Gene expression analysis provides genome-wide insights into the transcriptional activity of a cell. One of the first computational steps in exploration and analysis of the gene expression data is clustering. With a number of standard clustering methods routinely used, most of the methods do not take prior biological information into account. Here, we propose a new approach for gene expression clustering analysis. The approach benefits from a new deep learning architecture, Robust Autoencoder, which provides a more accurate high-level representation of the feature sets, and from incorporating prior system-wide biological information into the clustering process. We tested our approach on two gene expression datasets and compared the performance with two widely used clustering methods, hierarchical clustering and k-means, and with a recent deep learning clustering approach. Our approach outperformed all other clustering methods on the labeled yeast gene expression dataset. Furthermore, we showed that it is better in identifying the functionally common clusters than k-means on the unlabeled human gene expression dataset. The results demonstrate that our new deep learning architecture can generalize well the specific properties of gene expression profiles. Furthermore, the results confirm our hypothesis that the prior biological network knowledge is helpful in the gene expression clustering.

Deep learning is usually applied to static datasets. If used for classification based on data streams, it is not easy to take into account a non-stationarity. This thesis presents work in progress on a new method for online deep classifi- cation learning in data streams with slow or moderate drift, highly relevant for the application domain of malware detection. The method uses a combination of multilayer perceptron and variational autoencoder to achieve constant mem- ory consumption by encoding past data to a generative model. This can make online learning of neural networks more accessible for independent adaptive sys- tems with limited memory. First results for real-world malware stream data are presented, and they look promising. 1

Predictive Maintenance (PM) has been increasingly adopted in the Automotive industry, in the recent decades along with conventional approaches such as the Preventive Maintenance and Diagnostic/Corrective Maintenance, since it provides many advantages to estimate the failure before the actual occurrence proactively, and also being adaptive to the present status of the vehicle, in turn allowing flexible maintenance schedules for efficient repair or replacing of faulty components. PM necessitates the storage and analysis of large amounts of sensor data. This requirement can be a challenge in deploying this method on-board the vehicles due to the limited storage and computational power on the hardware of the vehicle. Hence, this thesis seeks to obtain low dimensional descriptive features from high dimensional data using Representation Learning. This low dimensional representation will be used for predicting vehicle faults, specifically Turbocharger related failures. Since the Logged Vehicle Data (LVD) was base on all the data utilized in this thesis, it allowed for the evaluation of large populations of trucks without requiring additional measuring devices and facilities. The gradual degradation methodology is considered for describing vehicle condition, which allows for modeling the malfunction/ failure as a continuous process rather than a discrete flip from healthy to an unhealthy state. This approach eliminates the challenge of data imbalance of healthy and unhealthy samples. Two important hypotheses are presented. Firstly, Parallel StackedClassical Autoencoders would produce better representations com-pared to individual Autoencoders. Secondly, employing Learned Em-beddings on Categorical Variables would improve the performance of the Dimensionality reduction. Based on these hypotheses, a model architecture is proposed and is developed on the LVD. The model is shown to achieve good performance, and in close standards to the previous state-of-the-art research. This thesis, finally, illustrates the potential to apply parallel stacked architectures with Learned Embeddings for the Categorical features, and a combination of feature selection and extraction for numerical features, to predict the Remaining Useful Life (RUL) of a vehicle, in the context of the Turbocharger. A performance improvement of 21.68% with respect to the Mean Absolute Error (MAE) loss with an 80.42% reduction in the size of data was observed.

Wireless communications technologies have experienced an exponential development during the last decades. 5G is a prominent exponent whose one of its crucial component is the Massive MIMO technology. By supporting multiple streams of signals it allows a revamped signal reconstruction in terms of mobile traffic size, data rate, latency, and reliability. In this thesis work, we isolated this technology into a SIMOapproach (Single-Input Multiple-Output) to explore a Machine Learning modeling to address the so-called Channel Prediction problem. Generally, the algorithms available to perform Channel Estimation in FDD and TDD deployments incur computational complexity downsides and require explicit feedback from client devices, which is typically prohibitive. This thesis work focuses on Channel Prediction by aims of employing Machine and deep Learning models in order to reduce the computational complexity by further relying in statistical modeling/learning. We explored the cross-Frequency Subband prediction intra-TTI (Transmission Time Interval) by means of proposing 3 three models. These intended to leverage frequency Multipath Components dependencies along TTIs. The first two ones are Probabilistic Principal Components Analysis (PPCA) and its Bayesiancounterpart, Bayesian Principal Components Analysis (BPCA). Then, we implemented Deep Learning Variational Encoder-Decoder (VED) architecture. These three models are intended to deal with the hugely high-dimensional space of the 4 datasets used by its intrinsic dimensionality reduction. The PPCA method was on average five times better than the VED alternative in terms of MSE accounting for all the datasets used.

<p>Queueing systems are everywhere: in transportation networks, service centers, communication systems, clinics, manufacturing systems, etc. In this dissertation, we contribute to the theory of queueing in two aspects. In the first part, we dilate the interplay between retrials and strategic arrival behavior in single-class queueing networks. Specifically, we study a variation of the ‘Network Concert Queueing Game,’ wherein a fixed but large number of strategic users arrive at a network of queues where they can be routed to other queues in the network following a fixed routing matrix, or potentially fedback to the end of the queue they arrive at. Working in a non-atomic setting, we prove the existence of Nash equilibrium arrival and routing profiles in three simple, but non-trivial, network topologies/architectures. In two of them, we also prove the uniqueness of the equilibrium. Our results prove that Nash equilibrium decisions on when to arrive and which queue to join in a network are substantially impacted by routing, inducing ‘herding’ behavior under certain conditions on the network architecture. Our theory raises important design implications for capacity-sharing in systems with strategic users, such as ride-sharing and crowdsourcing platforms.</p> <p><br></p> <p>In the second part, we develop a new method of data-driven model calibration or estimation for queueing models. Statistical and theoretical analyses of traffic traces show that the doubly stochastic Poisson processes are appropriate models of high intensity traffic arriving at an array of service systems. On the other hand, the statistical estimation of the underlying latent stochastic intensity process driving the traffic model involves a rather complicated nonlinear filtering problem. In this thesis we use deep neural networks to ‘parameterize’ the path measures induced by the stochastic intensity process, and solve this nonlinear filtering problem by maximizing a tight surrogate objective called the evidence lower bound (ELBO). This framework is flexible in the sense that we can also estimate other stochastic processes (e.g., the queue length process) and their related parameters (e.g., the service time distribution). We demonstrate the effectiveness of our results through extensive simulations. We also provide approximation guarantees for the estimation/calibration problem. Working with the Markov chain induced by the Euler-Maruyama discretization of the latent diffusion, we show that (1) there exists a sequence of approximate data generating distributions that converges to the “ground truth” distribution in total variation distance; (2) the variational gap is strictly positive for the optimal solution to the ELBO. Extending to the non-Markov setting, we identify the variational gap minimizing approximate posterior for an arbitrary (known) posterior and further, prove a lower bound on the optimal ELBO. Recent theoretical results on optimizing the ELBO for related (but ultimately different) models show that when the data generating distribution equals the ground truth distribution and the variational gap is zero, the probability measures that achieve these conditions also maximize the ELBO. Our results show that this may not be true in all problem settings.</p>

The most common approach to analysing satellite imagery is building or object segmentation,which expects an algorithm to find and segment objects with specific boundaries thatare present in the satellite imagery. The company Vricon takes satellite imagery analysisfurther with the goal of reproducing the entire world into a 3D mesh. This 3D reconstructionis performed by a set of complex algorithms excelling in different object reconstructionswhich need sufficient labeling in the original 2D satellite imagery to ensure validtransformations. Vricon believes that the labeling of areas can be used to improve the algorithmselection process further. Therefore, the company wants to investigate if multinomiallarge area classification can be performed successfully using the satellite image data availableat the company. To enable this type of classification, the company’s gold-standarddataset containing labeled objects such as individual buildings, single trees, roads amongothers, has been transformed into an large area gold-standard dataset in an unsupervisedmanner. This dataset was later used to evaluate large area classification using several stateof-the-art Deep Convolutional Neural Network (DCNN) semantic segmentation architectureson both RGB as well as RGB and Digital Surface Model (DSM) height data. Theresults yield close to 63% mIoU and close to 80% pixel accuracy on validation data withoutusing the DSM height data in the process. This thesis additionally contributes with a novelapproach for large area gold-standard creation from existing object labeled datasets.

京都大学 / 新制・課程博士 / 博士(情報学) / 甲第23540号 / 情博第770号 / 新制||情||131(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)准教授 吉井 和佳, 教授 河原 達也, 教授 西野 恒, 教授 鹿島 久嗣 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DFAM

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.