module (gnu packages machine-learning)
30 #:use-module ((guix licenses) #:prefix license:)
31 #:use-module (guix packages)
32 #:use-module (guix utils)
33 #:use-module (guix download)
34 #:use-module (guix svn-download)
35 #:use-module (guix build-system cmake)
36 #:use-module (guix build-system gnu)
37 #:use-module (guix build-system ocaml)
38 #:use-module (guix build-system python)
39 #:use-module (guix build-system r)
40 #:use-module (guix git-download)
41 #:use-module (gnu packages)
42 #:use-module (gnu packages algebra)
43 #:use-module (gnu packages autotools)
44 #:use-module (gnu packages boost)
45 #:use-module (gnu packages check)
46 #:use-module (gnu packages compression)
47 #:use-module (gnu packages cran)
48 #:use-module (gnu packages dejagnu)
49 #:use-module (gnu packages gcc)
50 #:use-module (gnu packages image)
51 #:use-module (gnu packages maths)
52 #:use-module (gnu packages mpi)
53 #:use-module (gnu packages ocaml)
54 #:use-module (gnu packages onc-rpc)
55 #:use-module (gnu packages perl)
56 #:use-module (gnu packages pkg-config)
57 #:use-module (gnu packages python)
58 #:use-module (gnu packages python-xyz)
59 #:use-module (gnu packages statistics)
60 #:use-module (gnu packages swig)
61 #:use-module (gnu packages xml)
62 #:use-module (gnu packages xorg))
65 ;; The last release is >100 commits behind, so we package from git.
66 (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
69 (version (string-append "2.2.0-1." (string-take commit 8)))
73 (url "https://github.com/libfann/fann.git")
75 (file-name (string-append name "-" version "-checkout"))
78 "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
79 (build-system cmake-build-system)
82 (modify-phases %standard-phases
84 (lambda* (#:key outputs #:allow-other-keys)
85 (let* ((out (assoc-ref outputs "out")))
86 (with-directory-excursion (string-append (getcwd) "/tests")
87 (invoke "./fann_tests"))))))))
88 (home-page "http://leenissen.dk/fann/wp/")
89 (synopsis "Fast Artificial Neural Network")
91 "FANN is a free open source neural network library, which implements
92 multilayer artificial neural networks in C with support for both fully
93 connected and sparsely connected networks.")
94 (license license:lgpl2.1))))
103 (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
104 name "-" version ".tar.gz"))
107 "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
108 (build-system gnu-build-system)
110 `(#:tests? #f ;no "check" target
111 #:phases (modify-phases %standard-phases
114 'install ; no ‘install’ target
115 (lambda* (#:key outputs #:allow-other-keys)
116 (let* ((out (assoc-ref outputs "out"))
117 (bin (string-append out "/bin/")))
119 (for-each (lambda (file)
120 (copy-file file (string-append bin file)))
125 (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
126 (synopsis "Library for Support Vector Machines")
128 "LIBSVM is a machine learning library for support vector
129 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
130 distribution estimation (one-class SVM). It supports multi-class
132 (license license:bsd-3)))
134 (define-public python-libsvm
135 (package (inherit libsvm)
136 (name "python-libsvm")
137 (build-system gnu-build-system)
139 `(#:tests? #f ;no "check" target
140 #:make-flags '("-C" "python")
142 (modify-phases %standard-phases
145 'install ; no ‘install’ target
146 (lambda* (#:key inputs outputs #:allow-other-keys)
147 (let ((site (string-append (assoc-ref outputs "out")
151 (assoc-ref inputs "python") 5) 3)
153 (substitute* "python/svm.py"
154 (("../libsvm.so.2") "libsvm.so.2"))
156 (for-each (lambda (file)
157 (copy-file file (string-append site (basename file))))
158 (find-files "python" "\\.py"))
159 (copy-file "libsvm.so.2"
160 (string-append site "libsvm.so.2")))
163 `(("python" ,python)))
164 (synopsis "Python bindings of libSVM")))
167 ;; The latest release candidate is several years and a couple of fixes have
168 ;; been published since. This is why we download the sources from the SVN
170 (let ((svn-revision 2341))
173 (version (string-append "0.9-rc3-0." (number->string svn-revision)))
177 (url "http://svn.code.sf.net/p/ghmm/code/trunk")
178 (revision svn-revision)))
179 (file-name (string-append name "-" version))
182 "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
183 (build-system gnu-build-system)
185 `(#:imported-modules (,@%gnu-build-system-modules
186 (guix build python-build-system))
188 (modify-phases %standard-phases
189 (add-after 'unpack 'enter-dir
190 (lambda _ (chdir "ghmm") #t))
192 (add-after 'install 'check
193 (assoc-ref %standard-phases 'check))
194 (add-before 'check 'fix-PYTHONPATH
195 (lambda* (#:key inputs outputs #:allow-other-keys)
196 (let ((python-version ((@@ (guix build python-build-system)
198 (assoc-ref inputs "python"))))
200 (string-append (getenv "PYTHONPATH")
201 ":" (assoc-ref outputs "out")
202 "/lib/python" python-version
205 (add-after 'enter-dir 'fix-runpath
206 (lambda* (#:key outputs #:allow-other-keys)
207 (substitute* "ghmmwrapper/setup.py"
208 (("^(.*)extra_compile_args = \\[" line indent)
209 (string-append indent
210 "extra_link_args = [\"-Wl,-rpath="
211 (assoc-ref outputs "out") "/lib\"],\n"
214 (assoc-ref outputs "out")
217 (add-after 'enter-dir 'disable-broken-tests
219 (substitute* "tests/Makefile.am"
220 ;; GHMM_SILENT_TESTS is assumed to be a command.
221 (("TESTS_ENVIRONMENT.*") "")
222 ;; Do not build broken tests.
226 (("label_higher_order_test.*$")
227 "label_higher_order_test\n"))
229 ;; These Python unittests are broken as there is no gato.
230 ;; See https://sourceforge.net/p/ghmm/support-requests/3/
231 (substitute* "ghmmwrapper/ghmmunittests.py"
232 (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
234 (string-append indent
235 "@unittest.skip(\"Disabled by Guix\")\n"
238 (add-after 'disable-broken-tests 'autogen
240 (invoke "bash" "autogen.sh"))))))
242 `(("python" ,python-2) ; only Python 2 is supported
243 ("libxml2" ,libxml2)))
245 `(("pkg-config" ,pkg-config)
248 ("autoconf" ,autoconf)
249 ("automake" ,automake)
250 ("libtool" ,libtool)))
251 (home-page "http://ghmm.org")
252 (synopsis "Hidden Markov Model library")
254 "The General Hidden Markov Model library (GHMM) is a C library with
255 additional Python bindings implementing a wide range of types of @dfn{Hidden
256 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
257 training, HMM clustering, HMM mixtures.")
258 (license license:lgpl2.0+))))
267 "http://micans.org/mcl/src/mcl-"
268 (string-replace-substring version "." "-")
272 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
273 (build-system gnu-build-system)
275 `(#:configure-flags (list "--enable-blast")))
278 (home-page "http://micans.org/mcl/")
279 (synopsis "Clustering algorithm for graphs")
281 "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
282 fast and scalable unsupervised cluster algorithm for graphs (also known as
283 networks) based on simulation of (stochastic) flow in graphs.")
284 ;; In the LICENCE file and web page it says "The software is licensed
285 ;; under the GNU General Public License, version 3.", but in several of
286 ;; the source code files it suggests GPL3 or later.
287 ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
288 (license license:gpl3)))
290 (define-public ocaml-mcl
293 (version "12-068oasis4")
298 "https://github.com/fhcrc/mcl/archive/"
300 (file-name (string-append name "-" version ".tar.gz"))
303 "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
304 (build-system ocaml-build-system)
306 `(#:ocaml ,ocaml-4.02
307 #:findlib ,ocaml4.02-findlib
309 (modify-phases %standard-phases
310 (add-before 'configure 'patch-paths
312 (substitute* "configure"
313 (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
314 (substitute* "setup.ml"
316 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
318 (home-page "https://github.com/fhcrc/mcl")
319 (synopsis "OCaml wrappers around MCL")
321 "This package provides OCaml bindings for the MCL graph clustering
323 (license license:gpl3)))
325 (define-public randomjungle
327 (name "randomjungle")
333 "https://www.imbs.uni-luebeck.de/fileadmin/files/Software"
334 "/randomjungle/randomjungle-" version ".tar_.gz"))
335 (patches (search-patches "randomjungle-disable-static-build.patch"))
338 "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
339 (build-system gnu-build-system)
342 (list "--disable-static"
343 (string-append "--with-boost="
344 (assoc-ref %build-inputs "boost")))
346 (modify-phases %standard-phases
348 'configure 'set-CXXFLAGS
350 (setenv "CXXFLAGS" "-fpermissive ")
358 `(("gfortran" ,gfortran)
359 ("gfortran:lib" ,gfortran "lib")))
360 ;; Non-portable assembly instructions are used so building fails on
361 ;; platforms other than x86_64 or i686.
362 (supported-systems '("x86_64-linux" "i686-linux"))
363 (home-page "https://www.imbs.uni-luebeck.de/forschung/software/details.html#c224")
364 (synopsis "Implementation of the Random Forests machine learning method")
366 "Random Jungle is an implementation of Random Forests. It is supposed to
367 analyse high dimensional data. In genetics, it can be used for analysing big
368 Genome Wide Association (GWA) data. Random Forests is a powerful machine
369 learning method. Most interesting features are variable selection, missing
370 value imputation, classifier creation, generalization error estimation and
371 sample proximities between pairs of cases.")
372 (license license:gpl3+)))
374 (define-public shogun
382 "ftp://shogun-toolbox.org/shogun/releases/"
383 (version-major+minor version)
384 "/sources/shogun-" version ".tar.bz2"))
387 "1rn9skm3nw6hr7mr3lgp2gfqhi7ii0lyxck7qmqnf8avq349s5jp"))
388 (modules '((guix build utils)
392 ;; Remove non-free sources and files referencing them
393 (for-each delete-file
394 (find-files "src/shogun/classifier/svm/"
395 "SVMLight\\.(cpp|h)"))
396 (for-each delete-file
397 (find-files "examples/undocumented/libshogun/"
399 "(classifier_.*svmlight.*|"
400 "evaluation_cross_validation_locked_comparison).cpp")))
401 ;; Remove non-free functions.
402 (define (delete-ifdefs file)
403 (with-atomic-file-replacement file
405 (let loop ((line (read-line in 'concat))
407 (if (eof-object? line)
412 "#endif //USE_SVMLIGHT" line)))
414 "#ifdef USE_SVMLIGHT" line))))
415 (when (or (not skipping?)
416 (and skipping? (not skip-next?)))
418 (loop (read-line in 'concat) skip-next?)))))))
419 (for-each delete-ifdefs
421 (find-files "src/shogun/classifier/mkl"
422 "^MKLClassification\\.cpp")
423 (find-files "src/shogun/classifier/svm"
424 "^SVMLightOneClass\\.(cpp|h)")
425 (find-files "src/shogun/multiclass"
426 "^ScatterSVM\\.(cpp|h)")
427 (find-files "src/shogun/kernel/"
428 "^(Kernel|CombinedKernel|ProductKernel)\\.(cpp|h)")
429 (find-files "src/shogun/regression/svr"
430 "^(MKLRegression|SVRLight)\\.(cpp|h)")
431 (find-files "src/shogun/transfer/domain_adaptation"
432 "^DomainAdaptationSVM\\.(cpp|h)")))
434 (build-system cmake-build-system)
436 '(#:tests? #f ;no check target
438 (modify-phases %standard-phases
439 (add-after 'unpack 'delete-broken-symlinks
441 (for-each delete-file '("applications/arts/data"
442 "applications/asp/data"
443 "applications/easysvm/data"
444 "applications/msplicer/data"
445 "applications/ocr/data"
447 "examples/undocumented/data"))
449 (add-after 'unpack 'change-R-target-path
450 (lambda* (#:key outputs #:allow-other-keys)
451 (substitute* '("src/interfaces/r/CMakeLists.txt"
452 "examples/meta/r/CMakeLists.txt")
453 (("\\$\\{R_COMPONENT_LIB_PATH\\}")
454 (string-append (assoc-ref outputs "out")
457 (add-after 'unpack 'fix-octave-modules
458 (lambda* (#:key outputs #:allow-other-keys)
459 (substitute* "src/interfaces/octave/CMakeLists.txt"
460 (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
461 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave")
462 ;; change target directory
463 (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
464 (string-append (assoc-ref outputs "out")
465 "/share/octave/packages")))
466 (substitute* '("src/interfaces/octave/swig_typemaps.i"
467 "src/interfaces/octave/sg_print_functions.cpp")
468 ;; "octave/config.h" and "octave/oct-obj.h" deprecated in Octave.
469 (("octave/config\\.h") "octave/octave-config.h")
470 (("octave/oct-obj.h") "octave/ovl.h"))
472 (add-after 'unpack 'move-rxcpp
473 (lambda* (#:key inputs #:allow-other-keys)
474 (let ((rxcpp-dir "shogun/third-party/rxcpp"))
476 (install-file (assoc-ref inputs "rxcpp") rxcpp-dir)
478 (add-before 'build 'set-HOME
479 ;; $HOME needs to be set at some point during the build phase
480 (lambda _ (setenv "HOME" "/tmp") #t)))
482 (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
483 "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
484 "-DBUILD_META_EXAMPLES=OFF" ;requires unpackaged ctags
485 ;;"-DINTERFACE_JAVA=ON" ;requires unpackaged jblas
486 ;;"-DINTERFACE_RUBY=ON" ;requires unpackaged ruby-narray
487 ;;"-DINTERFACE_PERL=ON" ;"FindPerlLibs" does not exist
488 ;;"-DINTERFACE_LUA=ON" ;fails because lua doesn't build pkgconfig file
489 "-DINTERFACE_OCTAVE=ON"
490 "-DINTERFACE_PYTHON=ON"
491 "-DINTERFACE_R=ON")))
494 ("numpy" ,python-numpy)
495 ("r-minimal" ,r-minimal)
496 ("octave" ,octave-cli)
501 ("arpack" ,arpack-ng)
508 `(("pkg-config" ,pkg-config)
510 ;; Non-portable SSE instructions are used so building fails on platforms
511 ;; other than x86_64.
512 (supported-systems '("x86_64-linux"))
513 (home-page "http://shogun-toolbox.org/")
514 (synopsis "Machine learning toolbox")
516 "The Shogun Machine learning toolbox provides a wide range of unified and
517 efficient Machine Learning (ML) methods. The toolbox seamlessly allows to
518 combine multiple data representations, algorithm classes, and general purpose
519 tools. This enables both rapid prototyping of data pipelines and extensibility
520 in terms of new algorithms.")
521 (license license:gpl3+)))
530 (uri (string-append "https://github.com/ReactiveX/RxCpp/archive/v"
534 "0y2isr8dy2n1yjr9c5570kpc9lvdlch6jv0jvw000amwn5d3krsh"))
535 (file-name (string-append name "-" version ".tar.gz"))))
536 (build-system cmake-build-system)
539 (modify-phases %standard-phases
540 (add-after 'unpack 'remove-werror
542 (substitute* (find-files ".")
547 (invoke "ctest"))))))
549 `(("catch" ,catch-framework)))
550 (home-page "http://reactivex.io/")
551 (synopsis "Reactive Extensions for C++")
553 "The Reactive Extensions for C++ (RxCpp) is a library of algorithms for
554 values-distributed-in-time. ReactiveX is a library for composing asynchronous
555 and event-based programs by using observable sequences.
557 It extends the observer pattern to support sequences of data and/or events and
558 adds operators that allow you to compose sequences together declaratively while
559 abstracting away concerns about things like low-level threading,
560 synchronization, thread-safety, concurrent data structures, and non-blocking
562 (license license:asl2.0)))
564 (define-public r-adaptivesparsity
566 (name "r-adaptivesparsity")
570 (uri (cran-uri "AdaptiveSparsity" version))
573 "0imr5m8mll9j6n4icsv6z9rl5kbnwsp9wvzrg7n90nnmcxq2cz91"))))
575 `((upstream-name . "AdaptiveSparsity")))
576 (build-system r-build-system)
579 (modify-phases %standard-phases
580 (add-after 'unpack 'link-against-armadillo
582 (substitute* "src/Makevars"
583 (("PKG_LIBS=" prefix)
584 (string-append prefix "-larmadillo"))))))))
587 ("r-matrix" ,r-matrix)
589 ("r-rcpparmadillo" ,r-rcpparmadillo)))
591 `(("armadillo" ,armadillo)))
592 (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
593 (synopsis "Adaptive sparsity models")
595 "This package implements the Figueiredo machine learning algorithm for
596 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
598 (license license:lgpl3+)))
600 (define-public r-kernlab
607 (uri (cran-uri "kernlab" version))
610 "1m0xqf6gyvwayz7w3c83y32ayvnlz0jicj8ijk808zq9sh7dbbgn"))))
611 (build-system r-build-system)
612 (home-page "https://cran.r-project.org/web/packages/kernlab")
613 (synopsis "Kernel-based machine learning tools")
615 "This package provides kernel-based machine learning methods for
616 classification, regression, clustering, novelty detection, quantile regression
617 and dimensionality reduction. Among other methods @code{kernlab} includes
618 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
620 (license license:gpl2)))
629 "http://dlib.net/files/dlib-" version ".tar.bz2"))
632 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
633 (modules '((guix build utils)))
636 ;; Delete ~13MB of bundled dependencies.
637 (delete-file-recursively "dlib/external")
638 (delete-file-recursively "docs/dlib/external")
640 (build-system cmake-build-system)
643 (modify-phases %standard-phases
644 (add-after 'unpack 'disable-asserts
646 ;; config.h recommends explicitly enabling or disabling asserts
647 ;; when building as a shared library. By default neither is set.
648 (substitute* "dlib/config.h"
649 (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
651 (add-after 'disable-asserts 'disable-failing-tests
653 ;; One test times out on MIPS, so we need to disable it.
654 ;; Others are flaky on some platforms.
655 (let* ((system ,(or (%current-target-system)
657 (disabled-tests (cond
658 ((string-prefix? "mips64" system)
659 '("object_detector" ; timeout
661 ((string-prefix? "armhf" system)
662 '("learning_to_track"))
663 ((string-prefix? "i686" system)
668 (substitute* "dlib/test/makefile"
669 (((string-append "SRC \\+= " test "\\.cpp")) "")))
674 ;; No test target, so we build and run the unit tests here.
675 (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
676 (with-directory-excursion test-dir
677 (invoke "make" "-j" (number->string (parallel-job-count)))
678 (invoke "./dtest" "--runall"))
680 (add-after 'install 'delete-static-library
681 (lambda* (#:key outputs #:allow-other-keys)
682 (delete-file (string-append (assoc-ref outputs "out")
686 `(("pkg-config" ,pkg-config)
695 ("openblas" ,openblas)
698 "Toolkit for making machine learning and data analysis applications in C++")
700 "Dlib is a modern C++ toolkit containing machine learning algorithms and
701 tools. It is used in both industry and academia in a wide range of domains
702 including robotics, embedded devices, mobile phones, and large high performance
703 computing environments.")
704 (home-page "http://dlib.net")
705 (license license:boost1.0)))
707 (define-public python-scikit-learn
709 (name "python-scikit-learn")
715 (url "https://github.com/scikit-learn/scikit-learn.git")
717 (file-name (git-file-name name version))
720 "0fkhwg3xn1s7ln9q1szq6kwc4jhwvjh8w4kmv9wcrqy7cq3lbv0d"))))
721 (build-system python-build-system)
724 (modify-phases %standard-phases
725 (add-after 'build 'build-ext
726 (lambda _ (invoke "python" "setup.py" "build_ext" "--inplace") #t))
729 ;; Restrict OpenBLAS threads to prevent segfaults while testing!
730 (setenv "OPENBLAS_NUM_THREADS" "1")
732 ;; Some tests require write access to $HOME.
733 (setenv "HOME" "/tmp")
735 (invoke "pytest" "sklearn" "-m" "not network")))
736 ;; FIXME: This fails with permission denied
737 (delete 'reset-gzip-timestamps))))
739 `(("openblas" ,openblas)))
741 `(("python-pytest" ,python-pytest)
742 ("python-pandas" ,python-pandas) ;for tests
743 ("python-cython" ,python-cython)))
745 `(("python-numpy" ,python-numpy)
746 ("python-scipy" ,python-scipy)))
747 (home-page "http://scikit-learn.org/")
748 (synopsis "Machine Learning in Python")
750 "Scikit-learn provides simple and efficient tools for data mining and
752 (license license:bsd-3)))
754 (define-public python2-scikit-learn
755 (package-with-python2 python-scikit-learn))
757 (define-public python-autograd
758 (let* ((commit "442205dfefe407beffb33550846434baa90c4de7")
760 (version (git-version "0.0.0" revision commit)))
762 (name "python-autograd")
763 (home-page "https://github.com/HIPS/autograd")
771 "189sv2xb0mwnjawa9z7mrgdglc1miaq93pnck26r28fi1jdwg0z4"))
772 (file-name (git-file-name name version))))
774 (build-system python-build-system)
776 `(("python-nose" ,python-nose)
777 ("python-pytest" ,python-pytest)))
779 `(("python-future" ,python-future)
780 ("python-numpy" ,python-numpy)))
782 `(#:phases (modify-phases %standard-phases
785 (invoke "py.test" "-v"))))))
786 (synopsis "Efficiently computes derivatives of NumPy code")
787 (description "Autograd can automatically differentiate native Python and
788 NumPy code. It can handle a large subset of Python's features, including loops,
789 ifs, recursion and closures, and it can even take derivatives of derivatives
790 of derivatives. It supports reverse-mode differentiation
791 (a.k.a. backpropagation), which means it can efficiently take gradients of
792 scalar-valued functions with respect to array-valued arguments, as well as
793 forward-mode differentiation, and the two can be composed arbitrarily. The
794 main intended application of Autograd is gradient-based optimization.")
795 (license license:expat))))
797 (define-public python2-autograd
798 (package-with-python2 python-autograd))
800 (define-public lightgbm
807 "https://github.com/Microsoft/LightGBM/archive/v"
811 "132zf0yk0545mg72hyzxm102g3hpb6ixx9hnf8zd2k55gas6cjj1"))
812 (file-name (string-append name "-" version ".tar.gz"))))
814 `(("python-pytest" ,python-pytest)
815 ("python-nose" ,python-nose)))
817 `(("openmpi" ,openmpi)))
819 `(("python-numpy" ,python-numpy)
820 ("python-scipy" ,python-scipy)))
825 (modify-phases %standard-phases
827 (lambda* (#:key outputs #:allow-other-keys)
828 (with-directory-excursion ,(string-append "../LightGBM-" version)
829 (invoke "pytest" "tests/c_api_test/test_.py")))))))
830 (build-system cmake-build-system)
831 (home-page "https://github.com/Microsoft/LightGBM")
832 (synopsis "Gradient boosting framework based on decision tree algorithms")
833 (description "LightGBM is a gradient boosting framework that uses tree
834 based learning algorithms. It is designed to be distributed and efficient with
835 the following advantages:
838 @item Faster training speed and higher efficiency
839 @item Lower memory usage
840 @item Better accuracy
841 @item Parallel and GPU learning supported (not enabled in this package)
842 @item Capable of handling large-scale data
844 (license license:expat)))
846 (define-public vowpal-wabbit
847 ;; Language bindings not included.
849 (name "vowpal-wabbit")
854 "https://github.com/JohnLangford/vowpal_wabbit/archive/"
858 "0clp2kb7rk5sckhllxjr5a651awf4s8dgzg4659yh4hf5cqnf0gr"))
859 (file-name (string-append name "-" version ".tar.gz"))))
865 (list (string-append "--with-boost="
866 (assoc-ref %build-inputs "boost")))))
867 (build-system gnu-build-system)
868 (home-page "https://github.com/JohnLangford/vowpal_wabbit")
869 (synopsis "Fast machine learning library for online learning")
870 (description "Vowpal Wabbit is a machine learning system with techniques
871 such as online, hashing, allreduce, reductions, learning2search, active, and
872 interactive learning.")
873 (license license:bsd-3)))
875 (define-public python2-fastlmm
877 (name "python2-fastlmm")
882 (uri (pypi-uri "fastlmm" version ".zip"))
885 "1q8c34rpmwkfy3r4d5172pzdkpfryj561897z9r3x22gq7813x1m"))))
886 (build-system python-build-system)
888 `(#:python ,python-2)) ; only Python 2.7 is supported
890 `(("python2-numpy" ,python2-numpy)
891 ("python2-scipy" ,python2-scipy)
892 ("python2-matplotlib" ,python2-matplotlib)
893 ("python2-pandas" ,python2-pandas)
894 ("python2-scikit-learn" ,python2-scikit-learn)
895 ("python2-pysnptools" ,python2-pysnptools)))
898 ("python2-cython" ,python2-cython)
899 ("python2-mock" ,python2-mock)
900 ("python2-nose" ,python2-nose)))
901 (home-page "http://research.microsoft.com/en-us/um/redmond/projects/mscompbio/fastlmm/")
902 (synopsis "Perform genome-wide association studies on large data sets")
904 "FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed
905 Models, is a program for performing both single-SNP and SNP-set genome-wide
906 association studies (GWAS) on extremely large data sets.")
907 (license license:asl2.0)))