A latent factor model for count data is popularly applied when deconvoluting mixed signals in biological data as exemplified by sequencing data for transcriptome or microbiome studies. Due to the availability of pure samples such as single-cell transcriptome data, the estimators can enjoy much better accuracy by utilizing the extra information. However, such an advantage quickly disappears in the presence of excessive zeros. To correctly account for such a phenomenon, we propose a zero-inflated non-negative matrix factorization that models excessive zeros in both mixed and pure samples and derive an effective multiplicative parameter updating rule. In simulation studies, our method yields smaller bias comparing to other deconvolution methods. We applied our approach to gene expression from brain tissue as well as fecal microbiome datasets, illustrating the superior performance of the approach. Our method is implemented as a publicly available R-package, iNMF. In zero-inflated non-negative matrix factorization (iNMF) for the deconvolution of mixed signals of biological data, pure-samples play a significant role by solving the identifiability issue as well as improving the accuracy of estimates. One of the main issues of using single-cell data is that the identities(labels) of the cells are not given. Thus, it is crucial to sort these cells into their correct types computationally. We propose a nonlinear latent variable model that can be used for sorting pure-samples as well as grouping mixed-samples via deep neural networks. The computational difficulty will be handled by adopting a method known as variational autoencoding. While doing so, we keep the NMF structure in a decoder neural network, which makes the output of the network interpretable.

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This report aims to present a project in the field of unsupervised clustering on human behavior in a parking application. With increasing opportunities to collect and store data, the demands to utilize the data in meaningful ways also increase. The purpose of this work is to explore common behaviors within the app and what those reveal about its usage. Transforming event based data into user sessions was the first step. The next step was to establish how to measure the similarity between sequences. This was achieved using two different approaches. One approach based on a combination of string metrics and heuristics. The other approach creates array representations of the sessions using an autoencoder. With these two ways of representing the similarity between sessions, we utilize clustering algorithms to assign labels to all sessions. Due to the unknown attributes of the data set, the versatile clustering algorithm HDBSCAN was employed on both representations of the session separately. The clusters produced by HDBSCAN were compared to those produced by simple partitioning algorithms. The noisy nature of human behavior allowed HDBSCAN to create better clusters with distinct behaviors in comparison to the simpler partitioning algorithms. Without a ground truth to rely on, evaluating the models proved to be a difficult part of the project. We utilized both quantitative metrics, as well as qualitative methods for evaluation. In conclusion, our work provides a new way of evaluating user behavior. It brings new insights into different ways the customer achieves their goals within the app. And finally it lays ground for connecting user behavior with transaction data. / Denna rapport syftar till att presentera ett projekt inom oövervakat klustrande av mänskligt beteende i en parkeringsapplikation. Med ökande möjligheter att samla in och lagra data ökar också kraven på att använda informationen på meningsfulla sätt. Syftet med detta arbete är att undersöka vanligt förekommande beteenden inom applikationen och vad dessa avslöjar om användningen. Första steget var att omvandla händelsesbaserad data till användarsessioner. Nästa steg var att etablera hur man mäter likheten mellan sekvenser. Detta uppnåddes genom att använda två olika metoder. Första metoden var baserad på en kombination av strängmått och heuristik. Den andra metoden skapade vektorreprestation av sessionerna med hjälp av en autokodare. Med dessa två sätt att representera likheten mellan sessioner användes klustringsalgoritmer för att tilldela etiketter till alla sessioner. På grund av de okända attributen hos datasetet applicerades den mångsidiga klustringsalgoritmen HDBSCAN för båda representationer av sessionerna. Klustren som skapades från HDBSCAN jämfördes med de kluster som skapades med hjälp av enkla partitioneringsalgoritmer. Bruset som mänskligt beteende medför gjorde att HDBSCAN kunde skapa bättre kluster med tydliga beteenden jämfört med de simpla partitionsalgoritmerna. Utan en grundläggande sanning att utgå ifrån visade sig utvärderingen av modellerna vara en svår del av projektet. Vi använde både kvantitativa mätvärden och kvalitativa metoder för utvärderingen. Sammanfattningsvis resulterade vårt arbete i ett nytt sätt att utvärdera användarbeteende. Vidare skapades nya insikter kring de olika sätt som användare navigerar applikationen för att uträtta olika ärenden. Slutligen lägger arbetet grunden för att koppla samman användarbeteende med transaktionsdata i framtida projekt.

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京都大学 / 新制・課程博士 / 博士(情報学) / 甲第24725号 / 情博第813号 / 新制||情||137(附属図書館) / 京都大学大学院情報学研究科知能情報学専攻 / (主査)教授 鹿島 久嗣, 教授 山本 章博, 教授 吉川 正俊 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

The aim of explainable machine learning is to aid humans in understanding how exactly complex machine learning models work. Machine learning models have offered great performance in various areas. However, the mechanisms behind how the model works and how decisions are being made remain unknown. This specific constraint increases the user’s hesitation to trust the results of the model and even to improve their performance further. Counterfactual explanation is one method to offer explainability in machine learning by indicating what would have happened if the input of a model was modified in a specific way. Fraud is the action of acquiring something from someone else in a dishonest manner. Companies’ and organizations’ vulnerability to malicious actions has been increasing due to the development of digitalization. Machine learning applications have been successfully put in place to tackle fraudulent actions. However, the severity of the impact of fraudulent actions has highlighted the need for further scientific exploration of the topic. The current research will attempt to do so by studying counterfactual explanations related to fraud detection. Latent-CF is a method for counterfactual generation that utilizes an autoencoder and gradient descent in its latent space. LatentCF++ is an extension of Latent-CF. It utilizes a classifier and an autoencoder. The aim is to perturb the encoded latent representation through a gradient descent optimization for counterfactual generation so that the initially undesired class is then classified with the desired prediction. Compared to Latent-CF, LatentCF++ uses Adam optimization and adds further constraints to ensure that the generated counterfactual’s class probability surpasses the set decision boundary. The research question the current thesis addresses is: “To what extent can LatentCF++ provide reliable counterfactual explanations in fraud detection?”. In order to provide an answer to this question, the study is applying an experiment to implement a new application of LatentCF++. The current experiment utilizes a onedimensional convolutional neural network as a classifier and a deep autoencoder for counterfactual generation in fraud data. This study reports satisfying results regarding counterfactual explanation production of LatentCF++ on fraud detection. The classification is quite accurate, while the reconstruction loss of the deep autoencoder employed is very low. The validity of the counterfactual examples produced is lower than the original study while the proximity is lower. Compared to baseline models, k-nearest neighbors outperform LatentCF++ in terms of validity and Feature Gradient Descent in terms of proximity.

MRI is favorable for brain imaging due to its excellent soft tissue contrast and absence of harmful ionizing radiation. Many have proposed supervised multimodal neural networks for automatic brain tumor segmentation and showed promising results. However, they rely on large amounts of labeled data to generalize well. The trained network is also highly specific to the task and input. Missing inputs will most likely have a detrimental effect on the network’s predictions, if it works at all. The aim of this thesis work is to implement a deep neural network that learns the general representation of multimodal MRI images in an unsupervised manner and is insensitive to missing modalities. With the latent representation, labeled data are then used for brain tumor segmentation. A variational autoencoder and an unified representation network are used for repre- sentation learning. Fine-tuning or joint training was used for segmentation task. The performances of the algorithms at the reconstruction task was evaluated using the mean- squared error and at the segmentation task using the Dice coefficient. Both networks demonstrated the possibility in learning brain MR representations, but the unified representation network was more successful at the segmentation task.

The widespread of machine learning and deep learning in commercial and industrial settings has seen a dramatic up-rise. While the traditional software engineering techniques have overlap between machine learning model development, fundamental differences exist which affect both scientific disciplines. The current state-of-the-art argues that most challenges in software engineering of deep learning applications stem from poorly defined software requirements, tightly coupled architecturesand hardware-induced development issues. However the majority of the current work on this topic stems from literature reviews and requires validation in an industrial context. The work aims to validate the findings of the academia through the development of the autoencoder model for gearbox fault detection. The model has been developed as a part of the ongoing campaign from Volvo Construction Equipment towards introducing AI-based solution in quality control and production. Findings of the work are mostly aligned with the current state-of-the-art, where poorly defined software requirements and hardware-induced issues have been experienced, but the tightly-coupled architecture did not characterize the final product. Along with the confirmation of the previous findings, the work presents a recommendation for practitioners of software engineering for deep learning models in the form of technological rule which addresses the hardware-induced issues of development through the contribution of a method for calculating the memory requirements of the model and batch during the training phase. / <p>Collaboration with Volvo Construction Equipment</p>

京都大学 / 新制・論文博士 / 博士(医学) / 乙第13501号 / 論医博第2260号 / 新制||医||1061(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 小林 恭, 教授 中本 裕士, 教授 黒田 知宏 / 学位規則第4条第2項該当 / Doctor of Medical Science / Kyoto University / DFAM