Adding seqlearn library and hmm code

Python/rough_ankur.py

@@ -0,0 +1,28 @@
+import pandas as pd
+import numpy as np
+import sys
+
+sys.path.insert(0,'../lib/seqlearn/')
+
+from seqlearn.hmm import MultinomialHMM
+from hmmlearn.hmm import GaussianHMM
+
+
+input_data = pd.read_csv('../data/train_subject1_psd01.csv', header=None)
+
+d1 = pd.read_csv('../data/train_subject1_psd01.csv',header=None)
+d2 = pd.read_csv('../data/train_subject1_psd02.csv',header=None)
+d3 = pd.read_csv('../data/train_subject1_psd03.csv',header=None)
+
+input_data = pd.concat([d1, d2, d3], axis=0)
+lengths = [len(d1), len(d2), len(d3)]
+
+clf = MultinomialHMM()
+clf.fit(input_data.iloc[:,:-1], input_data.iloc[:,-1], lengths)
+pred = clf.predict(d3.iloc[:,:-1])
+actual = d3.iloc[:,-1]
+accuracy = sum(pred == actual)/float(len(actual))
+
+print accuracy
+
+

Rscripts/eda.R

@@ -1,4 +1,4 @@
-dataset.test1 = read.csv('train_subject1_psd01.csv')
+dataset.test1 = read.csv('../data/training_data_complete.csv')
 plot(density(dataset.test1[dataset.test1$X7.00E.00==7,1]))
 lines(density(dataset.test1[dataset.test1$X7.00E.00==2,1]))
 lines(density(dataset.test1[dataset.test1$X7.00E.00==3,1]))
@@ -17,7 +17,7 @@ correlationDataframe = data.frame(correlationMatrix)
 
 for(i in seq(1,96,1)){
   for(j in seq(i,96,1)){
-    if(abs(correlationMatrix[i,j])>0.6 && i!=j){
+    if(abs(correlationMatrix[i,j])>0.70 && i!=j){
       print(paste(i,j,correlationMatrix[i,j]))
     }
   }

lib/seqlearn/.gitignore

@@ -0,0 +1,19 @@
+*.py[cdo]
+*.c
+*.so
+*~
+.#*
+*.sw[op]
+.DS_Store
+build/
+
+pip-log.txt
+
+*.tar.gz
+*.tgz
+*.zip
+
+*.html
+*.lprof
+
+MANIFEST

lib/seqlearn/.travis.yml

@@ -0,0 +1,32 @@
+language: python
+python:
+  - "2.7"
+  - "3.4"
+
+sudo: required
+dist: trusty    # We want a recent SciPy.
+
+addons:
+  apt:
+    packages:
+      - python-numpy
+      - python-scipy
+      - python3-numpy
+      - python3-scipy
+      - libatlas-dev
+      - liblapack-dev
+      - gfortran
+
+virtualenv:
+  system_site_packages: true
+
+install:
+  - deactivate
+  - virtualenv --system-site-packages testenv
+  - source testenv/bin/activate
+  - pip install -U Cython nose scikit-learn
+  - pip install .
+
+script:
+  - cd /tmp
+  - nosetests --exe seqlearn

lib/seqlearn/COPYING

@@ -0,0 +1,19 @@
+Copyright 2013-2014 Lars Buitinck / University of Amsterdam and contributors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

lib/seqlearn/MANIFEST.in

@@ -0,0 +1,4 @@
+include README.rst
+
+recursive-include doc *.rst Makefile conf.py
+recursive-include examples *.bio *.py

lib/seqlearn/Makefile

@@ -0,0 +1,2 @@
+here:
+	python setup.py build_ext --inplace

lib/seqlearn/README.rst

@@ -0,0 +1,64 @@
+.. -*- mode: rst -*-
+
+seqlearn
+========
+
+seqlearn is a sequence classification toolkit for Python. It is designed to
+extend `scikit-learn <http://scikit-learn.org>`_ and offer as similar as
+possible an API.
+
+
+Compiling and installing
+------------------------
+
+Get NumPy >=1.6, SciPy >=0.11, Cython >=0.20.2 and a recent version of
+scikit-learn. Then issue::
+
+    python setup.py install
+
+to install seqlearn.
+
+If you want to use seqlearn from its source directory without installing,
+you have to compile first::
+
+    python setup.py build_ext --inplace
+
+
+Getting started
+---------------
+
+The easiest way to start using seqlearn is to fetch a dataset in CoNLL 2000
+format. Define a task-specific feature extraction function, e.g.::
+
+    >>> def features(sequence, i):
+    ...     yield "word=" + sequence[i].lower()
+    ...     if sequence[i].isupper():
+    ...         yield "Uppercase"
+    ...
+
+Load the training file, say ``train.txt``::
+
+    >>> from seqlearn.datasets import load_conll
+    >>> X_train, y_train, lengths_train = load_conll("train.txt", features)
+
+Train a model::
+
+    >>> from seqlearn.perceptron import StructuredPerceptron
+    >>> clf = StructuredPerceptron()
+    >>> clf.fit(X_train, y_train, lengths_train)
+
+Check how well you did on a validation set, say ``validation.txt``::
+
+    >>> X_test, y_test, lengths_test = load_conll("validation.txt", features)
+    >>> from seqlearn.evaluation import bio_f_score
+    >>> y_pred = clf.predict(X_test, lengths_test)
+    >>> print(bio_f_score(y_test, y_pred))
+
+For more information, see the `documentation
+<http://larsmans.github.io/seqlearn>`_.
+
+
+|Travis|_
+
+.. |Travis| image:: https://api.travis-ci.org/larsmans/seqlearn.png?branch=master
+.. _Travis: https://travis-ci.org/larsmans/seqlearn

lib/seqlearn/doc/.gitignore

@@ -0,0 +1 @@
+_build

lib/seqlearn/doc/Makefile

@@ -0,0 +1,136 @@
+# Makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+PAPER         =
+BUILDDIR      = _build
+
+# User-friendly check for sphinx-build
+ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $$?), 1)
+$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+# the i18n builder cannot share the environment and doctrees with the others
+I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
+
+.PHONY: help clean html dirhtml singlehtml pickle json latex latexpdf text changes linkcheck doctest gettext
+
+help:
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  gh-pages   to make HTML files and commit them to gh-pages"
+	@echo "  html       to make standalone HTML files"
+	@echo "  dirhtml    to make HTML files named index.html in directories"
+	@echo "  singlehtml to make a single large HTML file"
+	@echo "  pickle     to make pickle files"
+	@echo "  json       to make JSON files"
+	@echo "  latex      to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  text       to make text files"
+	@echo "  texinfo    to make Texinfo files"
+	@echo "  info       to make Texinfo files and run them through makeinfo"
+	@echo "  gettext    to make PO message catalogs"
+	@echo "  changes    to make an overview of all changed/added/deprecated items"
+	@echo "  xml        to make Docutils-native XML files"
+	@echo "  pseudoxml  to make pseudoxml-XML files for display purposes"
+	@echo "  linkcheck  to check all external links for integrity"
+	@echo "  doctest    to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	rm -rf $(BUILDDIR)/*
+
+gh-pages: html
+	touch $(BUILDDIR)/html/.nojekyll
+	./commit-to-gh-pages.sh $(BUILDDIR)/html
+
+html:
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+singlehtml:
+	$(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
+	@echo
+	@echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	$(MAKE) -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+text:
+	$(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
+	@echo
+	@echo "Build finished. The text files are in $(BUILDDIR)/text."
+
+texinfo:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo
+	@echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
+	@echo "Run \`make' in that directory to run these through makeinfo" \
+	      "(use \`make info' here to do that automatically)."
+
+info:
+	$(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
+	@echo "Running Texinfo files through makeinfo..."
+	make -C $(BUILDDIR)/texinfo info
+	@echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
+
+gettext:
+	$(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
+	@echo
+	@echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+xml:
+	$(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
+	@echo
+	@echo "Build finished. The XML files are in $(BUILDDIR)/xml."
+
+pseudoxml:
+	$(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
+	@echo
+	@echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."

lib/seqlearn/doc/commit-to-gh-pages.sh

@@ -0,0 +1,14 @@
+#! /bin/sh
+
+# Commit the generated HTML pages to the branch gh-pages.
+# Will not push them to GitHub.
+
+set -e -v
+
+treehash=$(./hash-tree.py "${1:-_build/html}")
+parent=$(git rev-parse gh-pages)
+
+msg="Regenerated docs for $(git rev-parse HEAD)"
+commithash=$(echo "$msg" | git commit-tree $treehash -p $parent)
+echo "Updating gh-pages to $commithash"
+git update-ref refs/heads/gh-pages "$commithash"