Report section 1 and 2 done

.gitignore

@@ -1,4 +1,3 @@
-env/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -158,4 +157,303 @@ cython_debug/
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-.idea/
+.idea/
+**/.DS_Store
+out/model/*.pt
+
+## Core latex/pdflatex auxiliary files:
+*.aux
+*.lof
+*.lot
+*.fls
+*.out
+*.toc
+*.fmt
+*.fot
+*.cb
+*.cb2
+.*.lb
+
+## Intermediate documents:
+*.dvi
+*.xdv
+*-converted-to.*
+# these rules might exclude image files for figures etc.
+# *.ps
+# *.eps
+# *.pdf
+
+## Generated if empty string is given at "Please type another file name for output:"
+
+## Bibliography auxiliary files (bibtex/biblatex/biber):
+*.bbl
+*.bcf
+*.blg
+*-blx.aux
+*-blx.bib
+*.run.xml
+
+## Build tool auxiliary files:
+*.fdb_latexmk
+*.synctex
+*.synctex(busy)
+*.synctex.gz
+*.synctex.gz(busy)
+*.pdfsync
+
+## Build tool directories for auxiliary files
+# latexrun
+latex.out/
+
+## Auxiliary and intermediate files from other packages:
+# algorithms
+*.alg
+*.loa
+
+# achemso
+acs-*.bib
+
+# amsthm
+*.thm
+
+# beamer
+*.nav
+*.pre
+*.snm
+*.vrb
+
+# changes
+*.soc
+
+# comment
+*.cut
+
+# cprotect
+*.cpt
+
+# elsarticle (documentclass of Elsevier journals)
+*.spl
+
+# endnotes
+*.ent
+
+*.lox
+
+# feynmf/feynmp
+*.mf
+*.mp
+*.t[1-9]
+*.t[1-9][0-9]
+*.tfm
+
+#(r)(e)ledmac/(r)(e)ledpar
+*.end
+*.?end
+*.[1-9]
+*.[1-9][0-9]
+*.[1-9][0-9][0-9]
+*.[1-9]R
+*.[1-9][0-9]R
+*.[1-9][0-9][0-9]R
+*.eledsec[1-9]
+*.eledsec[1-9]R
+*.eledsec[1-9][0-9]
+*.eledsec[1-9][0-9]R
+*.eledsec[1-9][0-9][0-9]
+*.eledsec[1-9][0-9][0-9]R
+
+# glossaries
+*.acn
+*.acr
+*.glg
+*.glo
+*.gls
+*.glsdefs
+*.lzo
+*.lzs
+*.slg
+*.slo
+*.sls
+
+# uncomment this for glossaries-extra (will ignore makeindex's style files!)
+# *.ist
+
+# gnuplot
+*.gnuplot
+*.table
+
+# gnuplottex
+*-gnuplottex-*
+
+# gregoriotex
+*.gaux
+*.glog
+*.gtex
+
+# htlatex
+*.4ct
+*.4tc
+*.idv
+*.lg
+*.trc
+*.xref
+
+# hyperref
+*.brf
+
+# knitr
+*-concordance.tex
+# *.tikz
+*-tikzDictionary
+
+# listings
+*.lol
+
+# luatexja-ruby
+*.ltjruby
+
+# makeidx
+*.idx
+*.ilg
+*.ind
+
+# minitoc
+*.maf
+*.mlf
+*.mlt
+*.mtc[0-9]*
+*.slf[0-9]*
+*.slt[0-9]*
+*.stc[0-9]*
+
+# minted
+_minted*
+*.pyg
+
+# morewrites
+*.mw
+
+# newpax
+*.newpax
+
+# nomencl
+*.nlg
+*.nlo
+*.nls
+
+# pax
+*.pax
+
+# pdfpcnotes
+*.pdfpc
+
+# sagetex
+*.sagetex.sage
+*.sagetex.py
+*.sagetex.scmd
+
+# scrwfile
+*.wrt
+
+# svg
+svg-inkscape/
+
+# sympy
+*.sout
+*.sympy
+sympy-plots-for-*.tex/
+
+# pdfcomment
+*.upa
+*.upb
+
+# pythontex
+*.pytxcode
+pythontex-files-*/
+
+# tcolorbox
+*.listing
+
+# thmtools
+*.loe
+
+# TikZ & PGF
+*.dpth
+*.md5
+*.auxlock
+
+# titletoc
+*.ptc
+
+# todonotes
+*.tdo
+
+# vhistory
+*.hst
+*.ver
+
+*.lod
+
+# xcolor
+*.xcp
+
+# xmpincl
+*.xmpi
+
+# xindy
+*.xdy
+
+# xypic precompiled matrices and outlines
+*.xyc
+*.xyd
+
+# endfloat
+*.ttt
+*.fff
+
+# Latexian
+TSWLatexianTemp*
+
+## Editors:
+# WinEdt
+*.bak
+*.sav
+
+# Texpad
+.texpadtmp
+
+# LyX
+*.lyx~
+
+# Kile
+*.backup
+
+# gummi
+.*.swp
+
+# KBibTeX
+*~[0-9]*
+
+# TeXnicCenter
+*.tps
+
+# auto folder when using emacs and auctex
+./auto/*
+*.el
+
+# expex forward references with \gathertags
+*-tags.tex
+
+# standalone packages
+*.sta
+
+# Makeindex log files
+*.lpz
+
+# xwatermark package
+*.xwm
+
+# REVTeX puts footnotes in the bibliography by default, unless the nofootinbib
+# option is specified. Footnotes are the stored in a file with suffix Notes.bib.
+# Uncomment the next line to have this generated file ignored.
+#*Notes.bib

README.md

@@ -69,3 +69,13 @@ performance of the classifiers in terms of average precision and recall, which a
 | freq     | 27.00%              | 40.00%           |
 | lsi      | 4.00%               | 20.00%           |
 | doc2vec  | 10.00%              | 10.00%           |
+
+## Report
+
+To compile the report run:
+
+```shell
+cd report
+pdflatex -interaction=nonstopmode -output-directory=. main.tex
+pdflatex -interaction=nonstopmode -output-directory=. main.tex
+```

out/lsi_prec_recall.txt

@@ -1,2 +1,2 @@
-Precision: 4.00%
+Precision: 4.50%
 Recall: 20.00%

prec-recall.py

@@ -107,7 +107,7 @@ def evaluate(method_name: str, file_path: str) -> tuple[float, float]:
 
     if len(dfs) > 0:
         df = pd.concat(dfs)
-        plt.figure(figsize=(20, 16))
+        plt.figure(figsize=(12, 10))
         sns.scatterplot(
             x="tsne-2d-one", y="tsne-2d-two",
             hue="Query",

report/main.tex

@@ -16,7 +16,7 @@
 \usepackage{multicol}
 \usepackage{multirow}
 \usepackage{pbox}
-\usepackage{enumitem}	
+\usepackage{enumitem}
 \usepackage{colortbl}
 \usepackage{pifont}
 \usepackage{xspace}
@@ -28,7 +28,6 @@
 \usepackage{color}
 \usepackage{anyfontsize}
 \usepackage{comment}
-\usepackage{soul}
 \usepackage{multibib}
 \usepackage{float}
 \usepackage{caption}
@@ -47,23 +46,22 @@
 
 \subsection*{Section 1 - Data Extraction}
 
-The data extraction process scans through the files in the TensorFlow project to extract Python docstrings and symbol
+The data extraction (implemented in the script \texttt{extract-data.py}) process scans through the files in the
-names for functions, classes and methods. A summary of the number of features extracted can be found in
+TensorFlow project to extract Python docstrings and symbol names for functions, classes and methods. A summary of the
-table~\ref{tab:count1}.
+number of features extracted can be found in table~\ref{tab:count1}. The collected figures show that the number of
-
+classes is more than half the number of files, while the number of functions is about twice the number of files.
-Report and comment figures about the extracted data (e.g., number of files; number of code
+Additionally, the data shows that a class has slightly more than 2 methods in it on average.
-entities of different kinds).
 
 \begin{table}[H]
-\centering \scriptsize
+\centering
-\begin{tabular}{cccc}
+\begin{tabular}{cc}
 \hline
 Type & Number \\
 \hline
-Python files & ? \\
+Python files & 2817 \\
-Classes & ? \\
+Classes & 1882 \\
-Functions & ? \\
+Functions & 4565 \\
-Methods & ? \\
+Methods & 5817 \\
 \hline
 \end{tabular}
 \caption{Count of created classes and properties.}
@@ -72,39 +70,196 @@ Methods & ? \\
 
 \subsection*{Section 2: Training of search engines}
 
-Report and comment an example of a query and the results.
+The training and model execution of the search engines is implemented in the Python script \texttt{search-data.py}.
+The script is able to search a given natural language query among the extracted TensorFlow corpus using four techniques.
+These are namely: Word Frequency Similarity, Term-Frequency Inverse Document-Frequency (TF-IDF) Similarity, Latent
+Semantic Indexing (LSI), and Doc2Vec.
 
+An example output of results generated from the query ``Gather gpu device info'' for the word frequency, TF-IDF, LSI
+and Doc2Vec models are shown in
+figures~\ref{fig:search-freq},~\ref{fig:search-tfidf},~\ref{fig:search-lsi}~and~\ref{fig:search-doc2vec} respectively.
+Both the word frequency and TF-IDF model identify the correct result (according to the provided ground truth for this
+query) as the first recommendation to output. Both the LSI and Doc2Vec models fail to report the correct function in
+all 5 results.
 
-\subsection*{Section 3: Evaluation of search engines}
+\begin{figure}
+    \small
+    \begin{verbatim}
+Similarity: 87.29%
+Python function: gather_gpu_devices
+Description: Gather gpu device info. Returns: A list of test_log_pb2.GPUInf...
+File: tensorflow/tensorflow/tools/test/gpu_info_lib.py
+Line: 167
 
-Using the ground truth provided, evaluate and report recall and average precision for each of the four search engines; comment the differences among search engines.
+Similarity: 60.63%
+Python function: compute_capability_from_device_desc
+Description: Returns the GpuInfo given a DeviceAttributes proto. Args: devi...
+File: tensorflow/tensorflow/python/framework/gpu_util.py
+Line: 35
 
+Similarity: 60.30%
+Python function: gpu_device_name
+Description: Returns the name of a GPU device if available or the empty str...
+File: tensorflow/tensorflow/python/framework/test_util.py
+Line: 129
+
+Similarity: 58.83%
+Python function: gather_available_device_info
+Description: Gather list of devices available to TensorFlow. Returns: A lis...
+File: tensorflow/tensorflow/tools/test/system_info_lib.py
+Line: 126
+
+Similarity: 57.74%
+Python function: gather_memory_info
+Description: Gather memory info.
+File: tensorflow/tensorflow/tools/test/system_info_lib.py
+Line: 70
+        \end{verbatim}
+    \caption{Search result output for the query ``Gather gpu device info'' using the word frequency similarity model.}
+    \label{fig:search-freq}
+\end{figure}
+
+\begin{figure}
+    \small
+    \begin{verbatim}
+Similarity: 86.62%
+Python function: gather_gpu_devices
+Description: Gather gpu device info. Returns: A list of test_log_pb2.GPUInf...
+File: tensorflow/tensorflow/tools/test/gpu_info_lib.py
+Line: 167
+
+Similarity: 66.14%
+Python function: gather_memory_info
+Description: Gather memory info.
+File: tensorflow/tensorflow/tools/test/system_info_lib.py
+Line: 70
+
+Similarity: 62.52%
+Python function: gather_available_device_info
+Description: Gather list of devices available to TensorFlow. Returns: A lis...
+File: tensorflow/tensorflow/tools/test/system_info_lib.py
+Line: 126
+
+Similarity: 57.98%
+Python function: gather
+File: tensorflow/tensorflow/compiler/tf2xla/python/xla.py
+Line: 452
+
+Similarity: 57.98%
+Python function: gather_v2
+File: tensorflow/tensorflow/python/ops/array_ops.py
+Line: 4736
+        \end{verbatim}
+    \caption{Search result output for the query ``Gather gpu device info'' using the TF-IDF model.}
+    \label{fig:search-tfidf}
+\end{figure}
+
+\begin{figure}
+    \small
+    \begin{verbatim}
+Similarity: 92.11%
+Python function: device
+Description: Uses gpu when requested and available.
+File: tensorflow/tensorflow/python/framework/test_util.py
+Line: 1581
+
+Similarity: 92.11%
+Python function: device
+Description: Uses gpu when requested and available.
+File: tensorflow/tensorflow/python/keras/testing_utils.py
+Line: 925
+
+Similarity: 89.04%
+Python function: compute_capability_from_device_desc
+Description: Returns the GpuInfo given a DeviceAttributes proto. Args: devi...
+File: tensorflow/tensorflow/python/framework/gpu_util.py
+Line: 35
+
+Similarity: 85.96%
+Python class: CUDADeviceProperties
+File: tensorflow/tensorflow/tools/test/gpu_info_lib.py
+Line: 51
+
+Similarity: 85.93%
+Python function: gpu_device_name
+Description: Returns the name of a GPU device if available or the empty str...
+File: tensorflow/tensorflow/python/framework/test_util.py
+Line: 129
+        \end{verbatim}
+    \caption{Search result output for the query ``Gather gpu device info'' using the LSI model.}
+    \label{fig:search-lsi}
+\end{figure}
+
+\begin{figure}
+    \small
+    \begin{verbatim}
+Similarity: 81.85%
+Python method: benchmark_gather_nd_op
+File: tensorflow/tensorflow/python/kernel_tests/gather_nd_op_test.py
+Line: 389
+
+Similarity: 81.83%
+Python function: gather_hostname
+File: tensorflow/tensorflow/tools/test/system_info_lib.py
+Line: 66
+
+Similarity: 81.07%
+Python method: benchmarkNontrivialGatherAxis1XLA
+File: tensorflow/tensorflow/compiler/tests/gather_test.py
+Line: 210
+
+Similarity: 80.53%
+Python method: benchmarkNontrivialGatherAxis4
+File: tensorflow/tensorflow/compiler/tests/gather_test.py
+Line: 213
+
+Similarity: 80.45%
+Python method: benchmarkNontrivialGatherAxis4XLA
+File: tensorflow/tensorflow/compiler/tests/gather_test.py
+Line: 216
+        \end{verbatim}
+    \caption{Search result output for the query ``Gather gpu device info'' using the Doc2Vec model.}
+    \label{fig:search-doc2vec}
+\end{figure}
+
+\subsection*{TBD Section 3: Evaluation of search engines}
+
+Using the ground truth provided, evaluate and report recall and average precision for each of the four search engines;
+comment the differences among search engines.
 
 \begin{table} [H]
-\centering \scriptsize
+\centering
 \begin{tabular}{cccc}
 \hline
 Engine & Avg Precision & Recall \\
 \hline
-Frequencies & ? & ? \\
+Frequencies & 27.00\% & 40.00\% \\
-TD-IDF & ? & ? \\
+TD-IDF & 20.00\% & 20.00\% \\
-LSI & ? & ? \\
+LSI & 4.00\% & 20.00\% \\
-Doc2Vec & ? & ? \\
+Doc2Vec & 10.00\% & 10.00\% \\
 \hline
 \end{tabular}
 \caption{Evaluation of search engines.}
 \label{tab:tab2}
 \end{table}
 
-\subsection*{Section 4: Visualisation of query results}
+\subsection*{TBD Section 4: Visualisation of query results}
 
 Include, comment and compare the t-SNE plots for LSI and for Doc2Vec.
 
 \begin{figure}[H]
 \begin{center}
-\includegraphics[width=0.3\textwidth]{Figures/dummy_pic.png}
+\includegraphics[width=\textwidth]{../out/doc2vec_plot}
-\caption{Caption.}
+\caption{T-SNE plot for the Doc2Vec model over the queries and ground truths given in \texttt{ground-truth-unique.txt}.}
-\label{fig:fig1}
+\label{fig:tsne-doc2vec}
+\end{center}
+\end{figure}
+
+\begin{figure}[H]
+\begin{center}
+\includegraphics[width=\textwidth]{../out/lsi_plot}
+\caption{T-SNE plot for the LSI model over the queries and ground truths given in \texttt{ground-truth-unique.txt}.}
+\label{fig:lsi-doc2vec}
 \end{center}
 \end{figure}
 \end{document}