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docs/thesis/chapters/5_cases/naive-bayes.tex

@@ -50,7 +50,7 @@ MAG needs no further preprocessing if we aim to match SciBERT's setup \cite{belt
 
 Our aims are twofold: (1) to evaluate a sentence classification model on MAG and compare it with the prior art; and (2) to retrain and apply this model for classifying publication metadata (including abstracts). This would allow the ScoutinScience Platform to select an appropriate processing pipeline which has been trained on a matching vocabulary (and domain) for each publication. 
 
-It seems reasonable that only considering the distribution (frequencies) of individual terms may be sufficient. For testing this hypothesis, a unigram language model --- Multinomial Naïve Bayes (MNB) --- is constructed, and its accuracy is compared with SciBERT's. The former definitely aligns with the advice to \textit{Use The Most Efficient Models}. Using the MNB implementation of scikit-learn \cite{pedregosa2011scikit}, it only took 71 lines of code to create, hyperparameter optimise, and test a text classifier.\footnote{The code is available at \href{https://great-ai.scoutinscience.com/tutorial/}{great-ai.scoutinscience.com/tutorial}.} This further proves how simple it is to use standard packages. The code can be considered for satisfying the \textit{Automate Hyper-Parameter Optimisation} best practice since it also implements an automated hyperparameter sweep. 
+It seems reasonable that only considering the distribution (frequencies) of individual terms may be sufficient. For testing this hypothesis, a unigram language model --- Multinomial Naïve Bayes (MNB) --- is constructed, and its accuracy is compared with SciBERT's. The former definitely aligns with the advice to \textit{Use The Most Efficient Models}. Using the MNB implementation of scikit-learn \cite{pedregosa2011scikit}, it only took 71 lines of code to create, hyperparameter optimise, and test a text classifier.\footnote{The code is available at \href{https://great-ai.schmelczer.dev/tutorial/}{great-ai.schmelczer.dev/tutorial}.} This further proves how simple it is to use standard packages. The code can be considered for satisfying the \textit{Automate Hyper-Parameter Optimisation} best practice since it also implements an automated hyperparameter sweep.
 
 The sentences are tokenised into words and vectorised with TF-IDF (with logarithmic term frequency) \cite{buckley1985implementation}, the hyperparameters found via 10-fold cross-validation on the \textit{train} split lead to filtering out tokens which occur in fewer than five documents or more than 5\% of the documents.
 
@@ -80,7 +80,7 @@ When this model is applied to the \textit{test} split of MAG, we get the confusi
 
 It is, of course, not entirely surprising that the sophisticated transformer architecture of SciBERT is not necessary for a straightforward task like this. Apart from phrases, the relations between separate words of a sentence do not carry nearly as much discriminative power as the identity of the terms \cite{hand2001idiot}; hence, there is little reason for using an attention mechanism. The fact that SciBERT even works in any way on this task is already a testament to its general applicability. Nevertheless, this short experiment has proved that we can safely opt for using MNB for production.
 
-Since Multinomial Naïve Bayes is best at returning a single label and SSC has multiple labels per datapoint: for evaluation purposes, it is checked whether the returned label is contained in the labels of the ground truth. On this dataset, MNB achieves a lower macro-average than on MAG, with an F1-score of 0.59.\footnote{The code for this is available at \href{https://great-ai.scoutinscience.com/examples/simple/deploy}{great-ai.scoutinscience.com/examples/simple/deploy}.} The weighted-average F1 is 0.70, and the overall accuracy is also 70\%. The substantial difference between the macro and weighted averages comes from the unbalanced distribution of the labels. The lower F1-score is not surprising because this dataset has more than twice as many classes. Additionally, the mistakes made are defensible when we look at Figure \ref{fig:ss-confusion}: most of them are between related domains.
+Since Multinomial Naïve Bayes is best at returning a single label and SSC has multiple labels per datapoint: for evaluation purposes, it is checked whether the returned label is contained in the labels of the ground truth. On this dataset, MNB achieves a lower macro-average than on MAG, with an F1-score of 0.59.\footnote{The code for this is available at \href{https://great-ai.schmelczer.dev/examples/simple/deploy}{great-ai.schmelczer.dev/examples/simple/deploy}.} The weighted-average F1 is 0.70, and the overall accuracy is also 70\%. The substantial difference between the macro and weighted averages comes from the unbalanced distribution of the labels. The lower F1-score is not surprising because this dataset has more than twice as many classes. Additionally, the mistakes made are defensible when we look at Figure \ref{fig:ss-confusion}: most of them are between related domains.
 
 \begin{displayquote}
 This is the usual point where papers conclude: a proof-of-concept/prototype has been built, and its performance demonstrated, measured --- and usually --- explained. Nonetheless, in an industrial setting, our problem is far from being solved: it has yet to be deployed.
@@ -186,7 +186,7 @@ assert add_number(12).output == 417
 
 Coincidentally, deployment best practices can be easily implemented in this wrapper layer. In the first iteration, these are input validation, persisting traces, online monitoring, and generating documentation. Input validation may be used to \textit{Check that Input Data is Complete, Balanced and Well Distributed}. Traces are essential for both \textit{Log Production Predictions with the Model's Version and Input Data} and \textit{Provide Audit Trails}. However, traces can also indirectly help \textbf{Robustness} because even production systems cannot be expected to be perfect. Saving and letting the users filter on encountered errors while allowing them to correlate those with the inputs producing them is imperative for facilitating debugging. Lastly, monitoring and documentation correspond with helping best practices: \textit{Continuously Monitor the Behaviour of Deployed Models} and \textit{Communicate, Align, and Collaborate With Others} respectively.
 
-To allow customising the service's behaviour to fit different use cases, the default configurations can be overridden by calling some library functions. An example of this can be seen in Listing \ref{listing:complex}, while more details of the semantics can be found in the documentation\footnote{\href{https://great-ai.scoutinscience.com/how-to-guides/create-service/}{great-ai.scoutinscience.com/how-to-guides/create-service}}.
+To allow customising the service's behaviour to fit different use cases, the default configurations can be overridden by calling some library functions. An example of this can be seen in Listing \ref{listing:complex}, while more details of the semantics can be found in the documentation\footnote{\href{https://great-ai.schmelczer.dev/how-to-guides/create-service/}{great-ai.schmelczer.dev/how-to-guides/create-service}}.
 
 \subsection{Summary}
 

docs/thesis/chapters/5_cases/scibert.tex

@@ -53,7 +53,7 @@ For the first iteration, 1500 sentences were selected for two experts to annotat
     \label{fig:scibert-confusion}
 \end{figure}
 
-The next step is fine-tuning SciBERT with the help of Hugging Face \texttt{transformers} \cite{wolf2019huggingface}. The data are divided into training and test splits with a ratio of 4:1. A validation split, used for early stopping, is also derived from the train split. The objective function is the F1-score of the positive class, and the early stopping patience is five epochs. The learning rate is $5 \times 10^{-5}$ and AdamW \cite{loshchilov2017decoupled} is used for optimisation with a weight decay of 0.05. The code can be found in the documentation\footnote{\href{https://great-ai.scoutinscience.com/examples/scibert/train/}{great-ai.scoutinscience.com/examples/scibert/train}}, it is surprisingly slightly shorter than the code of Section \ref{section:simple-case}.
+The next step is fine-tuning SciBERT with the help of Hugging Face \texttt{transformers} \cite{wolf2019huggingface}. The data are divided into training and test splits with a ratio of 4:1. A validation split, used for early stopping, is also derived from the train split. The objective function is the F1-score of the positive class, and the early stopping patience is five epochs. The learning rate is $5 \times 10^{-5}$ and AdamW \cite{loshchilov2017decoupled} is used for optimisation with a weight decay of 0.05. The code can be found in the documentation\footnote{\href{https://great-ai.schmelczer.dev/examples/scibert/train/}{great-ai.schmelczer.dev/examples/scibert/train}}, it is surprisingly slightly shorter than the code of Section \ref{section:simple-case}.
 
 \begin{displayquote}
 \textbf{Utility of LargeFiles} For the purposes of the documentation, the fine-tuning was conducted in the Google Colab online environment, which is excellent for providing anyone with GPU time for free. However, notebook environments are ephemeral, resulting in the need to manually upload and download all relevant data whenever a new virtual machine instance is granted. The \texttt{LargeFile} implementation alleviated this problem by automatically handling the uploads and downloads. Of course, first, backwards compatibility had to be solved for Python 3.7, the only available environment in Colab.