From 8e8cf0f2d39b9bce0c4192e34162bfb1afa2a559 Mon Sep 17 00:00:00 2001 From: Martin Thoma Date: Mon, 11 Jan 2016 17:34:04 +0100 Subject: [PATCH] Add review --- documents/paper-peer-review/Makefile | 7 + documents/paper-peer-review/README.md | 31 +++ .../paper-peer-review/paper-peer-review.tex | 214 ++++++++++++++++++ 3 files changed, 252 insertions(+) create mode 100644 documents/paper-peer-review/Makefile create mode 100644 documents/paper-peer-review/README.md create mode 100644 documents/paper-peer-review/paper-peer-review.tex diff --git a/documents/paper-peer-review/Makefile b/documents/paper-peer-review/Makefile new file mode 100644 index 0000000..d692819 --- /dev/null +++ b/documents/paper-peer-review/Makefile @@ -0,0 +1,7 @@ +SOURCE = paper-peer-review +make: + pdflatex $(SOURCE).tex -output-format=pdf + make clean + +clean: + rm -rf $(TARGET) *.class *.html *.log *.aux *.out diff --git a/documents/paper-peer-review/README.md b/documents/paper-peer-review/README.md new file mode 100644 index 0000000..6e135b7 --- /dev/null +++ b/documents/paper-peer-review/README.md @@ -0,0 +1,31 @@ +## About + +A peer-review paper for a seminar at KIT (Karlsruhe, Germany). + +### Gegeben + +Die Beurteilung von anderen wissenschaftlichen Arbeiten ist ein wichtiger Teil +der Forschung. Aus diesem Grund werdet ihr in diesem Seminar die Möglichkeit +erhalten, ein solches „Review“ für eure Partnerarbeit zu erstellen. Da ihr in +diesem Fall kein Expertenwissen über die Arbeit verfügt, liegt der Schwerpunkt +auf der Beurteilung des formalen und allgemeinen logischen Aufbaus: + +* Ist die Arbeit logisch Strukturiert? +* Gibt es eine klare Fragestellung, die sich auch in der Arbeit wiederspiegelt? +* Werden alle erwähnten Aspekte verständlich und ausreichend erklärt? +* Werden alle Fachbegriffe eingeführt? +* Sind die einzelnen Bestandteile der Arbeit aufeinander bezogen? +* Gibt es einen besseren Weg etwas zu beschreiben/erklären? + + +Kritik sollte immer konstruktiv sein. Ein „die Erklärung von X ist schlecht“ +hilft dem Autor nicht viel weiter. Deshalb ist es wichtig die Kritik zu +begründen: „… ist schlecht, weil sie …“. + +Ein gutes Review zu schreiben hilft euren Kommilitonen! Sie können die +Anmerkungen einarbeiten und somit die Qualität ihrer Arbeit erhöhen. Ein +„negatives“ Review wird niemals zu einer schlechteren Bewertung der Arbeit +führen. + +* Review-Vorlage im ILIAS verwenden +* Das Review sollte 200-300 Wörter umfassen \ No newline at end of file diff --git a/documents/paper-peer-review/paper-peer-review.tex b/documents/paper-peer-review/paper-peer-review.tex new file mode 100644 index 0000000..d7d75b8 --- /dev/null +++ b/documents/paper-peer-review/paper-peer-review.tex @@ -0,0 +1,214 @@ +\documentclass[a4paper,9pt]{scrartcl} +\usepackage{amssymb, amsmath} % needed for math +\usepackage[utf8]{inputenc} % this is needed for umlauts +\usepackage[USenglish]{babel} % this is needed for umlauts +\usepackage[T1]{fontenc} % this is needed for correct output of umlauts in pdf +\usepackage[margin=2.5cm]{geometry} %layout +\usepackage{hyperref} % hyperlinks +\usepackage{color} +\usepackage{framed} +\usepackage{enumerate} % for advanced numbering of lists +\usepackage{csquotes} % for enquote + +\newcommand\titletext{Peer-Review of\\"Deep Neuronal Networks for Semantiv Segmentation in Medical +Informatics"} + +\title{\titletext} +\author{Martin Thoma} + +\hypersetup{ + pdfauthor = {Martin Thoma}, + pdfkeywords = {peer review}, + pdftitle = {Lineare Algebra} +} + +\usepackage{microtype} + +\begin{document} +\maketitle +\section{Introduction} +This is a peer-review of \enquote{Deep Neuronal Networks for Semantiv +Segmentation in Medical Informatics} by Marvin Teichmann. The reviewed document +is available under \href{https://github.com/MarvinTeichmann/seminar-pixel-exact-classification.git}{https://github.com/MarvinTeichmann/seminar-pixel-exact-classification.git}, version +\texttt{b1bdb4802c8e268ebf7ca66adb7f806e29afb413}. + +\section{Summary of the Content} +The author wants to describe how convolutional networks can be used for +semantic segmentation tasks in medicine. To do so, he introduces Convolutional +Neural Networks. + +As the introduction, section~2 (Computer Vision Tasks) and section~5 +(Application in Medical Informatics) are not written yet, it can only be said +that the plan of writing them is good. + +The author expects the reader to know how neural networks work in general, but +gives a detailed introduction into CNNs. He continues with explaining fully +convolutional networks (FCNs). This leads in a natural fashion to the +application of neural networks for segmentation. + + +\section{Overall Feedback} +Gramatical errors make it sometimes difficult to understand relatively easy +sentences. Also, the missing parts make it difficult to see if there is a +consistent overall structure. + +I recommend adding more source to claims made in the paper. + +The overall structure seems to be logical, definitions are given most of the +time (see the feedback below for some exceptions where it should be added). + + +\section{Major Remarks} +\subsection{Section 3 / 3.1: CNNs} +\begin{itemize} + \item What is \enquote{stationarity of statistics}? + \item What are \enquote{translation invariance functions}? + \item The term \enquote{Kernel} and \enquote{reception field} were neither + introduced nor a source was given where the reader could find + definitions. + \item What is a \enquote{channel size}? Do you mean the number of channels + or the channel dimension? + \item What is $F_{nm}$? A function, but on which domain does it operate and + to which domain does it map? What does this function mean? Is it + an activation function? + \item What does $n << h,w$ mean? $n \ll \min(h, w)$? + \item It was not explained what \enquote{a sliding window fashion} means. + \item I miss an~image in section 3.1 (definitions and notation). +\end{itemize} + +\subsection{Section 3.2: Layer types} + +\begin{itemize} + \item I've never heard of activation layers. Do you mean fully connected + layers? If not, then you should probably cite a publication which + calls it like that. + \item \enquote{curtained weights} - what is that? (The problem might be + my lack of knowledge of the English language). However, I think + you should cite a source here for the claim that this is possible. + \item \enquote{a variety of tasks including edge and area detection, + contrast sharpening and image blurring}: I miss a source. + \item \enquote{big ($k \geq 7$). [KSH12, SZ14, SLJ + 14].} - What exactly + do you cite here? + \item An image with a tiny example would make the pooling layer much + easier to understand. However, you can also cite a source which + explains this well. + \item The sentence \enquote{Firstly it naturally reduces the spatial dimension +enabling the network to learn more compact representation if the data and decreasing the +amount of parameters in the succeeding layers.} sounds wrong. You forgot something + At \enquote{if the data}. + \item The sentence is gramatically wrong and makes it hard to understand + \enquote{Secondly it introduces robust translation invariant.}. + \item \enquote{Minor shifts in the input data will not result in the same activation after pooling.} + Not? I thought that was the advantage of pooling, that you get + invariant? + \item \enquote{Recently ReLU Nonlinearities [KSH12](AlexNet, Bolzmann)}: + It is possible to make that easier to read: + \enquote{Recently ReLU nonlinearities, as introduced by~[KSH12](AlexNet, Bolzmann)} + - However, I'm not too sure what you mean with \enquote{Bolzmann}. + \item It was not explained / defined what ReLU means / is. +\end{itemize} + + +\subsection{Section 4: Neural Networks for Segmentation} +\begin{itemize} + \item \enquote{After the overwhelming successes of DCNNs in image classification}: Add source + \item \enquote{in combination with traditional classifiers} - What are \enquote{traditional} classifiers? + \item \enquote{Other authors used the idea described in Section 2} - Don't make me jump back. Can you give that idea a short name? Then you can write something like \enquote{the idea of sliding windows}. As you wrote about sliding windows in the rest of the sentence, I guess restrucuting the sentence might help. + \item \enquote{are currently the state-of-the art in several semantic segmentation benchmarks.} - name at least one. +\end{itemize} + +\subsection{Section 4.1: Sliding Window efficiency in CNNs} +\begin{itemize} + \item \enquote{The input image will be down sampled by a factor of s corresponding to the product of all strides being applied in $C'$.} - I don't think that is obvious. Please explain it or give a source for that claim. + \item \enquote{shift-and-stitch} - What is that? +\end{itemize} + +\subsection{Section 4.2: FCNs} + +\begin{itemize} + \item \enquote{builds up on the ideas presented of Section 4.1} - which ones? + The \textit{sliding-window-as-a-convoluton} idea and which other idea? + \item \enquote{they are not trying to avoid downsampling as part of the progress} + - do you mean process? + \item Explain what an \enquote{upsampling layer} is. +\end{itemize} + +\subsection{Section 4.2.1: Deconvolution} +This section is still to be done. + + +\subsection{Section 4.2.2: Skip-Architecture} +An image would help, although I guess it is already easy to understand. + + +\subsection{4.2.3 Transfer Learning} +\begin{itemize} + \item What is transfer lerning? + \item What is VGG16 (cite paper) - same for AlexNet and GoogLeNet, if it + wasn't done already. People who don't know what a CNN is will also + not know what AlexNet / GoogLeNet is. +\end{itemize} + + +\subsection{4.3 Extensions of FCN} +\begin{itemize} + \item \enquote{Several extensions of FCN have been proposed} - give sources + \item \enquote{of strong labeled data} what is \textbf{strong} labeled data? +\end{itemize} + + +\section{Minor Remarks} +I stopped looking for typos in section 4.1. + +\begin{itemize} + \item \enquote{we}: It is a single author. Why does he write \enquote{we}? + \item should be lower case: + \begin{itemize} + \item \enquote{Architecture} should be lower case + \item \enquote{Classification Challenge} should be lower case + \item \enquote{Classification}, \enquote{Localization}, \enquote{Detection}, \enquote{Segmentation} + \item \enquote{Tasks} + \item \enquote{Layer} + \item \enquote{Nonlinearities} + \item \enquote{Semantic Segmentation} + \end{itemize} + \item typos (missing characters like commas, switched characters, \dots) + \begin{itemize} + \item \enquote{as fellows} + \item \enquote{descripe} + \item \enquote{architeture} + \item \enquote{a translation invariance functions} + \item \enquote{$f$ is than applied} + \item \enquote{To archive that $f_{ks}$ is chosen} + \item \enquote{an MLP} + \item \enquote{In convolutional layers stride is usually choose to be $s = 1$ ,} + \item \enquote{applies non-learnable function} + \item \enquote{to learn nonlinear function} - \enquote{a} is missing + \item \enquote{this models} + \item \enquote{Fully Convolutional Networks (FCN)} - missing plural s in (FCNs) + \item \enquote{FCN are an architecture} - mixed singular and plural. \enquote{A FCN is an architecture\dots} + \item \enquote{approaches ConvNets} - comma missing + \item \enquote{relevant} $\neq$ \enquote{relevance} + \item \enquote{itself will be a ConvNet, that means} - replace the comma by a point. This sentence is too long. + \item \enquote{only downside is, that} - remove comma + \end{itemize} + \item Typography + \begin{itemize} + \item Why don't you include \texttt{hyperref}? I really like being able + to directly jump to the sections, without having to manually + search them. + \item I prefer $\mathbb{R}$ instead of $R$. This makes it more obvious + that it is not a variable, but the set of real numbers. + \item \verb+\ll+ is nicer than \verb+<<+: $\ll$ vs $<<$. + \item \verb+exp+ ($exp$) are three variables. The function is \verb+\exp+ ($\exp$). Same for $\tanh$. + \item \enquote{A recent break-trough has been achieved with} - That seems to be a good point to start a new paragraph. + \end{itemize} + \item \enquote{[...], the ImageNet Classification Challenge} should be + followed by a comma + \item \enquote{have broken new records}: either \enquote{have broken records} + or something like \enquote{have set new records} + \item \enquote{For the pooling layer typically s is choose to be k} - I would write \enquote{For the pooling layer $s$ is typically choosen to be equal to $k$} + \item \enquote{to further computer vision tasks} - I'm not too sure if you can say \enquote{further} in this context +\end{itemize} + +\end{document}