Comment out response to reviewers

Makefile

@@ -6,6 +6,6 @@ build_folder:
 letter.pdf: letter.tex
 	latexmk -pdf letter.tex
 
-
 clean:
 	rm -rf build
+

README.md

@@ -1,2 +1,35 @@
 # ba-letter
 
+Repository containing the latex source for the bachelor's thesis letter.
+
+After cloning, make sure to initialize the submodules containing the dependencies:
+```bash
+$ git submodule update --init
+```
+
+## Build
+
+### Build on host
+
+For a list of dependencies consult one of the dockerfiles in the `dockerfiles` directory. Build document:
+
+```bash
+$ make
+```
+
+After compiling, the PDF can be found in the `build` directory.
+
+### Build using docker
+
+Be warned that `texlive` installations can take some time.
+Building the docker image may take a few minutes.
+
+1. Build docker image
+    ```bash
+    $ docker build -f dockerfiles/Dockerfile.alpine . -t ba-letter
+    ```
+2. Build document
+    ```bash
+    $ docker run --rm -v $PWD:$PWD -w $PWD -u `id -u`:`id -g` ba-letter make
+    ```
+

dockerfiles/Dockerfile.alpine

@@ -2,6 +2,13 @@ FROM alpine:3.19
 
 RUN apk update && apk upgrade
 RUN apk add make texlive texmf-dist-pictures
-RUN apk add texmf-dist-publishers
-RUN apk add texmf-dist-science
-RUN apk add texmf-dist-fontsextra
+RUN apk add texmf-dist-publishers texmf-dist-science texmf-dist-fontsextra texmf-dist-latexextra
+RUN apk add biber texmf-dist-bibtexextra
+
+# The 'bbm' package insists on generating stuff in the home directory. In
+# order to guarantee access to the home directory no matter the user the
+# docker container is run with, create a temporary one anyone can write to
+RUN mkdir /tmp/home
+RUN chmod -R 777 /tmp/home
+ENV HOME=/tmp/home
+

dockerfiles/Dockerfile.arch

@@ -0,0 +1,25 @@
+FROM archlinux:latest
+
+RUN pacman-key --init
+RUN pacman-key --populate archlinux
+RUN pacman -Sy archlinux-keyring --noconfirm && pacman -Su --noconfirm
+
+RUN pacman -Syu --noconfirm
+RUN pacman -S make perl texlive texlive-binextra texlive-pictures --noconfirm
+RUN pacman -S texlive-publishers texlive-mathscience texlive-fontsextra texlive-latexextra --noconfirm
+RUN pacman -Syu biber texlive-bibtexextra --noconfirm
+
+# The 'bbm' package insists on generating stuff in the home directory. In
+# order to guarantee access to the home directory no matter the user the
+# docker container is run with, create a temporary one anyone can write to
+RUN mkdir /tmp/home
+RUN chmod -R 777 /tmp/home
+ENV HOME=/tmp/home
+
+# Generate font necessary for \mathbbm{1}
+RUN mktexpk --mfmode / --bdpi 600 --mag 1+0/600 --dpi 600 bbm10
+RUN chmod -R 777 /tmp/home
+
+# For some reason simply installing 'biber' does not set the path
+ENV PATH="${PATH}:/usr/bin/vendor_perl"
+

dockerfiles/Dockerfile.archlinux

@@ -1,9 +0,0 @@
-FROM archlinux:latest
-
-RUN pacman-key --init
-RUN pacman-key --populate archlinux
-RUN pacman -Sy archlinux-keyring --noconfirm && pacman -Su --noconfirm
-
-RUN pacman -Syu --noconfirm
-RUN pacman -S make perl texlive texlive-binextra texlive-pictures --noconfirm
-RUN pacman -S texlive-publishers texlive-mathscience texlive-fontsextra --noconfirm

dockerfiles/Dockerfile.ubuntu

@@ -4,4 +4,13 @@ ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt update -y && apt upgrade -y
 RUN apt install make texlive latexmk texlive-pictures -y
-RUN apt install make texlive-publishers texlive-science texlive-fonts-extra -y
+RUN apt install texlive-publishers texlive-science texlive-fonts-extra texlive-latex-extra -y
+RUN apt install biber texlive-bibtex-extra -y
+
+# The 'bbm' package insists on generating stuff in the home directory. In
+# order to guarantee access to the home directory no matter the user the
+# docker container is run with, create a temporary one anyone can write to
+RUN mkdir /tmp/home
+RUN chmod -R 777 /tmp/home
+ENV HOME=/tmp/home
+

letter.bib

@@ -0,0 +1,115 @@
+@ARTICLE{ADMM,
+  author={Barman, Siddharth and Liu, Xishuo and Draper, Stark C. and Recht, Benjamin},
+  journal={Trans. Inf. Theory}, 
+  title={Decomposition Methods for Large Scale LP Decoding}, 
+  year={2013},
+  volume={59},
+  number={12},
+  pages={7870-7886},
+%  doi={10.1109/TIT.2013.2281372}
+}
+
+@ARTICLE{feldman_paper,
+  author={Feldman, J. and Wainwright, M.J. and Karger, D.R.},
+  journal={IEEE Trans. Inf. Theory}, 
+  title={Using linear programming to Decode Binary linear codes}, 
+  year={2005},
+  volume={51},
+  number={3},
+  pages={954-972},
+%  doi={10.1109/TIT.2004.842696}
+}
+
+@ARTICLE{ml_in_the_list,
+	author={Geiselhart, Marvin and Elkelesh, Ahmed and Ebada, Moustafa and Cammerer, Sebastian and Brink, Stephan ten},
+	journal={IEEE Trans. Commun.}, 
+	title={Automorphism Ensemble Decoding of Reed–Muller Codes}, 
+	year={2021},
+	volume={69},
+	number={10},
+	pages={6424-6438},
+%	doi={10.1109/TCOMM.2021.3098798}
+}
+
+@ARTICLE{mackay99,
+  author={MacKay, D.J.C.},
+  journal={IEEE Trans. Inf. Theory}, 
+  title={Good error-correcting codes based on very sparse matrices}, 
+  year={1999},
+  volume={45},
+  number={2},
+  pages={399-431},
+%  doi={10.1109/18.748992}
+}
+
+@online{mackay,
+    author = {MacKay, David J.C.},
+    title  = {Encyclopedia of Sparse Graph Codes},
+    date   = {2023-04},
+    url    = {www.inference.org.uk/mackay/codes/data.html}
+}
+
+@book{proximal_algorithms,
+  title={Proximal algorithms},
+  author={Parikh, Neal and Boyd, Stephen and others},
+  journal={Foundations and trends{\textregistered} in Optimization},
+  volume={1},
+  number={3},
+  pages={127--239},
+  year={2014},
+  publisher={Now Publishers, Inc.}
+}
+
+@book{channel_codes_book,
+    place={Cambridge},
+    title={Channel Codes: Classical and Modern},
+%    DOI={10.1017/CBO9780511803253},
+    publisher={Cambridge University Press},
+    author={Ryan, William and Lin, Shu},
+    year={2009},
+%    url={https://d1.amobbs.com/bbs_upload782111/files_35/ourdev_604508GHLFR2.pdf}
+}
+
+@INPROCEEDINGS{adaptive_lp_decoding,
+  author={Taghavi, Mohammad H. and Siegel, Paul H.},
+  booktitle={IEEE Proc. ISIT}, 
+  title={Adaptive Linear Programming Decoding}, 
+  year={2006},
+  volume={},
+  number={},
+  pages={1374-1378},
+%  doi={10.1109/ISIT.2006.262071}
+}
+
+@INPROCEEDINGS{interior_point_decoding,
+  author={Vontobel, Pascal O.},
+  booktitle={Proc. ITA}, 
+  title={Interior-point algorithms for linear-programming decoding}, 
+  year={2008},
+  volume={},
+  number={},
+  pages={433-437},
+%  doi={10.1109/ITA.2008.4601085}
+}
+
+@article{proximal_paper,
+    title={Proximal Decoding for {LDPC} Codes},
+    author={Tadashi Wadayama and Satoshi Takabe},
+    journal={IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences},
+%    volume={advpub},
+%    pages={2022TAP0002},
+    year={2022},
+%    doi={10.1587/transfun.2022TAP0002}
+}
+
+@ARTICLE{chase_decoding,
+  author={Chase, D.},
+  journal={IEEE Trans. Inf. Theory}, 
+  title={Class of algorithms for decoding block codes with channel measurement information}, 
+  year={1972},
+ % volume={18},
+ % number={1},
+ % pages={170-182},
+ % keywords={},
+ % doi={10.1109/TIT.1972.1054746}}
+}

res/bp_20433484.csv

@@ -0,0 +1,14 @@
+SNR,FER,BER,num_frame_errors
+1.0, 0.654723127035831   , 0.0888101168806285  , 201
+1.5, 0.392578125000000   , 0.0482345281862745  , 201
+2.0, 0.182561307901907   , 0.0213175188331463  , 201
+2.5, 0.0620753551575046  , 0.00605856919667188 , 201
+3.0, 0.0130012936610608  , 0.00128034396164675 , 201
+3.5, 0.00176298778188070 , 0.000150054320523940, 201
+4.0, 0.000267259157615091, 1.51866607463458e-05, 201
+4.5, 5.33724908622844e-05, 1.98370100658768e-06, 201
+5.0, 1.34177489983751e-05, 3.66497875284852e-07, 201
+5.5, 4.12634778374169e-06, 1.04658123477986e-07, 201
+6.0, 1.08000000000000e-06, 2.41176470588235e-08, 108
+6.5, 3.60000000000000e-07, 8.62745098039216e-09, 36
+

res/p_error.csv

@@ -1,205 +1,205 @@
 index,p_error
-0,6.78e-06
-1,6.68e-06
-2,5.82e-06
-3,1.37e-06
-4,5.7e-07
-5,2.9e-07
-6,1.6e-07
-7,1.3e-07
-8,1.3e-07
-9,7e-08
-10,6e-08
-11,7e-08
-12,3e-08
-13,2e-08
-14,1e-08
-15,5e-08
-16,4e-08
-17,0.0
-18,1e-08
-19,2e-08
-20,2e-08
-21,1e-08
-22,2e-08
-23,0.0
-24,1e-08
-25,5e-08
-26,2e-08
-27,1e-08
-28,2e-08
-29,0.0
-30,1e-08
-31,1e-08
-32,1e-08
-33,3e-08
-34,0.0
-35,1e-08
-36,2e-08
-37,1e-08
-38,0.0
-39,0.0
-40,1e-08
-41,1e-08
-42,2e-08
-43,0.0
-44,1e-08
-45,0.0
-46,0.0
-47,1e-08
-48,0.0
-49,0.0
-50,0.0
-51,1e-08
-52,0.0
-53,1e-08
-54,0.0
-55,0.0
-56,0.0
-57,0.0
-58,0.0
-59,0.0
-60,1e-08
-61,0.0
-62,0.0
-63,0.0
-64,0.0
-65,0.0
-66,0.0
-67,1e-08
-68,0.0
-69,2e-08
-70,0.0
-71,0.0
-72,1e-08
-73,0.0
-74,0.0
-75,0.0
-76,0.0
-77,0.0
-78,0.0
-79,0.0
-80,0.0
-81,0.0
-82,0.0
-83,0.0
-84,0.0
-85,0.0
-86,0.0
-87,0.0
-88,0.0
-89,2e-08
-90,0.0
-91,0.0
-92,0.0
-93,0.0
-94,1e-08
-95,0.0
-96,0.0
-97,0.0
-98,0.0
-99,0.0
-100,1e-08
-101,0.0
-102,0.0
-103,0.0
-104,0.0
-105,0.0
-106,0.0
-107,0.0
-108,0.0
-109,0.0
-110,0.0
-111,0.0
-112,1e-08
-113,1e-08
-114,0.0
-115,0.0
-116,2e-08
-117,0.0
-118,0.0
-119,0.0
-120,0.0
-121,0.0
-122,0.0
-123,1e-08
-124,0.0
-125,0.0
-126,0.0
-127,0.0
-128,0.0
-129,0.0
-130,0.0
-131,0.0
-132,0.0
-133,0.0
-134,0.0
-135,0.0
-136,0.0
-137,0.0
-138,0.0
-139,0.0
-140,0.0
-141,0.0
-142,0.0
-143,0.0
-144,0.0
-145,0.0
-146,0.0
-147,0.0
-148,0.0
-149,0.0
-150,0.0
-151,0.0
-152,0.0
-153,0.0
-154,0.0
-155,0.0
-156,1e-08
-157,0.0
-158,1e-08
-159,0.0
-160,0.0
-161,0.0
-162,0.0
-163,0.0
-164,0.0
-165,0.0
-166,0.0
-167,0.0
-168,0.0
-169,0.0
-170,0.0
-171,0.0
-172,0.0
-173,0.0
-174,0.0
-175,0.0
-176,0.0
-177,0.0
-178,0.0
-179,0.0
-180,0.0
-181,0.0
-182,0.0
-183,0.0
-184,0.0
-185,0.0
-186,0.0
-187,1e-08
-188,0.0
-189,0.0
-190,0.0
-191,0.0
-192,0.0
-193,0.0
-194,0.0
-195,0.0
-196,0.0
-197,0.0
-198,0.0
-199,0.0
-200,0.0
-201,0.0
-202,0.0
-203,1e-08
+0,0.001972541
+1,0.00184933
+2,0.001619784
+3,0.000671981
+4,0.000330856
+5,0.000186121
+6,0.000117411
+7,8.0073e-05
+8,5.7761e-05
+9,4.3332e-05
+10,3.3405e-05
+11,2.6124e-05
+12,2.102e-05
+13,1.7142e-05
+14,1.425e-05
+15,1.1871e-05
+16,9.983e-06
+17,8.707e-06
+18,7.293e-06
+19,6.256e-06
+20,5.442e-06
+21,4.955e-06
+22,4.34e-06
+23,3.781e-06
+24,3.306e-06
+25,3.026e-06
+26,2.752e-06
+27,2.458e-06
+28,2.208e-06
+29,2.104e-06
+30,1.84e-06
+31,1.628e-06
+32,1.538e-06
+33,1.447e-06
+34,1.354e-06
+35,1.175e-06
+36,1.089e-06
+37,1.049e-06
+38,9.17e-07
+39,8.59e-07
+40,8.42e-07
+41,7.75e-07
+42,6.93e-07
+43,7.08e-07
+44,6.11e-07
+45,6.12e-07
+46,5.98e-07
+47,5.86e-07
+48,4.91e-07
+49,4.63e-07
+50,4.57e-07
+51,4.11e-07
+52,4.13e-07
+53,4.15e-07
+54,3.85e-07
+55,3.76e-07
+56,3.77e-07
+57,3.58e-07
+58,3.18e-07
+59,2.86e-07
+60,2.94e-07
+61,3.11e-07
+62,2.8e-07
+63,2.61e-07
+64,2.56e-07
+65,2.48e-07
+66,2.73e-07
+67,2.28e-07
+68,2.33e-07
+69,2.26e-07
+70,2.01e-07
+71,1.88e-07
+72,2.11e-07
+73,2.14e-07
+74,1.86e-07
+75,2.03e-07
+76,1.89e-07
+77,2.07e-07
+78,2.02e-07
+79,1.91e-07
+80,2.01e-07
+81,1.88e-07
+82,2.15e-07
+83,1.68e-07
+84,1.88e-07
+85,1.86e-07
+86,1.82e-07
+87,1.8e-07
+88,2.01e-07
+89,1.88e-07
+90,1.84e-07
+91,1.92e-07
+92,1.88e-07
+93,1.85e-07
+94,1.71e-07
+95,1.78e-07
+96,1.44e-07
+97,1.4e-07
+98,1.65e-07
+99,1.33e-07
+100,1.67e-07
+101,1.56e-07
+102,1.42e-07
+103,1.35e-07
+104,1.4e-07
+105,1.22e-07
+106,1.42e-07
+107,1.43e-07
+108,1.19e-07
+109,1.25e-07
+110,1.02e-07
+111,1.06e-07
+112,1.19e-07
+113,1.2e-07
+114,1.19e-07
+115,1.03e-07
+116,9.8e-08
+117,1.15e-07
+118,1.01e-07
+119,1e-07
+120,1.01e-07
+121,9.6e-08
+122,8.6e-08
+123,7.8e-08
+124,9.6e-08
+125,7.7e-08
+126,8.6e-08
+127,9.9e-08
+128,7.9e-08
+129,8.4e-08
+130,9.1e-08
+131,8.3e-08
+132,7.7e-08
+133,8.4e-08
+134,6.1e-08
+135,6.7e-08
+136,6.6e-08
+137,7.6e-08
+138,7e-08
+139,7.4e-08
+140,6.9e-08
+141,6.4e-08
+142,6.6e-08
+143,6.5e-08
+144,6.9e-08
+145,5.5e-08
+146,5.8e-08
+147,6.2e-08
+148,6.4e-08
+149,6.4e-08
+150,6.4e-08
+151,5.3e-08
+152,5.7e-08
+153,4.9e-08
+154,6.1e-08
+155,5.6e-08
+156,4.2e-08
+157,5.6e-08
+158,4e-08
+159,5.7e-08
+160,6.3e-08
+161,7.5e-08
+162,3.3e-08
+163,5.7e-08
+164,4.5e-08
+165,5.1e-08
+166,6e-08
+167,4.3e-08
+168,3.8e-08
+169,4.3e-08
+170,4.2e-08
+171,5.1e-08
+172,6.4e-08
+173,3.9e-08
+174,4.3e-08
+175,3.5e-08
+176,2.9e-08
+177,4.3e-08
+178,4e-08
+179,5.1e-08
+180,4.8e-08
+181,6e-08
+182,5.1e-08
+183,4.2e-08
+184,3.9e-08
+185,3.4e-08
+186,4.7e-08
+187,2.4e-08
+188,3.9e-08
+189,5.2e-08
+190,6.7e-08
+191,3.2e-08
+192,4e-08
+193,3.3e-08
+194,3.9e-08
+195,4.5e-08
+196,5e-08
+197,5.3e-08
+198,7.4e-08
+199,6.8e-08
+200,8.3e-08
+201,1.2e-07
+202,1.94e-07
+203,2.52e-07