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@@ -5,6 +5,7 @@
\DeclareLanguageMapping{british}{british-apa} \DeclareLanguageMapping{british}{british-apa}
\usepackage{url} \usepackage{url}
\usepackage{float} \usepackage{float}
\usepackage{ragged2e}
\usepackage{caption} \usepackage{caption}
\usepackage{multicol} \usepackage{multicol}
\newcommand{\tabitem}{~~\llap{\textbullet}~~} \newcommand{\tabitem}{~~\llap{\textbullet}~~}
@@ -203,7 +204,7 @@ fundamental method for detecting heart valve disorders for over a century.
However, auscultation is a skill that requires training and can only usually be However, auscultation is a skill that requires training and can only usually be
performed by a medical professional, such as a GP. As a result, manual performed by a medical professional, such as a GP. As a result, manual
auscultation is significantly susceptible to human error~\parencite{Hanna2002}. auscultation is significantly susceptible to human error~\parencite{Hanna2002}.
Automation of this method using technology may be provide a solution, and Automation of this method using technology may provide a solution, and
recent research has shown promise in this area. A large amount of research has recent research has shown promise in this area. A large amount of research has
focused on analysis of Electrocardiogram (ECG) signals. Although useful for focused on analysis of Electrocardiogram (ECG) signals. Although useful for
detecting pathologies, ECG equipment is expensive and requires a trained detecting pathologies, ECG equipment is expensive and requires a trained
@@ -221,7 +222,7 @@ earlier diagnosis of conditions that may have otherwise been overlooked, this
technology could have a significant impact on reducing mortality rates as a technology could have a significant impact on reducing mortality rates as a
result of heart conditions. result of heart conditions.
\section{Related Work} \section{Related work}
There are currently a wide variety of methods employed for the analysis and There are currently a wide variety of methods employed for the analysis and
classification of PCG signals. Current methods can typically be divided into 3 classification of PCG signals. Current methods can typically be divided into 3
areas, each of which are combined to create a full classification system. These areas, each of which are combined to create a full classification system. These
@@ -230,7 +231,7 @@ extraction/classification. The performance and evaluation of complete systems
are also discussed in section~\ref{Classification} are also discussed in section~\ref{Classification}
\subsection{Signal Preprocessing} \subsection{Signal preprocessing}
There are a large number of factors that lead to variation in quality of PCG There are a large number of factors that lead to variation in quality of PCG
recordings: stethoscope type, make and model, its microphone/sensors, the recordings: stethoscope type, make and model, its microphone/sensors, the
position used to record (i.e.\ lower left sternal border, apex, pulmonic area, position used to record (i.e.\ lower left sternal border, apex, pulmonic area,
@@ -267,7 +268,7 @@ decomposition~\parencite[p.93]{Ari2008}. This may be used for analysis of
transient events such as murmurs, that may consist of higher frequency transient events such as murmurs, that may consist of higher frequency
components than normal heart sounds. components than normal heart sounds.
\subsection{Signal Segmentation}\label{Segmentation} \subsection{Signal segmentation}\label{Segmentation}
Algorithms for the segmentation of PCG data aim to extract the structure of the Algorithms for the segmentation of PCG data aim to extract the structure of the
signal over time. This is a key stage in the analysis of PCG signals, as the signal over time. This is a key stage in the analysis of PCG signals, as the
structure of the signal and relationships between the fundamental heart sounds structure of the signal and relationships between the fundamental heart sounds
@@ -341,13 +342,13 @@ These features form vectors for training the HMM. Results of 98.6\%
sensitivity, 96.9\% positive predictivity for S1 sounds and 98.3\% sensitivity, sensitivity, 96.9\% positive predictivity for S1 sounds and 98.3\% sensitivity,
96.5\% positive predictivity for S2 sounds is reported. 96.5\% positive predictivity for S2 sounds is reported.
The issue of state duration was further addressed by Schmidt et.\ al through use The issue of state duration was further addressed by Schmidt et.\ al through use
of a duration-dependent hidden Markov (DHMM)~\parencite{Schmidt2015}. The of a Duration-dependent Hidden Markov Model (DHMM)~\parencite{Schmidt2015}. The
DHMM is a modified HMM that considers the duration of the current state when DHMM is a modified HMM that considers the duration of the current state when
calculating the probability of transition to another state. This modification calculating the probability of transition to another state. This modification
scored a reported sensitivity of 98.8\% and a positive predictivity of scored a reported sensitivity of 98.8\% and a positive predictivity of
98.6\%.\\ 98.6\%.\\
Building on previous work using HMMs, Springer et al.\ presented a segmentation Building on previous work using HMMs, Springer et al.\ presented a segmentation
algorithm by using hidden semi-markov models (HSMMs) in combination with algorithm by using Hidden Semi-Markov Models (HSMMs) in combination with
logistic regression~\parencite{Springer2016}. Use of Hidden semi markov model logistic regression~\parencite{Springer2016}. Use of Hidden semi markov model
allows for a priori information on the duration of the current state to be used allows for a priori information on the duration of the current state to be used
in probability calculation of the subsequent state. In this case, the knowledge in probability calculation of the subsequent state. In this case, the knowledge
@@ -395,7 +396,7 @@ $Ac = \text{Accuracy}, Se = \text{Sensitivity}, P_+ = \text{Positive predictivit
\doublespacing \doublespacing
\subsection{Feature extraction/Classification models}\label{Classification} \subsection{Feature extraction/classification models}\label{Classification}
A wide variety of methods exist for the extraction of statistical features and A wide variety of methods exist for the extraction of statistical features and
classification of PCG data. Most notably, the range of methods that were classification of PCG data. Most notably, the range of methods that were
@@ -671,8 +672,8 @@ identified as necessary for the success of the proposed project:
classification would likely be performed in sub-optimal conditions. If classification would likely be performed in sub-optimal conditions. If
this is not possible, noise could potentially be added to clean signals this is not possible, noise could potentially be added to clean signals
to simulate this. to simulate this.
\item Healthy signals must be able to be differentiated from a variety of \item It must be possible to differentiate healthy signals from a variety of
individual pathologies in order to provide a general abnormality individual pathologies, in order to provide a general abnormality
detection algorithm. This should be reflected in the database through detection algorithm. This should be reflected in the database through
inclusion of a variety of signals representing different pathological inclusion of a variety of signals representing different pathological
heart conditions. heart conditions.
@@ -688,7 +689,7 @@ Two viable options were then considered based on the above criteria:
by Almasi et al.~\parencite{Almasi2011} by Almasi et al.~\parencite{Almasi2011}
\end{enumerate} \end{enumerate}
Generation of synthetic data was considered as few well-formed alternative Generation of synthetic data was considered, as few well-formed alternative
databases exist, other than the Physionet challenge data. The database curated databases exist, other than the Physionet challenge data. The database curated
for the Physionet challenge was selected for this project, as it fulfilled the for the Physionet challenge was selected for this project, as it fulfilled the
criteria sufficiently and posed less of a risk in terms of signal quality, due criteria sufficiently and posed less of a risk in terms of signal quality, due
@@ -697,37 +698,37 @@ of PCG data remains an interesting possibility for improving evaluation of
classification systems and could be considered for the generation of additional classification systems and could be considered for the generation of additional
samples in future work. samples in future work.
\subsection{Database Summary} \subsection{Database summary}
The selected database is significantly larger and contains a wider variety of The selected database is significantly larger and contains a wider variety of
signal conditions than any database used for previous research (as detailed in signal conditions than any database used for previous research (as detailed in
table~\ref{PriorWorkTable}). It is released as an open-source resource and is table~\ref{PriorWorkTable}). It is released as an open-source resource and is
documented in significant detail by Liu et al.~\parencite{Liu2016}. The lack documented in significant detail by Liu et al.~\parencite{Liu2016}. The lack of
of any alternative databases, comparable in size or variety of content, perhaps any alternative databases, comparable in size or variety of content, perhaps
makes this resource the current standard for PCG analysis projects. In makes this resource the current standard for PCG analysis projects. In
addition, by replicating the conditions of the Physionet challenge, results can addition, by replicating the conditions of the Physionet challenge, results can
also be directly compared with those of the challenge participant's, with the be directly compared with those of the challenge participant's, with the aim of
aim of understanding how the proposed algorithm compares to the current state understanding how the proposed algorithm compares to the current state of PCG
of PCG analysis. analysis.
\begin{itemize} \begin{itemize}
\item The database consists of 6 sub-databases, labelled $a$ to $f$. \item The database consists of 6 sub-databases, labelled $a$ to $f$.
\item These sub-databases have been sourced from a variety of professionals, \item These sub-databases have been sourced from a variety of professionals,
over the course of a decade. over the course of a decade.
\item A total of 3,126 recordings are included, created using varying equipment. \item A total of 3,240 recordings are included, created using varying equipment.
\item 2575 recordings are labelled as normal, 665 are labelled as abnormal. \item 2575 recordings are labelled as normal, 665 are labelled as abnormal.
\item All samples have been resampled to 2KHz \item All samples have been resampled to 2KHz
\item Samples were recorded in a range of environments, both clinical and \item Samples were recorded in a range of both clinical and
non-clinical. non-clinical environments.
\item Many recordings are corrupted with environmental noise, such as \item Many recordings are corrupted with environmental noise, such as
microphone friction, breathing, talking etc\ldots microphone friction, breathing, talking etc\ldots
\item Sections of silence are present in some recordings, most \item Sections of silence are present in some recordings, most
significantly in database $e$ significantly in database $e$.
\end{itemize} \end{itemize}
\subsection{Considerations}\label{DBCons} \subsection{Considerations}\label{DBCons}
There are a number of issues with the acquired database that have been There are a number of issues with the acquired database that have been
highlighted, both through previous literature and through development of the highlighted, both through previous literature and through development of the
project. These have been considered throughout development and evaluation of proposed system. These have been considered throughout development and evaluation of
the project.\\ the project.\\
A significant issue highlighted by Liu et al.\ is the large number of normal A significant issue highlighted by Liu et al.\ is the large number of normal
recordings compared to pathological recordings. This creates a clear class recordings compared to pathological recordings. This creates a clear class
@@ -738,18 +739,18 @@ Another key issue is the difference between the databases used by participants o
Physionet challenge, and the available data that was acquired for this project. Physionet challenge, and the available data that was acquired for this project.
For unknown reasons, information such as patient labels used for training many For unknown reasons, information such as patient labels used for training many
of the challenge participant's models have not been made publicly available and of the challenge participant's models have not been made publicly available and
so could not be used in this project.\\ so could not be used for training of the proposed system.\\
The lack of access to the hidden test set used for evaluating challenge entries The lack of access to the hidden test set used for evaluating challenge entries
also had a significant impact on evaluation. An alternative method for also had a significant impact on evaluation. An alternative method for
evaluating using only the data provided has been proposed in evaluating using only the data provided has been proposed in
Section~\ref{Eval}.\\ Section~\ref{metrics}.\\
Finally, an issue is highlighted by Bobillo with regards to database Finally, an issue is highlighted by Bobillo with regards to database
$e$~\parencite{Bobillo2016}. The recording of normal and pathological signals using $e$~\parencite{Bobillo2016}. The recording of normal and pathological signals using
separate devices is likely to cause issues and is discussed in separate devices is likely to cause issues and is discussed in
Section~\ref{Eval} Section~\ref{Eval}.
%BEGIN NEW MATERIAL %BEGIN NEW MATERIAL
\pagebreak
\section{Design} \section{Design}
This project aims to provide robust heart abnormality detection for PCG This project aims to provide robust heart abnormality detection for PCG
signals, such that use of the system could reliably recommend further medical signals, such that use of the system could reliably recommend further medical
@@ -801,7 +802,7 @@ classification of the minor class. In this context, class imbalance could
potentially impact classification accuracy for abnormal samples, so must be potentially impact classification accuracy for abnormal samples, so must be
handled appropriately. This issue can be approached using a number of methods. handled appropriately. This issue can be approached using a number of methods.
Sophisticated oversampling methods such as SMOTE (Synthetic Minority Sophisticated oversampling methods such as SMOTE (Synthetic Minority
oversampling Technique) offer one solution. SMOTE generates synthetic samples Oversampling Technique) offer one solution. SMOTE generates synthetic samples
using interpolation and adds these to the data set to balance the classes, using interpolation and adds these to the data set to balance the classes,
without using direct copies of existing data. However, oversampling techniques without using direct copies of existing data. However, oversampling techniques
such as this can increase overfitting of models, and don't always offer such as this can increase overfitting of models, and don't always offer
@@ -811,10 +812,17 @@ major class. This has the obvious disadvantage of reducing data available for
training. However, an improved method using $k$-Means clustering has been shown training. However, an improved method using $k$-Means clustering has been shown
to be effective in previous cardiovascular classifications to be effective in previous cardiovascular classifications
problems~\parencite{Rahman2013}. This method was seen to be the best choice for problems~\parencite{Rahman2013}. This method was seen to be the best choice for
the proposed system. the proposed system. This method is illustrated using a small generated
2-dimesional dataset in Figure~\ref{cent}.
\subsubsection{Signal Segmentation} \begin{figure}[H]
%TODO: Generate segmentation plot \caption[caption of centroid]{Example resampling of synthesised dataset using cluster centroids\footnotemark}
\makebox[\textwidth]{\includegraphics[width=\textwidth]{centroid}}
\label{cent}
\end{figure}
\footnotetext{This figure was adapted from: \url{http://contrib.scikit-learn.org/imbalanced-learn/stable/}}
\subsubsection{Signal segmentation}
With one notable exception~\parencite{Langley2016}, previous classification With one notable exception~\parencite{Langley2016}, previous classification
algorithms rely heavily on the ability to segment signals into the four algorithms rely heavily on the ability to segment signals into the four
fundamental heart sounds. This is a key prerequisite to the extraction of fundamental heart sounds. This is a key prerequisite to the extraction of
@@ -835,10 +843,18 @@ quality. As methods proposed by previous literature, such as hand correction by
a professional~\parencite[p.2203]{Liu2016} are not feasible in this context, a professional~\parencite[p.2203]{Liu2016} are not feasible in this context,
and considering the low number of erroneous results produced by the and considering the low number of erroneous results produced by the
algorithm~\parencite[p.2]{Goda2016} it was decided that these errors would not algorithm~\parencite[p.2]{Goda2016} it was decided that these errors would not
pose a significant problem. pose a significant problem. An illustration of PCG data segmentation can be
seen in Figure~\ref{segs}.
\begin{figure}[H]
\caption{Example segmentation of PCG data}
\makebox[\textwidth]{\includegraphics[width=\textwidth]{segs}}
\label{segs}
\end{figure}
\subsection{Feature Extraction}\label{featEx}
\subsection{Feature extraction}\label{featEx}
The extraction of feature vectors from data is a fundamental component of most The extraction of feature vectors from data is a fundamental component of most
machine learning based systems. The aim is to construct meaningful machine learning based systems. The aim is to construct meaningful
representations of the data that emphasize information relevant to the representations of the data that emphasize information relevant to the
@@ -954,19 +970,25 @@ the wavelet transform is to represent an input signal as a set of scaled and
shifted finite oscillations. By comparing the signal with each scale of wavelet shifted finite oscillations. By comparing the signal with each scale of wavelet
at all points in time, a set of $N\times A$ (Where $A$ is the number of scales) at all points in time, a set of $N\times A$ (Where $A$ is the number of scales)
coefficients are generated. These define the scale and position needed for coefficients are generated. These define the scale and position needed for
each wavelet in order to fully reconstruct the signal (For further details, each wavelet in order to fully reconstruct the signal (This is illustrated in Figure~\ref{wave}. For further details,
refer to~\parencite{Polikar1994}). The benefit of this transform is that it is refer to~\parencite{Polikar1994}). The benefit of this transform is that it is
well localized in both time and frequency domains. This allows for accurate well localized in both time and frequency domains. This allows for accurate
representation of transient events such as clicks and snaps that are representation of transient events such as clicks and snaps that are
characteristic of heart conditions such as Mitral valve prolapse or characteristic of heart conditions such as Mitral valve prolapse or
stenosis~\parencite{Brown2008}.\\ stenosis~\parencite{Brown2008}.\\
For the proposed system, a 5 level DWT using debauchies-4 mother wavelet was For the proposed system, a 5 level DWT using daubechies wavelets-4 mother wavelet was
used for decomposition and reconstruction. Statistical features such as entropy used for decomposition and reconstruction. Statistical features such as entropy
were then calculated, both on the reconstructed signal and directly on were then calculated, both on the reconstructed signal and directly on
coefficients to attain a total of 48 features.~\parencite{Homsi2016} coefficients to attain a total of 48 features.~\parencite{Homsi2016}
% TODO: Insert wavelet diagram here % TODO: Insert wavelet diagram here
\subsubsection{Feature Scaling and Imputing} \begin{figure}[H]
\caption{Example 5 level daubechies 4 wavelet decomposition and reconstruction (normalised). Plots in descending order: D1, D2, \ldots, D5, A1}
\makebox[\textwidth]{\includegraphics[width=1.0\textwidth]{wavelet}}
\label{wave}
\end{figure}
\subsubsection{Feature scaling and imputing}
A common problem when working with multiple features is the difference in scale A common problem when working with multiple features is the difference in scale
between features. This problem can cause many machine learning algorithms to place between features. This problem can cause many machine learning algorithms to place
bias on larger scale features and can significantly impact the time taken for bias on larger scale features and can significantly impact the time taken for
@@ -980,7 +1002,7 @@ result of $\log(0)$ or division by 0 calculations, amongst other edge cases. A
standard method for handling these values is to apply an imputer, replacing standard method for handling these values is to apply an imputer, replacing
values with the mean of the feature vector~\parencite{VanderPlas2017}. values with the mean of the feature vector~\parencite{VanderPlas2017}.
\subsection{Stacking Classifier with Cross-Validation}\label{class} \subsection{Stacking classifier with cross-validation}\label{class}
The stacking classifier is an ensemble classifier, that uses the results of The stacking classifier is an ensemble classifier, that uses the results of
multiple base classifiers as input to a 2nd level meta-classifier, which in multiple base classifiers as input to a 2nd level meta-classifier, which in
turn is used to generate a final prediction. $k$-fold cross validation is used turn is used to generate a final prediction. $k$-fold cross validation is used
@@ -988,14 +1010,21 @@ across base classifiers, training on $k-1$ folds of input data, and applying
to the remaining validation set. The results of these predictions from each to the remaining validation set. The results of these predictions from each
base classifier are combined and used to train the 2nd level classifier which base classifier are combined and used to train the 2nd level classifier which
produces the final predictions based on the probabilities and predictions produces the final predictions based on the probabilities and predictions
provided.\\ provided. This is illustrated in figure~\ref{stack}\\
Given it's proven accurate performance across a range of tasks, it was Given it's proven accurate performance across a range of tasks, it was
expected that this classification model could be applied effectively to produce expected that this classification model could be applied effectively to produce
an alternative method for abnormality detection than those presented in an alternative method for abnormality detection than those presented in
previous literature. previous literature.
% TODO:Insert stacking classifier diagram % TODO:Insert stacking classifier diagram
\subsubsection{Base Classifiers} \begin{figure}[H]
\caption[caption of stack]{Stacking classifier overview\footnotemark}
\makebox[\textwidth]{\includegraphics[width=0.5\textwidth]{stacking_cv_classification_overview}}
\label{stack}
\end{figure}
\footnotetext{Figure retrieved from:\url{http://rasbt.github.io/mlxtend/user_guide/classifier/StackingCVClassifier/}}
\subsubsection{Base classifiers}
Clearly, an important consideration when using any ensemble method is the Clearly, an important consideration when using any ensemble method is the
selection of the base classifiers. In order for any ensemble method to perform selection of the base classifiers. In order for any ensemble method to perform
well, it must be constructed using a selection of classifiers that individually well, it must be constructed using a selection of classifiers that individually
@@ -1061,7 +1090,7 @@ quickly, to obtain initial results. Despite the inclusion of more complex
models, this model was chosen via automatic selection for the final model. models, this model was chosen via automatic selection for the final model.
Refer to section~\ref{PSOp} for further details. Refer to section~\ref{PSOp} for further details.
\paragraph{Logistic Regression} \paragraph{Logistic regression}
Logistic regression is a regression model that aims to fit as hyperplane to Logistic regression is a regression model that aims to fit as hyperplane to
data points by minimizing a cost function using weighted features. data points by minimizing a cost function using weighted features.
By applying weights to feature vectors then applying a sigmoid function, a By applying weights to feature vectors then applying a sigmoid function, a
@@ -1074,15 +1103,12 @@ $x$ is a feature vector\\
$y$ is a class label vector \\ $y$ is a class label vector \\
$\theta$ is a weight vector \\ $\theta$ is a weight vector \\
A cost function can then be defined as: A cost function can then be defined as:
\begin{equation}
J(\theta)=\argmin\limits_\theta\frac{1}{2m}\sum\limits_{i=1}^m\Big(h_\theta(x^{(i)})-y^{(i)}\Big)^2+\text{Regularization}(\theta)
\end{equation}
\begin{align} \begin{align}
&J(\theta)=\argmin\limits_\theta\frac{1}{2m}\sum\limits_{i=1}^m\Big(h_\theta(x^{(i)})-y^{(i)}\Big)^2+\text{Regularization}(\theta)\\
&\text{Regularization}{(\theta)}_\text{L1}=\lambda\sum\limits_{j=1}^n\mid\theta_i\mid\\ &\text{Regularization}{(\theta)}_\text{L1}=\lambda\sum\limits_{j=1}^n\mid\theta_i\mid\\
&\text{Regularization}{(\theta)}_\text{L2}=\lambda\sum\limits_{j=1}^n\theta_i^2 &\text{Regularization}{(\theta)}_\text{L2}=\lambda\sum\limits_{j=1}^n\theta_i^2
\end{align} \end{align}
Where: Where:\\
$\lambda$ is the regularization parameter used to help prevent overfitting\\ $\lambda$ is the regularization parameter used to help prevent overfitting\\
By minimizing the cost function, classification predictions can then be made By minimizing the cost function, classification predictions can then be made
using the hypothesis function~\parencite{Ng2012}.\\ using the hypothesis function~\parencite{Ng2012}.\\
@@ -1095,7 +1121,7 @@ range of meta-classifiers have been proposed for different tasks that utilise
stacking~\parencite[p.29]{Sesmero2015}. Further work in this area could stacking~\parencite[p.29]{Sesmero2015}. Further work in this area could
potentially provide improved results. potentially provide improved results.
\subsection{Model Optimisation}\label{optimise} \subsection{Model optimisation}\label{optimise}
As discussed in previous sections, two of the most important aspects that affect As discussed in previous sections, two of the most important aspects that affect
the performance of a classification system are it's models, and the input the performance of a classification system are it's models, and the input
features. A combination of relevant features and well tuned models is therefore features. A combination of relevant features and well tuned models is therefore
@@ -1107,14 +1133,14 @@ proposed system. To address this issue, two automatic optimisation approaches
were implemented, with the aim of maximising the accuracy of the proposed were implemented, with the aim of maximising the accuracy of the proposed
system. system.
\subsubsection{Sequential Feature Selection}\label{SFS} \subsubsection{Sequential feature selection}\label{SFS}
It was recognised that the extraction of such large numbers of features in the It was recognised that the extraction of such large numbers of features in the
proposed system would likely result in a large amount of redundant information. proposed system would likely result in a large amount of redundant information.
There are two commonly used methods for addressing this problem: feature There are two commonly used methods for addressing this problem: feature
reduction and feature selection. Feature reduction involves reducing features reduction and feature selection. Feature reduction involves reducing features
to a lower dimensionality using techniques such as PCA. Conversely, feature to a lower dimensionality using techniques such as PCA. Conversely, feature
selection involves selectively removing features entirely via methods such as selection involves selectively removing features entirely via methods such as
Sequential Floating Selection (SFFS). Both aim to reduce the amount of Sequential Floating Forward Selection (SFFS). Both aim to reduce the amount of
redundant information in features by removing or reducing features that are not redundant information in features by removing or reducing features that are not
expected to benefit the model. As a selection of models were to be used, each expected to benefit the model. As a selection of models were to be used, each
potentially handling dimensionality differently (SVMs in particular), it was potentially handling dimensionality differently (SVMs in particular), it was
@@ -1134,19 +1160,18 @@ set of features. An exhaustive feature selection algorithm is capable of this
but this would incur significant computational cost. For further details on but this would incur significant computational cost. For further details on
SFFS please refer to~\parencite[p.3]{Ferri1994} SFFS please refer to~\parencite[p.3]{Ferri1994}
\subsubsection{Particle Swarm Hyperparameter Optimisation}\label{PSOp} \subsubsection{Particle swarm optimisation}\label{PSOp}
The particle swarm optimisation algorithm is an iterative meta-heuristic algorithm that The particle swarm optimisation algorithm is an iterative meta-heuristic algorithm that
aims to find the set of parameters that maximises a given function. Given a aims to find the set of parameters that maximises a given function. Given a
$n$ dimensional parameter space, the algorithm randomly initialises sets of $n$ dimensional parameter space, the algorithm randomly initialises sets of
`particles' representing random combinations of parameters. As the algorithm `particles' representing random combinations of parameters. As the algorithm
progresses particle travel through the parameter space, updating their progresses particles travel through the parameter space, updating their
position based on their velocity, best historical score and the best historical position based on their velocity, best historical score and the best historical
score of the swarm. As the algorithm iterates, particles will converge on local score of the swarm. As the algorithm iterates, particles will converge on local
optima, producing potential solutions. The best score is chosen after the final optima, producing potential solutions. The best score is chosen after the final
iteration as the best parameter selection. Annotated pseudocode for this iteration as the best parameter selection. Annotated pseudocode for this
algorithm is shown in code block~\ref{PSCode}~\parencite{Clerc2002} algorithm is shown in code block~\ref{PSCode}~\parencite{Clerc2002}
\pagebreak
\onehalfspacing \onehalfspacing
\begin{lstlisting}[escapeinside={(*}{*)}, label={PSCode}, caption={Particle \begin{lstlisting}[escapeinside={(*}{*)}, label={PSCode}, caption={Particle
Swarm Optimisation Pseudocode}] Swarm Optimisation Pseudocode}]
@@ -1176,8 +1201,9 @@ The use of this algorithm allowed for the efficient optimisation of all
parameters relating to the stacking classifier and it's base classifiers, parameters relating to the stacking classifier and it's base classifiers,
resulting in a finely tuned classification model that would not have been resulting in a finely tuned classification model that would not have been
producible using traditional trial and error methods to search for optimal producible using traditional trial and error methods to search for optimal
parameters.\\ During the initial design phase, it was found that the abundance parameters.\\
of machine learning algorithms available make selection of the optimal model a During the initial design phase, it was found that the abundance
of machine learning algorithms available make selection of the optimal model
difficult, requiring in depth knowledge of a range of machine learning difficult, requiring in depth knowledge of a range of machine learning
techniques. A novel approach used by recent stacking classifier applications techniques. A novel approach used by recent stacking classifier applications
has been in the use of meta-heuristic algorithm to select models automatically, has been in the use of meta-heuristic algorithm to select models automatically,
@@ -1196,7 +1222,7 @@ optimal solution. It was thought that for the proposed system a locally optimal
system would suffice, particularly given the highly complex parameter space system would suffice, particularly given the highly complex parameter space
used in implementation. This is discussed in detail in Section~\ref{ModOp}. used in implementation. This is discussed in detail in Section~\ref{ModOp}.
\subsection{Model Performance Evaluation Method}\label{metrics} \subsection{Model performance evaluation method}\label{metrics}
In order to fully understand the performance of the system (and to evaluate the In order to fully understand the performance of the system (and to evaluate the
impact of design decisions throughout development), a group of scoring methods impact of design decisions throughout development), a group of scoring methods
were implemented to test the system's performance in a selection of scenarios. were implemented to test the system's performance in a selection of scenarios.
@@ -1270,7 +1296,7 @@ such issues. Rationale is given for decisions made throughout
production of the proposed system and any known issues with the current implementation are production of the proposed system and any known issues with the current implementation are
outlined. outlined.
\subsection{Development Strategy} \subsection{Development strategy}
Early in the design process it became apparent that in order for this project Early in the design process it became apparent that in order for this project
to produce reasonable results, it would need to utilise a number of complex to produce reasonable results, it would need to utilise a number of complex
algorithms to handle the various non-trivial problems that were encountered algorithms to handle the various non-trivial problems that were encountered
@@ -1306,8 +1332,8 @@ throughout the project alongside other packages detailed in the following
sections. sections.
\subsection{System overview} \subsection{System overview}
The proposed system can be broken down into 4 key components: the user The proposed system can be broken down into 5 key components: the user
interface, feature generation module, classification module and optimisation interface, feature generation module, classification module, optimisation
module and evaluation module. The overall architecture of the system follows a module and evaluation module. The overall architecture of the system follows a
common design pattern for machine learning based systems; Taking a set of input common design pattern for machine learning based systems; Taking a set of input
data, augmenting to produce associated data, extracting patterns from said data, augmenting to produce associated data, extracting patterns from said
@@ -1334,9 +1360,9 @@ particularly in long-running iterative processes used for optimisation.\\
A file based logging system was developed using Python's built-in logging A file based logging system was developed using Python's built-in logging
module to allow for the monitoring of threaded processes. This allowed for module to allow for the monitoring of threaded processes. This allowed for
detailed monitoring of the systems progress, even when running multiple detailed monitoring of the systems progress, even when running multiple
operation concurrently.\\ operations concurrently.\\
A significant issues that developed as the project grew in size and complexity A significant issue that developed as the project grew in size and complexity
was the running time. As more complex methods were implemented for feature was the running time. As more complex methods were implemented for feature
extraction and model optimisation, the time taken to process the relatively extraction and model optimisation, the time taken to process the relatively
large dataset grew considerably. Primarily using Python's object pickling large dataset grew considerably. Primarily using Python's object pickling
@@ -1391,7 +1417,7 @@ Appendix~\ref{appendixA}.\\
Given the large number of operation required for feature extraction, a large Given the large number of operation required for feature extraction, a large
amount of time needed to compute features was an unavoidable consequence of amount of time needed to compute features was an unavoidable consequence of
the design. To help alleviate this issue, processing of features was the design. To help alleviate this issue, processing of features was
parallelised, using each sample as an individual job. The speed-up incurred parallelised, using each sample as an individual job. The speed-up aquired
through parellisation is inherently dependant on the system running the through parellisation is inherently dependant on the system running the
program, however, this significantly reduced the computation time of features. program, however, this significantly reduced the computation time of features.
A modified implementation of Python's multiprocessing module was used for task A modified implementation of Python's multiprocessing module was used for task
@@ -1479,9 +1505,9 @@ evaluations, resulting in 50 iterations using 20 particles. Final parameters
and selected features and selected features
for the chosen algorithms are detailed in table~\ref{OpParam}.\\ for the chosen algorithms are detailed in table~\ref{OpParam}.\\
The final scores produced for this model, evaluated using the full dataset, can The final scores produced for this model, evaluated using the full dataset, can
be found in Table~\ref{TestSet} (Hidden test set scores), Table~\ref{LOGO} be found in Table~\ref{TestSet}. Scores for Leave-one-out cross-validation and
(Leave-one-out scores) and 10-fold cross-validation can be seen in Figure~\ref{fig1} and Figure~\ref{fig2}
Table~\ref{KFCV} (Stratified cross-validation scores). respectively. Details can be found in Appendix~\ref{appendixD}.
\begin{table}[H] \begin{table}[H]
\centering \centering
@@ -1494,40 +1520,6 @@ $Acc$ & $Se$ & $Sp$ \\ \midrule
\end{tabular} \end{tabular}
\end{table} \end{table}
\begin{table}[H]
\doublespacing
\caption{Leave-one-out scores}
\label{LOGO}
\footnotesize
All scores are an average of 10 iterations $\pm$ standard-deviation
\scriptsize
\centering
\begin{tabulary}{\linewidth}{LCCCCCCC}
\toprule
& A & B & C & D & E & F & Mean \\ \midrule
$Acc$ & $0.5395\pm0.0104$ & $0.4896\pm0.0129$ & $0.5673\pm0.0298$ & $0.5173\pm0.0223$ & $0.5869\pm0.0300$ & $0.5492\pm0.0140$ & $0.5416\pm0.0318$ \\
$Se$ & $0.7281\pm0.0164$ & $0.8664\pm0.0240$ & $0.6775\pm0.0208$ & $0.7865\pm0.0218$ & $0.5397\pm0.0459$ & $0.7387\pm0.0493$ & $0.7228\pm0.1005$ \\
$Sp$ & $0.3509\pm0.0264$ & $0.1127\pm0.012$ & $0.4571\pm0.0571$ & $0.2481\pm0.0416$ & $0.6340\pm0.0387$ & $0.3596\pm0.0464$ & $0.3604\pm0.1624$ \\ \bottomrule
\end{tabulary}
\end{table}
\begin{table}[H]
\caption{10-fold cross-validation score}
\footnotesize
All scores are an average of 10 iterations $\pm$ standard-deviation
\doublespacing
\label{KFCV}
\scriptsize
\centering
\begin{tabulary}{\linewidth}{LCCCCCCCCCCC}
\toprule
& 1 & 2 & 3 & 4 & 5 & 6 & 7 & 8 & 9 & 10 & Mean \\ \midrule
$Acc$ & $0.7969\pm0.0246$ & $0.8049\pm0.0244$ & $0.8043\pm0.0153$ & $0.8111\pm0.0295$ & $0.8095\pm0.0261$ & $0.7999\pm0.0208$ & $0.8061\pm0.0299$ & $0.8150\pm0.0198$ & $0.8140\pm0.0245$ & $0.7928\pm0.0224$ & $0.8055\pm0.0069$ \\
$Se$ & $0.8121\pm0.0420$ & $0.8164\pm0.0360$ & $0.8193\pm0.0302$ & $0.8184\pm0.0634$ & $0.8158\pm0.0484$ & $0.8061\pm0.0438$ & $0.8325\pm0.0546$ & $0.8421\pm0.0321$ & $0.8246\pm0.0474$ & $0.7798\pm0.0302$ & $0.8167\pm0.0157$ \\
$Sp$ & $0.7818\pm0.0293$ & $0.7935\pm0.0267$ & $0.7894\pm0.0208$ & $0.8037\pm0.0280$ & $0.8033\pm0.0226$ & $0.7937\pm0.0214$ & $0.7798\pm0.0229$ & $0.7878\pm0.0206$ & $0.8035\pm0.0219$ & $0.8059\pm0.0228$ & $0.7942\pm0.0091$ \\ \bottomrule
\end{tabulary}
\end{table}
% Make lists without bullets and compact spacing % Make lists without bullets and compact spacing
\renewenvironment{itemize}{ \renewenvironment{itemize}{
\begin{list}{}{ \begin{list}{}{
@@ -1541,7 +1533,6 @@ $Sp$ & $0.7818\pm0.0293$ & $0.7935\pm0.0267$ & $0.7894\pm0.0208$ & $0.8037\pm0
} }
\setlist[enumerate]{itemsep=0.25em} \setlist[enumerate]{itemsep=0.25em}
\begin{table}[H] \begin{table}[H]
\centering \centering
\caption{Optimised model parameters and selected features} \caption{Optimised model parameters and selected features}
@@ -1604,28 +1595,37 @@ C: 4.2507 & C: 4.9452 & & C: 14.3611
\end{itemize} \end{itemize}
\end{multicols} \end{multicols}
\end{table} \end{table}
\begin{figure}[H]
Due to the mimicking of the approach taken for scoring entries to the physionet \caption{Leave-one-out cross-validation results (mean and std-dev)}
challenge, it was possible to directly compare results to challenge entries. \makebox[\textwidth]{\includegraphics[width=1.1\textwidth]{logo}}
\label{fig1}
\end{figure}
\begin{figure}[H]
\caption{Stratified 10-fold cross-validation results (mean and std-dev)}
\makebox[\textwidth]{\includegraphics[width=\textwidth]{10_fold}}
\label{fig2}
\end{figure}
Due to the replication of the approach taken for scoring entries to the Physionet
challenge, it is possible to directly compare results to challenge entries.
This aims to provide a thorough understanding of the performance of the This aims to provide a thorough understanding of the performance of the
proposed system in relation to other approaches. The system is further compared proposed system in relation to other approaches. The system is further compared
to some successful algorithms prior to the challenge in the subsequent section, to some successful algorithms prior to the challenge in the subsequent section,
in order to understand the performance of the system in a wider context of in order to understand the performance of the system in a wider context of
heart sound analysis.\\ heart sound analysis.\\
The most directly comparable results are to those presented by participant, The most directly comparable results are to those presented by challenge
used during the training of their algorithms. Many participants used similar participants, used during the training of their algorithms. Many participants
cross-validation scores to determine the performance of their algorithm before used similar cross-validation scores to determine the performance of their
testing on the final hidden dataset, and these provide a key insight into the algorithm before testing on the final hidden dataset, and these provide a key
performance with regard to a variety of aspects.\\ insight into the performance with regard to a variety of aspects.\\
Results obtained using the Leave-one-out cross-validation scoring are similar Results obtained using the Leave-one-out cross-validation scoring are similar
to those of the highest scoring algorithms in the to those of the highest scoring algorithms in the
challenge~\parencite{Homsi2017, Bobillo2016}. As a measure for performance on challenge~\parencite{Homsi2017, Bobillo2016}. As a measure for performance on
unseen data, this suggests that the proposed algorithm generalises to a similar unseen data, this suggests that the proposed algorithm generalises to a similar
degree. However, it is clear that algorithms score poorly in this area. This is degree. However, it is clear that algorithms generally score poorly in this
the general consensus across many of the algorithms presented for the area. This is the general consensus across many of the algorithms presented for
challenge and is a problem that requires further work. Higher scores in the challenge and is a problem that requires further work. Higher scores in
10-fold cross validation than those of Leave-one-out cross-validation further 10-fold cross validation than those of Leave-one-out cross-validation further
suggest that the algorithm is highly susceptible to degraded results, most suggest that the algorithm is highly susceptible to degraded results, most
likely as a consequence of signal qualities varying from those of the training likely as a consequence of signal qualities varying from those of the training
@@ -1635,7 +1635,7 @@ database. The aim of this was to remove class imbalance across the training
and test set, to gain an understanding of how the model performs on each class and test set, to gain an understanding of how the model performs on each class
equally. Results of these tests can be viewed in Appendix~\ref{appendixC}. It equally. Results of these tests can be viewed in Appendix~\ref{appendixC}. It
was found that, although hidden test set and 10-fold cross-validation scores was found that, although hidden test set and 10-fold cross-validation scores
aren't affected by class imbalance, there is a significant increase the overall aren't affected by class imbalance, there is a significant increase in the overall
leave-one-out cross-validation score from 54.16\% to 66.13\%. This is currently leave-one-out cross-validation score from 54.16\% to 66.13\%. This is currently
thought to be caused by the model not resampling by database during training. thought to be caused by the model not resampling by database during training.
As resampling during training does not maintain the balance between datasets, a As resampling during training does not maintain the balance between datasets, a
@@ -1663,7 +1663,7 @@ cross-validation scores. This may also be true in the case of the proposed
system as database $e$ has shown considerably higher specificity in results system as database $e$ has shown considerably higher specificity in results
than those the other database, both in balanced and unbalanced datasets. than those the other database, both in balanced and unbalanced datasets.
Further would be needed to understand the extent of the effect that this has on Further would be needed to understand the extent of the effect that this has on
the performance of the proposed system. the performance of the proposed system.\\
The final 10-fold cross-validation score was found to be between, 2 and 12\% The final 10-fold cross-validation score was found to be between, 2 and 12\%
less than those of the highest scoring models~\parencite{Zabihi2016, Homsi2017, less than those of the highest scoring models~\parencite{Zabihi2016, Homsi2017,
@@ -1696,7 +1696,7 @@ widely considered for the challenge.
\section{Discussion and further work}\label{FutureWork} \section{Discussion and further work}\label{FutureWork}
The current implementation of the system has provided promising results, The current implementation of the system has provided promising results,
suggest that the combination of techniques is well suited to the task of suggesting that the combination of techniques is well suited to the task of
abnormality detection. It is clear however, that further development of the abnormality detection. It is clear however, that further development of the
system could improve results further. This section defines some of the system could improve results further. This section defines some of the
recognised issues that could be addressed in each of the system's components, recognised issues that could be addressed in each of the system's components,
@@ -1709,8 +1709,8 @@ original signal, pre-processing (and other components of the system) currently
make little use of biomedical domain knowledge to aid in processing of the make little use of biomedical domain knowledge to aid in processing of the
input data. This is largely due to the author's lack of background in this input data. This is largely due to the author's lack of background in this
area, prior to development of this project. An example of a project that has area, prior to development of this project. An example of a project that has
implemented this is the work by Goda et al.\ who, by recognising that humans implemented this is the work by Goda et al.\ who, by recognising that trained professionals
can classify a heart sound with at least 5 seconds of audio, was able to can classify most heart conditions, given at least 5 seconds of audio, was able to
further segment audio in 5 second overlapping segments, essentially providing further segment audio in 5 second overlapping segments, essentially providing
additional atomic samples for training~\parencite{Goda2016}. It is thought that additional atomic samples for training~\parencite{Goda2016}. It is thought that
other such assumptions based on physiological understanding could be made in other such assumptions based on physiological understanding could be made in
@@ -1738,8 +1738,8 @@ For example, in the final selection of models, a linear SVM, RBF kernel SVM and
Naive Bayes models were chosen by the system. From intuition it is thought that Naive Bayes models were chosen by the system. From intuition it is thought that
the reason these worked well is due to the complex combination of linear and the reason these worked well is due to the complex combination of linear and
non-linear relationships in the input features. As the RBF kernel is well non-linear relationships in the input features. As the RBF kernel is well
suited to differentiating non linear patters, and the linear SVM is well suited suited to differentiating non linear patterns, and the linear SVM is well suited
for linear patters, these models would in theory compliment one another. This for linear patterns, these models would in theory compliment one another. This
is also true of the Naive-bayes model, which considers each feature in is also true of the Naive-bayes model, which considers each feature in
isolation from all others, contrasting the complex inter-feature relationships isolation from all others, contrasting the complex inter-feature relationships
(such as those most likely present in the MFCC and wavelet coefficients, for (such as those most likely present in the MFCC and wavelet coefficients, for
@@ -1798,12 +1798,6 @@ heart sound analysis.
\begin{table}[H] \begin{table}[H]
\centering \centering
\caption{Description of features} \caption{Description of features}
\scriptsize
Feature sources include:~\parencite{Homsi2016, Schmidt2015, Liang1998,
Lerch2012}\\
`*' --- denotes feature is applied to S1, systolic, S2 and diastolic segments
respectively.
\onehalfspacing \onehalfspacing
\tiny \tiny
\label{my-label} \label{my-label}
@@ -1846,6 +1840,12 @@ A5Shan & Approximation coefficient shannon entropy & S
\mbox{TotD[1-5]*Shan} & Total detail coefficient shannon entropy & Total Shannon entropy of DWT detail coefficient 1-5 across signal \\ \mbox{TotD[1-5]*Shan} & Total detail coefficient shannon entropy & Total Shannon entropy of DWT detail coefficient 1-5 across signal \\
TotA5*Shan & Total approximation coefficient shannon entropy & Total Shannon entropy of DWT approximation coefficient 1-5 across signal \\ \hline TotA5*Shan & Total approximation coefficient shannon entropy & Total Shannon entropy of DWT approximation coefficient 1-5 across signal \\ \hline
\end{tabulary} \end{tabulary}
\justifying
\scriptsize
Feature sources include:~\parencite{Homsi2016, Schmidt2015, Liang1998,
Lerch2012}\\
`*' --- denotes feature is applied to S1, systolic, S2 and diastolic segments
respectively.
\end{table} \end{table}
\pagebreak \pagebreak
@@ -1906,6 +1906,47 @@ optional arguments:
\doublespacing \doublespacing
\pagebreak{} \pagebreak{}
\subsection{Final results}\label{appendixD}
Results of of tests on final optimised model\\
Leave-one-out scores are shown in Table~\ref{LOGO}\\
Stratified cross-validation scores can be found in Table~\ref{KFCV}\\
\begin{table}[H]
\doublespacing
\caption{Leave-one-out scores}
\label{LOGO}
\footnotesize
All scores are an average of 10 iterations $\pm$ standard-deviation
\scriptsize
\centering
\begin{tabulary}{\linewidth}{LCCCCCCC}
\toprule
& A & B & C & D & E & F & Mean \\ \midrule
$Acc$ & $0.5395\pm0.0104$ & $0.4896\pm0.0129$ & $0.5673\pm0.0298$ & $0.5173\pm0.0223$ & $0.5869\pm0.0300$ & $0.5492\pm0.0140$ & $0.5416\pm0.0318$ \\
$Se$ & $0.7281\pm0.0164$ & $0.8664\pm0.0240$ & $0.6775\pm0.0208$ & $0.7865\pm0.0218$ & $0.5397\pm0.0459$ & $0.7387\pm0.0493$ & $0.7228\pm0.1005$ \\
$Sp$ & $0.3509\pm0.0264$ & $0.1127\pm0.012$ & $0.4571\pm0.0571$ & $0.2481\pm0.0416$ & $0.6340\pm0.0387$ & $0.3596\pm0.0464$ & $0.3604\pm0.1624$ \\ \bottomrule
\end{tabulary}
\end{table}
\begin{table}[H]
\caption{10-fold cross-validation score}
\footnotesize
All scores are an average of 10 iterations $\pm$ standard-deviation
\doublespacing
\label{KFCV}
\scriptsize
\centering
\begin{tabulary}{\linewidth}{LCCCCCCCCCCC}
\toprule
& 1 & 2 & 3 & 4 & 5 & 6 & 7 & 8 & 9 & 10 & Mean \\ \midrule
$Acc$ & $0.7969\pm0.0246$ & $0.8049\pm0.0244$ & $0.8043\pm0.0153$ & $0.8111\pm0.0295$ & $0.8095\pm0.0261$ & $0.7999\pm0.0208$ & $0.8061\pm0.0299$ & $0.8150\pm0.0198$ & $0.8140\pm0.0245$ & $0.7928\pm0.0224$ & $0.8055\pm0.0069$ \\
$Se$ & $0.8121\pm0.0420$ & $0.8164\pm0.0360$ & $0.8193\pm0.0302$ & $0.8184\pm0.0634$ & $0.8158\pm0.0484$ & $0.8061\pm0.0438$ & $0.8325\pm0.0546$ & $0.8421\pm0.0321$ & $0.8246\pm0.0474$ & $0.7798\pm0.0302$ & $0.8167\pm0.0157$ \\
$Sp$ & $0.7818\pm0.0293$ & $0.7935\pm0.0267$ & $0.7894\pm0.0208$ & $0.8037\pm0.0280$ & $0.8033\pm0.0226$ & $0.7937\pm0.0214$ & $0.7798\pm0.0229$ & $0.7878\pm0.0206$ & $0.8035\pm0.0219$ & $0.8059\pm0.0228$ & $0.7942\pm0.0091$ \\ \bottomrule
\end{tabulary}
\end{table}
\pagebreak
\subsection{Balanced dataset test results}\label{appendixC} \subsection{Balanced dataset test results}\label{appendixC}
Results of testing database using a resampled, balanced dataset.\\ Results of testing database using a resampled, balanced dataset.\\
Dataset was resampled by database, using jacknife resampling (Sampling without Dataset was resampled by database, using jacknife resampling (Sampling without