210 lines
13 KiB
TeX
210 lines
13 KiB
TeX
\documentclass[a4paper, final]{article}
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%\usepackage{literat} % Нормальные шрифты
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\usepackage[14pt]{extsizes} % для того чтобы задать нестандартный 14-ый размер шрифта
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\usepackage{tabularx}
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\usepackage[T2A]{fontenc}
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\usepackage[utf8]{inputenc}
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% \usepackage[russian]{babel}
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\usepackage{amsmath}
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\usepackage[left=25mm, top=20mm, right=20mm, bottom=20mm, footskip=10mm]{geometry}
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\usepackage{ragged2e} %для растягивания по ширине
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\usepackage{setspace} %для межстрочного интервала
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\usepackage{moreverb} %для работы с листингами
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\usepackage{indentfirst} % для абзацного отступа
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\usepackage{moreverb} %для печати в листинге исходного кода программ
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\usepackage{graphicx}
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\usepackage{array}
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\usepackage{multirow}
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\renewcommand\verbatimtabsize{4\relax}
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\renewcommand\listingoffset{0.2em} %отступ от номеров строк в листинге
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\renewcommand{\arraystretch}{1.4} % изменяю высоту строки в таблице
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\usepackage[font=small, singlelinecheck=false, justification=centering, format=plain, labelsep=period]{caption} %для настройки заголовка таблицы
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\usepackage{listings} %листинги
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\usepackage{xcolor} % цвета
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\usepackage{hyperref}% для гиперссылок
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\usepackage{enumitem} %для перечислений
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\newtheorem{theorem}{Теорема} % Создание нового окружения для теорем
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\setlist[enumerate,itemize]{leftmargin=1.2cm} %отступ в перечислениях
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\hypersetup{colorlinks,
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allcolors=[RGB]{010 090 200}} %красивые гиперссылки (не красные)
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% подгружаемые языки — подробнее в документации listings (это всё для листингов)
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\lstloadlanguages{ C++}
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% включаем кириллицу и добавляем кое−какие опции
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\lstset{tabsize=2,
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breaklines,
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basicstyle=\footnotesize,
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columns=fullflexible,
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flexiblecolumns,
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numbers=left,
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numberstyle={\footnotesize},
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keywordstyle=\color{blue},
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inputencoding=cp1251,
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extendedchars=true
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}
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\lstdefinelanguage{MyC}{
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language=C++,
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% ndkeywordstyle=\color{darkgray}\bfseries,
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% identifierstyle=\color{black},
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% morecomment=[n]{/**}{*/},
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% commentstyle=\color{blue}\ttfamily,
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% stringstyle=\color{red}\ttfamily,
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% morestring=[b]",
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% showstringspaces=false,
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% morecomment=[l][\color{gray}]{//},
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keepspaces=true,
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escapechar=\%,
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texcl=true
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}
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\textheight=24cm % высота текста
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\textwidth=16cm % ширина текста
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\oddsidemargin=0pt % отступ от левого края
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\topmargin=-1.5cm % отступ от верхнего края
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\parindent=24pt % абзацный отступ
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\parskip=5pt % интервал между абзацами
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\tolerance=2000 % терпимость к "жидким" строкам
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\flushbottom % выравнивание высоты страниц
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% Настройка листингов
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\lstset{
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language=C++,
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extendedchars=\true,
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inputencoding=utf8,
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keepspaces=true,
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% captionpos=b,
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}
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\begin{document} % начало документа
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% НАЧАЛО ТИТУЛЬНОГО ЛИСТА
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\begin{center}
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\hfill \break
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\hfill \break
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\normalsize{MINISTRY OF SCIENCE AND HIGHER EDUCATION OF THE RUSSIAN FEDERATION\\
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Federal State Autonomous Educational Institution of Higher Education Peter the Great St. Petersburg Polytechnic University\\[10pt]}
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\normalsize{Institute of Computer Science and Cybersecurity}\\[10pt]
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\normalsize{Higher School of Artificial Intelligence Technology}\\[10pt]
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\normalsize{Direction 02.03.01 Mathematics and computer Science}\\
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\hfill \break
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\hfill \break
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\hfill \break
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\hfill \break
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\large{\textbf{Literature Review}}\\
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\large{\textit{Machine learning approaches for assessing drug resistance in cancer treatment}}\\
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\hfill \break
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\hfill \break
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\end{center}
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\small{
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\begin{tabular}{lrrl}
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\!\!\!Student, & \hspace{2cm} & & \\
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\!\!\!group 5130201/20102 & \hspace{2cm} & \underline{\hspace{3cm}} &Tishenko А. А. \\\\
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\!\!\!Supervisor, Ph. D. & \hspace{2cm} & \underline{\hspace{3cm}} & Motorin D. E. \\\\
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&&\hspace{4cm}
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\end{tabular}
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\begin{flushright}
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<<\underline{\hspace{1cm}}>>\underline{\hspace{2.5cm}} 2024г.
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\end{flushright}
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}
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\hfill \break
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% \hfill \break
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\begin{center} \small{Saint-Petersburg, 2024} \end{center}
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\thispagestyle{empty} % выключаем отображение номера для этой страницы
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% КОНЕЦ ТИТУЛЬНОГО ЛИСТА
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\newpage
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% \tableofcontents
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% \newpage
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\section*{Introduction}
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\addcontentsline{toc}{section}{Introduction}
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Progress has been made in chemotherapy drugs, but drug resistance remains a major challenge in cancer treatment and the main cause of cancer progression and even death. However, there are no clear indicators for predicting the risk of drug resistance in patients. Existing drug sensitivity assessment methods has limitations such as low modeling success rates, high cost, and time-consuming process. Machine learning is both an expanding and evolving field of computing, and it seems that it can significantly help in solving chemotherapy resistance problem. Here we provide an overview of how different studies apply machine learning algorithms to predict and understand chemotherapy resistance in various cancer types. Also we consider the strengths and limitations of each approach and discuss obtained results.
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\newpage
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\begin{table}[h!]
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\centering
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\caption{Methods used in research papers.}
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\footnotesize
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\begin{tabularx}{\textwidth}{|X|p{2cm}|X|X|X|}
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\hline
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\textbf{Article} & \textbf{Cancer type} & \textbf{Machine learning algorithms} & \textbf{Datasets} & \textbf{Feature importance analysis} \\
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\hline
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Classification of paclitaxel-resistant ovarian cancer cells using holographic flow cytometry through interpretable machine learning~\cite{paclitaxel} & Epithelial ovarian cancer (EOC) & Tree, Naive Bayes, K-nearest neighbors
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(KNN), support vector machine (SVM), and neural network (NN) & Self-produced dataset of 2998 quantitative phase images (QPIs) of EOC cells & SHapley Additive
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exPlanations (SHAP), Pearson coefficient, Kruskal-Wallis test \\
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\hline
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Heterogeneity of computational pathomic signature predicts drug resistance and intra-tumor heterogeneity of ovarian cancer~\cite{heterogeneity} & Epithelial ovarian cancer (EOC) & CellProfiler~\cite{cellprofile}, least absolute shrinkage and selection operator (LASSO) regression & 494 ovarian and 70 paracarcinoma tissues images from The Cancer Genome Atlas (TCGA) database~\cite{tcga} & Statistical analysis using R~\cite{r-lang}. Various visualizations, including heatmaps, Venn diagrams, ROC curves, and survival curves. \\
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\hline
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Mitochondria-related chemoradiotherapy resistance genes-based machine learning model associated with immune cell infiltration on the prognosis of esophageal cancer and its value in pan-cancer~\cite{mitochondria} & Esophageal cancer & Generalized linear model (GLM), K-nearest neighbor (KNN), least absolute shrinkage and selection operator (LASSO) regression, neural network (NN), random forest (RF), support vector machine (SVM), extreme gradient boosting (XGB) & Nearly 500 tissue samples, RNA-sequences and some other clinical data from Gene Expression Omnibus (GEO) database~\cite{geo}, information on 183 esophageal cancer patients from The Cancer Genome Atlas (TCGA) database~\cite{tcga} & Statistical analysis using DALEX package~\cite{dalex} for~R~\cite{r-lang} \\
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\hline
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Molecular separation-assisted label-free SERS combined with machine learning for nasopharyngeal cancer screening and radiotherapy resistance prediction~\cite{sers} & Nasopharyng-eal cancer & Principal component analysis and linear discriminant analysis (PCA-LDA) & Self-produced dataset of 120 plasma samples, 60 of which from healthy volunteers, 30 from radiotherapy sensitivity patients and 30 from radiotherapy resistance patients & - \\
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\hline
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\end{tabularx}
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\end{table}
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\newpage
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\begin{table}[h!]
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\centering
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\caption{Results obtained in research papers.}
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\footnotesize
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\begin{tabularx}{\textwidth}{|X|X|X|X|}
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\hline
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\textbf{Article} & \textbf{Key results} & \textbf{Best algorithms} & \textbf{Metrics} \\
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\hline
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Classification of paclitaxel-resistant ovarian cancer cells using holographic flow cytometry through interpretable machine learning~\cite{paclitaxel} & Demonstrated that morphological changes in epithelial ovarian cancer (EOC) cells correlate with drug sensitivity, highlighting the potential for monitoring drug resistance.
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& Support vector machine (SVM) and neural network (NN) & Accuracy of 94.5\% for SVM and 93.4\% for NN \\
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\hline
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Heterogeneity of computational pathomic signature predicts drug resistance and intra-tumor heterogeneity of ovarian cancer~\cite{heterogeneity} & Demonstrated a strong correlation between intra-tumor heterogeneity (ITH) and drug resistance in epithelial ovarian cancer (EOC) cells & Least absolute shrinkage and selection operator (LASSO) regression & Area under curve (AUC) of 0.601, 0.594, and 0.589 for 1, 3, and 5 years survival time accordingly \\
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\hline
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Mitochondria-related chemoradiotherapy resistance genes-based machine learning model associated with immune cell infiltration on the prognosis of esophageal cancer and its value in pan-cancer~\cite{mitochondria} & Proposed a model that incorporates mitochondria-related chemoradiotherapy resistance (MRCRTR) genes. Identified six mitochondria-related genes that affect CRT and the prognosis of esophageal cancer. & Neural network (NN) and least absolute shrinkage and selection operator (LASSO) regression & Root mean squared error (RMSE) of 0.001 for NN and 0.003 for LASSO \\
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\hline
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Molecular separation-assisted label-free SERS combined with machine learning for nasopharyngeal cancer screening and radiotherapy resistance prediction~\cite{sers} & Developed a novel approach using label-free surface-enhanced Raman spectroscopy (SERS) to profile molecular patterns in the blood of nasopharyngeal cancer (NPC) patients, distinguishing those with radiotherapy sensitivity from those with resistance & Principal component analysis and linear discriminant analysis (PCA-LDA) & Accuracy of 96.7\% for identifying radiotherapy resistance subjects from sensitivity ones and 100\% for identifying the nasopharyngeal cancer (NPC) subjects from healthy ones \\
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\hline
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\end{tabularx}
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\end{table}
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% \section {Первый раздел}
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% \subsection{Первый подраздел}
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% Текст первого подраздела
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% \section*{Conclusion}
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% \addcontentsline{toc}{section}{Conclusion}
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% Conclusion text
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\newpage
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% \section*{Literature}
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% \addcontentsline{toc}{section}{Literature}
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\vspace{-1.5cm}
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\begin{thebibliography}{0}
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\bibitem{paclitaxel}
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Lu Xin, Wen Xiao, Huanzhi Zhang, Yakun Liu, Xiaoping Li, Pietro Ferraro, Feng Pan, Classification of paclitaxel-resistant ovarian cancer cells using holographic flow cytometry through interpretable machine learning, 2024.
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\bibitem{heterogeneity}
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Qiuli Zhu, Hua Dai, Feng Qiu, Weiming Lou, Xin Wang, Libin Deng, Chao Shi, Heterogeneity of computational pathomic signature predicts drug resistance and intra-tumor heterogeneity of ovarian cancer, 2024.
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\bibitem{mitochondria}
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Ziyu Liu, Zahra Zeinalzadeh, Tao Huang, Yingying Han, Lushan Peng, Dan Wang, Zongjiang Zhou, DIABATE Ousmane, Junpu Wang, Mitochondria-related chemoradiotherapy resistance genes-based machine learning model associated with immune cell infiltration on the prognosis of esophageal cancer and its value in pan-cancer, 2024.
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\bibitem{sers}
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Jun Zhang, Youliang Weng, Yi Liu, Nan Wang, Shangyuan Feng, Sufang Qiu, Duo Lin, Molecular separation-assisted label-free SERS combined with machine learning for nasopharyngeal cancer screening and radiotherapy resistance prediction, 2024.
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\bibitem{cellprofile}
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T. Misteli, C. McQuin, A. Goodman, V. Chernyshev, L. Kamentsky, B.A. Cimini, et al., CellProfiler 3.0: next-generation image processing for biology, 2018.
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\bibitem{tcga}
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The Cancer Genome Atlas (TCGA) database. Available at \url{https://www.cancer.gov/ccg/research/genome-sequencing/tcga}. Accessed October 8, 2024.
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\bibitem{geo}
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Gene Expression Omnibus (GEO) database. Available at \url{https://www.ncbi.nlm.nih.gov/geo/}. Accessed October 8, 2024.
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\bibitem{r-lang}
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The R Project for Statistical Computing. Available at \url{https://www.r-project.org/}. Accessed October 8, 2024.
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\bibitem{dalex}
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DALEX: explainers for complex predictive models, Przemyslaw Biecek, 2018.
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\end{thebibliography}
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\end{document} |